Deciphering the protein-RNA recognition code: Combining large-scale quantitative methods with structural biology

BioEssays ◽  
2015 ◽  
Vol 37 (8) ◽  
pp. 899-908 ◽  
Author(s):  
Janosch Hennig ◽  
Michael Sattler
Keyword(s):  
Structural Biology ◽  
Large Scale ◽  
Quantitative Methods ◽  
Rna Recognition ◽  
Recognition Code ◽  
Code Combining

scholarly journals Measuring the value of a digital supplemental resource

2021 ◽  
Vol 45 (4) ◽  
pp. 685-693
Author(s):  
Yvonne M. Baptiste ◽  
Samuel Abramovich ◽  
Cherylea J. Browne
Keyword(s):  
Factor Analysis ◽  
Science Education ◽  
Construct Validity ◽  
Student Perceptions ◽  
Large Scale ◽  
Quantitative Methods ◽  
Student Perception ◽  
Digital Learning ◽  
Internal Reliability ◽  
Traditional Component

Supplemental resources in science education are made available to students based on the belief that they will improve course-based student learning. This belief is ubiquitous, with supplemental resources being a traditional component of physiology education. In addition, the recent large-scale transition to remote learning caused by the Covid-19 pandemic suggests an increased relevance and necessity of digital versions of supplemental resources. However, the use of a supplemental resource is entirely dependent on whether students view it as beneficial. If students in a specific course do not perceive a supplemental resource as useful, there is little reason to believe the resources will be used and are worthy of investment. Consequently, measurement of student perception regarding the effectiveness of any digital learning tool is essential for educators and institutions in order to prioritize resources and make meaningful recommendations to students. In this study, a survey was used to determine student perceptions of a digital, supplemental resource. Quantitative methods, including exploratory factor analysis, were performed on data collected from the survey to examine the dimensionality and functionality of this survey. The findings from this study were used to devise an improved, standardized (i.e., reliable and valid) survey that can be used and adapted by physi3ology researchers and educators to determine student perception of a digital supplemental resource. The survey, with known construct validity and internal reliability, can provide useful information for administrators, instructors, and designers of digital supplemental resources.

scholarly journals Theoretical Analysis of S, M and N Structural Proteins by the Protein–RNA Recognition Code Leads to Genes/proteins that Are Relevant to the SARS-CoV-2 Life Cycle and Pathogenesis

2021 ◽  
Vol 12 ◽  
Author(s):  
Jozef Nahalka
Keyword(s):  
Life Cycle ◽  
Transcriptional Repression ◽  
Lipid Homeostasis ◽  
Epithelial Tissue ◽  
Rna Recognition ◽  
Review Of Literature ◽  
Recognition Code ◽  
Host Genes

In this conceptual review, based on the protein–RNA recognition code, some theoretical sequences were detected in the spike (S), membrane (M) and capsid (N) proteins that may post-transcriptionally regulate the host genes/proteins in immune homeostasis, pulmonary epithelial tissue homeostasis, and lipid homeostasis. According to the review of literature, the spectrum of identified genes/proteins shows that the virus promotes IL1α/β–IL1R1 signaling (type 1 immunity) and immunity defense against helminths and venoms (type 2 immunity). In the alteration of homeostasis in the pulmonary epithelial tissue, the virus blocks the function of cilia and the molecular programs that are involved in wound healing (EMT and MET). Additionally, the protein–RNA recognition method described here identifies compatible sequences in the S1A-domain for the post-transcriptional promotion of PIKFYVE, which is one of the critical factors for SARS-CoV-2 entry to the host cell, and for the post-transcriptional repression of xylulokinase XYLB. A decrease in XYLB product (Xu5P) in plasma was proposed as one of the potential metabolomics biomarkers of COVID-19. In summary, the protein–RNA recognition code leads to protein genes relevant to the SARS-CoV-2 life cycle and pathogenesis.

SEARCH FOR NEW METHODOLOGICAL APPROACHES AND METHODS IN RISK MANAGEMENT

2021 ◽  
Vol 54 (2) ◽  
pp. 35-47
Author(s):  
Svetlana N. Dvoryatkina ◽  
◽  
Arseny M. Lopukhin ◽  
Keyword(s):  
Risk Management ◽  
Large Scale ◽  
Quantitative Methods ◽  
Knowledge Bases ◽  
Fractal Model ◽  
Educational Process ◽  
Machine Learning Algorithms ◽  
Risk Modeling ◽  
Negative Consequences ◽  
Fractal Approach

The study actualized the complex and large-scale problem of adapting the theory of risk man-agement for the education system. A comprehensive analysis of domestic and international stud-ies revealed the lack of a theoretical framework, a general methodological vision of the problem of riskiness and risk-taking in the educational sphere. While effective management of education-al activities, ensuring the development of the competitiveness of the individual in the labor mar-ket and its potential for active participation in the life of society is possible on the basis of the modern paradigm of risk management, integrating achievements in pedagogical, economic, mathematical and computer sciences. A new methodology in the study is the fractal approach, which defines the idea of quantitative and qualitative analysis and assessment of the risk of non-formation of professional competencies, complex educational and cognitive constructs of subject activity. The fractal model of assessing the formation of knowledge and competencies, its risk landscape, taking into account the subject and cognitive divergence, will ensure the effective-ness of the structure of knowledge storage in the educational process, minimizing the time for building space and engineering knowledge bases, and the depth of solving the problem of pre-dicting educational risks. New methods of risk modeling based on machine learning algorithms and factor analysis, methods for constructing neural integrators, quantitative methods with and without taking into account the probability distribution will ensure the accuracy and speed of risk assessment and prediction, will allow one to identify new patterns of risk activity and further ways to develop the theory of risk. The presented effective strategies and innovative tools will solve the problem of minimizing unplanned chaos, the cascade of negative consequences of risky situations, including the COVID-19 epidemic.

A Multi-Methodological Approach to Study Systems Development in a Software Organization

2009 ◽  
pp. 2285-2306
Author(s):  
Paivi Ovaska
Keyword(s):  
Large Scale ◽  
Quantitative Methods ◽  
Development Process ◽  
Organizational Context ◽  
Methodological Approach ◽  
Research Process ◽  
Systems Development ◽  
Qualitative And Quantitative ◽  
Qualitative And Quantitative Methods ◽  
Software Organization

Large-scale systems development is a complex activity involving number of dependencies that people working together face. Only a few studies concentrate on the coordination of development activities in their organizational context. This research study tries to fill at least part of this gap by studying how systems development process is coordinated in practice. The study uses a multimethodological approach to interpret coordination of systems development process in a contemporary software organization in Finland. The methodology is based on the empirical casestudy approach in which the actions, conceptions, and artefacts of practitioners are analyzed using within-case and cross-case principles. In all the three phases of the study, namely multi-\site coordination, requirement understanding, and working with systems development methods, both the qualitative and quantitative methods were used to an understanding of coordination in systems development. The main contribution of this study is to demonstrate that contemporary systems development is much more complex and more driven by opportunity than is currently acknowledged by researchers. The most challenging part of the research process was the combination of qualitative and quantitative methods, because of the lack of multimethodological work done in IS discipline.

A Multi-Methodological Approach to Study Systems Development in a Software Organization

2009 ◽  
pp. 162-182
Author(s):  
Paivi Ovaska
Keyword(s):  
Large Scale ◽  
Quantitative Methods ◽  
Development Process ◽  
Organizational Context ◽  
Research Process ◽  
Systems Development ◽  
Qualitative And Quantitative ◽  
Qualitative And Quantitative Methods ◽  
Study Approach ◽  
Software Organization

Large-scale systems development is a complex activity involving number of dependencies that people working together face. Only a few studies concentrate on the coordination of development activities in their organizational context. This research study tries to fill at least part of this gap by studying how systems development process is coordinated in practice. The study uses a multimethodological approach to interpret coordination of systems development process in a contemporary software organization in Finland. The methodology is based on the empirical case-study approach in which the actions, conceptions, and artefacts of practitioners are analyzed using within-case and cross-case principles. In all the three phases of the study, namely multi-\site coordination, requirement understanding, and working with systems development methods, both the qualitative and quantitative methods were used to an understanding of coordination in systems development. The main contribution of this study is to demonstrate that contemporary systems development is much more complex and more driven by opportunity than is currently acknowledged by researchers. The most challenging part of the research process was the combination of qualitative and quantitative methods, because of the lack of multimethodological work done in IS discipline.

Network-Driven Analysis Methods and their Application to Drug Discovery

2011 ◽  
pp. 294-315
Author(s):  
Daniel Ziemek ◽  
Christoph Brockel
Keyword(s):  
Drug Discovery ◽  
Large Scale ◽  
Quantitative Methods ◽  
Primary Data ◽  
Success Rates ◽  
Parallel Methods ◽  
Development Face ◽  
Large Scale Data ◽  
Analysis Methods ◽  
Genome Scale

Drug discovery and development face tremendous challenges to find promising intervention points for important diseases. Any therapeutic agent targeting such an intervention point must prove its efficacy and safety in patients. Success rates measured from first studies in human to registration average around 10% only. Over the last decade, massive knowledge on biological systems has been accumulated and genome-scale primary data are produced at an ever increasing rate. In parallel, methods to use that knowledge have matured. This chapter will present some of the problems facing the pharmaceutical industry and elaborate on the current state of network-driven analysis methods. It will focus especially on semi-quantitative methods that are applicable to large-scale data analysis and point out their potential use in many relevant drug discovery challenges.

Investigating risk of bridge construction project: exploring Suramadu strait-crossing cable-stayed bridge in Indonesia

2020 ◽  
Vol 12 (1) ◽  
pp. 127-142
Author(s):  
Citra S. Ongkowijoyo ◽  
Argaw Gurmu ◽  
Andi Andi
Keyword(s):  
Large Scale ◽  
Quantitative Methods ◽  
Practical Implication ◽  
Rank Correlation ◽  
The Body ◽  
Content Type ◽  
Cable Stayed Bridge ◽  
Spearman’S Rank Correlation ◽  
Risk Event ◽  
Construction Risks

Purpose The complexities in strait-crossing cable-stayed bridge project are increasing the risks. This study aims to identify and analyze the significant and worth-considered construction risks of the first, biggest and longest spanned strait-crossing bridge project in Indonesia. Design/methodology/approach As many as 32 risk events were identified and determined as the risks that exist and can be represented in the Suramadu bridge project context. Data was collected through a design-based questionnaire disseminated to experts involved in the project as well as semi-formal interviews. Several quantitative methods were applied to analyze the significant risks, such as relative importance index, Spearman’s rank correlation test and Mann–Whitney U test. Findings The analyses reveal that “unexpected natural behavior” confirmed by both contractor and consultant parties is the most significant and crucial risk event. Another risk event found to be significant is the “delayed payment.” On the other hand, it is also found that several risks within the legal category are found to be less significant compared to other major risk events. Research limitations/implications The results of the present research should be interpreted in the context of several limitations. Given these possible concerns regarding the generalizability of the findings, along with the relatively low rate of participants in the current research, additional studies are needed to provide a more complete picture of stakeholder perceptions who are involved directly in the construction environment as well as to identify more construction risks specifically in the large-scale bridge project. Practical implications This study has provided fundamental contributions to the body of knowledge and practical implication to promote and assist decision-makers toward developing a comprehensive risk assessment of a large-scale bridge project. Originality/value The analyses of outcomes and discussion, as well as the findings of this research, have shed light on the construction risks understanding, which contributes to delivering a theoretical framework for achieving large-scale bridge project success.

scholarly journals Perspectives on the Capabilities for the Selection of Strategic Projects

2020 ◽  
Vol 12 (19) ◽  
pp. 8191
Author(s):  
Khalifa Mohammed Al-Sobai ◽  
Shaligram Pokharel ◽  
Galal M. Abdella
Keyword(s):  
Large Scale ◽  
Quantitative Methods ◽  
Project Selection ◽  
Economic Benefits ◽  
Research Directions ◽  
Qualitative And Quantitative Methods ◽  
Strategic Project ◽  
Managerial Capabilities ◽  
Selection Of

Strategic projects are large scale, complex, and require significant investments and resources. These projects aim at gaining long-term social and economic benefits. Therefore, organizations focusing on strategic projects should use a consistent approach that suits their strategy, capability, and long-term expectations. Based on the four research questions and content analysis of the literature, generic processes used for the strategic project selection in tandem with the managerial capabilities are identified in this paper. The generic processes and managerial capabilities are used to develop a generic framework for strategic project selection. The framework is used for literature analysis in the paper. The review shows that both qualitative and quantitative methods are used for strategic project selection. Some possible research directions have also been proposed at the end of the review. The paper provides value to both researchers and practitioners in terms of tools available and a guidance on project selection through a structured process framework.

Creation of firm performance through resource orchestration: the case of ÜLKER

2015 ◽  
Vol 25 (2) ◽  
pp. 179-204 ◽  
Author(s):  
Rifat Kamasak
Keyword(s):  
Firm Performance ◽  
Large Scale ◽  
Quantitative Methods ◽  
Business Processes ◽  
Empirical Studies ◽  
Complex Nature ◽  
Content Type ◽  
Study Approach ◽  
Multiple Data

Purpose – This study aims to investigate the complex interaction of different resource sets and capabilities in the process of performance creation within the context of resource-based theory. Design/methodology/approach – An inductive case study approach that included multiple data collection methods such as in-depth interviews, observation and documentation was utilized. Findings – Organizational culture, reputational assets, human capital, business processes and networking capabilities were found as the most important determinants of firm performance within the context of Ülker case study. Originality/value – Although large-scale empirical studies can be used to explore the direct resource–performance relationship, these quantitative methods bypass the complex and embedded nature of intangibles and provide only a limited understanding of why some resources are identified as strategic but others are not, what their roles are, and how these resources are converted into positions of competitive advantage. However, understanding of complex nature of resources that are embedded in organizations designates the need for more fieldwork-based qualitative studies. This study aims to address this gap by providing a thorough understanding about the managerial and organizational processes through which the resources become valuable.

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