bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transition to chaos separates learning regimes and relates to measure of consciousness in recurrent neural networks
Authors: Mastrovito Dana , Liu Yuhan Helena , Kusmierz Lukasz , Shea-Brown Eric , Koch Christof , Mihalas Stefan 
Published: May 2024

AbstractRecurrent neural networks exhibit chaotic dynamics when the variance in their connection strengths exceed a critical value. Recent work indicates connection variance also modulates learning strategies; networks learn ”rich” representations when initialized with low coupling and ”lazier”solutions with larger variance. Using Watts-Strogatz networks of varying sparsity, structure, and hidden weight variance, we find that the critical coupling strength dividing chaotic from ordered dynamics also differentiates rich and lazy learning strategies. Training moves both stable and chaotic networks closer to the edge of chaos, with networks learning richer representations before the transition to chaos. In contrast, biologically realistic connectivity structures foster stability over a wide range of variances. The transition to chaos is also reflected in a measure that clinically discriminates levels of consciousness, the perturbational complexity index (PCIst). Networks with high values of PCIst exhibit stable dynamics and rich learning, suggesting a consciousness prior may promote rich learning. The results suggest a clear relationship between critical dynamics, learning regimes and complexity-based measures of consciousness.
Meta-analyses reveal support for the Social Intelligence Hypothesis
Authors: Speechley Elizabeth M. , Ashton Benjamin J. , Foo Yong Zhi , Simmons Leigh W. , Ridley Amanda R. 
Published: May 2024

ABSTRACTThe Social Intelligence Hypothesis (SIH) is one of the leading explanations for the evolution of cognition. Since its inception a vast body of literature investigating the predictions of the SIH has accumulated, using a variety of methodologies and species. However, the generalisability of the hypothesis remains unclear. To gain an understanding of the robustness of the SIH as an explanation for the evolution of cognition, we systematically searched the literature for studies investigating the predictions of the SIH. Accordingly, we compiled 103 studies with 584 effect sizes from 17 taxonomic orders. We present the results of four meta-analyses which reveal support for the SIH across interspecific, intraspecific and developmental studies. However, effect sizes did not differ significantly between the cognitive or sociality metrics used, taxonomy or testing conditions. Thus, support for the SIH is similar across studies using neuroanatomy and cognitive performance, those using broad categories of sociality, group size and social interactions, across taxonomic groups, and for tests conducted in captivity or the wild. Overall, our meta-analyses support the SIH as an evolutionary and developmental explanation for cognitive variation.
Dissociable encoding of evolving beliefs and momentary belief updates in distinct neural decision signals
Authors: Parés-Pujolràs Elisabet , Kelly Simon P. , Murphy Peter R. 
Published: May 2024

AbstractMaking accurate decisions in noisy or otherwise uncertain environments requires integrating evidence over time. Using simple tasks requiring rapid evaluation of a stationary sensory feature, two human neurophysiological signals have been found to evolve with similar integration dynamics, with one (centroparietal positivity; CPP) appearing to compute the running integral and continuously feed it to the other (motor beta lateralisation; MBL). However, it remains unknown whether and how these signals serve more distinct functional roles in more complex scenarios where information arrives discontinuously and requires more computational steps to form appropriate belief updates. We employed a volatile expanded judgement task that permits dissociation of the encoding of raw sensory information in each of a series of discrete stimuli (‘objective evidence’), the appropriately transformed belief updates from that information (‘effective evidence’), and the evolving belief itself (accumulated evidence). Whereas MBL traced the evolving belief across stimuli, the CPP was found only to locally encode the effective evidence associated with each individual stimulus. Furthermore, fluctuations in CPP amplitude after each single stimulus could account for variability in the encoding of accumulated evidence in MBL. These results suggest a flexible computational hierarchy in which effective evidence can be computed sample-by-sample at an intermediate processing level to drive downstream belief updates for protracted decisions about discrete stimuli.
A Genetically Encoded System to Quantify and Evolve RuBisCO-Catalyzed Carbon Fixation
Authors: Lanster David L. , Li Zhiyi , Badran Ahmed H. 
Published: May 2024

AbstractStrategies to study and alter the biochemical properties of RuBisCO often couple CO2fixation to bacterial growth. However, these viability-coupled strategies are not quantitative and are limited by toxicity of the RuBisCO substrate RuBP, the slow kinetics of RuBisCO, and differences in RuBisCO expression. We report the development of the first genetically encoded system capable of accurately quantifying RuBisCO-dependent CO2fixationin cellulousing a tripartite approach that combines bacterial strains which insulate RuBisCO-derived products, an engineered pathway that eliminates RuBP toxicity, and biosensors to concurrently monitor RuBisCO abundance and catalysis. We extended this biosensing strategy to 43 Form II and II/III RuBisCO homologs, finding strong agreement within vitro-derived enzyme kinetics in living cells for the first time. Finally, we show how this system can be used to rapidly evolve functional RuBisCO enzymes. Our approach overcomes prior limitations by streamlining intracellular RuBisCO analyses and will enable the development of enzymes with improved CO2fixation capabilities.
Assessing pH-dependent Conformational Changes in the Fusion Peptide Proximal Region of the SARS-CoV-2 spike glycoprotein
Authors: Stepanenko Darya , Wang Yuzhang , Simmerling Carlos 
Published: May 2024

AbstractOne of the entry mechanisms of the SARS-CoV-2 coronavirus into host cells involves endosomal acidification. It has been proposed that under acidic conditions the Fusion Peptide Proximal Region (FPPR) of the SARS-CoV-2 spike glycoprotein acts as a pH-dependent switch, modulating immune response accessibility by influencing the positioning of the Receptor Binding Domain (RBD). This would provide an indirect coupling of RBD opening to environmental pH. Here, we explored this possible pH-dependent conformational equilibrium of the FPPR within the SARS-CoV-2 spike glycoprotein. We analyzed hundreds of experimentally determined spike structures from the Protein Data Bank, and carry out pH-Replica Exchange Molecular Dynamics, exploring the extent to which the FPPR conformation depends on pH and the positioning of the RBD. Meta-analysis of experimental structures identified alternate conformations of the FPPR among structures in which this flexible regions was resolved. However, the results did not support a correlation between the FPPR conformation and either RBD position or the reported pH of the cryo-EM experiment. We calculated pKa values for titratable side chains in the FPPR region using PDB structures, but these pKa values showed large differences between alternate PDB structures that otherwise adopt the same FPPR conformation type. This hampers comparison of pKa values in different FPPR conformations to rationalize a pH-dependent conformational change. We supplemented these PDB-based analyses with all-atom simulations, using constant pH-Replica Exchange Molecular Dynamics to estimate pKa values in the context of flexibility and explicit water. The resulting titration curves show good reproducibility between simulations, but also suggest that the titration curves of the different FPPR conformations are the same within error bars. In summary, we were unable to find evidence supporting the previously published hypothesis of FPPR pH-dependent equilibrium, either from existing experimental data, or from constant pH MD simulations. The study underscores the complexity of the spike system and opens avenues for further exploration into the interplay between pH and SARS-CoV-2 viral entry mechanisms.
S100A9 interacts with a dynamic region on CD14 to activate Toll-like receptor 4
Authors: Chisholm Lauren O. , Jaeger Natalie M. , Murawsky Hannah E. , Harms Michael J. 
Published: May 2024

AbstractS100A9 is a Damage Associated Molecular Pattern (DAMP) that activates inflammatory pathways via Toll-like receptor 4 (TLR4). This activity plays important homeostatic roles in tissue repair, but can also contribute to inflammatory diseases. The mechanism of activation is unknown. Here, we follow up on a previous observation that the protein CD14 is an important co-receptor that enables S100A9 to activate TLR4. Using cell-based functional assays and a combination of mutations and pharmocological perturbations, we found that CD14 must be membrane bound to potentiate TLR4 activation by S100A9. Additionally, S100A9 is sensitive to inhibitors of pathways downstream of TLR4 internalization. Together, this suggests that S100A9 induces activity via CD14-dependent internalization of TLR4. We then used mutagenesis, structural modeling, andin vitrobinding experiments to establish that S100A9 binds to CD14’s N-terminus in a region that overlaps with, but is not identical to, the region where CD14 binds its canonical ligand, lipopolysaccharide (LPS). In molecular dynamics simulations, this region of the protein is dynamic, allowing it to reorganize to recognize both S100A9 (a soluble protein) and LPS (a small hydrophobic molecule). Our work is the first attempt at a molecular characterization of the S100A9/CD14 interaction, bringing us one step closer to unraveling the full mechanism by which S100A9 activates TLR4/MD-2.
Engineering Bacterial Biomanufacturing: Characterization and Manipulation ofSphingomonas sp.LM7 Extracellular Polymers
Authors: van Wijngaarden Ellen W. , Goetsch Alexandra G. , Brito Ilana L. , Hershey David M. , Silberstein Meredith N. 
Published: May 2024

AbstractBiologically produced materials are an attractive alternative to traditional materials such as metals and plastics and offer improved functionalities such as better biodegradability and biocompatibility. Polysaccharides are an example of a biologically produced materials that can have a range of chemical and physical properties including high stiffness to weight ratios and thermal stability. Biomanufactured bacterial polysaccharides can come with many advantages such as being non-toxic and are mechanically robust relative to proteins and lipids, which are also secreted by bacteria to generate a biofilm. One major goal in biomanufacturing is to produce quality material quickly and cost-effectively. Biomanufacturing offers additional benefits compared to traditional manufacturing including low resource investment and equipment requirements, providing an alternative to sourcing fossil fuel byproducts, and relatively low temperatures needed for production. However, many biologically produced materials require complex and lengthy purification processes before use. This paper 1) identifies the material properties of a novel polysaccharide, dubbed promonan, isolated from the extracellular polymeric substances ofSphingomonas sp.LM7; 2) demonstrates that these properties can be manipulated to suit specific applications; and 3) presents two alternative methods of processing to shorten purification time by more than 50% while maintaining comparable material.
Computational structural prediction and chemical inhibition of the human mitochondrial pyruvate carrier protein heterodimer complex
Authors: Hadfield Christy M. , Walker John K. , Arnatt Chris , McCommis Kyle S. 
Published: May 2024

ABSTRACTThe mitochondrial pyruvate carrier (MPC) plays a role in numerous diseases including neurodegeneration, metabolically dependent cancers, and the development of insulin resistance. Several previous studies in genetic mouse models or with existing inhibitors suggest that inhibition of the MPC could be used as a viable therapeutic strategy in these diseases. However, the MPC’s structure is unknown, making it difficult to screen for and develop therapeutically viable inhibitors. Currently known MPC inhibitors would make for poor drugs due to their poor pharmacokinetic properties, or in the case of the thiazolidinediones (TZDs), off-target specificity for peroxisome-proliferator activated receptor gamma (PPARγ) leads to unwanted side effects. In this study, we develop several structural models for the MPC heterodimer complex and investigate the chemical interactions required for the binding of these known inhibitors to MPC and PPARγ. Based on these models, the MPC most likely takes on outward-facing (OF) and inward-facing (IF) conformations during pyruvate transport, and inhibitors likely plug the carrier to inhibit pyruvate transport. Although some chemical interactions are similar between MPC and PPARγ binding, there is likely enough difference to reduce PPARγ specificity for future development of novel, more specific MPC inhibitors.
Charting the financial odyssey: a literature review on history and evolution of investment strategies in the stock market (1900–2022)
Authors: Jagirdar Sharneet Singh , Gupta Pradeep Kumar 
Published: May 2024

PurposeThe present study reviews the literature on the history and evolution of investment strategies in the stock market for the period from 1900 to 2022. Conflicts and relationships arising from such diverse seminal studies have been identified to address the research gaps.Design/methodology/approachThe studies for this review were identified and screened from electronic databases to compile a comprehensive list of 200 relevant studies for inclusion in this review and summarized for the cognizance of researchers.FindingsThe study finds a coherence to complex theoretical documentation of more than a century of evolution on investment strategy in stock markets, capturing the characteristics of time with a chronological study of events.Research limitations/implicationsThere were complications in locating unpublished studies leading to biases like publication bias, the reluctance of editors to publish studies, which do not reveal statistically significant differences, and English language bias.Practical implicationsPractitioners can refine investment strategies by incorporating behavioral finance insights and recognizing the influence of psychological biases. Strategies span value, growth, contrarian, or momentum indicators. Mitigating overconfidence bias supports effective risk management. Social media sentiment analysis facilitates real-time decision-making. Adapting to evolving market liquidity curbs volatility risks. Identifying biases guides investor education initiatives.Originality/valueThis paper is an original attempt to pictorially depict the seminal works in stock market investment strategies of more than a hundred years.
Innovative technology for converting automobile tire waste bead wires into recycled steel fibers for sustainable concrete composites: insights for the Al-Kharj Governorate construction industry
Authors: Amran Mugahed 
Published: May 2024

PurposeThe initiative for sustainability in the construction industry has led to the innovative utilization of automobile tire waste, transforming it into value-added products, toward decarbonization in the construction industry, aligning with the development and sustainability goals of Al-Kharj Governorate. However, the disposal of these materials generates significant environmental concerns. As a payoff for these efforts, this study aims to contribute to a fruitful shift toward eco-friendly recycling techniques, particularly by studying the transformation of tire waste bead wires into recycled steel tire fibers (RSTFs) for sustainable concrete composites.Design/methodology/approachThis research delves into how this technological transformation not only addresses environmental concerns but also propels sustainable tire innovation forward, presenting a promising solution for waste management and material efficiency in building materials. Recent studies have highlighted the superior tensile strength of RSTFs from discarded tires, making them suitable for various structural engineering applications. Recently, there has been a notable shift in research focus to the use of RSTFs as an alternative to traditional fibers in concrete. In this study, however, efforts have paid off in outlining a comprehensive assessment to investigate the viability and efficacy of repurposing tire bead wires into RSTFs for use in concrete composites, as reported in the literature.FindingsThis study examined the Saudi waste management, the geometrical properties of RSTFs, and their impact on the strength properties of concrete microstructure. It also examined the economic, cost, and environmental impacts of RSTFs on concrete composites, underscoring the need for the construction industry to adopt more sustainable and adaptable practices. Furthermore, the main findings of this study are proposed insights and a blueprint for the construction industry in Al-Kharj Governorate, calling for collective action from both public and private sectors, and the community to transform challenges into job opportunities for growth and sustainability.Originality/valueThis study pointed to thoroughly demonstrate the technological advancement in converting tire waste to reinforcing fibers by evaluating the effectiveness, environmental sustainability, and practicality of these fibers in eco-friendly concrete composites. Besides, the desired properties and standards for RSTFs to enhance the structural integrity of concrete composites are recommended, as is the need to establish protocols and further study into the long-term efficacy of RSTF-reinforced concrete composites.
Elderly clothing upgrading in product-service system design using extended Kansei Engineering methodology
Authors: Wang Mingrun , Shaari Nazlina , Abidin Sazrinee Zainal , He Yan 
Published: May 2024

PurposeThis study aims to integrate fall-protection function into the elderly clothing to meet both the daily life and fall-protection needs of the elderly people, thereby upgrading the performance of elderly clothing.Design/methodology/approachThis study identified the design strategies of elderly clothing using an Extended Kansei Engineering methodology. Extended Kansei Engineering methodology is a new design framework developed from the traditional Kansei Engineering methodology to meet the design requirements of the product-service system. This study focuses on the product section of product-service system design. According to the product design process of the Extended Kansei Engineering methodology, this study first collected and organized the design elements and Kansei words of elderly clothing. Then a questionnaire was designed using Semantic Differential Scale. Finally, the questionnaire survey was conducted and the collected data was analysed to understand the consumption preferences of elderly people. A total of 399 elderly people aged 65 and older provided valuable design insights for this survey.FindingsThe research findings include the product design strategies for the development of elderly clothing, as well as a product prototype canvas and a product prototype elderly clothing developed based on the design strategies.Practical implicationsThe research findings can provide competitive design strategies for the development of elderly clothing, thereby upgrading the performance of elderly clothing.Social implicationsThis elderly clothing integrates fall-protection function to reduce the risk of injury for elderly people due to falls, thereby helping society alleviate the medical and healthcare pressure caused by falls for elderly people.Originality/valueThe research findings can provide competitive design strategies for the development of elderly clothing. Furthermore, the Extended Kansei Engineering methodology introduced in this study can provide product and service designers with design methods that are more in line with the development trend of modern product-service system business models.
Can smart supply chain bring agility and resilience for enhanced sustainable business performance?
Authors: Sharma Mahak , Antony Rose , Sharma Ashu , Daim Tugrul 
Published: May 2024

PurposeSupply chains need to be made viable in this volatile and competitive market, which could be possible through digitalization. This study is an attempt to explore the role of Industry 4.0, smart supply chain, supply chain agility and supply chain resilience on sustainable business performance from the lens of natural resource-based view.Design/methodology/approachThe study tests the proposed model using a covariance-based structural equation modelling and further investigates the ranking of each construct using the artificial neural networks approach in AMOS and SPSS respectively. A total of 234 respondents selected using purposive sampling aided in capturing the industry practices across supply chains in the UK. The full collinearity test was carried out to study the common method bias and the content validity was carried out using the item content validity index and scale content validity index. The convergent and discriminant validity of the constructs and mediation study was carried out in SPSS and AMOS V.23.FindingsThe results are overtly inferring the significant impact of Industry 4.0 practices on creating smart and ultimately sustainable supply chains. A partial relationship is established between Industry 4.0 and supply chain agility through a smart supply chain. This work empirically reinstates the combined significance of green practices, Industry 4.0, smart supply chain, supply chain agility and supply chain resilience on sustainable business value. The study also uses the ANN approach to determine the relative importance of each significant variable found in SEM analysis. ANN determines the ranking among the significant variables, i.e. supply chain resilience > green practices > Industry 4.0> smart supply chain > supply chain agility presented in descending order.Originality/valueThis study is a novel attempt to establish the role of digitalization in SCs for attaining sustainable business value, providing empirical support to the mediating role of supply chain agility, supply chain resilience and smart supply chain and manifests a significant integrated framework. This work reinforces the integrated model that combines all the constructs dealt with in silos so far in prior literature.