Basic Tutorial Research Articles

A Basic Tutorial on Novelty and Activation Functions for Music Signal Processing

A Basic Tutorial on Novelty and Activation Functions for Music Signal Processing

Exploring the Feasibility of At-Home Lung Ultra-Portable Ultrasound: Parent-Performed Pediatric Lung Imaging.

To determine if caregivers would be able to successfully perform in home lung ultrasounds on their children without direct supervision after undergoing a basic tutorial that would allow for expert interpretation. A prospective exploratory single-center cohort study was conducted on patients (0-18 years) presenting to a pediatric emergency department with a respiratory complaint or COVID-related illness. Caregivers underwent a brief hands-on session and were instructed to scan the lungs daily for 7 days. Images were assessed using a modified POCUS IQ score. Descriptive statistics were used to describe the data and bivariate analysis was used to compare groups. Eighteen patients were enrolled; the average age of the parent scanner was 31.9 years and 78% were female. Of all participants, 77.8% scanned on day one. Parents were able to successfully perform some part of the daily scan session for an average of 3.8 out of 7 days. The average POCUS IQ score overall was 6.7 (out of 12). Our study demonstrates the feasibility and acceptability of caregiver ability to obtain adequate lung ultrasound images, at home under no guidance, using the Butterfly iQ probe. Further studies are needed to investigate the accessibility of ultra-portable ultrasound and the ability to integrate with the at-home hospital model, specifically in the pediatric population.

The Use of Laser Ablation Inductively Coupled Plasma Mass Spectrometry (LA-ICP-MS) for the Quantification of Rare Earth Elements in Geological Samples: A Basic Tutorial

The Use of Laser Ablation Inductively Coupled Plasma Mass Spectrometry (LA-ICP-MS) for the Quantification of Rare Earth Elements in Geological Samples: A Basic Tutorial

Blending Moodle and Closed Facebook Group in Interdisciplinary Reading Course: A Collaborative Action Research

Learning management system has been an innovative practice in Nepalese higher education to foster interaction and keep track of day-to-day teaching-learning activities. This article explores using technology applications: Moodle and closed Facebook group in face-to-face class for promoting participation in an interdisciplinary reading course and to find out students’ perception in blending Moodle in face-to-face class. The research study was mainly based on collaborative action research. The primary sources of data were collected from the use of Moodle as learning management system. The students of four intact classes (consists 120 students) were selected purposively under department of English Education, University Campus, Kirtipur. The systematically collected narratives and observation have been analyzed and interpreted descriptively. This study found that the basic tutorials in using technology is prerequisite for the students in using the basics of moodle, email log and the ways to interact on reading text in Moodle platform as a part of pre-instructional activity. Many students felt that they come from remote area, have studied in the technology outreached area, cannot explore the resources, and feel hesitation in exploring the technological tools. In addition, the use of resources in the Moodle and blend of closed Facebook group was found to be highly motivating and resourceful for both the low- level learners and high-level readers in assisting resources.

A Beginner's Guide to the COBRA Toolbox.

COBRA toolbox is one of the most popular tools for systems biology analyses using genome-scale metabolic reconstructions. The toolbox permits the use of many constraint-based analytical methods for examining characteristics of metabolism in the biosystems ranging in complexity from single cells to microbial communities and ultimately multicellular organisms. The toolbox has a number of different variants that can be used depending on a user's choice ofprogramming language. Here, I provide a basic tutorial for beginners that plan to use the original MATLAB version of the toolbox.

A Novel Mobile Platform Enhances Motivation and Satisfaction of Academic Teachers

ABSTRACT With rising numbers of students, shorter hospital stays and increasing workload of academic teachers, teaching time have become a scarce resource. Thus, optimal preparation by teachers is key for good clinical teaching. Though a lot of teaching duties are performed by residents in Germany, they are not likely to have been educated in didactic techniques. We developed and evaluated a mobile teaching application using the “Learning Toolbox (LTB)” platform (Raycom BV, Utrecht, Netherlands) that was offered to academic teachers for preparation and support during curricular courses at our medical school. Courses were part of the curricula in Anaesthesiology, Emergency Medicine, and Orthopaedic and Trauma Surgery, and course length could vary up to 40 h per week. Information provided by the novel platform included logistic information, learning objectives, and curricula for the individual courses. A basic tutorial on didactic techniques, suggestions for providing feedback and for enhancing students’ participation was also part of the platform. After one semester, interviews with teachers indicated an increase in overall satisfaction. Residents appreciated didactic aids and content provided for preparation, leading to higher motivation and self-confidence. The more experienced teachers were particularly satisfied with easy access to scheduling, teaching assignments and daily planning. The app increased teachers’ satisfaction with their performance and enabled better integration of teaching in the daily schedule.

Basic Features of the Analysis of Germination Data with Generalized Linear Mixed Models

Germination data are discrete and binomial. Although analysis of variance (ANOVA) has long been used for the statistical analysis of these data, generalized linear mixed models (GzLMMs) provide a more consistent theoretical framework. GzLMMs are suitable for final germination percentages (FGP) as well as longitudinal studies of germination time-courses. Germination indices (i.e., single-value parameters summarizing the results of a germination assay by combining the level and rapidity of germination) and other data with a Gaussian error distribution can be analyzed too. There are, however, different kinds of GzLMMs: Conditional (i.e., random effects are modeled as deviations from the general intercept with a specific covariance structure), marginal (i.e., random effects are modeled solely as a variance/covariance structure of the error terms), and quasi-marginal (some random effects are modeled as deviations from the intercept and some are modeled as a covariance structure of the error terms) models can be applied to the same data. It is shown that: (a) For germination data, conditional, marginal, and quasi-marginal GzLMMs tend to converge to a similar inference; (b) conditional models are the first choice for FGP; (c) marginal or quasi-marginal models are more suited for longitudinal studies, although conditional models lead to a congruent inference; (d) in general, common random factors are better dealt with as random intercepts, whereas serial correlation is easier to model in terms of the covariance structure of the error terms; (e) germination indices are not binomial and can be easier to analyze with a marginal model; (f) in boundary conditions (when some means approach 0% or 100%), conditional models with an integral approximation of true likelihood are more appropriate; in non-boundary conditions, (g) germination data can be fitted with default pseudo-likelihood estimation techniques, on the basis of the SAS-based code templates provided here; (h) GzLMMs are remarkably good for the analysis of germination data except if some means are 0% or 100%. In this case, alternative statistical approaches may be used, such as survival analysis or linear mixed models (LMMs) with transformed data, unless an ad hoc data adjustment in estimates of limit means is considered, either experimentally or computationally. This review is intended as a basic tutorial for the application of GzLMMs, and is, therefore, of interest primarily to researchers in the agricultural sciences.

AQUA-DUCT: Analysis of Molecular Dynamics Simulations of Macromolecules with the use of Molecular Probes [Article v1.0

AQUA-DUCT software reverses the standard approach of the molecular dynamics simulations analysis of macromolecules, focusing on solvent, cosolvent and small ligands analysis considered as specific molecular probes instead of analysis of macromolecules atoms movement. In this article we present six basic tutorials instructing the users in the best practices for preparing, carrying out, and analysing AQUA-DUCT results in various applications. Users are expected to already have significant experience with running standard molecular dynamics simulations in any dedicated software (e.g., Amber, GROMACS, NAMD), and usage of PyMOL visualising software. The tutorials range from a basic analysis of multiple solvents trajectory used for identification of the entries/exits to the protein core, to a complex one, like identification of the key hot-spots in cosolvent MD simulations that can be used as an insight for macromolecules description, analysis, re-engineering, and for drug design.

Exploration of temporal bone anatomy using mixed reality (HoloLens): development of a mixed reality anatomy teaching resource prototype

Mixed reality (MR), a technology which supplements the real world with virtual objects, is increasingly becoming available as a teaching tool in medical education. The Microsoft HoloLens device allows operators to experience MR using a head-mounted device without interfering with their physical reality, stimulating a realistic learning experience using virtual objects. This project aimed to develop a MR anatomy teaching application with HoloLens for exploring the anatomy of the temporal bone. The educational application was developed from a multidisciplinary collaboration between undergraduate and postgraduate students across several academic disciplines with Medtronic, a medical technology company. 3D anatomical models were built using ZBrush and Blender, while the HoloLens1 application was developed using Windows 10, Visual Studio 2017, Unity and Mixed Reality Toolkit (MRTK). Modules developed within the application included a basic HoloLens tutorial, a virtual temporal bone with surgical anatomy landmarks and free drilling of the temporal bone. The basic tutorial allows the operator to adapt to the MR environment prior to exploring the anatomical landmarks of the 3D temporal bone. The free drilling of the temporal bone using vertex displacement and texture stretching replicates a real-time bone drilling experience and allows the operator to explore the anatomical relationship between different otological structures.

Model Evaluation of Continuous Data Pharmacometric Models: Metrics and Graphics.

This article represents the first in a series of tutorials on model evaluation in nonlinear mixed effect models (NLMEMs), from the International Society of Pharmacometrics (ISoP) Model Evaluation Group. Numerous tools are available for evaluation of NLMEM, with a particular emphasis on visual assessment. This first basic tutorial focuses on presenting graphical evaluation tools of NLMEM for continuous data. It illustrates graphs for correct or misspecified models, discusses their pros and cons, and recalls the definition of metrics used.

Crowdsourcing for translational research: analysis of biomarker expression using cancer microarrays

Background:Academic pathology suffers from an acute and growing lack of workforce resource. This especially impacts on translational elements of clinical trials, which can require detailed analysis of thousands of tissue samples. We tested whether crowdsourcing – enlisting help from the public – is a sufficiently accurate method to score such samples.Methods:We developed a novel online interface to train and test lay participants on cancer detection and immunohistochemistry scoring in tissue microarrays. Lay participants initially performed cancer detection on lung cancer images stained for CD8, and we measured how extending a basic tutorial by annotated example images and feedback-based training affected cancer detection accuracy. We then applied this tutorial to additional cancer types and immunohistochemistry markers – bladder/ki67, lung/EGFR, and oesophageal/CD8 – to establish accuracy compared with experts. Using this optimised tutorial, we then tested lay participants’ accuracy on immunohistochemistry scoring of lung/EGFR and bladder/p53 samples.Results:We observed that for cancer detection, annotated example images and feedback-based training both improved accuracy compared with a basic tutorial only. Using this optimised tutorial, we demonstrate highly accurate (>0.90 area under curve) detection of cancer in samples stained with nuclear, cytoplasmic and membrane cell markers. We also observed high Spearman correlations between lay participants and experts for immunohistochemistry scoring (0.91 (0.78, 0.96) and 0.97 (0.91, 0.99) for lung/EGFR and bladder/p53 samples, respectively).Conclusions:These results establish crowdsourcing as a promising method to screen large data sets for biomarkers in cancer pathology research across a range of cancers and immunohistochemical stains.

Tensor Computation: A New Framework for High-Dimensional Problems in EDA

Many critical EDA problems suffer from the curse of dimensionality, i.e. the very fast-scaling computational burden produced by large number of parameters and/or unknown variables. This phenomenon may be caused by multiple spatial or temporal factors (e.g. 3-D field solvers discretizations and multi-rate circuit simulation), nonlinearity of devices and circuits, large number of design or optimization parameters (e.g. full-chip routing/placement and circuit sizing), or extensive process variations (e.g. variability/reliability analysis and design for manufacturability). The computational challenges generated by such high dimensional problems are generally hard to handle efficiently with traditional EDA core algorithms that are based on matrix and vector computation. This paper presents "tensor computation" as an alternative general framework for the development of efficient EDA algorithms and tools. A tensor is a high-dimensional generalization of a matrix and a vector, and is a natural choice for both storing and solving efficiently high-dimensional EDA problems. This paper gives a basic tutorial on tensors, demonstrates some recent examples of EDA applications (e.g., nonlinear circuit modeling and high-dimensional uncertainty quantification), and suggests further open EDA problems where the use of tensor computation could be of advantage.

Wireless Communication: A Basic Tutorial on Radio Technology

RADIO-FREQUENCY (RF) COMMUNIcation is an important smart grid enabler for functions such as voltage variability (VAR) levels and reactive power control, recloser control, and feeder restorations and isolation. This article will provide a basic tutorial on the types of RF communications and the benefits and liabilities of each. The specific topics to be explored are licensed versus unlicensed frequencies, the distance between remote radios and base stations, and communication architectures.

A Virtual Microscopy Learning Platform - a High Quality, Innovative and Interactive Tool for Training Haematologists of the Future: A UK Pilot Study

Abstract Introduction: Virtual microscopy (VM) allows a whole slide once scanned, to be visualised, navigated and annotated at different magnifications on a digital viewing platform. Advantages for trainees are numerous; slides can be viewed simultaneously by large numbers of students or accessed remotely at the student’s time and place of preference. In the UK all Haematology trainees are required to be competent in diagnostic evaluation of blood films, bone marrow aspirates and trephines. The drive towards laboratory centralisation, increasing automation and full shift working patterns has decreased access to traditional small group teaching using a multi-headed microscope. VM has the potential to realise new modes of training delivery and to prepare haematologists for the advent of VM as a mainstream diagnostic tool. Aim: To review the utility and acceptability of incorporating virtual microscopy into a virtual learning environment (VLE) for haematology trainees. Methods : Over a 6 month period a VLE has been developed centred on the use of VM comprising of: basic morphology tutorials including interactive learning modules and instructional videosannotated image bankclinical case scenario simulationmock examination practice Curriculum mapped content was created to develop acquisition of morphological skills from first principles. 4 interactive modules take users through a step-wise approach to examining a blood film, recognising normal appearances, identifying morphological abnormalities and interpreting their findings in the film report. Case scenarios, requiring trainees to identify morphological abnormalities and put these into clinical context were developed using structured questioning, providing instant feedback on performance at each stage of the case. Additional resources include an annotated image bank of >250 slides and mock examination cases. The use of VM to support large group teaching was piloted at an afternoon for haematology trainees in London. Haematopathology slides were made available on-line prior to the session with videos introducing an approach to examining trephines and lymph nodes. Questions to facilitate examination of the slides were built in to promote learning. The interactive session was facilitated by trainees using the VLE site and case discussions made available on-line for future reference. Informal feedback on the site was encouraged alongside its development and formal surveys were undertaken to evaluate the quality and utility of the VLE both for self-directed and large group teaching. Results: The VLE was piloted to 40 trainee haematology physicians and 10 biomedical scientists only 1 of whom had previous experience of VM. 100% of participants viewed the experience as ‘useful’ or ‘very useful’ and would recommend to other colleagues. Junior trainees particularly valued the structured tutorials on blood film reporting and annotated practice cases. The novel application of the VLE for simulating haematological emergencies presenting with laboratory abnormalities (e.g. APML) was found to be invaluable by new trainees in preparation for out of hours work. 88 trainees attended the large group teaching session. Slides were viewed on-line by 53/88 (60%) trainees in preparation. 78% of trainees rated the training experience as 5/5 (very good). Free text comments included: “pre-course material very useful; really liked the digital microscopy; the most useful day this year”. The use of VLE in this context has been incorporated into future training events. When comparing to light microscopy the key benefits of VM identified by users were: AccessibilityAbility to return to review material as desiredAnnotation of digital imagesAbility to compare different slides side by side within the same screen windowAvailability of slides of rare diagnoses. Overall, image quality was rated as equivalent to viewing glass slides. Technicalities of viewing the slides (panning, changing magnification and adjusting focus) were easier using a light microscope compared to the digital microscope interface. Conclusions: Incorporation of VM into a VLE is an innovative and effective platform for transforming haematology training for the 21st century. Its versatility, quality and accessibility facilitate its implementation into a wide range of learning settings. Minor technical limitations can be easily addressed to improve the user experience. Disclosures No relevant conflicts of interest to declare.

An Introduction to Propensity Scores

The use of propensity scores as a method to promote causality in studies that cannot use random assignment has increased dramatically since its original publication in 1983. While the utility of these approaches is important, the concepts underlying their use are complex. The purpose of this article is to provide a basic tutorial for conducting analyses using propensity scores and what researchers should be aware of in reading papers that choose propensity scores as a method, as well as in conducting their own research. In addition to the explanations given, examples are presented, based on actual studies, which illustrate the use of propensity scores for regression adjustment, stratification, and matching. The syntax, datasets, and output used for these examples are available on http://jea.sagepub.com/content/early/recent for readers to download and follow.

A Basic Tutorial on Cyclic Voltammetry for the Investigation of Electroactive Microbial Biofilms

Electroactive microbial biofilms and the microorganisms embedded therein are not only of crucial fundamental interest because they play an important role in redox cycles that occur in nature, they are also attracting increasing attention as key component of microbial bioelectrochemcial systems (BES). In these systems, interconversion of chemical and electrical energy and the associated exchange of electrons between living microbial cells and solid electrodes take place. The fascinating prospects and promise of BES technology have considerably increased the research on electroactive microbial biofilms over recent years. As a consequence, the research community is truly multifaceted, with backgrounds and interests ranging from molecular biology, via chemistry, to engineering. One of the most-important and most-widespread applied electrochemical techniques is cyclic voltammetry (CV). This Focus Review illustrates the power of this electrochemical technique and the versatility of the information that can be gained by its application for the electrochemical freshman. This Review will also pinpoint hurdles in using this technique, especially for the non-electrochemist, and the limitations of present models for data analysis. Because it aims to be a basic introduction, this Review will not discuss the latest intricacies in the field.

Implementation of Dynamic Plotting for a Ventilation Simulator on Android Mobile Devices

A ventilation simulator is implemented in android mobile devices to simulate the mechanics of the human lung. The simulation results shall be displayed by a dynamic plot to illustrate the trend of the ventilation parameters in real-time. The chosen software library to perform the plots is AndrodPlot [1]. The library provides basic features and tutorials for dynamic plotting. Tests were performed to find out whether dynamic plotting with dynamic speed and in real-time is possible and feasible with AndroidPlot. The tests consist of temporal analyses of redraw durations for the two used redrawing methods. Both methods use a separate thread to redraw the plot in fixed time intervals or to pass a signal which indicates a necessity for redrawing the plot. The tests showed that dynamic plotting with static speed and close to real-time is possible. Occurring limitations are the sampling frequency and domain width. These limitations should be dealt with to make the dynamic plotting more widely useable.

Binocular rivalry for beginners.

How to create and use binocular rivalry David Carmel, Michael Arcaro, Sabine Kastner, and Uri Hasson www.jove.com/video/2030/how-to-create-and-use-binocular-rivalry Binocular rivalry is a remarkable phenomenon of vision—two dissimilar images are presented simultaneously to each eye, and perception alternates between them. For example, if the left eye views horizontal lines and the right eye views vertical lines, an observer will report seeing one of the images for a few seconds, then the other, then the first again, and so on for as long as he or she cares to look (Wheatstone, 1838). You can experience this for yourself at www.psy.vanderbilt.edu/faculty/blake/rivalry/BR.html. Binocular rivalry is a popular tool for studying perception and awareness, because perception changes even when the physical stimulus does not. For this reason, rivalry is championed as a useful tool for studying the neural correlates of visual consciousness (Crick & Koch, 1990). However, despite there being a rich literature on rivalry, there are few teaching and learning resources devoted to the subject. Carmel, Arcaro, Kastner, and Hasson (2010) address this in their video: How to create and use binocular rivalry. The video begins with a brief description of binocular rivalry. It then provides a basic tutorial on the importance of stable vergence, because it ensures the two images fall on corresponding locations on the retina, as well as how it can be maintained during a rivalry experiment. For example, vergence can be maintained by surrounding each image with an identical frame of some sort, such as a simple or patterned border, and by placing an identical fixation point or cross in the centre of each image. The video also discusses some of the advantages and disadvantages of different methods to induce binocular rivalry. For example, chromatic (e.g., red-blue, red-green, etc.) goggles are inexpensive (a few dollars) and can be used with fMRI, but are prone to bleed-through and require careful stimulus preparation to ensure that each image can pass through only one of the chromatic filters. The video provides the same level of detail for the mirror stereoscope and prism goggles. Next, the video discusses the appearance of binocular rivalry. In particular, there is a neat demonstration of continuous flash suppression, a form of rivalry where a high-contrast image dominates perception indefinitely, and piecemeal rivalry, when patches of both images are perceived. Finally, the video discusses the distribution of dominance durations where time is plotted on the x-axis of a histogram and frequency is plotted on the y-axis, and that the data can be fitted with a gamma-like function. Overall, the video is professional and easy to use: the descriptions are accurate, the described methods are clear, and the accompanying pictures and demonstrations are crisp. Indeed, the video achieves what its title promises, but it does at the cost of some omission of important features of binocular rivalry. For example, the video mentions shutter and display goggles as methods to induce binocular rivalry, but fails to provide a discussion on the advantages and disadvantages of these techniques, and there is no discussion of the characteristics that affect rivalry. Also, there is no information about how to measure rivalry, such as by pressing one of two keys to report visibility of one of the images. This is especially surprising, because the video gives advice about the statistical tests to be used when analysing such data. Despite these minor omissions, How to create and use binocular rivalry covers a good chunk of material. It is also accompanied by a paper in which some of the video's deficiencies are redressed and in which there is a useful set of references. Although binocular-rivalry enthusiasts will be well-versed in the video's content, it is unlikely that students and newcomers to the field will be, too. For this reason, I strongly endorse Carmel et al.'s (2010) video for teaching and learning purposes. Bradley N. Jack, Discipline of Psychology and Cognitive Neuroscience Research Cluster, School of Health and Human Sciences, Southern Cross University, Coffs Harbour, Australia

ウィキペディアの基本的な編集方法と考え方 間違いを正しく編集する

本稿では，ウィキペディアの簡単な編集方法を解説することで，参加への障壁を取り除くことを試みる。ごく単純な間違いの修正，アカウントの登録とその取り扱い，自分自身または自分に密接に関わりのある記事の編集を扱う。

SYNTAX Score Reproducibility and Variability Between Interventional Cardiologists, Core Laboratory Technicians, and Quantitative Coronary Measurements

In the Synergy between Percutaneous Coronary Intervention with Taxus and Cardiac Surgery (SYNTAX) trial, the SYNTAX score was useful in risk stratifying patients with complex coronary artery disease. The reproducibility of this score may affect its clinical utility. We therefore assessed SYNTAX score interobserver and intraobserver variability among a group of interventional cardiologists (ICs) and an experienced group of angiographic core laboratory (ACL) technicians. After basic training from the SYNTAX score website, 3 ICs and 4 ACL technicians, each working independently, assessed the SYNTAX score of 30 multivessel disease angiograms. The ICs then underwent an intensive training session with ACL technicians, after which the SYNTAX score from 50 additional angiograms were assessed independently by both groups. Interobserver Fleiss κ statistic values were determined. A third assessment was performed using quantitative coronary angiography (QCA). The ACL technician interobserver strength of agreement from both periods was substantial or greater (k=0.82; 95% CI [0.72, 1.00] and 0.84 [0.76, 1.00]) and not different than QCA. The IC interobserver agreement was initially estimated to be at least slight (k=0.33 [0.18, 0.44]), improving to substantial or greater after advanced training (k=0.76 [0.64, 1.00]). Despite advanced training, ICs underscored the number of lesions, bifurcations, and small-vessel disease (P<0.001), resulting in a lower score than ACL technicians (mean difference=7.5, P<0.001). Highly reproducible SYNTAX score measurements were quickly achieved by experienced ACL technicians. In contrast, agreement among ICs after the basic tutorial was initially poor but improved considerably after further training with the ACL, although differences still remained in interpretation of several lesion types. These findings have important implications for adoption of SYNTAX score methodology in routine practice and future clinical trials.