Drag-and-drop genome insertion without DNA cleavage with CRISPR-directed integrases

Programmable and multiplexed genome integration of large, diverse DNA cargo independent of DNA repair remains an unsolved challenge of genome editing. Current gene integration approaches require double-strand breaks that evoke DNA damage responses and rely on repair pathways that are inactive in terminally differentiated cells. Furthermore, CRISPR-based approaches that bypass double stranded breaks, such as Prime editing, are limited to modification or insertion of short sequences. We present Programmable Addition via Site-specific Targeting Elements, or PASTE, which achieves efficient and versatile gene integration at diverse loci by directing insertion with a CRISPR-Cas9 nickase fused to both a reverse transcriptase and serine integrase. Without generating double stranded breaks, we demonstrate integration of sequences as large as ~36 kb with rates between 10-50% at multiple genomic loci across three human cell lines, primary T cells, and quiescent non-dividing primary human hepatocytes. To further improve PASTE, we discover thousands of novel serine integrases and cognate attachment sites from metagenomes and engineer active orthologs for high-efficiency integration using PASTE. We apply PASTE to fluorescent tagging of proteins, integration of therapeutically relevant genes, and production and secretion of transgenes. Leveraging the orthogonality of serine integrases, we engineer PASTE for multiplexed gene integration, simultaneously integrating three different genes at three genomic loci. PASTE has editing efficiencies comparable to or better than those of homology directed repair or non-homologous end joining based integration, with activity in non-dividing cells and fewer detectable off-target events. For therapeutic applications, PASTE can be delivered as mRNA with synthetically modified guides to programmably direct insertion of DNA templates carried by AAV or adenoviral vectors. PASTE expands the capabilities of genome editing via drag-and-drop gene integration, offering a platform with wide applicability for research, cell engineering, and gene therapy.

Extracting SBVR Business Vocabularies from UML Use Case Models Using M2M Transformations Based on Drag-and-Drop Actions

In the domain of model-driven system engineering, model-to-model (M2M) transformations present a very relevant topic because they may provide much-needed automation capabilities to the whole CASE-supported system development life cycle. Nonetheless, it is observed that throughout the whole development process M2M transformations are spread unevenly; in this respect, the phases of Business Modeling and System Analysis are arguably the most underdeveloped ones. The main novelty and contributions of this paper are the presented set of model-based transformations for extracting well-structured SBVR business vocabularies from visual UML use case models, which utilizes M2M transformation technology based on the so-called drag-and-drop actions. The conducted experiments show that this new development provides the same transformation power while introducing more flexibility to the model development process as compared to our previously developed approach for (semi-)automatic extraction of SBVR business vocabularies from UML use case models.

PsyBuilder: An open-source cross-platform graphical experiment builder with built-in performance optimization for behavioral and neural sciences

Central in an experimental psychologist’s toolkit is software for stimulus presentation and response collection. An ideal package should combine flexibility and power in the choice of stimuli and responses, precision in control and timing, and ease of use. Psychtoolbox has remained the most popular open-source package, but it suffers from two major long-standing limitations: being script-based only, Psychtoolbox is challenging to learn and time-consuming to program and debug; scripting can also lead to timing inaccuracies unwittingly. We dissolve these limitations by developing the first general-purpose graphical experiment builder for Psychtoolbox, called PsyBuilder, which allows users to graphically implement sophisticated experimental tasks through intuitive drag-and-drop without the need of coding and with built-in optimized timing precision. PsyBuilder is poised to facilitate wider adoption of Psychtoolbox in teaching and research in lieu of proprietary software, fueling the open science movement. Furthermore, its built-in performance optimization and drag-and-drop design can improve data-collection efficiency and accuracy to accelerate scientific progress.

Object adaptation of Drag and Drop technology for web-system interface components

Today, in the development of information systems, cloud technologies are often used for remote computing and data processing. There are web technologies, and on their basis, libraries and frameworks have been developed for creating web applications and user interfaces designed for the operation of information systems in browsers. Ready-made JavaScript libraries have been developed to add drag and drop functionality to a web application. However, in some situations, the library may not be available, or there may be overhead or dependencies that the project does not need to use it. In such situations, an alternative solution provides the functionality of APIs available in modern browsers. The article discusses the current state of the methods of the Drag and Drop mechanism and proposes a programmatic way to improve the interface by creating a class for dragging and dropping elements when organizing work in multi-user information web systems. Drag and Drop is a convenient way to improve the interface. Grabbing an element with the mouse and moving it visually simplifies many operations: from copying and moving documents, as in file managers, to placing orders in online store services. The HTML drag and drop API uses the DOM event model to retrieve information about a dragged element and update that element after the drag. Using JavaScript event handlers, it is possible to turn any element of the web system into a drag-and-drop element or drop target. To solve this problem, a JavaScript object was developed with methods that allow you to create a copy of any object and handle all events of this object aimed at organizing the Drag and Drop mechanism. Basic algorithm of Drag and Drop technology based on processing mouse events. The software implementation is considered and the results of the practical use of object adaptation of the Drag and Drop technology for the interface components of the web system - the medical information system MedSystem, in which the application modules have the implementation of the dispatcher and the interactive window interface are presented. In the "Outpatient clinic" module, the Drag and Drop mechanism is used when working with the "Appointment sheet". In the "Hospital" module of the MedSystem medical information system, the Drag and Drop mechanism is used in the "List of doctor's appointments". The results of using object adaptation of Drag and Drop technology have shown that this mechanism organically fits into existing technologies for building web applications and has sufficient potential to facilitate and automate work in multi-user information systems and web services.

Using process data to understand problem-solving strategies and processes for drag-and-drop items in a large-scale mathematics assessment

In 2017, the mathematics assessments that are part of the National Assessment of Educational Progress (NAEP) program underwent a transformation shifting the administration from paper-and-pencil formats to digitally-based assessments (DBA). This shift introduced new interactive item types that bring rich process data and tremendous opportunities to study the cognitive and behavioral processes that underlie test-takers’ performances in ways that are not otherwise possible with the response data alone. In this exploratory study, we investigated the problem-solving processes and strategies applied by the nation’s fourth and eighth graders by analyzing the process data collected during their interactions with two technology-enhanced drag-and-drop items (one item for each grade) included in the first digital operational administration of the NAEP’s mathematics assessments. Results from this research revealed how test-takers who achieved different levels of accuracy on the items engaged in various cognitive and metacognitive processes (e.g., in terms of their time allocation, answer change behaviors, and problem-solving strategies), providing insights into the common mathematical misconceptions that fourth- and eighth-grade students held and the steps where they may have struggled during their solution process. Implications of the findings for educational assessment design and limitations of this research are also discussed.