bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antibiotic-Induced Morphological Changes Enhance Phage Propagation: A Mathematical Model of Plaque Formation in Structured Environments
Authors: Bulssico Julián , Panigrahi Swapnesh , Ginet Nicolas , Ansaldi Mireille 
Published: September 2024

AbstractA distinctive manifestation of phage infection in solid media is the appearance of lysis plaques, which correspond to the circular thinning of a bacterial lawn. During plaque formation, successive cycles of phage replication generally take place from a single point of infection and spread radially in a matrix of immobilized bacterial hosts. Many different factors affect plaque size, such as the composition and the reticulation of the propagation matrix, the characteristics of the phage, but also parameters related to the physiology of the bacterial host.Since combined administration of both antibiotics and phages is a common practice during compassionate treatments, our research focuses on the effects of antibiotics on phage predation, which can be of crucial importance for the therapeutic applications of phages.It has been previously observed that the presence of antibiotics at sublethal concentrations can affect drastically bacterial physiology, allowing phages to spread more rapidly and resulting in better bacterial eradication. Previous experimental work has focused on the phage characteristics that influence plaque size. However, as plaque formation is strongly influenced by host growth dynamics, a comprehensive model integrating both the host growth and phage infection parameters is required.In this work, we suggest that plaque enlargement is linked to morphological changes of the host that have an impact on the rate of epidemic propagation and certainly on phage diffusion into the matrix. To support this hypothesis, we characterized the growth parameters of two different phages and bacteria in semi-solid media in the presence of various antibiotics. By combining these data, we have produced a mathematical model that accounts for these observations and explains the increase in plaque size when the host morphology is affected.Significance StatementThis study provides new insights into the phenomenon of Phage-Antibiotic Synergy (PAS) by demonstrating that antibiotic-induced morphological changes in bacterial hosts play a critical role in enhancing phage propagation in structured environments. By linking these morphological alterations—such as cell filamentation and bloating—to increased lysis plaque size, the research underscores the importance of host dynamics in phage therapy. The development of a mathematical model integrating both host growth and phage infection parameters offers a novel framework for understanding and optimizing phage-based treatments in the presence of antibiotics, potentially improving therapeutic outcomes.
Single Distal Mutation Enhances Activity of known PETases via Stabilisation of PET-binding
Authors: Fu Xiaozhi , Gracia I. Carmona Oriol , Abrusan Gyorgy , Jiao Xiang , Diaciuc Alexander , Gautel Mathias , Fraternali Franca , Zelezniak Aleksej 
Published: September 2024

AbstractAs a major source of plastic pollution, PET has attracted significant interest for biodegradation due to its potential in the circular economy. Finding effective enzymes still remains a challenge as screening methods are limited by either the low throughput or dependence on alternative non-PET substrates due to PET’s insolubility. Here, we report a highly active, stable and robust enzyme, Fast_2.9, identified while directly screening for PET-degrading activity in mesophilic conditions using droplet-based encapsulation of PET nanoparticles with the throughput above 1 kHz. We identified a distal S269T mutation that improves activity in the majority of all known PETases with up to 400 times over wildtype, and more than twice of known engineered PETases, as tested on untreated post-consumer plastics. Microsecond time scale molecular dynamics analyses indicate that this distant mutation possibly influences residues near the substrate-binding cleft via a common mechanism across PETases. Compared to the state-of-the-art FastPETase and LCCICCGenzymes, the engineered Fast_2.9 enzyme requires up to 8 and 42 times lower enzyme concentrations to reach the same enzymatic activity, ultimately requiring significantly less enzyme. As such our engineered enzyme degrades multiple post-consumer PET substrates, including polyester textiles, within as least as just 2 days with up to nearly 100% terephthalic acid conversion using as little as 0.72 mgenzyme/gPETat 50℃. Our study presents a universal methodology for direct screening of insoluble substrates at ultra-high-throughput and highlights the techno-economic potential of Fast_2.9 for PET depolymerisation.
PathMHC: a workflow to selectively target pathogen-derived MHC peptides in discovery immunopeptidomics experiments for vaccine target identification
Authors: Leddy Owen , Yuki Yuko , Carrington Mary , Bryson Bryan D. , White Forest M. 
Published: September 2024

AbstractVaccine-elicited T cell responses can contribute to immune protection against emerging infectious disease risks such as antimicrobials-resistant (AMR) microbial pathogens and viruses with pandemic potential, but rapidly identifying appropriate targets for T cell priming vaccines remains challenging. Mass spectrometry (MS) analysis of peptides presented on major histocompatibility complexes (MHCs) can identify potential targets for protective T cell responses in a proteome-wide manner. However, pathogen-derived peptides are outnumbered by self peptides in the MHC repertoire and may be missed in untargeted MS analyses. Here we present a novel approach, termed PathMHC, that uses computational analysis of untargeted MS data followed by targeted MS to discover novel pathogen-derived MHC peptides more efficiently than untargeted methods alone. We applied this workflow to identify MHC peptides derived from multiple microbes, including potential vaccine targets presented on MHC-I by human dendritic cells infected withMycobacterium tuberculosis. PathMHC will facilitate antigen discovery campaigns for vaccine development.
The transcriptome of playfulness is sex-biased in the juvenile rat medial amygdala: a role for inhibitory neurons
Authors: Marquardt Ashley E. , Basu Mahashweta , VanRyzin Jonathan W. , Ament Seth A. , McCarthy Margaret M. 
Published: September 2024

AbstractSocial play is a dynamic behavior known to be sexually differentiated; in most species, males play more than females, a sex difference driven in large part by the medial amygdala (MeA). Despite the well-conserved nature of this sex difference and the importance of social play for appropriate maturation of brain and behavior, the full mechanism establishing the sex bias in play is unknown. Here, we explore “the transcriptome of playfulness” in the juvenile rat MeA, assessing differences in gene expression between high- and low-playing animals of both sexes via bulk RNA-sequencing. Using weighted gene co-expression network analysis (WGCNA) to identify gene modules combined with analysis of differentially expressed genes (DEGs), we demonstrate that the transcriptomic profile in the juvenile rat MeA associated with playfulness is largely distinct in males compared to females. Of the 13 play-associated WGCNA networks identified, only two were associated with play in both sexes, and very few DEGs associated with playfulness were shared between males and females. Data from our parallel single-cell RNA-sequencing experiments using amygdala samples from newborn male and female rats suggests that inhibitory neurons drive this sex difference, as the majority of sex-biased DEGs in the neonatal amygdala are enriched within this population. Supporting this notion, we demonstrate that inhibitory neurons comprise the majority of play-active cells in the juvenile MeA, with males having a greater number of play-active cells than females, of which a larger proportion are GABAergic. Through integrative bioinformatic analyses, we further explore the expression, function, and cell-type specificity of key play-associated modules and the regulator “hub genes” predicted to drive them, providing valuable insight into the sex-biased mechanisms underlying this fundamental social behavior.
The transmembrane glycoprotein Gpnmb is required for the immune and fibrotic responses during zebrafish heart regeneration
Authors: Gupta Savita , Bajwa Gursimran Kaur , El-Sammak Hadil , Mattonet Kenny , Günther Stefan , Looso Mario , Stainier Didier Y. R. , Marín-Juez Rubén 
Published: September 2024

AbstractMyocardial infarction occurs when coronary supply of oxygen and nutrients to part of the heart is interrupted. In contrast to adult mammals, adult zebrafish have a unique ability to regenerate their heart after cardiac injury. Several processes are involved in this regenerative response including inflammation, coronary endothelial cell proliferation and revascularization, endocardial expansion, cardiomyocyte repopulation, and transient scar formation. To identify potential regulators of zebrafish cardiac regeneration, we profiled the transcriptome of regenerating coronary endothelial cells at 7 days post cryoinjury (dpci) and observed the significant upregulation of dozens of genes includinggpnmb. Gpnmb (glycoprotein non-metastatic melanoma protein B) is a transmembrane glycoprotein implicated in inflammation resolution and tissue regeneration. Transcriptomic profiling data of cryoinjured zebrafish hearts reveal thatgpnmbis mostly expressed by macrophages. To investigategpnmbfunction during zebrafish cardiac regeneration, we generated a full locus deletion (FLD) allele. We find that after cardiac cryoinjury, animals lackinggpnmbexhibit neutrophil retention and decreased macrophage recruitment as well as reduced myofibroblast numbers. Moreover, loss ofgpnmbimpairs coronary endothelial cell regeneration and cardiomyocyte dedifferentiation. Transcriptomic analyses of cryoinjuredgpnmbmutant hearts identified enhanced collagen gene expression and the activation of extracellular matrix (ECM) related pathways. Furthermore,gpnmbmutant hearts exhibit larger fibrotic scars revealing additional defects in cardiac regeneration. Altogether, these data indicate thatgpnmbexpressing macrophages modulate inflammation and ECM deposition after cardiac cryoinjury in zebrafish and further highlight the importance of this subset of immune cells to support a regenerative response.
Model for efficient dynamical ranking in networks
Authors: Della Vecchia Andrea , Neocosmos Kibidi , Larremore Daniel B. , Moore Cristopher , De Bacco Caterina 
Published: September 2024

We present a physics-inspired method for inferring dynamic rankings in directed temporal networks—networks in which each directed and timestamped edge reflects the outcome and timing of a pairwise interaction. The inferred ranking of each node is real-valued and varies in time as each new edge, encoding an outcome like a win or loss, raises or lowers the node's estimated strength or prestige, as is often observed in real scenarios including sequences of games, tournaments, or interactions in animal hierarchies. Our method works by solving a linear system of equations and requires only one parameter to be tuned. As a result, the corresponding algorithm is scalable and efficient. We test our method by evaluating its ability to predict interactions (edges' existence) and their outcomes (edges' directions) in a variety of applications, including both synthetic and real data. Our analysis shows that in many cases our method's performance is better than existing methods for predicting dynamic rankings and interaction outcomes.

Published by the American Physical Society
2024
Protocols for trainable and differentiable quantum generative modeling
Authors: Kyriienko Oleksandr , Paine Annie E. , Elfving Vincent E. 
Published: September 2024

We propose an approach for learning probability distributions as differentiable quantum circuits (DQC) that enable efficient quantum generative modeling (QGM) and synthetic data generation. Contrary to existing QGM approaches, we perform training of a DQC-based model, where data is encoded in a latent space with the proposed phase feature map of exponential capacity. This is followed by a trainable quantum circuit, forming the model. We then map the trained model to the bit basis using a fixed unitary transformation, in this case corresponding to a quantum Fourier transform circuit. It allows fast sampling from parametrized distributions using a single-shot readout. Importantly, latent space training provides models that are automatically differentiable, and we show how samples from solutions of stochastic differential equations (SDEs) can be accessed by solving stationary and time-dependent Fokker-Planck equations with a quantum protocol. Our approach opens a route to multidimensional generative modeling with qubit registers explicitly correlated via a (fixed) entangling layer. In this case quantum computers can offer advantage as efficient samplers, which perform complex inverse transform sampling enabled by the fundamental laws of quantum mechanics. On a technical side the advances are multiple, as we introduce the phase feature map, analyze its properties, and develop frequency-taming techniques that include qubitwise training and feature map sparsification.

Published by the American Physical Society
2024
Green supply chain management and sustainable performance: exploring the role of circular economy capability and green ambidexterity innovation
Authors: Martínez-Falcó Javier , Sánchez-García Eduardo , Marco-Lajara Bartolomé , Andreu Rosario 
Published: September 2024

PurposeThe present research aims to analyze the influence of Green Supply Chain Management (GSCM) on the Sustainable Performance (SP) of Spanish wineries, examining the intermediary roles of Circular Economy Capability (CEC) and Green Ambidexterity Innovation (GAI) within this primary relationship. In particular, the study seeks to answer the following Research Questions (RQs): (RQ1), does GSCM exert a positive impact on wineries’ SP? (RQ2), does CEC play a mediating role in the interconnection between GSCM and wineries’ SP? And (RQ3), does GAI function as a mediator in the interplay between GSCM and wineries’ SP?Design/methodology/approachThe research utilizes Partial Least Squares Structural Equation Modeling (PLS-SEM) to evaluate the hypothesized theoretical model using primary data collected from 196 Spanish wineries from September 2022 to January 2023.FindingsThe results reveal a positive relationship between GSCM and SP in Spanish wineries, as well as the existence of positive partial mediations of CEC and GAI in this main linkage, which allows an affirmative answer to the three RQs formulated.Originality/valueDistinguished by its innovative exploration, this research marks a pioneering effort in the uncharted field of scrutinizing CEC and GAI as mediating factors in the GSCM-SP nexus, thereby enriching the existing body of knowledge and opening new avenues for future academic research on sustainability in the wine industry.
Framing effects in non-GMO labels: an empirical study of the impact of non-GMO label frames on consumers' food preferences
Authors: Chen Zhouhai , Wang Hong , Hu Jiahao 
Published: September 2024

PurposeFood labels are increasingly used to provide information to consumers. As a common design strategy used for food package labels globally, label frame is often used to expand the perceived breadth of a brand and create a broader brand image. We evaluated the effect of the presence or absence of a non-genetically modified organism (non-GMO) label frame on consumers' preferences for non-GMO foods.Design/methodology/approachThis study collected data from 120 MBA students at a university in Sichuan, China, and 126 foreign volunteers in a shopping mall in Chengdu, Sichuan Province. The study investigates the effect of the presence or absence of non-GMO label frame (i.e. label with or without an outline) on non-GMO food preferences through a field survey and two controlled experiments. To empirically analyse the psychological mechanisms by which non-GMO label frames affect consumers' preferences for non-GMO food, we set up the mediating variable of food association of safety.FindingsFor ordinary consumers, a framed non-GMO label is more likely to evoke food association of safety and further enhance consumer preference for non-GMO foods. It facilitates consumers' choice of healthier foods. This finding did not otherwise vary across demographic characteristics.Originality/valueThis study is the first to examine the influence of non-GMO label frames on consumers' non-GMO food preferences, which is an innovative research question. The findings of this study are instructive for food manufacturers and policymakers to better design and use non-GMO label frames to attract more consumers to choose non-GMO foods.
Technological and market sensing capabilities as drivers of SME participation in public procurement: an empirical test of the moderating role of financial capability
Authors: Israel Baraka , Mwenda Beny 
Published: September 2024

PurposePublic procurement presents substantial market opportunities for small- and medium-sized enterprises (SMEs), which can contribute to their economic growth. However, limited dynamic capabilities often pose challenges for SMEs to participate effectively in public procurement markets. Drawing on dynamic capability (DC) theory, this study explores whether financial capability (FNCP) influences SMEs’ ability to leverage their technological capability (TECC) and marketing sensing capability (MKSC) and actively engage in public procurement.Design/methodology/approachData for this study were collected from 248 SME managers in the Ilala District, Tanzania, using a cross-sectional questionnaire survey and stratified random sampling technique. The proposed hypotheses were tested empirically through confirmatory factor analysis (CFA) and the Hayes PROCESS macro.FindingsTECC and MKSC demonstrated significant positive associations with SME participation in public procurement (SMPP). Moreover, the interaction between TECC and FNCP as well as the interaction between MKSC and FNCP demonstrate a significant positive effect, suggesting that FNCP strengthens the impact of TECC and MKSC on SMPP.Research limitations/implicationsThe scope of this study was limited to SMEs in the Ilala District of Tanzania, hence affecting the generalizability of the findings to other contexts. More importantly, the study findings enrich the understanding of DC theory, signifying that the integration and reconfiguration of MKSC, TECC and FNCP add significant value to SMPP.Practical implicationsThe findings suggest that policymakers, support institutions and SME managers should focus on enhancing SMEs' MKSC and TECC to improve their participation in public procurement. In addition, improving SMEs' access to financial resources can further strengthen these effects, enabling more inclusive participation in public procurement.Originality/valueThe study contributes to the literature on SMPP by highlighting the critical roles of MKSC and TECC. It also underscores the importance of FNCP as a moderator in these relationships, which has not been addressed in the existing literature. By integrating these factors, the study offers a comprehensive framework for understanding the dynamics that influence SMPP from financial, technological and marketing perspectives, particularly in developing economies like Tanzania.
Influence of customer intention on patronizing halal logo in the food premises of Malaysia
Authors: Pauzi Norhidayah , Razali Asbah , Man Saadan , Syed Jaafar Syed Mohd Jeffri , Jamaludin Mohd Hafiz 
Published: September 2024

Purpose
This study aims to examine attitude, perceived behavioral and religiosity that influence Muslim consumers’ intention in patronizing at food premises with halal logo.

Design/methodology/approach
The data were collected from 450 respondents on random sampling basis. Quantitative analysis was conducted using SEM SMARTPLS version 3.3.

Findings
Based on the findings gathered using PLS analysis with n = 450, it was indicated that attitude, perceived behavioral control and religiosity significantly influence Muslim consumers’ intention on patronizing at food premise with halal logo.

Research limitations/implications
The data collection for the present study was limited to the respondents in Kuala Lumpur among Muslim consumers, and limited to 450 sample sizes.

Practical implications
The presence of halal logo should be crucial in attracting consumers due to the comprehensive meaning it brings.

Social implications
In the context of food premises, the results of the research suggest that the halal logo shown by the food premise seems to operate significantly in attracting Muslim consumers toward the food premises. Muslim consumers need to be nourished by proper Islamic teachings and have a good understanding of halal principle.

Originality/value
The halal logo of food premise concerns the Muslims. Muslim consumers are relying on surrogates in selecting the alternatives for packaged goods in Islamic marketing literature. However, it is little known how Muslims use indicators to select food premises when there is no halal logo.
Analysis of the influence of printing parameters on the compression resistance of PLA in the FDM process
Authors: Passari Émerson dos Santos , Lauermann Carlos Henrique , Souza André J. , Silva Fabio Pinto , Barros Rodrigo Rodrigues de 
Published: September 2024

Purpose
The rapid growth of 3D printing has transformed the cost-effective production of prototypes and functional items, primarily using extrusion technology with thermoplastics. This study aims to focus on optimizing mechanical properties, precisely highlighting the crucial role of mechanical compressive strength in ensuring the functionality and durability of 3D-printed components, especially in industrial and engineering applications.

Design/methodology/approach
Using the Box−Behnken experimental design, the research investigated the influence of layer thickness, wall perimeter and infill level on mechanical resistance through compression. Parameters such as maximum force, printing time and mass utilization are considered for assessing and enhancing mechanical properties.

Findings
The layer thickness was identified as the most influential parameter over the compression time, followed by the degree of infill. The number of surface layers significantly influences both maximum strength and total mass. Optimization strategies suggest reducing infill percentage while maintaining moderate to high values for surface layers and layer thickness, enabling the production of lightweight components with adequate mechanical strength and reduced printing time. Experimental validation confirms the effectiveness of these strategies, with generated regression equations serving as a valuable predictive tool for similar parameters.

Practical implications
This research offers valuable insights for industries using 3D printing in creating prototypes and functional parts. By identifying optimal parameters such as layer thickness, surface layers and infill levels, the study helps manufacturers achieve stronger, lighter and more cost-efficient components. For industrial and engineering applications, adopting the outlined optimization strategies can result in components with enhanced mechanical strength and durability, while also reducing material costs and printing times. Practitioners can use the developed regression equations as predictive tools to fine-tune their production processes and achieve desired mechanical properties more effectively.

Originality/value
This research contributes to the ongoing evolution of additive manufacturing, providing insights into optimizing structural rigidity through polylactic acid (PLA) selection, Box−Behnken design and overall process optimization. These findings advance the understanding of fused deposition modeling (FDM) technology and offer practical implications for more efficient and economical 3D printing processes in industrial and engineering applications.