scholarly journals Making molecules vibrate: Interactive web environment for the teaching of infrared spectroscopy

2021 ◽  
Author(s):  
Kevin Maik Jablonka ◽  
Luc Patiny ◽  
Berend Smit
Keyword(s):  
Infrared Spectroscopy ◽  
Chemistry Education ◽  
Vibrational Frequencies ◽  
Ease Of Use ◽  
Electronic Effects ◽  
Immediate Feedback ◽  
Structural Modifications ◽  
Interactive Interface ◽  
Web App ◽  
Semi Empirical

Infrared spectroscopy (IR) is a staple structural elucidation and characterization technique due to its ability to identify functional groups and its ease of use. Interestingly, it allows capturing electronic effects via their influence on the bond strength of "probes" such as the carbonyl group and also offers a wealth of examples for discussion on the theory of electronic transitions. For this reason, IR spectroscopy is typically taught both in theoretical classes and in applied structural analysis courses. In practice, there is rarely a link between those courses, and both suffer from the lack of exploratory learning, i.e., tools with which students can explore the interplay between symmetry and selection rules, as well as electronic effects and vibrational frequencies — with almost immediate feedback. In practice, this might lead to students that are well skilled in looking up vibrational frequencies in lookup tables but do not understand the links to electronic effects and reactivity. Here, we introduce a web app that leverages semi-empirical quantum mechanical (or force-field based) calculations, performed on a web service, in an interactive interface to provide an environment in which students can explore how slight changes to the structure manifest in changes of the spectrum. This approach avoids the time-consuming handling of potentially hazardous materials that might not be readily available and invites students to play with spectroscopy — to "see" and "test" electronic effects that are so commonplace in organic chemistry education. As a "side effect" our web app also provides a powerful aid for research scientists to investigate how different structural modifications, such as substitution, isomerism, or steric strain, would manifest in the infrared spectrum.

scholarly journals The Collaborative Metadata Repository (CoMetaR) Web App: Quantitative and Qualitative Usability Evaluation (Preprint)

2021 ◽  
Author(s):  
Mark R Stöhr ◽  
Andreas Günther ◽  
Raphael W Majeed
Keyword(s):  
Qualitative Analysis ◽  
Medical Informatics ◽  
Ease Of Use ◽  
Metadata Management ◽  
System Usability Scale ◽  
Standards And Guidelines ◽  
Use Efficiency ◽  
Metadata Repository ◽  
Web App ◽  
Further Development

BACKGROUND In the field of medicine and medical informatics, the importance of comprehensive metadata has long been recognized, and the composition of metadata has become its own field of profession and research. To ensure sustainable and meaningful metadata are maintained, standards and guidelines such as the FAIR (Findability, Accessibility, Interoperability, Reusability) principles have been published. The compilation and maintenance of metadata is performed by field experts supported by metadata management apps. The usability of these apps, for example, in terms of ease of use, efficiency, and error tolerance, crucially determines their benefit to those interested in the data. OBJECTIVE This study aims to provide a metadata management app with high usability that assists scientists in compiling and using rich metadata. We aim to evaluate our recently developed interactive web app for our collaborative metadata repository (CoMetaR). This study reflects how real users perceive the app by assessing usability scores and explicit usability issues. METHODS We evaluated the CoMetaR web app by measuring the usability of 3 modules: <i>core module</i>, <i>provenance module</i>, and <i>data integration module</i>. We defined 10 tasks in which users must acquire information specific to their user role. The participants were asked to complete the tasks in a live web meeting. We used the System Usability Scale questionnaire to measure the usability of the app. For qualitative analysis, we applied a modified think aloud method with the following thematic analysis and categorization into the ISO 9241-110 usability categories. RESULTS A total of 12 individuals participated in the study. We found that over 97% (85/88) of all the tasks were completed successfully. We measured usability scores of 81, 81, and 72 for the 3 evaluated modules. The qualitative analysis resulted in 24 issues with the app. CONCLUSIONS A usability score of 81 implies very good usability for the 2 modules, whereas a usability score of 72 still indicates acceptable usability for the third module. We identified 24 issues that serve as starting points for further development. Our method proved to be effective and efficient in terms of effort and outcome. It can be adapted to evaluate apps within the medical informatics field and potentially beyond.

scholarly journals Experimental and Computational Vibration Study of Amino Acids

2013 ◽  
Vol 15 ◽  
pp. 1-17 ◽  
Author(s):  
Musa E. Mohamed ◽  
Abdelhafeez M.A. Mohammed
Keyword(s):  
Amino Acids ◽  
Glutamic Acid ◽  
Ab Initio ◽  
Vibrational Frequencies ◽  
Empirical Methods ◽  
Vibrational Studies ◽  
Semi Empirical

Vibrational studies of amino acids experimentally and theoretically have been performed. The Semi-empirical methods optimization by PM6 and RM1 on the l- and d-amino acids (alanine, phenylalanine, aspartic and glutamic acid), showed no difference in energy between l-and d-isomers. The vibrational frequencies were calculated by semi-emprical methods (PM6 and RM1) and Ab Initio methods (B3LYP/6-31+G(d) and were scaled down by factors of 0.925 (RM1), 1.09 (PM6) and 0.89 (B3LYP/6-31+G(d)). The calculated and experimental vibrational frequencies have shown good general agreement.

Exploring the Player Flow Experience in E-Game Playing

2010 ◽  
Vol 6 (2) ◽  
pp. 47-64 ◽  
Author(s):  
Chin-Lung Hsu
Keyword(s):  
Information Technology ◽  
Game Design ◽  
Ease Of Use ◽  
Flow Experience ◽  
Perceived Ease Of Use ◽  
Immediate Feedback ◽  
Related Literature ◽  
Proposed Model ◽  
Research Questions ◽  
Electronic Games

Flow theory has been widely applied in the context of information technology and is useful in understanding users’ behavior; however, few studies empirically examine what factors influence players’ flow, and what the facets and consequences of flow are in the context of electronic games (e-games). In this study, the author reviews previous flow-related literature to develop the proposed model to explore these research questions. The proposed model is empirically evaluated using survey data collected from 277 users responding about their perception of e-game. Results of this empirical study show that perceived ease of use, immediate feedback, skill and challenge are antecedents of flow, while enjoyment is the most salient facet of flow. The results provide further insights into e-game design and development.

scholarly journals Replacement of Trifluoroacetic Acid with HCl in the Hydrophobic Purification Steps of Pediocin PA-1: a Structural Effect

2002 ◽  
Vol 68 (10) ◽  
pp. 4803-4808 ◽  
Author(s):  
Hélène Gaussier ◽  
Hélène Morency ◽  
Marc C. Lavoie ◽  
Muriel Subirade
Keyword(s):  
Antimicrobial Activity ◽  
Fourier Transform ◽  
Infrared Spectroscopy ◽  
Trifluoroacetic Acid ◽  
Good Alternative ◽  
Structural Effect ◽  
Purification Procedure ◽  
Protein Loss ◽  
Structural Modifications ◽  
Procedural Change

ABSTRACT Trifluoroacetic acid (TFA) is a purification contaminant associated with pediocin PA-1 that interferes with Fourier transform infrared spectroscopy structural analysis. As revealed by circular dichroism, its presence affects the structural folding of pediocin. Consequently, we propose a new pediocin PA-1 purification procedure using HCl instead of TFA in all of the hydrophobic steps. This procedural change does not affect the purification yield or the amount of pediocin PA-1 purified. Furthermore, removing HCl, as opposed to TFA, after purification is an easier procedure to carry out. In fact, the removal of TFA requires more experimentation and results in protein loss. Thus, HCl is a good alternative to TFA in pediocin PA-1 purification and can be extended to the purification of other proteins. We also show that TFA-induced structural modifications do not significantly affect the antimicrobial activity of pediocin PA-1.

Graphene Infrared Spectroscopy: DFT Vibrational Frequencies

2010 ◽  
Author(s):  
Nazrul Ahmad Rosli ◽  
Hasan Abu Kassim ◽  
Keshav N. Shrivastava ◽  
A. K. Yahya ◽  
Shah Alam
Keyword(s):  
Infrared Spectroscopy ◽  
Vibrational Frequencies

Near-Infrared Spectroscopy: A Promising Prehospital Tool for Management of Traumatic Brain Injury

2017 ◽  
Vol 32 (4) ◽  
pp. 414-418 ◽  
Author(s):  
Joost Peters ◽  
Bas Van Wageningen ◽  
Nico Hoogerwerf ◽  
Edward Tan
Keyword(s):  
Traumatic Brain Injury ◽  
Infrared Spectroscopy ◽  
Brain Injury ◽  
Near Infrared Spectroscopy ◽  
Near Infrared ◽  
Ease Of Use ◽  
Treatment Change ◽  
Publication Type ◽  
Scan Time ◽  
Severe Tbi

AbstractIntroductionEarly identification of traumatic brain injury (TBI) is essential. Near-infrared spectroscopy (NIRS) can be used in prehospital settings for non-invasive monitoring and the diagnosis of patients who may require surgical intervention.MethodsThe handheld NIRS Infrascanner (InfraScan Inc.; Philadelphia, Pennsylvania USA) uses eight symmetrical scan points to detect intracranial bleeding. A scanner was tested in a physician-staffed helicopter Emergency Medical Service (HEMS). The results were compared with those obtained using in-hospital computed tomography (CT) scans. Scan time, ease-of-use, and change in treatment were scored.ResultsA total of 25 patients were included. Complete scans were performed in 60% of patients. In 15 patients, the scan was abnormal, and in one patient, the scan resulted in a treatment change. Compared with the results of CT scanning, the Infrascanner obtained a sensitivity of 93.3% and a specificity of 78.6%. Most patients had severe TBI with indication for transport to a trauma center prior to scanning. In one patient, the scan resulted in a treatment change. Evaluation of patients with less severe TBI is needed to support the usefulness of the Infrascanner as a prehospital triage tool.ConclusionPromising results were obtained using the InfraScan NIRS device in prehospital screening for intracranial hematomas in TBI patients. High sensitivity and good specificity were found. Further research is necessary to determine the beneficial effects of enhanced prehospital screening on triage, survival, and quality of life in TBI patients.PetersJ, Van WageningenB, HoogerwerfN, TanE. Near-infrared spectroscopy: a promising prehospital tool for management of traumatic brain injury. Prehosp Disaster Med. 2017;32(4):414–418.

scholarly journals Examining Chemistry Students’ Perceptions Toward Multiple-Choice Assessment Tools that Vary in Feedback and Partial Credit

2021 ◽  
Author(s):  
Michael Williams ◽  
Eileen Wood ◽  
Fatma Arslantas ◽  
Steve MacNeil
Keyword(s):  
Multiple Choice ◽  
Ease Of Use ◽  
Interview Data ◽  
Assessment Tools ◽  
Partial Credit ◽  
Immediate Feedback ◽  
Chemistry Students ◽  
Testing Method ◽  
Choice Testing ◽  
Dichotomous Scoring

Multiple-choice testing with dichotomous scoring is one of the most common assessment methods utilized in undergraduate education. Determining students’ perceptions toward different types of multiple-choice testing formats is important for effective assessment. The present study compared two alternative multiple-choice testing formats used in a second-year required chemistry course: (1) The Immediate Feedback Assessment Technique (IFAT®) and (2) Personal Point Allocation (PPA). Both testing methods allow for partial credit but only the IFAT® provides immediate feedback on students’ responses. Both survey and interview data indicated that, overall, most students preferred IFAT® to the PPA testing method. These positive ratings were related to potential increase in reward, ease of use, and confidence. IFAT® was also perceived to be less stress producing, and anxiety provoking than PPA. Interview data supported these findings but also indicated individual differences in preference for each of these two methods. Additionally, students’ feedback on strategies used for either testing method and suggestions on how to improve the methods are discussed.

scholarly journals Near-Infrared Spectroscopy and Its Potential for Point-Of-Care Testing

2017 ◽  
Vol 5 (1) ◽  
pp. 93-100
Author(s):  
Rammohan V Maikala
Keyword(s):  
Infrared Spectroscopy ◽  
Near Infrared Spectroscopy ◽  
Near Infrared ◽  
Point Of Care ◽  
Ease Of Use ◽  
Healthcare Sector ◽  
Tissue Oxygen Saturation ◽  
Point Of Care Testing ◽  
Point Of Care Technology ◽  
Care Technology

Point-of-care or ‘near-patient’ testing has received attention in recent years for its usefulness in rapid and reliable delivery of healthcare to a patient in a variety of clinical settings. Near-infrared spectroscopy (NIRS)-derived optical biomarkers (e.g., tissue oxygen saturation) have been utilized to monitor tissue vascularity and oxygenation status continuously in normal and patient populations. Despite its ease of use and modest cost, the NIRS modality is still not at point-of-care use in the healthcare sector as extensively as other physiological modalities such as Pulse Oximetry. This short communication examines the case for point-of-care testing with two examples of FDA-approved NIRS systems, and discusses the feasibility and implementation of the NIRS modality as a point-of-care technology.

scholarly journals REDLE: A Platform in the Cloud for Elderly Fall Detection and Push Response Tracking

2017 ◽  
Vol 10 (2) ◽  
pp. 185-195
Author(s):  
Piyanuch Silapachote ◽  
Ananta Srisuphab ◽  
Jinkawin Phongpawarit ◽  
Sirikorn Visetpalitpol ◽  
Sirima Jirapasitchai
Keyword(s):  
Fall Detection ◽  
Detection Algorithm ◽  
Ease Of Use ◽  
Physically Active ◽  
Interactive Interface ◽  
Emotional Wellness ◽  
Global Positioning ◽  
Risk Of Falls ◽  
Global Aging

Caring for a rapid and ever-increasing older population, providing social support and monitoring emotional wellness, is the most immediate and most urgent challenge prompted by the global aging of baby boomers. Elderly assisted systems do not only promote independent lifestyles, enhancing their quality of life, but also reduce stress and worry of families and friends. While being physically active is beneficial and much encouraged, it does increase the risk of falls. We developed an affordable fall detection and response tracking application on the cloud platform; mobile cloud computing is a major evolution with rising impact in information technology and enterprises. Our system, named REDLE, features push notifications for fall alerts and real-time maps for tracking and providing locations and phone numbers of nearby hospitals. Implemented on Android, it captures signals from an embedded tri-axial accelerometer and a global positioning system sensor. Coupled with an efficient threshold-based fall detection algorithm for instantaneous responses, REDLE achieved a near perfect fall detection rate and accurate tracking. Users enjoyed the smoothness of our interactive interface, and complimented on its ease of use and familiarity.

scholarly journals cgbind: A Python Module and Web App for Automated Metallocage Construction and Host-Guest Characterization

2020 ◽  
Author(s):  
Tom A. Young ◽  
Razvan Gheorghe ◽  
Fernanda Duarte
Keyword(s):  
Chemical Space ◽  
Chemical Properties ◽  
Computationally Efficient ◽  
Web Based ◽  
Electronic Structure Methods ◽  
New Hosts ◽  
Web App ◽  
Semi Empirical ◽  
Better Than ◽  
And Chemical Properties

Metallocages offer a diverse and underexplored region of chemical space to search for novel catalysts and substrate hosts. However, the ability to tailor such structures towards applications in binding and catalysis is a challenging task. Here, we present an open-source computational toolkit, cgbind, that facilitates the characterization and prediction of functional metallocages. It employs known structural scaffolds as starting points, and computationally efficient approaches for the evaluation of geometric and chemical properties. To illustrate the applicability of cgbind, we evaluate the likelihood of 102 substrates to bind within M2L4 and M4L6 cages and achieve accuracy comparable or better than semi-empirical electronic structure methods. The cgbind code presented here is freely available at github.com/duartegroup/cgbind and also via a web-based graphical user interface at cgbind.chem.ox.ac.uk. The protocol described here paves the way for high-throughput virtual screening of potential supramolecular structures, accelerating the search for new hosts and catalysts.

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