Demystification of RNAseq Quality Control

Next Generation Sequencing (NGS) analysis has become a widely used method for studying the structure of DNA and RNA, but complexity of the procedure leads to obtaining error-prone datasets which need to be cleansed in order to avoid misinterpretation of data. We address the usage and proper interpretations of characteristic metrics for RNA sequencing (RNAseq) quality control, implemented in and reported by FastQC, and provide a comprehensive guidance for their assessment in the context of total RNAseq quality control of Illumina raw reads. Additionally, we give recommendations how to adequately perform the quality control preprocessing step of raw total RNAseq Illumina reads according to the obtained results of the quality control evaluation step; the aim is to provide the best dataset to downstream analysis, rather than to get better FastQC results. We also tested effects of different preprocessing approaches to the downstream analysis and recommended the most suitable approach.

EVALUATION INSTRUMENTS OF COMPREHENSIVE GUIDANCE AND COUNSELING PROGRAM IN THE CULTURE OF HIGHER EDUCATION INSTITUTIONS IN INDONESIA

Program evaluation in comprehensive guidance and counseling is very important to determine the level of goal achievement. In order for the evaluation results to provide the right information, a valid and reliable instrument is needed. At the higher education level, the comprehensive guidance and counseling program, including the program evaluation component, does not have many references that users can refer to. The available references focus more on primary and secondary education levels. This research is intended to produce the intended evaluation instrument. Descriptive methods and literature review were used in this study. The data were revealed using a Delphi technique questionnaire involving three experts, then analyzed qualitatively and quantitatively. In this study, the constructs of evaluation instruments for comprehensive guidance and counseling programs were synthesized and modified from various expert opinions and professional organizations with two patterns of answers: yes and no, translated into 294 statements. The resulting evaluation instrument needs to be empirically tested for its feasibility by involving adequate participants.

Organized structure of real-world evidence best practices: moving from fragmented recommendations to comprehensive guidance

Decision-makers have become increasingly interested in incorporating real-world evidence (RWE) into their decision-making process. Due to concerns regarding the reliability and quality of RWE, stakeholders have issued numerous recommendation documents to assist in setting RWE standards. The fragmented nature of these documents poses a challenge to researchers and decision-makers looking for guidance on what is ‘high-quality’ RWE and how it can be used in decision-making. We offer researchers and decision-makers a structure to organize the landscape of RWE recommendations and identify consensus and gaps in the current recommendations. To provide researchers with a much needed pathway for generating RWE, we discuss how decision-makers can move from fragmented recommendations to comprehensive guidance.

The International Federation for Emergency Medicine report on emergency department crowding and access block: a brief summary

Objective To develop comprehensive guidance that captures international impacts, causes, and solutions related to emergency department crowding and access block Methods Emergency physicians representing 15 countries from all IFEM regions composed the Task Force. Monthly meetings were held via video-conferencing software to achieve consensus for report content. The report was submitted and approved by the IFEM Board on June 1, 2020. Results A total of 14 topic dossiers, each relating to an aspect of ED crowding, were researched and completed collaboratively by members of the Task Force. Conclusions The IFEM report is a comprehensive document intended to be used in whole or by section to inform and address aspects of ED crowding and access block. Overall, ED crowding is a multifactorial issue requiring systems-wide solutions applied at local, regional, and national levels. Access block is the predominant contributor of ED crowding in most parts of the world.

The International Federation for Emergency Medicine report on emergency department crowding and access block: A brief summary

ObjectiveTo develop comprehensive guidance that captures international impacts, causes and solutions related to emergency department (ED) crowding and access block.MethodsEmergency physicians representing 15 countries from all International Federation of Emergency Medicine (IFEM) regions composed the Task Force. Monthly meetings were held via video-conferencing software to achieve consensus for report content. The report was submitted and approved by the IFEM Board on June 1, 2020.ResultsA total of 14 topic dossiers, each relating to an aspect of ED crowding, were researched and completed collaboratively by members of the Task Force.ConclusionsThe IFEM report is a comprehensive document intended to be used in whole or by section to inform and address aspects of ED crowding and access block. Overall, ED crowding is a multifactorial issue requiring systems-wide solutions applied at local, regional, and national levels. Access block is the predominant contributor of ED crowding in most parts of the world.

Recognizing the value of software: a software citation guide

Software is as integral as a research paper, monograph, or dataset in terms of facilitating the full understanding and dissemination of research. This article provides broadly applicable guidance on software citation for the communities and institutions publishing academic journals and conference proceedings. We expect those communities and institutions to produce versions of this document with software examples and citation styles that are appropriate for their intended audience. This article (and those community-specific versions) are aimed at authors citing software, including software developed by the authors or by others. We also include brief instructions on how software can be made citable, directing readers to more comprehensive guidance published elsewhere. The guidance presented in this article helps to support proper attribution and credit, reproducibility, collaboration and reuse, and encourages building on the work of others to further research.

The importance of software citation

Software is as integral as a research paper, monograph, or dataset in terms of facilitating the full understanding and dissemination of research. This article provides broadly applicable guidance on software citation for the communities and institutions publishing academic journals and conference proceedings. We expect those communities and institutions to produce versions of this document with software examples and citation styles that are appropriate for their intended audience. This article (and those community-specific versions) are aimed at authors citing software, including software developed by the authors or by others. We also include brief instructions on how software can be made citable, directing readers to more comprehensive guidance published elsewhere. The guidance presented in this article helps to support proper attribution and credit, reproducibility, collaboration and reuse, and encourages building on the work of others to further research.