bluuebunny/crossref_metadata_2025_split huggingface dataset:
Computational Mesoscale Framework for Biological Clustering and Fractal Aggregation
Authors: Zohravi Elnaz , Moreno Nicolas , Ellero Marco 
Published: February 2023

AbstractComplex hierarchical clustering mediated by diffusion and reaction is ubiquitous to many naturally occurring phenomena. The aggregates typically exhibit a fractal behavior or non-integer size scaling compared to their intrinsic dimensionality (2 – 3 dimensions). Such fractal aggregates have attracted attention in studying biological (i.e. bronchi and nervous system morphogenesis, blood clotting) and synthetic (i.e. colloids, polymers, catalysts, nano-dendrites, multicellular organisms) systems. In general, biological clustering can occur on a wide range of spatial/temporal scales, and depending on the type of interactions, multiple mechanisms (or stages) can be involved. As a consequence, the modeling of biological clustering is typically a challenging task, requiring the use of a variety of methods to capture the characteristic behavior of specific biological systems. Herein, we proposed a generalized-mesoscale-clustering (GMC) framework that incorporates hydrodynamic interactions, bonding, and surface tension effects. This framework allows for studying both static and dynamic states of cluster development. We showcase the framework using a variety of biological clustering mechanisms, and further illustrate its versatility to model different scales, focusing on blood-related clustering ranging from fibrin network formation to platelet aggregation. Besides the introduction of the mesoscale clustering framework, we show that a single biomarker (such as fractal dimension) is insufficient to fully characterize and distinguish different cluster structures (morphologies). To overcome this limitation, we propose a comprehensive characterization that relates the structural properties of the cluster using four key parameters, namely the fractal dimension, pore-scale diffusion, as well as the characteristic times for initiation and consolidation of the cluster. Additionally, we show that the GMC framework allows tracking of bond density providing another biomarker for cluster temporal evolution and final steady-state. Furthermore, this feature and built-in hydrodynamics interactions offer the potential to investigate cluster mechanical properties in a variety of biological systems.
The evolution of democratic peace in animal societies
Authors: Hunt KL , Patel M , Croft DP , Franks DW , Green PA , Thompson FJ , Johnstone RA , Cant MA , Sankey DWE 
Published: February 2023

ABSTRACTA major goal in evolutionary biology is to elucidate common principles that drive human and other animal societies to adopt either a warlike or peaceful nature. One proposed explanation for the variation in aggression between human societies is the ‘democratic peace’ hypothesis. According to this theory, autocracies are more warlike than democracies because autocratic leaders can pursue fights for private gain. However, autocratic and democratic decision-making processes are not unique to humans and are widely observed across a diverse range of non-human animal societies. We use evolutionary game theory to evaluate whether the logic of democratic peace may apply across taxa; specifically adapting the classic Hawk-Dove model to consider conflict decisions made by groups rather than individuals. We find support for the democratic peace hypothesis without mechanisms involving complex human institutions and discuss how these findings might be relevant to non-human animal societies. We suggest that the degree to which collective decisions are shared may explain variation in the intensity of intergroup conflict in nature.
Uncovering the BIN1-SH3 interactome underpinning centronuclear myopathy
Authors: Zambo Boglarka , Edelweiss Evelina , Morlet Bastien , Negroni Luc , Pajkos Mátyás , Dosztányi Zsuzsanna , Ostergaard Soren , Trave Gilles , Laporte Jocelyn , Gogl Gergo 
Published: February 2023

AbstractTruncation of the protein-protein interaction SH3 domain of the membrane remodeling Bridging Integrator 1 (BIN1, Amphiphysin 2) protein leads to centronuclear myopathy. Here, we assessed the impact of a set of naturally observed, previously uncharacterized BIN1 SH3 domain variants using conventionalin vitroand cell-based assays monitoring the BIN1 interaction with dynamin 2 (DNM2) and identified potentially harmful ones that can be also tentatively connected to neuromuscular disorders. However, SH3 domains are typically promiscuous and it is expected that other, so-far unknown partners of BIN1 exist besides DNM2, that also participate in the development of centronuclear myopathy. In order to shed light on these other relevant interaction partners and to get a holistic picture of the pathomechanism behind BIN1 SH3 domain variants, we used affinity interactomics. We identified hundreds of new BIN1 interaction partners proteome-wide, among which many appear to participate in cell division, suggesting a critical role of BIN1 in the regulation of mitosis. Finally, we show that the identified BIN1 mutations indeed cause proteome-wide affinity perturbation, signifying the importance of employing unbiased affinity interactomic approaches.
Sarbecoviruses of British Horseshoe Bats; Sequence Variation and Epidemiology
Authors: Apaa Ternenge , Withers Amy J. , Staley Ceri , Blanchard Adam , Bennett Malcolm , Bremner-Harrison Samantha , Chadwick Elizabeth A. , Hailer Frank , Harrison Stephen W.R. , Loose Mathew , Mathews Fiona , Tarlinton Rachael 
Published: February 2023

AbstractHorseshoe bats are the natural hosts of theSarbecovirussubgenus that includes SARS-CoV-1 and 2. Despite the devastating impacts of the COVID-19 pandemic, there is still little known about the underlying epidemiology and virology of sarbecoviruses in their natural hosts, leaving large gaps in our pandemic preparedness. Here we describe the results of PCR testing for sarbecoviruses in the two horseshoe bat species (Rhinolophus hipposiderosandR. ferrumequinum) present in Great Britain, collected in 2021-22 during the peak of COVID-19 pandemic. One hundred and ninety sevenR. hipposiderossamples from 33 roost sites and 277R. ferremequinumsamples from 20 roost sites were tested. No coronaviruses were detected in any samples fromR. ferrumequinumwhereas 44% and 56% of individual and pooled (respectively) faecal samples fromR. hipposiderosacross multiple roost sites tested positive in a sarbecovirus-specific qPCR. Full genome sequences were generated from three of the positive samples (and partial genomes from two more) using Illumina RNAseq on unenriched samples. Phylogenetic analyses showed that the obtained sequences belong to the same monophyletic clade, with >95% similarity, as previously reported European isolates fromR. hipposideros. The sequences differed in the presence or absence of accessory genes ORF 7b, 9b and 10. All lacked the furin cleavage site of SARS-CoV-2 spike gene and are therefore unlikely to be infective for humans. These results demonstrate a lack, or at least low incidence, of SARS-CoV-2 spill over from humans to susceptible GB bats, and confirm that sarbecovirus infection is widespread inR. hipposideros. Despite frequently sharing roost sites withR. ferrumequinum, no evidence of cross-species transmission was found.
IL-33 drives polyfunctionality and antitumor activity of a unique ST2+ NK cell population
Authors: Eberhardt Anaïs , Blanc Elena , Picant Valentin , Alcazer Vincent , Rocca Yamila , Ardin Maude , Voissière Aurélien , Onodi Fanny , Rodriguez Céline , Tonon Laurie , Estavoyer Benjamin , Moudombi Lyvia , Charrier Emily , Wang Xi , Stojanovic Ana , Rau Tilman , Tredan Olivier , Treilleux Isabelle , Michallet Marie-Cécile , Valladeau-Guilemond Jenny , Marçais Antoine , Walzer Thierry , Krebs Philippe , Cerwenka Adelheid , Hubert Margaux , Caux Christophe , Bendriss-Vermare Nathalie 
Published: February 2023

AbstractNatural Killer (NK) cell subsets differ to ensure complementary and crucial roles in tumor immunosurveillance. Their biology is critically regulated by cytokines. Here, we show that IL-33 synergizes with IL-12 to strongly activate a subset of CD56dimNK cells acquiring ST2 expression. Transcriptomic and biological analysis of human ST2+CD56dimNK cells revealed a distinct intermediate differentiation state between canonical CD56brightand CD56dimNK cells, combining high proliferative properties, cytokines/chemokines production, and cytotoxicity. NK cells expressing ST2 protein or exhibiting a ST2-linked transcriptional signature were identified in human and mouse tumors. Accordingly, IL-12 unleashes human breast tumor ST2+NK cell potential to produce IFN-γ in response to IL-33 and IL-33/IL-12 co-injection resulted in a NK-dependent IFN-γ secretion and anti-tumor effects in murine mammary tumors. AnIL33hi-NKhiscore in solid tumors correlated with increased progression-free patient survival. Our findings thus identify polyfunctional ST2+NK cells which effector functions can be harnessed by IL-33 to boost anti-tumor immunity.One sentence summaryThe IL-33/IL-33R(ST2)/NK cell axis is a key determinant of cancer immunity and immunotherapy.
Structural insight into guanylyl cyclase receptor hijacking of the kinase–Hsp90 regulatory mechanism
Authors: Caveney Nathanael A , Tsutsumi Naotaka , Garcia K Christopher 
Published: February 2023

AbstractMembrane receptor guanylyl cyclases play a role in many important facets of human physiology, from regulating blood pressure to intestinal fluid secretion. The structural mechanisms which influence these important physiological processes have yet to be explored. We present the 3.9 Å resolution cryo-EM structure of the human membrane receptor guanylyl cyclase GC-C in complex with Hsp90 and its co-chaperone Cdc37, providing insight into the mechanism of Cdc37 mediated binding of GC-C to the Hsp90 regulatory complex. As a membrane protein and non-kinase client of Hsp90–Cdc37, this work shows the remarkable plasticity of Cdc37 to interact with a broad array of clients with significant sequence variation. Further, this work shows how membrane receptor guanylyl cyclases hijack the regulatory mechanisms used for active kinases to facilitate their regulation. Given the known druggability of Hsp90, these insights can guide the further development of membrane receptor guanylyl cyclase-targeted therapeutics and lead to new avenues to treat hypertension, inflammatory bowel disease, and other membrane receptor guanylyl cyclase-related conditions.
Transcription regulation of SARS-CoV-2 receptor ACE2 by Sp1: a potential therapeutic target
Authors: Han Hui , Luo Rong-Hua , Long Xin-Yan , Wang Li-Qiong , Zhu Qian , Tang Xin-Yue , Zhu Rui , Ma Yi-Cheng , Zheng Yong-Tang , Zou Cheng-Gang 
Published: February 2023

AbstractAngiotensin-converting enzyme 2 (ACE2) is a major cell entry receptor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Induction of ACE2 expression may represent an effective tactic employed by SARS-CoV-2 to facilitate its own propagation. However, the regulatory mechanisms of ACE2 expression after viral infection remain largely unknown. By employing an array of 45 different luciferase reporters, we identify that the transcription factor Sp1 positively and HNF4α negatively regulate the expression of ACE2 at the transcriptional levels in HPAEpiC cells, a human lung epithelial cell line. SARS-CoV-2 infection promotes and inhibits the transcription activity of Sp1 and HNF4α, respectively. The PI3K/AKT signaling pathway, which is activated by SARS-CoV-2 infection, is a crucial node for induction of ACE2 expression by increasing Sp1 phosphorylation, an indicator of its activity, and reducing HNF4α nuclear location. Furthermore, we show that colchicine could inhibit the PI3K/AKT signaling pathway, thereby suppressing ACE2 expression. Inhibition of Sp1 by either its inhibitor mithramycin A or colchicine reduces viral replication and tissue injury in Syrian hamsters infected with SARS-CoV-2. In summary, our study uncovers a novel function of Sp1 in regulating ACE2 expression and suggests that Sp1 is a potential target to reduce SARS-CoV-2 infection.
2-Photon imaging of fluorescent proteins in living swine
Authors: Costine-Bartell Beth A. , Martinez-Ramirez Luis , Normoyle Kieran , Stinson Tawny , Staley Kevin J. , Lillis Kyle P. 
Published: February 2023

ABSTRACTA common point of failure in translation of preclinical neurological research to successful clinical trials comes in the giant leap from rodent models to humans. Non-human primates are phylogenetically close to humans, but cost and ethical considerations prohibit their widespread usage in preclinical trials. Swine have large, gyrencencephalic brains, which are biofidelic to human brains. Their classification as livestock makes them a readily accessible model organism. However, their size has precluded experiments involving intravital imaging with cellular resolution. Here, we present a suite of techniques and tools forin vivoimaging of porcine brains with subcellular resolution. Specifically, we describe surgical techniques for implanting a synthetic, flexible, transparent dural window for chronic optical access to the neocortex. We detail optimized parameters and methods for injecting adeno-associated virus vectors through the cranial imaging window to express fluorescent proteins. We introduce a large-animal 2-photon microscope that was constructed with off-the shelf components, has a gantry design capable of accommodating animals > 80 kg, and is equipped with a high-speed digitizer for digital fluorescence lifetime imaging. Finally, we delineate strategies developed to mitigate the substantial motion artifact that complicates high resolution imaging in large animals, including heartbeat-triggered high-speed image stack acquisition. The effectiveness of this approach is demonstrated in sample images acquired from pigs transduced with the chloride-sensitive fluorescent protein SuperClomeleon.
Future climate change impacts on anchoveta (Engraulis ringens) in the Northern Peru Current Ecosystem
Authors: Oliveros-Ramos Ricardo , Shin Yunne-Jai 
Published: February 2023

AbstractThe Northern Peru Current Ecosystem (NPCE) is the most productive ecosystem in terms of fish biomass and sustains the world’s largest small pelagic fishery, the Peruvian anchovy fishery. A cooling of this system has been observed during recent decades but the potential regional impacts of rising atmospheric CO2concentrations on upwelling dynamics and productivity are still unknown. We used the ecosystem model OSMOSE to forecast the impacts of several scenarios of climate change on Peruvian anchovy in the NPCE. The OSMOSE model was forced by plankton production and climate drivers from the Earth System Models IPSL CM5A-LR and GFDL-ESM2M for the period 2009-2100. For each earth system model, representative concentration pathways (RCP) scenarios 2.6, 4.5, 6.0 and 8.5 were run. Our results showed that an optimistic trajectory for anchovy is a reduction of biomass at a rate of 14% per decade until mid-21st century, followed by a collapse and late recovery by the end of the 21st century, while no changes in the spatial distribution of the population were observed. The pessimistic trajectory for anchovy is a reduction of biomass of 22% per decade, with a collapse after 2020 and near extinction by 2060, with a spatial displacement of the population to the south and to more coastal areas. Further research is needed to include additional key environmental variables such as oxygen as well as more realistic fisheries management intervention scenarios to evaluate future options for the sustainability of anchovy resource and fisheries.
Chemically-induced targeted protein degradation in mycobacteria uncovers antibacterial effects and potentiates antibiotic efficacy
Authors: Won Harim I. , Zhu Junhao , Kandror Olga , Akopian Tatos , Wolf Ian D. , Chao Michael C. , Waldor Maya , Rubin Eric J. 
Published: February 2023

AbstractProteolysis-targeting chimeras (PROTACs) represent a new therapeutic modality involving selectively directing disease-causing proteins for degradation through proteolytic systems. Our ability to exploit this targeted protein degradation (TPD) approach for antibiotic development remains nascent due to our limited understanding of which bacterial proteins will be labile TPD targets. Here, we use a genetic system to model chemically-induced proximity and degradation to screen essential proteins inMycobacterium smegmatis(Msm), a model for the major human pathogenM. tuberculosis(Mtb). We find that drug-induced proximity to the bacterial ClpC1P1P2 proteolytic complex is sufficient to degrade many, but not all, endogenousMsmproteins, profoundly inhibiting bacterial growth for some targets. We also show that TPD can potentiate the effects of existing antibiotics targeting the same pathways and complexes. Together, our results identify specific endogenous mycobacterial proteins as attractive targets for futureMtbPROTAC development, as both standalone antibiotics and potentiators of existing antibiotic efficacy.
Naupliar exposure to acute warming does not affect ontogenetic patterns in respiration, size, or development time in the cosmopolitan copepodAcartia tonsa
Authors: Holmes-Hackerd Mathew , Sasaki Matthew , Dam Hans G. 
Published: February 2023

AbstractShort-term, acute warming events are increasing in frequency across the world’s oceans. For short-lived species like most copepods, these extreme events can occur over both within- and between-generational time scales. Yet, it is unclear whether exposure to acute warming during early life stages of copepods can cause lingering effects on metabolism through development, even after the event has ended. These lingering effects would reduce the amount of energy devoted to growth and affect copepod population dynamics. We exposed nauplii of an ecologically important coastal species, Acartia tonsa, to a 24-hour warming event (control: 18°C; treatment: 28°C), and then tracked individual respiration rate, body length, and stage duration through development. As expected, we observed a decrease in massspecific respiration rates as individuals developed. However, exposure to acute warming had no effect on the ontogenetic patterns in per-capita or mass-specific respiration rates, body length, or development time. The lack of these carryover effects through ontogeny suggests within-generational resilience to acute warming in this copepod species.
Data mining analytics investigate WeChat users’ behaviours: online social media and social commerce development
Authors: Liao Shu-Hsien , Widowati Retno , Lin Wei-Can 
Published: February 2023

Purpose
As of December 2021, WeChat had more than 1.2 billion active users worldwide, making it the most active online social media in mainland China. The term social commerce is used to describe new online sales through a mix of social networks and/or peer-to-peer communication or marketing strategies in terms of allowing consumers to satisfy their shopping behaviour through online social media. Thus, given the numerous active users, the development of online social media and social commerce on WeChat is a critical issue of internet research.

Design/methodology/approach
This empirical study takes WeChat as the online social media research object. Questionnaires for WeChat users in China were designed and distributed. All items are designed as nominal and ordinal scales (not Likert scale). The obtained data was put into a relational database (N = 2,342), and different meaningful patterns and rules were examined through data mining analytics, including clustering analysis and association rules, to explore the role of WeChat in the development of online social media and social commerce.

Findings
Practical implications are presented according to the research findings of meaningful patterns and rules. In addition, alternatives to WeChat in terms of further development are also proposed according to the investigation findings of WeChat users’ behaviour and preferences in China.

Originality/value
This study concludes that online social media, such as WeChat, will be able to transcend the current development pattern of most online social media and make good use of investigating users’ behaviour and preferences, not only to stimulate the interaction of users in the social network, but also to create social commerce value in social sciences.
Effectiveness of banking card security in the Ethiopian financial sector: PCI-DSS security standard as a lens
Authors: Lessa Lemma , Gebrehawariat Daniel 
Published: February 2023

PurposeThis study is aimed at assessing the information security management practice with a focus on banking card security in selected financial institutions in Ethiopia, using an international information security standard as a benchmark. It is to identify the gaps and recommend best security practices to help financial institutions meet the required security compliance.Design/methodology/approachTwo financial sectors were purposively selected. A total of twenty-five respondents (IT executives and IT staff) were included in the study. Quantitative data was collected using the PCI-DSS (Payment Card Industry Data Security Standard) security standard questionnaire. In addition, observation and document analysis were made.FindingsThe result shows that most of the essential security management activities in the financial sectors do not comply with the international security standard. Similarly, the level of most of the indispensable security requirements that should be in place is found to be below the acceptable level. The study also revealed major security factors that prohibit the financial sectors from PCI-DSS security standard compliance.Originality/valueThis study assessed the information security management practice with a focus on banking card security and tried to figure out the limitations of security practices of the organizations surveyed based on the standard adopted. The topic has not been well explored especially in the Ethiopia context. Hence, the result can positively influence security policies, particularly in the banking sector.
Research on active disturbance rejection control technique for underwater welding robot based on model compensation
Authors: Li Shengqian , Zhang Xiaofan 
Published: February 2023

Purpose
An active disturbance rejection controller (ADRC) based on model compensation is proposed in this paper. The method should first be taken a nominal model of the robot to compensate. Subsequently, the uncertain external disturbance is estimated and compensated is used an expansion state observer (ESO) in real time, which can reduce the estimating range of observation for ESO. The purpose of this paper is to suggest a novel method to improve the system tracking performance, as well as the dynamic and static performance index.

Design/methodology/approach
A welding robot is a complicated system with uncertainty, time-varying, strong coupling and a nonlinear system; it is more complex as if it is used in an underwater environment, and it is difficult to establish an accurate dynamic model for an underwater welding robot. Aiming at the tracking control of an underwater welding robot, it is difficult to achieve the control performance requirements by the conventional proportional integral derivative method to realize automatic tracking of the seam.

Findings
The simulation experiment is carried out by MATLAB/Simulink, and the application experiment is recorded. The experimental results show that the control method is correct and effective, and the system’s tracking performance is stable, and the robustness and tracking accuracy of the system are also improved.

Originality/value
The seam gets plumper and smoother, with better continuity and no undercut phenomenon.