scholarly journals pChem: a modification-centric assessment tool for the performance of chemoproteomic probes

2021 ◽  
Author(s):  
Ji-Xiang He ◽  
Zheng-Cong Fei ◽  
Ling Fu ◽  
Cai-Ping Tian ◽  
Fu-Chu He ◽  
...  
Keyword(s):  
Assessment Tool ◽  
Protein Profiling ◽  
Metabolic Labeling ◽  
Experimental Setting ◽  
Computational Tool ◽  
On Demand ◽  
Manual Inspection ◽  
Search Tool ◽  
Blind Search ◽  
User Friendly

We report a modification-centric, blind-search tool termed pChem to provide a streamlined pipeline for unbiased assessing of the performance of chemoproteomic probes. The pipeline starts with an experimental setting for isotopically coding probe-derived modifications that can be automatically recognized, accurately calculated and precisely localized by pChem with neither prior knowledge nor manual inspection. Further, pChem exports on-demand reports by scoring the profiling efficiency, modification-homogeneity and proteome-wide residue selectivity of a tested probe. The performance and robustness of pChem were benchmarked by applying it to various bioorthogonal probes, including 15 activity-based protein profiling (ABPP) probes and 3 metabolic labeling probes. Together, pChem is a user-friendly computational tool for probe developers, even those with no experience in informatics, and aims to facilitate the development and optimization of probes for the ever-growing field of chemoproteomics.

LUU CHECKER: A Web-based Tool to Incorporate Emerging LUs in the SWAT Model

2019 ◽  
Vol 35 (5) ◽  
pp. 723-731 ◽  
Author(s):  
Gurdeep Singh ◽  
Dharmendra Saraswat ◽  
Naresh Pai ◽  
Benjamin Hancock
Keyword(s):  
Land Use ◽  
Management Practices ◽  
Assessment Tool ◽  
Urban Forest ◽  
Swat Model ◽  
Land Use Changes ◽  
Web Based ◽  
Large Size ◽  
Hydrologic Response Unit ◽  
User Friendly

Abstract. Standard practice of setting up Soil and Water Assessment Tool (SWAT) involves use of a single land use (LU) layer under the assumption that no change takes place in LU condition irrespective of the length of simulation period. This assumption leads to erroneous conclusions about efficacy of management practices in those watersheds where land use changes (LUCs) (e.g. agriculture to urban, forest to agriculture etc.) occur during the simulation period. To overcome this limitation, we have developed a user-friendly, web-based tool named LUU Checker that helps create a composite LU layer by integrating multiple years of LU layers available in watersheds of interest. The results show that the use of composite LU layer for hydrologic response unit (HRU) delineation in 2474-km2 L’Anguile River Watershed in Arkansas was able to capture changed LU at subbasin level by using LU data available in the year 1999 and 2006, respectively. The web-based tool is applicable for large size watersheds and is accessible to multiple users from anywhere in the world. Keywords: Land use, Web-based tool, SWAT, LUU Checker.

Methylphenidate Effect in Children With ADHD Can Be Measured by an Ecologically Valid Continuous Performance Test Embedded in Virtual Reality

CNS Spectrums ◽  
2010 ◽  
Vol 15 (2) ◽  
pp. 125-130 ◽  
Author(s):  
Yehuda Pollak ◽  
Hanan Barhoum Shomaly ◽  
Patrice L. Weiss ◽  
Albert A. Rizzo ◽  
Varda Gross-Tsur
Keyword(s):  
Virtual Reality ◽  
Classroom Environment ◽  
Performance Test ◽  
Assessment Tool ◽  
Similar Degree ◽  
Continuous Performance ◽  
Double Blind ◽  
Children With Adhd ◽  
Feedback Questionnaire ◽  
User Friendly

ABSTRACTBackground: Continuous performance tasks (CPTs) embedded in a virtual reality (VR) classroom environment have been shown to be a sensitive and user-friendly assessment tool to detect cognitive deficits related to attention-deficit/hyperactivity disorder (ADHD). The aim of the current study was to compare the performance of children with ADHD on a VR-CPT while on and off treatment with methylphenidate (MPH) and to compare the VR-CPT to a cgrrently used CPT, Test of Variables of Attention (TOVA).Methods:Twenty-seven children with ADHD underwent the VR-CPT, the same CPT without VR (no VR-CPT), and theTOVA, 1 hour after the. ingestion of either placebo or 0.3 mg/kg MPH, in a double-blind, placebo-controlled, crossover design. Immediately following CPT, subjects described their subjective experiences on the Short Feedback Questionnaire.Results: MPH reduced omission errors to a greater extent on the VR-CPT compared to the no VR-CPT and the TOVA, and decreased other CPT measures on all types of CPT to a similar degree. Children rated the VR-CPT as more enjoyable compared to the other types of CPT.Conclusions: It is concluded that the VR-CPT is a sensitive and user-friendly assessment tool in measuring the response to MPH in children with ADHD.

The use of websites by Mediterranean tourist ports

2019 ◽  
Vol 10 (2) ◽  
pp. 190-204 ◽  
Author(s):  
Clara Benevolo ◽  
Riccardo Spinelli
Keyword(s):  
Design Methodology ◽  
Assessment Tool ◽  
Qualitative Evaluation ◽  
Evaluation Tool ◽  
Content Type ◽  
Mediterranean Countries ◽  
Expected Information ◽  
User Friendly ◽  
Potential Customers

Purpose This paper aims to explore the use of websites by tourist ports to assess whether they support ports in communicating their image and provide information and services to actual and potential customers. Design/methodology/approach An analysis of 129 tourist ports websites from ten Mediterranean countries was conducted using the 2QCV3Q model, a multi-purpose qualitative evaluation tool based on experts’ judgments. Findings The findings show that tourist ports’ websites are typically beautiful and well-managed, give ports a clear image and link them with the local territory; however, sample websites are only partially user-friendly, offer limited room for interaction and fail to provide all the expected information and services to the visitors. Originality/value This research provides an unprecedented picture of the use and quality of websites by tourist ports located in the Mediterranean Sea and offers a robust and exhaustive assessment tool that might be of interest to researchers. The tool might also help managers of tourist ports to improve their websites by making them more business- and customer-oriented.

scholarly journals Indicator-Based Sustainability Assessment Tool to Support Coastal and Marine Management

2019 ◽  
Vol 11 (11) ◽  
pp. 3175 ◽  
Author(s):  
Donalda Karnauskaitė ◽  
Gerald Schernewski ◽  
Josianne G. Støttrup ◽  
Marija Kataržytė
Keyword(s):  
Assessment Tool ◽  
Systems Approach ◽  
Sustainability Assessment ◽  
Coastal Development ◽  
Decision Makers ◽  
Decision Making Process ◽  
Marine Management ◽  
Management Measures ◽  
Integrated Approaches ◽  
User Friendly

The applied Indicator-based Sustainability Assessment Tool (InSAT) serves as a user-friendly computer-aided tool to support coastal and marine management. Focus is on sustainable coastal development, including environmental, social, and economic aspects. We apply the InSAT to assess the changes in sustainability before, during, and after the implementation of management measures. The assessments address three case studies in Lithuania: the construction of a liquefied natural gas terminal in Klaipeda, the renewal of the port of Sventoji, and the opening of a beach in Nida. The application of core and optional indicators highlights the strengths and weaknesses of the management measures. We analyze to what extent, how, and when the InSAT can be applied within a stepwise Systems Approach Framework (SAF) to support sustainable coastal and marine management. Further, we assess how the tool can be applied within other integrated approaches. The application of tailor-made indicators helps to identify potential conflicts and raise discussions about sustainable development between stakeholders and decision-makers and therefore supports the decision-making process. The tool indicates the management measures’ weaknesses, but the assessment results do not indicate what kind of solutions should be undertaken. However, it can still serve to support, guide, and supplement the participation and discussion processes.

scholarly journals P29 A smartphone application to monitor nausea in pediatric cancer patients during chemotherapy

2019 ◽  
Vol 104 (6) ◽  
pp. e29.1-e29
Author(s):  
A Eliasen ◽  
MK Abildtoft ◽  
NS Krogh ◽  
JS Brok ◽  
R Mathiasen ◽  
...  
Keyword(s):  
Cancer Patients ◽  
Pediatric Cancer ◽  
Assessment Tool ◽  
Smartphone Application ◽  
List Type ◽  
Notification System ◽  
Pediatric Cancer Patients ◽  
Patient Reported ◽  
User Friendly ◽  
Nausea Severity

BackgroundNausea is a common and distressing side effect for children in chemotherapy. Antiemetic recommendations are based on limited literature and prospective evaluation of antiemetic efficacy is required. Smartphone applications (apps) may collect patient-reported outcomes with precision and effectiveness1. We developed a smartphone app to track nausea in pediatric cancer patients during chemotherapy.MethodsMedical researchers, pediatric oncologists and software engineers worked synergistically in the development. We translated the validated Pediatric Nausea Assessment Tool to score nausea severity2. We conducted three rounds of patient-feedback and modification.ResultsThe app has a definition module where the child centers the attention to the concept of nausea. The child can then express nausea severity with four faces and the child’s own definition of nausea is incorporated in the question2. The app includes a notification system to ensure high response rates. All participants felt that the app was user-friendly, intuitive and that time spent was acceptable.ConclusionThe app is a user-friendly tool to assess nausea in pediatric cancer patients that can ease future pediatric antiemetic trials.ReferencesStone AA, Shiffman S, Schwartz JE, et al. Patient compliance with paper and electronic diaries. Control Clin Trials 2003 Apr;24(2):182–99.Dupuis LL, Taddio A, Kerr EN, et al. Development and validation of the pediatric nausea assessment tool for use in children receiving antineoplastic agents. Pharmacotherapy 2006;26:1221–31.Disclosure(s)Nothing to disclose

scholarly journals Geospatial-based automated watershed modeling in Garhwal Himalaya

2010 ◽  
Vol 12 (4) ◽  
pp. 502-520 ◽  
Author(s):  
U. C. Kothyari ◽  
Raaj. Ramsankaran ◽  
D. Sathish Kumar ◽  
S. K. Ghosh ◽  
Nisha Mendiratta
Keyword(s):  
Spatial Distribution ◽  
Soil Erosion ◽  
Assessment Tool ◽  
Watershed Modeling ◽  
Erosion Rates ◽  
Erosion Processes ◽  
Runoff Potential ◽  
Soil Erosion Rates ◽  
Modelling Methodology ◽  
User Friendly

An automated GIS tool and its computational outcomes on the spatial distribution of runoff and soil erosion are presented. The developed tool, named Automated Soil Erosion Assessment Tool (ASEAT), simulates runoff and soil erosion rates based on the concept of erosion processes suggested by Morgan–Morgan–Finney (MMF) in 1984. ASEAT is provided with a user-friendly graphical user interface (GUI) to interact with the users. The computational algorithms used are made fully automated and have been developed using the ERDAS Macro Language (EML) and Spatial Macro Language (SML). The developed modelling methodology is applied to the data of an experimental watershed of Pathri Rao in the Indian lower Himalayan region. Generated spatial distribution of runoff potential and soil erosion rates for the studied watershed using ASEAT are depicted by maps. The model-computed surface runoff potential (145.63 mm) available in the watershed seems fair when compared with the runoff depth (176.07 mm) observed at the watershed outlet. The derived estimates of soil erosion are validated, albeit qualitatively, with field observations and seem reliable for making decisions on the adoption of soil erosion conservative measures in the watershed.

Subsea Pipelaying Simulation by the “Situa-Petropipe” Software: A User Friendly Alternative

2008 ◽  
Author(s):  
Danilo Machado Lawinscky da Silva ◽  
Carl Horst Albrecht ◽  
Breno Pinheiro Jacob ◽  
Isaias Quaresma Masetti ◽  
Claudio Roberto Mansur Barros ◽  
...  
Keyword(s):  
User Interface ◽  
Numerical Simulations ◽  
Environmental Conditions ◽  
Structural Behavior ◽  
Model Generation ◽  
Interface Model ◽  
Computational Tool ◽  
Hydrodynamic Behavior ◽  
User Friendly ◽  
Oil Company

Currently, Petrobras (the Brazilian state oil company) performs numerical simulations of pipelaying operations employing commercial software, such as OffPipe [1]. However, such tools presents restrictions/limitations related to the user interface, model generation and analysis formulations. These limitations hinder its efficient use for analyses of installation procedures for the scenarios considered by Petrobras, using the BGL-1 barge (owned by Petrobras) or other vessels, considering for instance particular types of stingers depending on depth and pipeline, with different lengths and geometries adapted to certain laying conditions in S-Lay procedures. Therefore, the objective of this work is to present the development and application of a tailored, in-house non-commercial computational tool in which the modules follow Petrobras users’ specifications, in order to overcome the limitations for specific needs and particular scenarios in the simulation of several types of pipeline procedures. Such tool, called SITUA-PetroPipe, presents a friendly interface with the user, for instance allowing the complete customization of the configuration of laybarge and stinger rollers. It also includes novel analysis methods and formulations, including the ability of coupling the structural behavior of the pipe with the hydrodynamic behavior of the vessel motions under environmental conditions.

scholarly journals A Federated Online Search Tool for Biospecimens (Sample Locator): Usability Study

10.2196/17739 ◽  
2020 ◽  
Vol 22 (8) ◽  
pp. e17739
Author(s):  
Christina Schüttler ◽  
Verena Huth ◽  
Magdaléna von Jagwitz-Biegnitz ◽  
Martin Lablans ◽  
Hans-Ulrich Prokosch ◽  
...  
Keyword(s):  
Sustainable Use ◽  
User Centered Design ◽  
Federated Search ◽  
Team Members ◽  
Related Data ◽  
System Usability Scale ◽  
System Usability ◽  
Usability Analysis ◽  
Search Tool ◽  
User Friendly

Background The German Biobank Alliance (GBA) aims to establish a cross-site biobank network. For this endeavor, the so-called Sample Locator, a federated search tool for biospecimens and related data, has been developed, forming the heart of its information technology (IT) infrastructure. Objective To ensure the sustainable use of such a tool, we included researchers as participants in an end user–based usability evaluation. Methods To develop a prototype ready for evaluation, we needed input from GBA IT experts. Thus, we conducted a 2-day workshop with 8 GBA IT team members. The focus was on the respective steps of a user-centered design process. With the acquired knowledge, the participants designed low-fidelity mock-ups. The main ideas of these mock-ups were discussed, extracted, and summarized into a comprehensive prototype using Microsoft PowerPoint. Furthermore, we created a questionnaire concerning the usability of the prototype, including the System Usability Scale (SUS), questions on negative and positive aspects, and typical tasks to be fulfilled with the tool. Subsequently, the prototype was pretested on the basis of this questionnaire with researchers who have a biobank background. Based on this preliminary work, the usability analysis was ultimately carried out with researchers and the results were evaluated. Results Altogether, 27 researchers familiar with sample requests evaluated the prototype. The analysis of the feedback certified a good usability, given that the Sample Locator prototype was seen as intuitive and user-friendly by 74% (20/27) of the participants. The total SUS score by the 25 persons that completed the questionnaire was 80.4, indicating good system usability. Still, the evaluation provided useful advice on optimization potential (eg, offering a help function). Conclusions The findings of this usability analysis indicate that the considerations regarding a user-friendly application that have been made in the development process so far strongly coincide with the perception of the study participants. Nevertheless, it was important to engage prospective end users to ensure that the previous development is going in the desired direction and that the Sample Locator will be used in the future. The user comments and suggestions for improvement will be considered in upcoming iterations for refinement.

scholarly journals A Federated Online Search Tool for Biospecimens (Sample Locator): Usability Study (Preprint)

2020 ◽  
Author(s):  
Christina Schüttler ◽  
Verena Huth ◽  
Magdaléna von Jagwitz-Biegnitz ◽  
Martin Lablans ◽  
Hans-Ulrich Prokosch ◽  
...  
Keyword(s):  
Sustainable Use ◽  
User Centered Design ◽  
Federated Search ◽  
Team Members ◽  
Related Data ◽  
System Usability Scale ◽  
System Usability ◽  
Usability Analysis ◽  
Search Tool ◽  
User Friendly

BACKGROUND The German Biobank Alliance (GBA) aims to establish a cross-site biobank network. For this endeavor, the so-called Sample Locator, a federated search tool for biospecimens and related data, has been developed, forming the heart of its information technology (IT) infrastructure. OBJECTIVE To ensure the sustainable use of such a tool, we included researchers as participants in an end user–based usability evaluation. METHODS To develop a prototype ready for evaluation, we needed input from GBA IT experts. Thus, we conducted a 2-day workshop with 8 GBA IT team members. The focus was on the respective steps of a user-centered design process. With the acquired knowledge, the participants designed low-fidelity mock-ups. The main ideas of these mock-ups were discussed, extracted, and summarized into a comprehensive prototype using Microsoft PowerPoint. Furthermore, we created a questionnaire concerning the usability of the prototype, including the System Usability Scale (SUS), questions on negative and positive aspects, and typical tasks to be fulfilled with the tool. Subsequently, the prototype was pretested on the basis of this questionnaire with researchers who have a biobank background. Based on this preliminary work, the usability analysis was ultimately carried out with researchers and the results were evaluated. RESULTS Altogether, 27 researchers familiar with sample requests evaluated the prototype. The analysis of the feedback certified a good usability, given that the Sample Locator prototype was seen as intuitive and user-friendly by 74% (20/27) of the participants. The total SUS score by the 25 persons that completed the questionnaire was 80.4, indicating good system usability. Still, the evaluation provided useful advice on optimization potential (eg, offering a help function). CONCLUSIONS The findings of this usability analysis indicate that the considerations regarding a user-friendly application that have been made in the development process so far strongly coincide with the perception of the study participants. Nevertheless, it was important to engage prospective end users to ensure that the previous development is going in the desired direction and that the Sample Locator will be used in the future. The user comments and suggestions for improvement will be considered in upcoming iterations for refinement.

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