Single Scaffolding Research Articles

The Combination of the Use of Customization and Personalization in a Three-Tier Test: Individualization vs. Non- Individualization

This study proposed a three-tier test (T3), where students were not only asked to give answers and reasons for their answers but also to engage in review questions. Furthermore, an individualized three-tier test (IT3) was implemented by incorporating customization and personalization into the T3. The T3 was utilized in Group A while the IT3 was used in Group B. Both tests were applied to help students learn English grammar. An empirical study was conducted to examine the varied reactions of these two groups, in terms of test performance, task performance, and learning behavior. Regarding test performance, Group B outperformed Group A. Regarding task performance, Group B obtained higher task scores than Group A. Regarding learning behavior, Group A tended to rely on a single scaffolding hint iteratively whereas Group B preferred utilizing various scaffolding hints concurrently. These results suggested that the IT3 was relatively beneficial to students. The aforementioned findings could provide guidance for the effective implementation of online tests.

Applying Real-Time Dynamic Scaffolding Techniques during Tutoring Sessions Using Intelligent Tutoring Systems

An intelligent tutoring system (ITS) is a computer system or software application that is built to replicate human tutors by supporting the theory of “learning by doing.” Even though ITSs have been proven to be successful in academic studies, they still have not found large adoption by the industry due to the complexities of building such systems due to the high technical expertise and domain knowledge requirements. Attempts have been made to build authoring tools that can provide assistance in building tutoring systems; however, most of these tools are targeted toward authors that have considerable programming experience. This research proposes an authoring tool for ITS, which is targeted at novice authors with minimum technical/programming experience and provides real-time scaffolding to learner’s incomplete/incorrect answers using the best scaffolding techniques. Two evaluation techniques were applied for the evaluation of the performance of the proposed authoring tool, e.g., paired t-test analysis and postexperiment survey. The learning gains obtained from paired t-test contend a significant learning gain and improvement in the learning process with enhanced learning performance with multiple scaffolding techniques as compared to single scaffolding technique experience. The postexperiment survey has a notable result that shows the effectiveness of the tutor model that ensures a very user-friendly interface, deploying scaffolding techniques and adequate control of selecting and deploying scaffolding techniques and making the authoring process easy.

Comparative Evaluation of Genome Assemblers from Long-Read Sequencing for Plants and Crops

The availability of recent state-of-the-art long-read sequencing technologies has significantly increased the ease and speed of producing high-quality plant genome assemblies. A wide variety of genome-related software tools are now available and they are typically benchmarked using microbial or model eukaryotic genomes such as Arabidopsis and rice. However, many plant species have much larger and more complex genomes than these, and the choice of tools, parameters, and/or strategies that can be used is not always obvious. Thus, we have compared the metrics of assemblies generated by various pipelines to discuss how assembly quality can be affected by two different assembly strategies. First, we focused on optimizing read preprocessing and assembler variables using eight different de novo assemblers on five different Pacific Biosciences long-read datasets of diploid and tetraploid species. Then, we examined a single scaffolding tool (quickmerge) that has been employed for the postprocessing step. We then merged the outputs from multiple assemblies to produce a higher quality consensus assembly. Then, we benchmarked the assemblies for completeness and accuracy (assembly metrics and BUSCO), computer memory, and CPU times. Two lightweight assemblers, Miniasm/Minimap/Racon and WTDBG, were deemed good for novice users because they involved smaller required learning curves and light computational resources. However, two heavyweight tools, CANU and Flye, should be the first choice when the goal is to achieve accurate and complete assemblies. Our results will provide valuable guidance in future plant genome projects and beyond.

Good for learning, bad for motivation? A meta-analysis on the effects of computer-supported collaboration scripts

Scripting computer-supported collaborative learning has been shown to greatly enhance learning, but is often criticized for hindering learners’ agency and thus undermining learners’ motivation. Beyond that, what makes some CSCL scripts particularly effective for learning is still a conundrum. This meta-analysis synthesizes the results of 53 primary studies that experimentally compared the effect of learning with a CSCL script to unguided collaborative learning on at least one of the variables motivation, domain learning, and collaboration skills. Overall, 5616 learners enrolled in K-12, higher education, or professional development participated in the included studies. The results of a random-effects meta-analysis show that learning with CSCL scripts leads to a non-significant positive effect on motivation (Hedges’ g = 0.13), a small positive effect (Hedges’ g = 0.24) on domain learning and a medium positive effect (Hedges’ g = 0.72) on collaboration skills. Additionally, the meta-analysis shows how scaffolding single particular collaborative activities and scaffolding a combination of collaborative activities affects the effectiveness of CSCL scripts and that synergistic or differentiated scaffolding is hard to achieve. This meta-analysis offers the first counterevidence against the widespread criticism that CSCL scripts have negative motivational effects. Furthermore, the findings can be taken as evidence for the robustness of the positive effects on domain learning and collaboration skills.

ReferenceSeeker: rapid determination of appropriate reference genomes

The large and growing number of microbial genomes available in public databases makes the optimal selection of reference genomes necessary for many in-silico analyses, e.g. single nucleotide polymorphism detection, scaffolding and comparative genomics, increasingly difficult. Here, we present ReferenceSeeker, a novel command line tool combining a fast kmer profile-based database lookup of candidate reference genomes with subsequent calculation of highly specific average nucleotide identity (ANI) values for the rapid determination of appropriate reference genomes. Pre-built databases for bacteria, archaea, fungi, protozoa and viruses based on the RefSeq database are provided for download. Availability and Implementation: ReferenceSeeker is open source software implemented in Python. Source code and binaries are freely available for download at https://github.com/oschwengers/referenceseeker​ under the GNU GPL3 license.

Protein phosphatase 2A is crucial for sarcomere organization in Caenorhabditis elegans striated muscle.

Protein phosphatase 2A (PP2A) is a heterotrimer composed of single catalytic and scaffolding subunits and one of several possible regulatory subunits. We identified PPTR-2, a regulatory subunit of PP2A, as a binding partner for the giant muscle protein UNC-89 (obscurin) in Caenorhabditis elegans. PPTR-2 is required for sarcomere organization when its paralogue, PPTR-1, is deficient. PPTR-2 localizes to the sarcomere at dense bodies and M-lines, colocalizing with UNC-89 at M-lines. PP2A components in C. elegans include one catalytic subunit LET-92, one scaffolding subunit (PAA-1), and five regulatory subunits (SUR-6, PPTR-1, PPTR-2, RSA-1, and CASH-1). In adult muscle, loss of function in any of these subunits results in sarcomere disorganization. rsa-1 mutants show an interesting phenotype: one of the two myosin heavy chains, MHC A, localizes as closely spaced double lines rather than single lines. This “double line” phenotype is found in rare missense mutants of the head domain of MHC B myosin, such as unc-54(s74). Analysis of phosphoproteins in the unc-54(s74) mutant revealed two additional phosphoserines in the nonhelical tailpiece of MHC A. Antibodies localize PPTR-1, PAA-1, and SUR-6 to I-bands and RSA-1 to M-lines and I-bands. Therefore, PP2A localizes to sarcomeres and functions in the assembly or maintenance of sarcomeres.

Single molecule sequencing-guided scaffolding and correction of draft assemblies

BackgroundAlthough single molecule sequencing is still improving, the lengths of the generated sequences are inevitably an advantage in genome assembly. Prior work that utilizes long reads to conduct genome assembly has mostly focused on correcting sequencing errors and improving contiguity of de novo assemblies.ResultsWe propose a disassembling-reassembling approach for both correcting structural errors in the draft assembly and scaffolding a target assembly based on error-corrected single molecule sequences. To achieve this goal, we formulate a maximum alternating path cover problem. We prove that this problem is NP-hard, and solve it by a 2-approximation algorithm.ConclusionsOur experimental results show that our approach can improve the structural correctness of target assemblies in the cost of some contiguity, even with smaller amounts of long reads. In addition, our reassembling process can also serve as a competitive scaffolder relative to well-established assembly benchmarks.

Multi-CAR: a tool of contig scaffolding using multiple references.

BackgroundA draft genome assembled by current next-generation sequencing techniques from short reads is just a collection of contigs, whose relative positions and orientations along the genome being sequenced are unknown. To further obtain its complete sequence, a contig scaffolding process is usually applied to order and orient the contigs in the draft genome. Although several single reference-based scaffolding tools have been proposed, they may produce erroneous scaffolds if there are rearrangements between the target and reference genomes or their phylogenetic relationship is distant. This may suggest that a single reference genome may not be sufficient to produce correct scaffolds of a draft genome.ResultsIn this study, we design a simple heuristic method to further revise our single reference-based scaffolding tool CAR into a new one called Multi-CAR such that it can utilize multiple complete genomes of related organisms as references to more accurately order and orient the contigs of a draft genome. In practical usage, our Multi-CAR does not require prior knowledge concerning phylogenetic relationships among the draft and reference genomes and libraries of paired-end reads. To validate Multi-CAR, we have tested it on a real dataset composed of several prokaryotic genomes and also compared its accuracy performance with other multiple reference-based scaffolding tools Ragout and MeDuSa. Our experimental results have finally shown that Multi-CAR indeed outperforms Ragout and MeDuSa in terms of sensitivity, precision, genome coverage, scaffold number and scaffold N50 size.ConclusionsMulti-CAR serves as an efficient tool that can more accurately order and orient the contigs of a draft genome based on multiple reference genomes. The web server of Multi-CAR is freely available at http://genome.cs.nthu.edu.tw/Multi-CAR/.

Enzyme Sequestration as a Tuning Point in Controlling Response Dynamics of Signalling Networks.

Signalling networks result from combinatorial interactions among many enzymes and scaffolding proteins. These complex systems generate response dynamics that are often essential for correct decision-making in cells. Uncovering biochemical design principles that underpin such response dynamics is a prerequisite to understand evolved signalling networks and to design synthetic ones. Here, we use in silico evolution to explore the possible biochemical design space for signalling networks displaying ultrasensitive and adaptive response dynamics. By running evolutionary simulations mimicking different biochemical scenarios, we find that enzyme sequestration emerges as a key mechanism for enabling such dynamics. Inspired by these findings, and to test the role of sequestration, we design a generic, minimalist model of a signalling cycle, featuring two enzymes and a single scaffolding protein. We show that this simple system is capable of displaying both ultrasensitive and adaptive response dynamics. Furthermore, we find that tuning the concentration or kinetics of the sequestering protein can shift system dynamics between these two response types. These empirical results suggest that enzyme sequestration through scaffolding proteins is exploited by evolution to generate diverse response dynamics in signalling networks and could provide an engineering point in synthetic biology applications.

Chimera distribution amplitudes for the pion and the longitudinally polarized ρ-meson

Using QCD sum rules with nonlocal condensates, we show that the distribution amplitude of the longitudinally polarized ρ-meson may have a shorttailed platykurtic profile in close analogy to our recently proposed platykurtic distribution amplitude for the pion. Such a chimera distribution de facto amalgamates the broad unimodal profile of the distribution amplitude, obtained with a Dyson–Schwinger equations-based computational scheme, with the suppressed tails characterizing the bimodal distribution amplitudes derived from QCD sum rules with nonlocal condensates. We argue that pattern formation, emerging from the collective synchronization of coupled oscillators, can provide a single theoretical scaffolding to study unimodal and bimodal distribution amplitudes of light mesons without recourse to particular computational schemes and the reasons for them.

Design Techniques for the DNA Cubic-Lattice

We use the Watson-Crick properties of DNA and the principles of graph theory to construct origami folding designs for self-assembling cubic lattices. Our objective is a mathematical design strategy that can be expanded systematically to any size cubic lattice. This design consists of threading a scaffolding strand of DNA through the lattice that is secured in place by short staple strands of DNA. We first add augmenting edges to the cubic lattice to enable a single scaffolding strand threading. We then thread the scaffolding strand through the augmented cube in a way that minimizes the number of different vertex configurations in the structure. Key Words: Watson-Crick, DNA Self-Assembly, Origami folding, Cubic Lattice, Scaffolding Strand, Threading, Staple Strands

Enhancing problem-based learning designs with a single e-learning scaffolding tool: Two case studies using challenge FRAP

Problem-based learning (PBL) is a powerful instructional approach. By working through assessable complex problem-solving tasks learners can be encouraged to actively engage in investigation and inquiry and to use high level cognitive thought processes to solve real-life problems in professional contexts. A critical element of a successful PBL design is the inclusion of instructional support, such as scaffolding, to guide and assist the learner through the reasoning process that is crucial to successful problem-solving. The e-learning tool ‘Challenge FRAP’ (Form for the Recording of the Analysis of Problems) is client-based public domain authoring software which facilitates the use of scaffolding, the provision of progressive feedback and can promote student reflection at key decision-making points. This paper illustrates the benefits of such an e-learning scaffolding tool through two PBL case studies; one group-based PBL task in science and technology and one self-directed PBL task in plant pathology.