Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment

We present the results for CAPRI Round 50, the fourth joint CASP-CAPRI protein assembly prediction challenge. The Round comprised a total of twelve targets, including six dimers, three trimers, and three higher-order oligomers. Four of these were easy targets, for which good structural templates were available either for the full assembly, or for the main interfaces (of the higher-order oligomers). Eight were difficult targets for which only distantly related templates were found for the individual subunits. Twenty-five CAPRI groups including eight automatic servers submitted ~1250 models per target. Twenty groups including six servers participated in the CAPRI scoring challenge submitted ~190 models per target. The accuracy of the predicted models was evaluated using the classical CAPRI criteria. The prediction performance was measured by a weighted scoring scheme that takes into account the number of models of acceptable quality or higher submitted by each group as part of their five top-ranking models. Compared to the previous CASP-CAPRI challenge, top performing groups submitted such models for a larger fraction (70–75%) of the targets in this Round, but fewer of these models were of high accuracy. Scorer groups achieved stronger performance with more groups submitting correct models for 70–80% of the targets or achieving high accuracy predictions. Servers performed less well in general, except for the MDOCKPP and LZERD servers, who performed on par with human groups. In addition to these results, major advances in methodology are discussed, providing an informative overview of where the prediction of protein assemblies currently stands.Cancer Research UK, Grant/Award Number: FC001003; Changzhou Science and Technology Bureau, Grant/Award Number: CE20200503; Department of Energy and Climate Change, Grant/Award Numbers: DE-AR001213, DE-SC0020400, DE-SC0021303; H2020 European Institute of Innovation and Technology, Grant/Award Numbers: 675728, 777536, 823830; Institut national de recherche en informatique et en automatique (INRIA), Grant/Award Number: Cordi-S; Lietuvos Mokslo Taryba, Grant/Award Numbers: S-MIP-17-60, S-MIP-21-35; Medical Research Council, Grant/Award Number: FC001003; Japan Society for the Promotion of Science KAKENHI, Grant/Award Number: JP19J00950; Ministerio de Ciencia e Innovación, Grant/Award Number: PID2019-110167RB-I00; Narodowe Centrum Nauki, Grant/Award Numbers: UMO-2017/25/B/ST4/01026, UMO-2017/26/M/ST4/00044, UMO-2017/27/B/ST4/00926; National Institute of General Medical Sciences, Grant/Award Numbers: R21GM127952, R35GM118078, RM1135136, T32GM132024; National Institutes of Health, Grant/Award Numbers: R01GM074255, R01GM078221, R01GM093123, R01GM109980, R01GM133840, R01GN123055, R01HL142301, R35GM124952, R35GM136409; National Natural Science Foundation of China, Grant/Award Number: 81603152; National Science Foundation, Grant/Award Numbers: AF1645512, CCF1943008, CMMI1825941, DBI1759277, DBI1759934, DBI1917263, DBI20036350, IIS1763246, MCB1925643; NWO, Grant/Award Number: TOP-PUNT 718.015.001; Wellcome Trust, Grant/Award Number: FC00100

Gereedschap om wiskunde in de vingers te krijgen

Over het gebruik van ICT-gereedschap in de wiskundeles zijn de meningen verdeeld. In dit themanummer over wiskunde en nieuwe media schetst Paul Drijvers twee theoretische invalshoeken om tegen deze inzet aan te kijken. Instrumentatietheorie beschrijft hoe ICT een instrument wordt voor wiskunde, en de theorie van belichaamde cognitie benadrukt de rol van het lichaam in het leren, ook van wiskunde. Na enkele voorbeelden pleit Paul voor een integratie van de twee, onder de noemer van belichaamde instrumentatie, om te bevorderen dat leerlingen wiskunde door de inzet van ICT in de vingers krijgen

Взаимодействует ли реальная форма с идеальной? Исследование овладения счетом на числовой прямой с помощью записи движений глаз

The article investigates acquisition of mathematical knowledge in collaboration with an adult as it is exemplified by preschoolers’ learning to count on the number line. A qualitative analysis of the eye-movements reveals the diversity of possible strategies in determination of a number on the number line. The developmental experiment discloses the mechanisms of emergence of these strategies in children. The quantitative comparison of the adults’ strategies, the strategies, which are involved in the teaching-learning process, and the strategies that the children used after the learning stage demonstrates the process of development (χ2= 44, 936; p<0,001). We distinguished the statistically significant differences between the stages in the ratio of counting up versus down along the number line and in the ratio of counting from versus towards the target point. The results demonstrate that children’s strategies after the learning stage are more similar to the adults’ inherent strategies than to the strategies that were introduced by the adults during the teaching stage. The analysis of the videos of shared activity that was synchronized with the eye movements showed that the adults demonstrated the basic strategy to the children at the teaching phase as they guided children’s perception by their pointing gestures and speech. However, the adults did not expose the ideal form, namely the diversity of their own strategies during their teaching. Nevertheless, the children were able to supplement the given teaching/learning formof counting from zero up along the number line to the target point with a variety of strategies by themselves, relying on their coherent notion of the number concept. The strategy that required the sequence-to-proportion shift was the only one that children were not able to constitute by themselves. According to our results, the ideal, cultural form of perception exists in the latent form, and a child needs to re-constitute it in their own practice. The children rely on the basic strategy and enrich this strategy as they include it in the integral conceptual knowledge about numbers. The results enrich our understanding of microgenesis of mathematical knowledge during the collaboration with an adult and open perspective on learning as an active reinvention of ideal form on the ground of cultural practice

Book Review: Networking theories as an example of boundary crossing.: Angelika Bikner-Ahsbahs and Susanne Prediger (Eds.) (2014) Networking of theories as a research practice in mathematics education

This review essay first discusses a book authored by the Networking Theories Group and argues that the strategies for networking of theories are very similar to the learning mechanisms identified in the literature on boundary crossing. I propose that these two theoretical perspectives may be put into a fruitful dialogue

Action-property duality in embodied design

For those working on embodied design it is a challenge to create tasks that enable students to develop abstract mathematical concepts. We approach this issue from the perspective of Sfard's notions of saming, encapsulation, and reification. We discuss a duality of properties and actions, and use this duality to review saming, encapsulation and reification from an action-and perceptionbased perspective. To illustrate the power of this theoretical contribution we discuss one new embodied task design and two from literature: MIT-P for proportion and a design for the gradient of a plane using the Augmented Reality Sandbox