Exploring the value of pro bono evaluation work as a method to build evaluator competencies and strengthen organizational capacity.

The Cultivating Evaluation Education and Development (CEED) program engages early career evaluators in an experiential learning experience by supporting them as they lead a pro bono evaluation for a local nonprofit community organization. We explored the value of this professional development to the early career evaluators, to the sponsor organization, and to the nonprofit organizations receiving CEED services by examining findings from six CEED projects. We found that early career evaluators self-reported gains in confidence and competence especially in four American Evaluation Association Evaluator Competencies (2018) domains - professional practice, methodology, planning and management, and interpersonal skills. The initiative allowed the sponsor organization to expand connections with community organizations, implement work consistent with the mission, and provide new mentoring opportunities. Representatives from the recipient nonprofit organizations reported they gained a deeper understanding of evaluation, improved their dissemination efforts, and built organizational evaluation capacity.

Bringing it home: expanding the local reach of dissemination and implementation training via a university-based workshop.

BACKGROUND: Currently, national training programs do not have the capacity to meet the growing demand for dissemination and implementation (D&I) workforce education and development. The Colorado Research in Implementation Science Program (CRISP) developed and delivered an introductory D&I workshop adapted from national programs to extend training reach and foster a local learning community for D&I. METHODS: To gauge interest and assess learning needs, a pre-registration survey was administered. Based on feedback, a 1.5-day workshop was designed. Day 1 introduced D&I frameworks, strategies, and evaluation principles. Local and national D&I experts provided ignite-style talks on key lessons followed by panel discussion. Breakout sessions discussed community engagement and applying for D&I grants. A workbook was developed to enhance the training and provided exercises for application to an individual's projects. Day 2 offered expert-led mentoring sessions with selected participants who desired advanced instruction. Two follow-up surveys (immediate post-workshop, 6 months) assessed knowledge gained from participation and utilization of workshop content. RESULTS: Ninety-three workshop registrants completed an assessment survey to inform workshop objectives and curriculum design; 43 % were new and 54 % reported a basic understanding of the D&I field. Pre-registrants intended to use the training to "apply for a D&I grant" (73 %); "incorporate D&I into existing projects" (76 %), and for quality improvement (51 %). Sixty-eight individuals attended Day 1; 11 also attended Day 2 mentoring sessions. In the 1-week post-workshop survey (n = 34), 100 % strongly agreed they were satisfied with the training; 97 % strongly agreed the workshop workbook was a valuable resource. All Day 2 participants strongly agreed that working closely with faculty and experts increased their overall confidence. In the 6-month follow-up evaluation (n = 23), evidence of new D&I-related manuscripts and grant proposals was found. Training materials were published online ( www.ucdenver.edu/implementation/workshops ) and disseminated via the National Institutes of Health (NIH) Clinical and Translational Science Awards Consortium. To sustain reach, CRISP adapted the materials into an interactive e-book ( www.CRISPebooks.org ) and launched a new graduate course. CONCLUSIONS: Local D&I training workshops can extend the reach of national training programs.

On the importance of cotranscriptional RNA structure formation.

The expression of genes, both coding and noncoding, can be significantly influenced by RNA structural features of their corresponding transcripts. There is by now mounting experimental and some theoretical evidence that structure formation in vivo starts during transcription and that this cotranscriptional folding determines the functional RNA structural features that are being formed. Several decades of research in bioinformatics have resulted in a wide range of computational methods for predicting RNA secondary structures. Almost all state-of-the-art methods in terms of prediction accuracy, however, completely ignore the process of structure formation and focus exclusively on the final RNA structure. This review hopes to bridge this gap. We summarize the existing evidence for cotranscriptional folding and then review the different, currently used strategies for RNA secondary-structure prediction. Finally, we propose a range of ideas on how state-of-the-art methods could be potentially improved by explicitly capturing the process of cotranscriptional structure formation.

Transient RNA structure features are evolutionarily conserved and can be computationally predicted.

Functional RNA structures tend to be conserved during evolution. This finding is, for example, exploited by comparative methods for RNA secondary structure prediction that currently provide the state-of-art in terms of prediction accuracy. We here provide strong evidence that homologous RNA genes not only fold into similar final RNA structures, but that their folding pathways also share common transient structural features that have been evolutionarily conserved. For this, we compile and investigate a non-redundant data set of 32 sequences with known transient and final RNA secondary structures and devise a dedicated computational analysis pipeline.

COFOLD: an RNA secondary structure prediction method that takes co-transcriptional folding into account.

Existing state-of-the-art methods that take a single RNA sequence and predict the corresponding RNA secondary structure are thermodynamic methods. These aim to predict the most stable RNA structure. There exists by now ample experimental and theoretical evidence that the process of structure formation matters and that sequences in vivo fold while they are being transcribed. None of the thermodynamic methods, however, consider the process of structure formation. Here, we present a conceptually new method for predicting RNA secondary structure, called CoFold, that takes effects of co-transcriptional folding explicitly into account. Our method significantly improves the state-of-art in terms of prediction accuracy, especially for long sequences of >1000 nt in length.

R-CHIE: a web server and R package for visualizing RNA secondary structures.

Visually examining RNA structures can greatly aid in understanding their potential functional roles and in evaluating the performance of structure prediction algorithms. As many functional roles of RNA structures can already be studied given the secondary structure of the RNA, various methods have been devised for visualizing RNA secondary structures. Most of these methods depict a given RNA secondary structure as a planar graph consisting of base-paired stems interconnected by roundish loops. In this article, we present an alternative method of depicting RNA secondary structure as arc diagrams. This is well suited for structures that are difficult or impossible to represent as planar stem-loop diagrams. Arc diagrams can intuitively display pseudo-knotted structures, as well as transient and alternative structural features. In addition, they facilitate the comparison of known and predicted RNA secondary structures. An added benefit is that structure information can be displayed in conjunction with a corresponding multiple sequence alignments, thereby highlighting structure and primary sequence conservation and variation. We have implemented the visualization algorithm as a web server R-chie as well as a corresponding R package called R4RNA, which allows users to run the software locally and across a range of common operating systems.