bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conventionalized creativity in the emergence of a mixed language – A case study of Light Warlpiri
Authors: O'Shannessy Carmel 
Published: September 2021

Abstract
Questions of how contact languages are best categorized and how their paths of development are most accurately described remain contentious. Mixed languages or split languages raise many unanswered questions about mechanisms of change in multilingual contexts, and how they lead to specific structural outcomes. An examination of the structure of Light Warlpiri, a mixed language spoken in a Warlpiri community in northern Australia, shows that the main mechanism of change is insertional code-switching where a verbal phrase from one language, Kriol (an English-lexified Creole) is inserted into a string of another language, Warlpiri. The result is a way of speaking that is mixed at every level, and can be categorized as underlyingly Warlpiri with innovative insertions and reanalyses from Kriol.
Learnability and ecological factors as motivators of language change
Authors: Efrat-Kowalsky Nour 
Published: September 2021

Abstract
This chapter adopts Mufwene’s (2001) framework according to which language acquisition is a process whereby competition and selection of linguistic features from the inputs create a unique idiolect. It examines the principles of selection of a given feature over others, and the mechanisms by which a feature spreads across a community (i.e., from one idiolect to another). These questions are addressed at the individual and population levels by analysing data from a twitter corpus. The frequency of a feature in the input as well as a suggested learnability factor are relevant to this discussion. Learnability is defined as the combination of the specific linguistic properties of a linguistic feature, and the universal human capacity to learn those specific properties.
Talking to children with atypical development
Authors: Fasulo Alessandra 
Published: September 2021

Abstract
Interactional studies of children with language impairments and their habitual interlocutors are key to understanding reciprocal adaptations in communication. The chapter is based on video recorded observations of three families at home, each with a child with Down Syndrome of approximately 6 years of age. The analysis focuses on the parental practice of asking the children ‘Are you going to’ questions. The results document two main uses: ‘request for information’ and ‘action solicit’. The analysis suggests that using the question as action solicit may hamper children’s comprehension and undermine their agency. A comparison with other action solicits and relative frequencies of use suggests family styles that either privilege a Requester’s Perspective or the Child’s Perspective. It is argued that, by privileging the Child’s Perspective, parents limit the imposition on children but subtract potential for normative and epistemic socialisation, as well as opportunities for the child to display their collaboration.
Language, interaction, and culture at school1
Authors: Caronia Letizia , Nasi Nicola 
Published: September 2021

Abstract
The chapter provides an overview of selected studies that, from the mid-twentieth century, have variously dealt with classroom language, interaction, and culture. Moving from the recognition that schools represent (at least in western societies) a major site for children’s socialization into the adult world, several ethnographic accounts of how this process concretely takes place in and through everyday classroom practices are presented and discussed. As the chapter illustrates, the focus on situated language use allows to appreciate how school is a lieu where the micro-macro dialectic emerges with particular evidence. Specifically, the chapter reports on research dealing with (a) classroom’ typical interactional structures, (b) teachers’ and pupils’ communicative practices, and (c) the interactional competence needed to appropriately participate in classroom everyday activities. An appraisal of the challenges that this multifaceted research field is facing in contemporary societies concludes the article.
Building bridges
Authors: Hughes Joanne , Loader Rebecca 
Published: September 2021

Abstract
This chapter examines group talk between Catholic and Protestant teachers in Northern Ireland as they discuss their collaboration on a Shared Education project. Shared Education is an initiative which offers opportunities for teachers and pupils from different communities to engage with each other and to promote positive and harmonious group interaction across the divided society in Northern Ireland. The chapter discusses the historical, social and geopolitical context in which teachers represent themselves and how this informs their views on the role of (cross-cultural) educational initiatives.Using discourse analysis, we illustrate how the teachers’ dialogue evidences both a struggle with competing and contested cultural positions and world views. We discuss how an exposition of teacher dialogue can be used as a tool of reflection in consideration of how to progress shared education.
Language, culture and social interaction
Authors: Caronia Letizia 
Published: September 2021

Abstract
In the 20th century, a theoretical insight surfaced and gradually prevailed as an agreed upon framework to (re)thinking children’s socialization and socio-cognitive development: language and interaction are the main tools through which cultures, social organization, moral orders as well as individuals’ identities are constituted on everyday bases. Philosophical arguments, anthropological systematic observations, psycho- and socio-linguistic empirical studies and some strands in developmental psychology converged toward a dialogical turn and set the premises for studying the constitutive role of language and social interaction in children becoming culturally competent members of their communities. This introductory essay reconstructs the landscape of theories and research that paved the way for contemporary sensitivity to children’s socio-cultural and cognitive development as a complex, multifaceted and radically dialogical phenomenon.
Can ionic concentration changes due to mechanical deformation be responsible for the neurostimulation caused by focused ultrasound? A simulation study
Authors: Filkin Vladimir , Kuznetsov Igor , Antonova Olga , Tarotin Ilya , Nemov Alexander , Aristovich Kirill 
Published: September 2021

Abstract

Objective. Ultrasound stimulation is an emerging neuromodulation technique, for which the exact mechanism of action is still unknown. Despite the number of hypotheses such as mechanosensitive ion channels and intermembrane cavitation, they fail to explain all of the observed experimental effects. Here we are investigating the ionic concentration change as a prime mechanism for the neurostimulation by the ultrasound. Approach. We derive the direct analytical relationship between the mechanical deformations in the tissue and the electric boundary conditions for the cable theory equations and solve them for two types of neuronal axon models: Hodgkin–Huxley and C-fibre. We detect the activation thresholds for a variety of ultrasound stimulation cases including continuous and pulsed ultrasound and estimate the mechanical deformations required for reaching the thresholds and generating action potentials (APs). Main results. We note that the proposed mechanism strongly depends on the mechanical properties of the neural tissues, which at the moment cannot be located in literature with the required certainty. We conclude that given certain common linear assumptions, this mechanism alone cannot cause significant effects and be responsible for neurostimulation. However, we also conclude that if the lower estimation of mechanical properties of neural tissues in literature is true, or if the normal cavitation occurs during the ultrasound stimulation, the proposed mechanism can be a prime cause for the generation of APs. Significance. The approach allows prediction and modelling of most observed experimental effects, including the probabilistic ones, without the need for any extra physical effects or additional parameters.
On the justification of the Poisson–Boltzmann equation in the context of technological plasmas
Authors: Köhn Kevin , Krüger Dennis , Kemaneci Efe , Xu Liang , Eremin Denis , Brinkmann Ralf Peter 
Published: September 2021

Abstract
The Poisson–Boltzmann (PB) equation is a nonlinear differential equation for the electric potential that describes equilibria of conducting fluids. Its standard justification is based on a variational principle which characterizes the thermodynamic equilibrium of a system in contact with a heat reservoir as a minimum of the Helmholtz free energy. The PB equation is also employed in the context of technological plasmas. There, however, the standard justification is inapplicable: technological plasmas are neither in thermodynamic equilibrium nor in contact with heat reservoirs. This study presents an alternative variational principle which is based on the functionals of entropy, particle number, and electromagnetic enthalpy. It allows to justify the PB equation for a wide class of technological plasmas under realistic assumptions.
Design and implementation of an inverter and its application in ring oscillator circuits using an organic-thin-film-transistor based on an FTM-derived channel
Authors: Singh Abhishek Kumar , Dwivedi A D D , Pandey A , Chakrabarti P 
Published: September 2021

Abstract
The organic thin film transistor (OTFT) has evolved in a big way, eventually replacing inorganic-based solid-state devices. An extensive survey of the literature reveals that the full potential of OTFTs has neither been explored nor exploited for circuit-level implementation for logic circuit design, despite the popularity of these devices. We have fabricated a PBTTT-C14 (poly (2,5-bis (3-tetradecylthiophen 2yl) thieno (3,2b) thiophene)) based OTFT by using a low-cost solution-processable technique via the floating transfer method (FTM). The fabricated OTFT using FTM shows better electrical behavior than its counterpart fabricated by using the conventional solution-processable technique. The superior electrical characteristics of the FTM-derived devices prompted us to develop a compact model of the p-channel OTFT. The compact modeling results of OTFT show a reasonably good agreement with our experimental results. We have also designed and implemented a PBTTT-C14 OTFT-based inverter circuit and ring oscillator circuit to explore the future of organic-based integrated circuits.
2D measurements of parallel counter-streaming flows in the W7-X scrape-off layer for attached and detached plasmas
Authors: Perseo V. , Winters V. , Feng Y. , Reimold F. , Ford O.P. , König R. , Bozhenkov S.A. , Brunner K.J. , Burhenn R. , Drewelow P. , Ennis D.A. , Gao Y. , Gradic D. , Hacker P. , Hergenhahn U. , Jakubowski M.W. , Knauer J. , Kremeyer T. , Kriete D.M. , Krychowiak M. , Kwak S. , Niemann H. , Pavone A. , Pisano F. , Puig Sitjes A. , Schlisio G. , Svensson J. , Zhang D. , Sunn Pedersen T. ,   the W7-X Team
Published: September 2021

Abstract
Investigations of particle parallel flow velocities have been carried out for the scrape-off layer (SOL) of the Wendelstein 7-X (W7-X) stellarator, in order to gain insights on the SOL transport properties during attached and detached plasma scenarios. The experimental evidence is based on the coherence imaging spectroscopy (CIS) diagnostic, able to measure 2D impurity emission intensity and flow velocity. The impurity monitored by CIS is C2+, characterized by a line-emission intensity observed to be linearly proportional to the total plasma radiated power in both attached and detached plasmas. The related C2+ velocity shows a strong dependence on the line-averaged electron density while remaining insensitive to the input power. During attached plasmas, the velocity increases with increasing line-averaged density. The tendency reverses in the transition to and during detachment, in which the velocity decreases by at least a factor of 2. The sharp drop in velocity, together with a rise in line-emission intensity, is reliably correlated to the detachment transition and can therefore be used as one of its signatures. The impurity flow velocity appears to be well coupled with the main ions’ one, thus implying the dominant role of impurity-main ion friction in the parallelimpurity transport dynamics. In view of this SOL impurity transport regime, the CIS measurement results are here interpreted with the help of EMC3-Eirene simulations, and their major trends are already explainable with a simple 1D fluid model.
MotorSkins—a bio-inspired design approach towards an interactive soft-robotic exosuit
Authors: Gutierrez Facundo , Razghandi Khashayar 
Published: September 2021

AbstractThe work presents a bio-inspired design approach to a soft-robotic solution for assisting the knee-bending in users with reduced mobility in lower limbs. Exosuits and fluid-driven actuators are fabric-based devices that are gaining increasing relevance as alternatives assistive technologies that can provide simpler, more flexible solutions in comparison with the rigid exoskeletons. These devices, however, commonly require an external energy supply or a pressurized-fluid reservoir, which considerably constrain the autonomy of such solutions. In this work, we introduce an event-based energy cycle (EBEC) design concept, that can harvest, store, and release the required energy for assisting the knee-bending, in a synchronised interaction with the user and the environment, thus eliminating any need for external energy or control input. Ice-plant hydro-actuation system served as the source of inspiration to address the specific requirements of such interactive exosuit through a fluid-driven material system. Based on the EBEC design concepts and the abstracted bio-inspired principles, a series of (material and process driven) design experimentations helped to address the challenges of realising various functionalities of the harvest, storage, actuation and control instances within a closed hydraulic circuit. Sealing and defining various areas of water-tight seam made out of thermoplastic elastomers provided the base material system to program various chambers, channels, flow-check valves etc of such EBEC system. The resulting fluid-driven EBEC-skin served as a proof of concept for such active exosuit, that brings these functionalities into an integrated ‘sense-acting’ material system, realising an auto-synchronised energy and information cycles. The proposed design concept can serve as a model for development of similar fluid-driven EBEC soft-machines for further applications. On the more general scheme, the work presents an interdisciplinary design-science approach to bio-inspiration and showcases how biological material solutions can be looked at from a design/designer perspective to bridge the bottom–up and top–down approach to bio-inspiration.
A survey on computational methods in discovering protein inhibitors of SARS-CoV-2
Authors: Liu Qiaoming , Wan Jun , Wang Guohua 
Published: September 2021

AbstractThe outbreak of acute respiratory disease in 2019, namely Coronavirus Disease-2019 (COVID-19), has become an unprecedented healthcare crisis. To mitigate the pandemic, there are a lot of collective and multidisciplinary efforts in facilitating the rapid discovery of protein inhibitors or drugs against COVID-19. Although many computational methods to predict protein inhibitors have been developed [ 1– 5], few systematic reviews on these methods have been published. Here, we provide a comprehensive overview of the existing methods to discover potential inhibitors of COVID-19 virus, so-called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). First, we briefly categorize and describe computational approaches by the basic algorithms involved in. Then we review the related biological datasets used in such predictions. Furthermore, we emphatically discuss current knowledge on SARS-CoV-2 inhibitors with the latest findings and development of computational methods in uncovering protein inhibitors against COVID-19.
epitope3D: a machine learning method for conformational B-cell epitope prediction
Authors: da Silva Bruna Moreira , Myung YooChan , Ascher David B , Pires Douglas E V 
Published: September 2021

AbstractThe ability to identify antigenic determinants of pathogens, or epitopes, is fundamental to guide rational vaccine development and immunotherapies, which are particularly relevant for rapid pandemic response. A range of computational tools has been developed over the past two decades to assist in epitope prediction; however, they have presented limited performance and generalization, particularly for the identification of conformational B-cell epitopes. Here, we present epitope3D, a novel scalable machine learning method capable of accurately identifying conformational epitopes trained and evaluated on the largest curated epitope data set to date. Our method uses the concept of graph-based signatures to model epitope and non-epitope regions as graphs and extract distance patterns that are used as evidence to train and test predictive models. We show epitope3D outperforms available alternative approaches, achieving Mathew’s Correlation Coefficient and F1-scores of 0.55 and 0.57 on cross-validation and 0.45 and 0.36 during independent blind tests, respectively.
PTMdyna: exploring the influence of post-translation modifications on protein conformational dynamics
Authors: Shi Xing-Xing , Wang Zhi-Zheng , Wang Yu-Liang , Huang Guang-Yi , Yang Jing-Fang , Wang Fan , Hao Ge-Fei , Yang Guang-Fu 
Published: September 2021

Abstract
Protein post-translational modifications (PTM) play vital roles in cellular regulation, modulating functions by driving changes in protein structure and dynamics. Exploring comprehensively the influence of PTM on conformational dynamics can facilitate the understanding of the related biological function and molecular mechanism. Currently, a series of excellent computation tools have been designed to analyze the time-dependent structural properties of proteins. However, the protocol aimed to explore conformational dynamics of post-translational modified protein is still a blank. To fill this gap, we present PTMdyna to visually predict the conformational dynamics differences between unmodified and modified proteins, thus indicating the influence of specific PTM. PTMdyna exhibits an AUC of 0.884 tested on 220 protein–protein complex structures. The case of heterochromatin protein 1α complexed with lysine 9-methylated histone H3, which is critical for genomic stability and cell differentiation, was used to demonstrate its applicability. PTMdyna provides a reliable platform to predict the influence of PTM on protein dynamics, making it easier to interpret PTM functionality at the structure level. The web server is freely available at http://ccbportal.com/PTMdyna.
DLAB: deep learning methods for structure-based virtual screening of antibodies
Authors: Schneider Constantin , Buchanan Andrew , Taddese Bruck , Deane Charlotte M 
Published: September 2021

Abstract

Motivation
Antibodies are one of the most important classes of pharmaceuticals, with over 80 approved molecules currently in use against a wide variety of diseases. The drug discovery process for antibody therapeutic candidates however is time- and cost-intensive and heavily reliant on in vivo and in vitro high throughput screens. Here, we introduce a framework for structure-based deep learning for antibodies (DLAB) which can virtually screen putative binding antibodies against antigen targets of interest. DLAB is built to be able to predict antibody–antigen binding for antigens with no known antibody binders.

Results
We demonstrate that DLAB can be used both to improve antibody–antigen docking and structure-based virtual screening of antibody drug candidates. DLAB enables improved pose ranking for antibody docking experiments as well as selection of antibody–antigen pairings for which accurate poses are generated and correctly ranked. We also show that DLAB can identify binding antibodies against specific antigens in a case study. Our results demonstrate the promise of deep learning methods for structure-based virtual screening of antibodies.

Availability and implementation
The DLAB source code and pre-trained models are available at https://github.com/oxpig/dlab-public.

Supplementary information
Supplementary data are available at Bioinformatics online.
ProFitFun: a protein tertiary structure fitness function for quantifying the accuracies of model structures
Authors: Kaushik Rahul , Zhang Kam Y J 
Published: September 2021

AbstractMotivationAn accurate estimation of the quality of protein model structures typifies as a cornerstone in protein structure prediction regimes. Despite the recent groundbreaking success in the field of protein structure prediction, there are certain prospects for the improvement in model quality estimation at multiple stages of protein structure prediction and thus, to further push the prediction accuracy. Here, a novel approach, named ProFitFun, for assessing the quality of protein models is proposed by harnessing the sequence and structural features of experimental protein structures in terms of the preferences of backbone dihedral angles and relative surface accessibility of their amino acid residues at the tripeptide level. The proposed approach leverages upon the backbone dihedral angle and surface accessibility preferences of the residues by accounting for its N-terminal and C-terminal neighbors in the protein structure. These preferences are used to evaluate protein structures through a machine learning approach and tested on an extensive dataset of diverse proteins.ResultsThe approach was extensively validated on a large test dataset (n = 25 005) of protein structures, comprising 23 661 models of 82 non-homologous proteins and 1344 non-homologous experimental structures. In addition, an external dataset of 40 000 models of 200 non-homologous proteins was also used for the validation of the proposed method. Both datasets were further used for benchmarking the proposed method with four different state-of-the-art methods for protein structure quality assessment. In the benchmarking, the proposed method outperformed some state-of-the-art methods in terms of Spearman’s and Pearson’s correlation coefficients, average GDT-TS loss, sum of z-scores and average absolute difference of predictions over corresponding observed values. The high accuracy of the proposed approach promises a potential use of the sequence and structural features in computational protein design.Availability and implementationhttp://github.com/KYZ-LSB/ProTerS-FitFun.Supplementary informationSupplementary data are available at Bioinformatics online.