A Kuramoto Model Approach to Predicting Chaotic Systems with Echo State Networks

An Echo State Network (ESN) with an activation function based on the Kuramoto model (Kuramoto ESN) is implemented, which can successfully predict the logistic map for a non-trivial number of time steps. The reservoir in the prediction stage exhibits binary dynamics when a good prediction is made, but the oscillators in the reservoir display a larger variability in states as the ESN’s prediction becomes worse. Analytical approaches to quantify how the Kuramoto ESN’s dynamics relate to its prediction are explored, as well as how the dynamics of the Kuramoto ESN relate to another widely studied physical model, the Ising model

The Dimerization of an α/β-Knotted Protein Is Essential for Structure and Function

Summaryα/β-Knotted proteins are an extraordinary example of biological self-assembly; they contain a deep topological trefoil knot formed by the backbone polypeptide chain. Evidence suggests that all are dimeric and function as methyltransferases, and the deep knot forms part of the active site. We investigated the significance of the dimeric structure of the α/β-knot protein, YibK, from Haemophilus influenzae by the design and engineering of monomeric versions of the protein, followed by examination of their structural, functional, stability, and kinetic folding properties. Monomeric forms of YibK display similar characteristics to an intermediate species populated during the formation of the wild-type dimer. However, a notable loss in structure involving disruption to the active site, rendering it incapable of cofactor binding, is observed in monomeric YibK. Thus, dimerization is vital for preservation of the native structure and, therefore, activity of the protein

Biomaterials Redesign of Microvascular Anastomotic Coupler

The key factors in the redesign of this part include the use of biomaterials, the redesign of the part geometry to include these biomaterials, and the proposition of production scale manufacturing methods suitable for these redesigns. The choice of biodegradable material was guided by previous literature, during which we found the PLGA polymer used in similar predicate devices with a biodegradability timeline similar to our goals. The model of coupler serving as the inspiration for the redesign utilizes two very strong but bioinert materials, polyethylene, and stainless steel. These high strength materials can withstand much greater forces than the biodegradable bulk material chosen for the redesign, so features of the old design were modified for robustness. This included to realize this new design on a production scale, the two most promising possibilities include injection molding with the PLGA polymer or additive manufacturing using stereo lithography printers and biodegradable resins. The commonality of these two processes is the ability to make complex shapes while retaining isotropic materials in the final part, which is essential for the strength of small features such as the pins. Key customer requirements for anastomotic procedures include successful attachments of vessels and low rates of dehiscence. These requirements are related to our coupler by successful attachment rate, max force withstood by coupler before assembly separates, max forces withstood by vessels before ripping. Different models of the coupler device were tested in assembled orientation with one blood vessel surrogate engaged. In both models, tensions upwards of 100N were experienced without a signal failure of the pins. This demonstrates that the pins are exceptionally stronger when assembled into the opposite coupler than when unengaged. Another factor in the improvement of the device is the time taken to film an implementation of the device using dissected cow arteries. The first round of prototypes required several people to affix the coupler and blood vessels and required additional processing of the cow arteries in the form of puncturing pilot holes for the spikes. Overall, the procedure took about an hour to perform. The latest model of prototypes was operated on in only a half hour and required only one person to perform the procedure. The improved placement and orientation of the spikes allow for much easier puncturing of the arterial wall for smoother attachments

A longitudinal study of theory of mind and listening comprehension: Is preschool theory of mind important?

Theory of mind has been shown to be important for listening comprehension for children at a range of ages. However, there is a lack of longitudinal evidence for a relationship between early theory of mind and later listening comprehension. The aim of this study was to examine whether preschool theory of mind has a longitudinal direct effect on later listening comprehension over and above the effects of concurrent theory of mind. A total of 147 children were tested on measures of theory of mind, working memory, vocabulary, and grammatical knowledge at Time 1 (mean age = 4;1 [years;months]) and Time 2 (mean age = 5;11). In addition, at Time 2 listening comprehension, comprehension monitoring, and inference making measures were taken. Data were fitted to concurrent and longitudinal models of listening comprehension. Concurrent findings at Time 2 showed theory of mind to have a direct effect on listening comprehension. However, longitudinal findings showed that earlier theory of mind in preschool (Time 1) did not have a direct effect on listening comprehension 22 months later; instead, there was only an indirect effect of earlier theory of mind on later listening comprehension via concurrent theory of mind (Time 2). Taken together, the results give further support for the importance of theory of mind for listening comprehension but show that there are limited additional benefits of early theory of mind acquisition. Implications for the development of children's listening comprehension are discussed. [Abstract copyright: Crown Copyright © 2022. Published by Elsevier Inc. All rights reserved.

Exploring the mutually reinforcing relationship between theory of mind and reading in adult readers

Background: Research with children shows that theory of mind predicts reading comprehension both concurrently and longitudinally, while research with adults shows increased print-exposure relates to theory of mind understanding. However, until now whether reading and theory of mind have a mutually reinforcing relationship in which they promote one another in parallel has not been explored. Therefore, this study aims to explore further the relationship between theory of mind and reading by investigating reading comprehension, print-exposure and theory of mind together. Method: Theory of mind (Reading the Eyes in the Mind test), reading comprehension (subset of the York Adult Assessment Battery-Revised) and print-exposure (Authors Recognition Test) were measured in a sample of U.K. adults (N = 220). Results: Findings showed that theory of mind was significantly related to both reading comprehension and reading print-exposure. Further, mediation analysis showed that this relationship does not operate with theory of mind mediating the relationship between print-exposure and reading comprehension as an indirect effect of print-exposure on reading comprehension through theory of mind was not found after controlling for age, income and education. Conclusions: The findings provide some initial evidence that, at least in adulthood, reading and theory of mind have a mutually reinforcing relationship in which they promote one another in parallel, but this relationship cannot be explained by theory of mind mediating the relationship between print-exposure and reading comprehension

Activity and Selectivity of Class B Sortase Enzymes

Gram-positive bacteria attach many proteins to their cell walls via sortase enzymes. Sortases are cysteine transpeptidases and are grouped into 6 classes, A-F. Sortase enzymes, particularly sortase A from Staphylococcus aureus, have been used extensively for in vitro protein ligations. Here, we investigate substrate-binding in sortase A from Streptococcus pyogenes. In addition, class B sortases are typically overlooked for research and development due to low in vitro activity and incomplete knowledge of substrate specificity. Here, we investigate the activity of class B sortases from Bacillus anthracis (baSrtB), Clostridioides difficile (cdSrtB), Listeria monocytogenes (lmSrtB), and Staphylococcus aureus (saSrtB). Of these, baSrtB was the most active in our hands and was selected for further study. Mutant enzymes were created to study the impact of a class B N-terminal α-helix and a structurally conserved, but sequentially variable, loop on baSrtB activity. Mutations to the structurally conserved loop were impactful on enzyme activity, with some mutations decreasing activity while others greatly increased it. A substrate-bound enzyme model generated using Alphafold2 (Galaxy) allowed us to explore enzyme-substrate interactions in greater detail. This model was validated through molecular dynamics simulations and mutagenesis. This work shows that baSrtB is a viable tool for protein engineering studies and lends greater insight into the structural features that underpin sortase activity and selectivity

Memory Affect: The Past and Present in Ross McElwee’s Photographic Memory (2011) and Terrence Malick’s The Tree of Life (2011)

This paper will explore the concept of Memory Affect - bringing together current thinking on affect in cinema and affect in the experiencing of memory by making specific reference to Terrence Malick’s feature film The Tree of Life (2011) and Ross McElwee’s documentary Photographic Memory (2011). In Photographic Memory, McElwee’s sixth wry autobiographical documentary since his groundbreaking film Sherman’s March, the director articulates the experiences of memory and it’s fragmentary subjective nature in relation to the photographic image, both moving and still, analogue and digital. Although not specifically stated, McElwee’s insights illustrate the notion of a Memory Affect. Building on the ideas exposed by McElwee, this paper also considers Malick’s equally personal Palme d’Or- winning The Tree of Life, where the director evokes memory within a fictional context, not only representing memory but also positioning the viewer within the act of remembering, creating an affective memory experience. With it’s particular ability to represent time and space, cinema is not only a metaphor for memory but also constitutive of memory, and this paper considers another layer of overlap – that of the affective, embodied experience of remembering, of calling the past into present. Drawing on a range of theoretical works, this paper uses these two very different films to explore the notion of Memory Affect and the creation of a memory experience shared between the viewer, the filmmaker and the memory