scholarly journals Learning structural bioinformatics and evolution with a snake puzzle

2016 ◽  
Vol 2 ◽  
pp. e100 ◽  
Author(s):  
Gonzalo S. Nido ◽  
Ludovica Bachschmid-Romano ◽  
Ugo Bastolla ◽  
Alberto Pascual-García
Keyword(s):  
Teaching Practice ◽  
Protein Structures ◽  
Simple Algorithm ◽  
Structural Bioinformatics ◽  
Data Availability ◽  
Folding Kinetics ◽  
Contact Order ◽  
Contact Matrix ◽  
Supplementary Material ◽  
High Level

We propose here a working unit for teaching basic concepts of structural bioinformatics and evolution through the example of a wooden snake puzzle, strikingly similar to toy models widely used in the literature of protein folding. In our experience, developed at a Master’s course at the Universidad Autónoma de Madrid (Spain), the concreteness of this example helps to overcome difficulties caused by the interdisciplinary nature of this field and its high level of abstraction, in particular for students coming from traditional disciplines. The puzzle will allow us discussing a simple algorithm for finding folded solutions, through which we will introduce the concept of the configuration space and the contact matrix representation. This is a central tool for comparing protein structures, for studying simple models of protein energetics, and even for a qualitative discussion of folding kinetics, through the concept of the Contact Order. It also allows a simple representation of misfolded conformations and their free energy. These concepts will motivate evolutionary questions, which we will address by simulating a structurally constrained model of protein evolution, again modelled on the snake puzzle. In this way, we can discuss the analogy between evolutionary concepts and statistical mechanics that facilitates the understanding of both concepts. The proposed examples and literature are accessible, and we provide supplementary material (see ‘Data Availability’) to reproduce the numerical experiments. We also suggest possible directions to expand the unit. We hope that this work will further stimulate the adoption of games in teaching practice.

scholarly journals Learning protein folding and evolution with a snake puzzle

2016 ◽  
Author(s):  
Gonzalo S Nido ◽  
Ludovica Bachschmid-Romano ◽  
Ugo Bastolla ◽  
Alberto Pascual-García
Keyword(s):  
Protein Folding ◽  
Teaching Practice ◽  
Protein Structures ◽  
Simple Algorithm ◽  
Folding Kinetics ◽  
Structure Comparison ◽  
Contact Matrix ◽  
Supplementary Material ◽  
The Stability ◽  
High Level

We propose here a working unit for teaching basic concepts of protein folding and evolution centred around the example of a wooden snake puzzle, strikingly similar to toy models widely used in the literature of protein folding. In our experience, developed at a Master course at the Universidad Autónoma de Madrid (Spain), the concreteness of this example helps to overcome difficulties caused by the interdisciplinary nature of this field and its high level of abstraction, in particular for students coming from traditional disciplines. The puzzle will allow us discussing a simple algorithm for finding folded solutions, through which we will introduce the concept of the configuration space and the contact matrix representation. This is a central tool for comparing protein structures, for studying simple models of protein energetics, and even for a qualitative discussion of folding kinetics, through the concept of the Contact Overlap. It also allows a simple representation of misfolded conformations and their free energy. These concepts, in particular protein structure comparison and the stability of the native state with respect to unfolded and misfolded conformations, will motivate evolutionary questions. We address these questions by simulating a structurally constrained model of protein evolution, again modelled on the snake puzzle. In this way, we can discuss the analogy between evolutionary concepts and statistical mechanics that facilitates the understanding of both concepts. The proposed examples and literature are accessible, and we provide supplementary material to reproduce the numerical experiments. We also suggest possible directions to expand the unit. We hope that this work will further stimulate the adoption of games in teaching practice.

scholarly journals Learning protein folding and evolution with a snake puzzle

2016 ◽  
Author(s):  
Gonzalo S Nido ◽  
Ludovica Bachschmid-Romano ◽  
Ugo Bastolla ◽  
Alberto Pascual-García
Keyword(s):  
Protein Folding ◽  
Teaching Practice ◽  
Protein Structures ◽  
Simple Algorithm ◽  
Folding Kinetics ◽  
Structure Comparison ◽  
Contact Matrix ◽  
Supplementary Material ◽  
The Stability ◽  
High Level

We propose here a working unit for teaching basic concepts of protein folding and evolution centred around the example of a wooden snake puzzle, strikingly similar to toy models widely used in the literature of protein folding. In our experience, developed at a Master course at the Universidad Autónoma de Madrid (Spain), the concreteness of this example helps to overcome difficulties caused by the interdisciplinary nature of this field and its high level of abstraction, in particular for students coming from traditional disciplines. The puzzle will allow us discussing a simple algorithm for finding folded solutions, through which we will introduce the concept of the configuration space and the contact matrix representation. This is a central tool for comparing protein structures, for studying simple models of protein energetics, and even for a qualitative discussion of folding kinetics, through the concept of the Contact Overlap. It also allows a simple representation of misfolded conformations and their free energy. These concepts, in particular protein structure comparison and the stability of the native state with respect to unfolded and misfolded conformations, will motivate evolutionary questions. We address these questions by simulating a structurally constrained model of protein evolution, again modelled on the snake puzzle. In this way, we can discuss the analogy between evolutionary concepts and statistical mechanics that facilitates the understanding of both concepts. The proposed examples and literature are accessible, and we provide supplementary material to reproduce the numerical experiments. We also suggest possible directions to expand the unit. We hope that this work will further stimulate the adoption of games in teaching practice.

Improved Proofs Of Retrievability And Replication For Data Availability In Cloud Storage

2020 ◽  
Vol 63 (8) ◽  
pp. 1216-1230 ◽  
Author(s):  
Wei Guo ◽  
Sujuan Qin ◽  
Jun Lu ◽  
Fei Gao ◽  
Zhengping Jin ◽  
...  
Keyword(s):  
Service Providers ◽  
Cloud Service ◽  
Data Availability ◽  
Forgery Attack ◽  
Common Strategy ◽  
Comparable Performance ◽  
Replication Scheme ◽  
High Level ◽  
Cloud Users ◽  
Proofs Of Retrievability

Abstract For a high level of data availability and reliability, a common strategy for cloud service providers is to rely on replication, i.e. storing several replicas onto different servers. To provide cloud users with a strong guarantee that all replicas required by them are actually stored, many multi-replica integrity auditing schemes were proposed. However, most existing solutions are not resource economical since users need to create and upload replicas of their files by themselves. A multi-replica solution called Mirror is presented to overcome the problems, but we find that it is vulnerable to storage saving attack, by which a dishonest provider can considerably save storage costs compared to the costs of storing all the replicas honestly—while still can pass any challenge successfully. In addition, we also find that Mirror is easily subject to substitution attack and forgery attack, which pose new security risks for cloud users. To address the problems, we propose some simple yet effective countermeasures and an improved proofs of retrievability and replication scheme, which can resist the aforesaid attacks and maintain the advantages of Mirror, such as economical bandwidth and efficient verification. Experimental results show that our scheme exhibits comparable performance with Mirror while achieving high security.

scholarly journals Immersive Gesture Interfaces for Navigation of 3D Maps in HMD-Based Mobile Virtual Environments

2018 ◽  
Vol 2018 ◽  
pp. 1-11 ◽  
Author(s):  
Yea Som Lee ◽  
Bong-Soo Sohn
Keyword(s):  
Virtual Environments ◽  
User Study ◽  
Simple Algorithm ◽  
3D Models ◽  
Google Earth ◽  
Depth Camera ◽  
Immersive Virtual Reality ◽  
Head Mounted Displays ◽  
Gesture Interfaces ◽  
High Level

3D maps such as Google Earth and Apple Maps (3D mode), in which users can see and navigate in 3D models of real worlds, are widely available in current mobile and desktop environments. Users usually use a monitor for display and a keyboard/mouse for interaction. Head-mounted displays (HMDs) are currently attracting great attention from industry and consumers because they can provide an immersive virtual reality (VR) experience at an affordable cost. However, conventional keyboard and mouse interfaces decrease the level of immersion because the manipulation method does not resemble actual actions in reality, which often makes the traditional interface method inappropriate for the navigation of 3D maps in virtual environments. From this motivation, we design immersive gesture interfaces for the navigation of 3D maps which are suitable for HMD-based virtual environments. We also describe a simple algorithm to capture and recognize the gestures in real-time using a Kinect depth camera. We evaluated the usability of the proposed gesture interfaces and compared them with conventional keyboard and mouse-based interfaces. Results of the user study indicate that our gesture interfaces are preferable for obtaining a high level of immersion and fun in HMD-based virtual environments.

The Use of Contract Adjustments to Lengthen the CEO Horizon in the Presence of Internal and External Monitoring

2013 ◽  
Vol 25 (1) ◽  
pp. 199-229 ◽  
Author(s):  
Shane S. Dikolli ◽  
Susan L. Kulp ◽  
Karen L. Sedatole
Keyword(s):  
Boards Of Directors ◽  
Data Availability ◽  
Shareholder Rights ◽  
Compensation Contracts ◽  
Job Change ◽  
External Monitoring ◽  
Increased Risk ◽  
Short Horizon ◽  
High Level ◽  
A Current

ABSTRACT We investigate whether boards of directors adjust compensation contracts to lengthen a CEO's decision horizon, and if the use of such contract adjustments depends on the levels of external (i.e., shareholder-based) and internal (i.e., board-based) CEO monitoring. Based on insights from the career-concerns literature, we identify short-horizon CEOs as those nearing retirement, at a firm with a current earnings decline or loss, and/or with an impending job change. We find that firms with a CEO identified as having a short-horizon place greater contract weight on forward-looking information. This horizon-lengthening contract adjustment is less pronounced when there is greater external monitoring (i.e., as proxied by a high level of shareholder rights), consistent with the intuition that increased shareholder rights mitigate CEO entrenchment, leading to less myopic decision making, independent of a contract adjustment. However, we also find that the horizon-lengthening contract adjustment is more pronounced when there is greater internal monitoring (i.e., as proxied by characteristics of the board), consistent with the intuition that increased employment risk from more intense internal monitoring itself creates a demand for increased incentive weights as a means of compensating the CEO for the increased risk. Data Availability: Data used for this study are derived from publicly available databases and proxy statements. JEL Classifications: M52; M41; J33.

scholarly journals A Globally Consistent Stress Testing Approach

2019 ◽  
Vol 4 (3) ◽  
pp. p153
Author(s):  
Colin Ellis
Keyword(s):  
Stress Testing ◽  
Expected Shortfall ◽  
Data Availability ◽  
Rank Ordering ◽  
Testing Approach ◽  
Bank Solvency ◽  
High Level ◽  
Loan Losses ◽  
Compare And Contrast ◽  
Expected Outcomes

This paper describes an approach for stress testing banks that is consistent across economies and geographies, in contrast to common “macro scenario” driven approaches. The latter would require economic scenarios to be both equally likely (in a probabilistic sense) and equally stressful (in a conditional loss sense) across countries in order to be comparable. The paper proposes a three-pronged approach for stressing bank solvency, which incorporates recalibrating pre-crisis Basel capital assumptions, adapting the BIS “expected shortfall” approach for securities, and using granular data for income haircuts. Loan losses are quantified using a simple “multiples” approach, starting from expected outcomes, which is derived from the pre-crisis Basel technical proposal. The approach is practical, can be more granular or conducted at a high level, depending on data availability, and offers a simple way for regulators, investors or risk assessors to compare and contrast stresses in different banking systems. Of the eight bank defaults recorded globally during 2017, this approach would have given a better “rank ordering” for seven of them, indicating the approach adds value to traditional solvency metrics.

scholarly journals Evaluation Results of an Online Teacher Training Course Specialized in Engineering Education

2021 ◽  
Vol 11 (5) ◽  
pp. 54
Author(s):  
Diego Gormaz-Lobos ◽  
Claudia Galarce-Miranda ◽  
Steffen Kersten
Keyword(s):  
Engineering Education ◽  
Teaching Practice ◽  
Academic Staff ◽  
Descriptive Analysis ◽  
Working Hours ◽  
Pilot Project ◽  
Research Process ◽  
Training Course ◽  
Online Teacher Training ◽  
High Level

The purpose of this article is to present the results of the evaluation of the imple-mentation of a teaching training course in Engineering Pedagogy (EP) at a Chilean university of applied sciences. The research questions that guided the research process were: (i) How do the participants evaluate the course in general? (ii) How do the participants evaluate the didactic design of the course? (iii) How do they evaluate the teaching competencies? (iv) How do they value the usefulness of the learning outcomes for their teaching practice? (v) How they self-evaluate their participation and their learning process? Based on different authors a questionnaire with closed and open-ended questions was developed and implemented online. For the statistical analysis was applied an exploratory-descriptive analysis. The training course consists of two online modules with 90 working hours in LMS, and was designed by the Center of Engineering Education (CIEI) at the University of Talca, according to the IGIP Curricula of the IGIP center at the Technische Universität Dresden (TU Dresden, Germany). From the first results of the pilot project, it can be noted that there is a high level of motivation and interest to participate in a teaching training course based on EP, which has been specially oriented and designed to meet the specific requirements of the academic staff of engineering schools.

scholarly journals Using the Nordic Geodetic Observing System for land uplift studies

Solid Earth ◽  
2014 ◽  
Vol 5 (2) ◽  
pp. 673-681 ◽  
Author(s):  
M. Nordman ◽  
M. Poutanen ◽  
A. Kairus ◽  
J. Virtanen
Keyword(s):  
International Association ◽  
Data Availability ◽  
Absolute Gravity ◽  
Data Sets ◽  
Land Uplift ◽  
Mantle Dynamics ◽  
Quaternary Climate ◽  
General Data ◽  
Supplementary Material ◽  
Observing Systems

Abstract. Geodetic observing systems have been planned and developed during the last decade. An ideal observing system consists of a network of geodetic observing stations with several techniques at the same site, publicly accessible databases, and as a product delivers data time series, combination of techniques or some other results obtained from the data sets. Globally, there is the International Association of Geodesy (IAG) Global Geodetic Observing System (GGOS), and there are ongoing attempts to create also regional observing systems. In this paper we introduce one regional system, the Nordic Geodetic Observing System (NGOS) hosted by the Nordic Geodetic Commission (NKG). Data availability and accessibility are one of the major issues today. We discuss in general data-related topics, and introduce a pilot database project of NGOS. As a demonstration of the use of such a database, we apply it for postglacial rebound studies in the Fennoscandian area. We compare land uplift values from three techniques, GNSS, tide gauges and absolute gravity, with the Nordic Geodetic Commission NKG2005LU land uplift model for Fennoscandia. The purpose is to evaluate the data obtained from different techniques and different sources and get the most reliable values for the uplift using publicly available data. The primary aim of observing systems will be to produce data and other products needed by multidisciplinary projects, such as Upper Mantle Dynamics and Quaternary Climate in Cratonic Areas (DynaQlim) or the European Plate Observing System (EPOS), but their needs may currently exceed the scope of an existing observing system. We discuss what requirements the projects pose to observing systems and their development. To make comparisons between different studies possible and reliable, the researcher should document what they have in detail, either in appendixes, supplementary material or some other available format.

Materiality Guidance of the Major Public Accounting Firms

2014 ◽  
Vol 34 (2) ◽  
pp. 3-26 ◽  
Author(s):  
Aasmund Eilifsen ◽  
William F. Messier
Keyword(s):  
Data Availability ◽  
Future Research ◽  
Public Accounting ◽  
Accounting Firms ◽  
Public Accounting Firms ◽  
Qualitative Factors ◽  
Research And Education ◽  
High Level ◽  
Implementation Of Standards

SUMMARY This paper examines the materiality guidance for eight of the largest U.S. public accounting firms. Knowledge of how materiality guidance is integrated into a firm's methodology is important for accounting and auditing researchers as well as for practitioners, regulators, and educators. Our results show a high level of consistency across the firms in terms of the quantitative benchmarks (e.g., income before taxes, total assets or revenues, and total equity) used to determine overall materiality, the related percentages applied to those benchmarks, the percentages applied to overall materiality for determining tolerable misstatement, and what constitutes a clearly trivial misstatement. We also find that the firms' guidance for evaluating detected misstatements, including qualitative factors and firm guidance for group audits, is consistent across firms. However, there are differences in how the firms consider the possibility of undetected misstatements when evaluating detected misstatements. The results of this study provide important insights into implementation of standards and valuable information for future research and education. Data Availability: The data used are proprietary to the firms and are not available for distribution.

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