bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterisation of anhydro-sialic acid transporters from mucosa-associated bacteria
Authors: Wu Yunhan , Bell Andrew , Thomas Gavin H. , Bolam David N. , Sargent Frank , Juge Nathalie , Palmer Tracy , Severi Emmanuele 
Published: January 2024

ABSTRACTSialic acid (Sia) transporters are critical to the capacity of host-associated bacteria to utilise sialic acid for growth and/or cell-surface modification. While N-acetyl-neuraminic acid (Neu5Ac)-specific transporters have been studied extensively, little is known on transporters dedicated to anhydro-sialic acid forms such as 2,7-anhydro-Neu5Ac (2,7-AN) or 2,3-dehydro-2-deoxy-Neu5Ac (Neu5Ac2en). Here, we used a Sia-transport-null strain ofEscherichia colito investigate the function of members of anhydro-Sia transporter families previously identified by computational studies. First, we showed that the transporter NanG, from the Glycoside-Pentoside-Hexuronide:cation symporter family, is a specific 2,7-AN transporter, and identified by mutagenesis a crucial functional residue within the putative substrate-binding site. We then demonstrated that NanX transporters, of the Major Facilitator Superfamily, also only transport 2,7-AN and not Neu5Ac2en nor Neu5Ac. Finally, we provided evidence that SiaX transporters, of the Sodium-Solute Symporter superfamily, are promiscuous Neu5Ac/Neu5Ac2en transporters able to acquire either substrate equally well. The characterisation of anhydro-Sia transporters expands our current understanding of prokaryotic Sia metabolism within host-associated microbial communities.
Glycan-costumed virus-like particles promote type 1 anti-tumor immunity
Authors: Lensch Valerie , Gabba Adele , Hincapie Robert , Bhagchandani Sachin H. , Basak Ankit , Alam Mohammad Murshid , Irvine Darrell J. , Shalek Alex K. , Johnson Jeremiah A. , Finn M. G. , Kiessling Laura L. 
Published: January 2024

AbstractCancer vaccine development is inhibited by a lack of strategies for directing dendritic cell (DC) induction of effective tumor-specific cellular immunity. Pathogen engagement of DC lectins and toll-like receptors (TLRs) shapes immunity by directing T cell function. Strategies to activate specific DC signaling pathways via targeted receptor engagement are crucial to unlocking type 1 cellular immunity. Here, we engineered a glycan-costumed virus-like particle (VLP) vaccine that delivers programmable peptide antigens to induce tumor-specific cellular immunityin vivo. VLPs encapsulating TLR7 agonists and decorated with a selective mannose-derived ligand for the lectin DC-SIGN induced robust DC activation and type 1 cellular immunity, whereas VLPs lacking this key DC-SIGN ligand failed to promote DC-mediated immunity. Vaccination with glycan-costumed VLPs generated tumor antigen-specific Th1 CD4+and CD8+T cells that infiltrated solid tumors, inhibiting tumor growth in a murine melanoma model. Thus, VLPs employing lectin-driven immune reprogramming provide a framework for advancing cancer immunotherapies.
Architecture of genome-wide transcriptional regulatory network reveals dynamic functions and evolutionary trajectories inPseudomonas syringae
Authors: Sun Yue , Li Jingwei , Huang Jiadai , Li Shumin , Li Youyue , Lu Beifang , Deng Xin 
Published: January 2024

AbstractThe model Gram-negative plant pathogenPseudomonas syringaeutilises hundreds of transcription factors (TFs) to regulate its functional processes, including virulence and metabolic pathways that control its ability to infect host plants. Although the molecular mechanisms of regulators have been studied for decades, a comprehensive understanding of genome-wide TFs inPsph1448A remains limited. Here, we investigated the binding characteristics of 170 of 301 annotated TFs through ChIP-seq. Fifty-four TFs, 62 TFs and 147 TFs were identified in top-level, middle-level and bottom-level, reflecting multiple higher-order network structures and direction of information-flow. More than forty thousand TF-pairs were classified into 13 three-node submodules which revealed the regulatory diversity of TFs inPsph1448A regulatory network. We found that bottom-level TFs performed high co-associated scores to their target genes. Functional categories of TFs at three levels encompassed various regulatory pathways. Three and 25 master TFs were identified to involve in virulence and metabolic regulation, respectively. Evolutionary analysis and topological modularity network revealed functional variability and various conservation of TFs inP. syringae(Psph1448A,PstDC3000,PssB728a andPsaC48). Overall, our findings demonstrated the global transcriptional regulatory network of genome-wide TFs inPsph1448A. This knowledge can advance the development of effective treatment and prevention strategies for related infectious diseases.
EmergingMycobacterium bovisin Lebanon: a snapshot based on whole-genome sequencing
Authors: El Jouaid Israa , Sobh Ghena , Araj George F , Achache Wafaa , Grine Ghiles , Tokajian Sima , Al Khoury Charbel , Abdel-Sater Fadi , Drancourt Michel , Saad Jamal 
Published: January 2024

ABSTRACTBackgroundTuberculosis is a pressing public health issue in Lebanon, a country of approximately five million people, including around 1.5 million refugees from Palestine and Syria. Prior research has revealed uncontrolled animal sources ofMycobacterium bovis, emphasizing the necessity for a comprehensive approach to combat tuberculosis in the region.Methods48 clinicalMycobacterium tuberculosiscomplex isolates were identified through whole genome sequence. Also, 43 animal fecal samples were collected from various farms across Lebanon to investigate the presence of theM. tuberculosiscomplex using CRISPR-csm4 PCR.ResultsGenomic analysis revealed that 39/48 (81.25%) of isolates wereM. tuberculosisand 9/48 (18.75%) wereM. bovis. M. tuberculosiswas distributed over four lineages, Indo-Oceanic L1 (n = 3/39)(7.6%), East-Asian L2 (n = 1/39)(2.5%), East-African Indian L3 (n = 5/39)(12.8%) and Euro-American L4 (n = 30/39)(76.9%). Sub-lineage L4.8 (Euro-American (mainly T), comprising 8/39 of the isolates (20.5%) was predominant, followed by sub-lineages L3 (East-African Indian, n = 5/39 isolates)(12.8%), L4.2.2.2 (Euro-American (Ural), n= 4/39 isolates)(10.2%) and L4.6.5 (Euro American, n=4/39 isolates)(10.2%). NineM. boviswere classified into two clades, designated as unknown2 (n=2/9; 22.2%) and unknown3 (n=7/9; 77.8%). Interestingly, none of the clades or others were detected in the 48 faecal samples using CRISPR standard PCR and qPCR.ConclusionsThis study offers insights into human and bovine tuberculosis in Lebanon, emphasizingM. tuberculosislineages prevalence andM. bovisdistribution into two clades, aiding the fight against tuberculosis, especially bovine tuberculosis, and renewing our understanding of tuberculosis dynamics in Lebanon.
Bridging Viruses and Prokaryotic Host through Miniature Inverted-repeat Transposable Elements (MITEs)
Authors: Nadal-Molero Francisco , Roselli Riccardo , Garcia-Juan Silvia , Campos-Lopez Alicia , Martin-Cuadrado Ana-Belen 
Published: January 2024

ABSTRACTTransposable elements (TEs) have a pivotal role in the evolution of genomes across all life domains. “Miniature Inverted-repeat Transposable-Elements” (MITEs) are non-autonomous TEs mainly located in intergenic regions, relying on external transposases for mobilization. The boundaries of MITEs’ mobilome were explored across nearly 1700 prokaryotic genera, 183232 genomes, revealing a widespread distribution. MITEs were identified in 56.5% of genomes, totaling over 1.4 million cMITEs (cellular). Cluster analysis revealed that a significant 97.4% of cMITEs were conserved within genera boundaries, with up to 23% being species-specific. Subsequently, this genus-specificity was evaluated as a tool to link microbial host to their viruses. A total of 51655 cMITEs had counterparts in viral sequences, termed vMITE (viral), resulting in the identification of 2798 viral sequences with vMITEs. Among these, 1501 sequences were positively assigned to a previously known host (41.8% were isolated virus, and 12.3% were assigned through CRISPR data), while 379 new host-virus associations were predicted. Deeper analysis in Neisseria and Bacteroidetes groups allowed the association of 242 and 530 new additional viral sequences, respectively. Given the abundance of non-culturable virus sequences accumulated in databases lacking affiliations with their microbial targets, MITEs are proposed as a novel approach to establishing valid virus-host relationships.GRAPHICAL ABSTRACT
Fluoride export is required for competitive fitness of pathogenic microorganisms in dental biofilm models
Authors: Banerjee Aditya , Kang Chia-Yu , An Minjun , Koff B. Ben , Sunder Sham , Kumar Anuj , Tenuta Livia M. A. , Stockbridge Randy B. 
Published: January 2024

AbstractMicroorganisms resist fluoride toxicity using fluoride export proteins from one of several different molecular families. Cariogenic speciesStreptococcus mutansandCandida albicansextrude intracellular fluoride using a CLCFF−/H+antiporter and FEX fluoride channel, respectively, whereas commensal eubacteria, such asStreptococcus gordonii,export fluoride using a Fluc fluoride channel. In this work, we examine how genetic knockout of fluoride export impacts pathogen fitness in single-species and three-species dental biofilm models. For biofilms generated usingS. mutanswith genetic knockout of the CLCFtransporter, exposure to low fluoride concentrations decreasedS. mutanscounts, synergistically reduced the populations ofC. albicans, increased the relative proportion of commensalS. gordonii, and reduced properties associated with biofilm pathogenicity, including acid production and hydroxyapatite dissolution. Biofilms prepared withC. albicanswith genetic knockout of the FEX channel also exhibited reduced fitness in the presence of fluoride, but to a lesser degree. Imaging studies indicate thatS. mutansis highly sensitive to fluoride, with the knockout strain undergoing complete lysis when exposed to low fluoride for a moderate amount of time, and biochemical purification theS. mutansCLCFtransporter and functional reconstitution establishes that the functional protein is a dimer encoded by a single gene. Together, these findings suggest that fluoride export by oral pathogens can be targeted by specific inhibitors to restore biofilm symbiosis in dental biofilms, and thatS. mutansis especially susceptible to fluoride toxicity.ImportanceDental caries is a globally prevalent condition that occurs when pathogenic species, includingStreptococcus mutansandCandida albicans, outcompete beneficial species, such asStreptococcus gordonii,in the dental biofilm. Fluoride is routinely used in oral hygiene to prevent dental caries. Fluoride also has antimicrobial properties, although most microbes possess fluoride exporters to resist its toxicity. This work shows that sensitization of cariogenic speciesStreptococcus mutansandCandida albicansto fluoride by genetic knockout of fluoride exporters alters the microbial composition and pathogenic properties of dental biofilms. These results suggest that the development of drugs that inhibit fluoride exporters could potentiate the anticaries effect of fluoride in over-the-counter products like toothpastes and mouth rinses. This is a novel strategy to treat dental caries.
C-di-AMP accumulation disrupts glutathione metabolism and inhibits virulence program expression inListeria monocytogenes
Authors: Siletti Cheta , Freeman Matthew , Tu Zepeng , Stevenson David M. , Amador-Noguez Daniel , Sauer John-Demian , Huynh TuAnh N. 
Published: January 2024

ABSTRACTC-di-AMP is an essential second messenger in many bacteria but its levels must be regulated. Unregulated c-di-AMP accumulation attenuates the virulence of many bacterial pathogens, including those that do not require c-di-AMP for growth. However, the mechanisms by which c-di-AMP regulates bacterial pathogenesis remain poorly understood. InListeria monocytogenes, a mutant lacking both c-di-AMP phosphodiesterases, denoted as the ΔPDE mutant, accumulates a high c-di-AMP level and is significantly attenuated in the mouse model of systemic infection. All keyL. monocytogenesvirulence genes are transcriptionally upregulated by the master transcription factor PrfA, which is activated by reduced glutathione (GSH) during infection. Our transcriptomic analysis revealed that the ΔPDE mutant is significantly impaired for the expression of virulence genes within the PrfA core regulon. Subsequent quantitative gene expression analyses validated this phenotype both at the basal level and upon PrfA activation by GSH. A constitutively active PrfA*variant, PrfA G145S, which mimics the GSH-bound conformation, restores virulence gene expression in ΔPDE but only partially rescues virulence defect. Through GSH quantification and uptake assays, we found that the ΔPDE strain is significantly depleted for GSH, and that c-di-AMP inhibits GSH uptake. Constitutive expression ofgshF(encoding a GSH synthetase) does not restore GSH levels in the ΔPDE strain, suggesting that c-di-AMP inhibits GSH synthesis activity or promotes GSH catabolism. Taken together, our data reveals GSH metabolism as another pathway that is regulated by c-di-AMP. C-di-AMP accumulation depletes cytoplasmic GSH levels withinL. monocytogenesthat leads to impaired virulence program expression.IMPORTANCEC-di-AMP regulates both bacterial pathogenesis and interactions with the host. Although c-di-AMP is essential in many bacteria, its accumulation also attenuates the virulence of many bacterial pathogens. Therefore, disrupting c-di-AMP homeostasis is a promising antibacterial treatment strategy, and has inspired several studies that screened for chemical inhibitors of c-di-AMP phosphodiesterases. However, the mechanisms by which c-di-AMP accumulation diminishes bacterial pathogenesis are poorly understood. Such understanding will reveal the molecular function of c-di-AMP, and inform therapeutic development strategies. Here, we identify GSH metabolism as a pathway regulated by c-di-AMP that is pertinent toL. monocytogenesreplication in the host. Given the role of GSH as a virulence signal, nutrient, and antioxidant, GSH depletion impairs virulence program expression and likely diminishes host adaptation.
Observer-based preview control for T-S fuzzy systems
Authors: Li Li , Ye Hui , Meng Xiaohua 
Published: January 2024

PurposeConsidering the unmeasurable states of the systems and the previewed reference signal, a novel fuzzy observer-based preview controller, which is a mixed controller of the fuzzy observer-based controller, fuzzy integrator and preview controller, is considered to address the tracking control problem.Design/methodology/approachThe authors employ an augmentation technique to construct an augmented error system for uncertain T-S fuzzy discrete-time systems with time-varying uncertainties. Additionally, the authors obtain the corresponding linear matrix inequality (LMI) conditions for designing the preview controller.FindingsThis paper discusses the preview tracking problem for nonlinear systems. First, considering the unmeasurable states of the systems and the previewed reference signal, a novel fuzzy observer-based preview controller, which is a mixed controller of the fuzzy observer-based controller, fuzzy integrator, and preview controller, is considered to address the tracking control problem. Then, using the fuzzy Lyapunov functional with the linear matrix inequality (LMI) technique, new sufficient conditions for the asymptotic stability of the augmented system are derived by applying the LMI technique. The preview controller and fuzzy observer can be designed in one step. Finally, a numerical example is used to illustrate the effectiveness of the results.Originality/valueAn augmented error system is successfully constructed by the state augmentation approach. A novel preview controller is designed to address the tracking control problem. The preview controller and fuzzy observer can be designed in one step.
Effect of ball–material ratio on Cu-Bi mixed powder and self-lubricating material properties
Authors: Liu Cong , Yin Yanguo , Li Rongrong 
Published: January 2024

Purpose
This study aims to investigate the effects of ball–material ratio on the properties of mixed powders and Cu-Bi self-lubricating alloy materials.

Design/methodology/approach
Cu-Bi mixed powder was ball milled at different ball–material ratios, and the preparation of Cu-Bi alloy materials was achieved through powder metallurgy technology. Scanning electron microscopy, X-ray diffraction and Raman spectroscopy were conducted to study the microstructure and phase composition of the mixed powder. The apparent density and flow characteristics of mixed powders were investigated using a Hall flowmeter. Tests on the crushing strength, impact toughness and tribological properties of self-lubricating alloy materials were conducted using a universal electronic testing machine, 300 J pendulum impact testing machine and M200 ring-block tribometer, respectively.

Findings
With the increase in ball–material ratio, the spherical copper matrix particles in the mixed powder became lamellar, the mechanical properties of the material gradually reduced, the friction coefficient of the material first decreased and then stabilized and the wear rate decreased initially and then increased. The increase in the ball–material ratio resulted in the fine network distribution of the Bi phase in the copper alloy matrix, which benefitted its enrichment on the worn surface for the formation a lubricating film and improvement of the material’s tribological performance. However, a large ball–material ratio can excessively weaken the mechanical properties of the material and reduce its wear resistance.

Originality/value
The effects of ball–material ratio on Cu-Bi mixed powder and material properties were clarified. This work provides a reference for the mechanical alloying process and its engineering applications.
Facilitating the role of quantity surveyors through integration of cyber-physical systems
Authors: Weerasooriya Dilan , Ranadewa K.A.T.O , Perera B.A.K.S 
Published: January 2024

Purpose
Cyber-physical systems (CPS) enable the synergistic integration of virtual models with the physical environment. This integration is gaining recognition for its potential to enhance construction project information management, thereby contributing to improved cost management in construction. Similarly, quantity surveyor (QS) plays a key role in construction projects by estimating and monitoring construction costs. Consequently, this research aims to explore redefining the role of QSs by integrating CPS.

Design/methodology/approach
The research adopted an interpretivism stance to collect and analyse data. Two rounds of 21 and 19 semi-structured interviews were conducted, with experts selected through heterogeneous purposive sampling. Code-based content analysis was used to analyse the data using NVivo12. MS Visio data visualisation tool was used to present the findings.

Findings
It is empirically proven the potential of CPS to facilitate nine key roles of QSs in all stages of the RIBA plan of work through the identification of 15 CPS applications and technologies. Nine key roles of QSs that CPS can facilitate were identified as preliminary estimation, measurement and quantification, contract administration, preparation of BOQ, interim valuation and payments, tender and contract documentation, cost planning, cost control and procurement advice. The study explored how adopting CPS technologies can transform traditional quantity surveying practices and enhance their value within the construction industry.

Originality/value
The findings add to the body of knowledge by redefining the role of QS through the integration of CPS for the first time and then by highlighting the usages of CPS in the construction industry rather than limiting it to a specific sector of the construction industry, as previous studies have done. This research uncovers several other research arenas on CPS as being the very first research to evaluate CPS to facilitate key roles of QSs. The findings can enhance the awareness and the practical implementation of CPS by intervening to form more partnerships among application developers and industry leaders.
Measuring corporate citizenship and public image: evidence from scale development and validation
Authors: Gulati Twinkle , Diwan Saloni Pawan 
Published: January 2024

Purpose
This study aims to measure the absolute impact of corporate citizenship actions on the operable elements of the public image by developing an adequate and parsimonious instrument.

Design/methodology/approach
Both qualitative and quantitative approaches are used, where initially a literature review is systematized, then related statements are created, examined and confirmed. Altogether, 296 responses have been tested at discrete points, allowing for a temporal split-up of observations, where the first 148 forms have been used for exploratory factor analysis and the remaining 148 for confirmatory factor analysis.

Findings
The results of exploratory factor analysis revealed that the proposed instrument contains 13 items under three components: corporate citizenship and public affiliation; corporate citizenship and public allegiance; and corporate citizenship and public accomplishment. Subsequently, confirmatory factor analysis findings attest to the completeness, robustness and fitness of the same.

Research limitations/implications
This experiment would serve as an inducement that would bridge the theoretical and empirical gap between corporate citizenship and public image by imparting an extensive perspective.

Originality/value
Perhaps on account of the lack of an inclusive instrument, the holistic view of corporate citizenship has secured quite less empirical attention so far, particularly from the perception of that group of stakeholders who manifest wholeness. This study, thus by making a ground-breaking methodological endeavor with the conceptually established construct of public image, would abet in shaping a new class of “wholistic”, i.e. whole and holistic corporations.
Exploring the Third Type of Agency Problem: An Empirical Study of the Impact of Debt Suspension Programmes on SMEs’ Resource Allocations
Authors: Savio Riccardo , Castellaneta Franceso , Vismara Silvio , Zattoni Alessandro 
Published: January 2024

AbstractThis study explores the third type of agency problem concerning the tension between shareholders and stakeholders. It does so by analysing whether small and medium‐sized enterprises (SMEs) eligible for a temporary debt suspension programme favour the short‐term interests of their shareholders or stakeholders, or the firm's long‐term competitiveness. Using information from an Italian debt moratorium programme aimed at alleviating the financial pressure on SMEs during the financial crisis, we built a rich database of 37,465 limited liability companies eligible for the programme between 2006 and 2015. We then used a difference‐in‐differences model to analyse the data. Our findings indicate that the debt suspension programme, designed to help eligible firms survive temporary financial constraints, did promote their long‐term competitiveness. However, it also produced some undesirable consequences, such as benefiting shareholders in the short term at the expense of other key stakeholders.