bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of the Entner-Douderoff Pathway inPseudomonas aeruginosaCatheter-associated Urinary Tract Infections
Authors: Husseini Nour El , Mekonnen Solomon A. , Hall Cherisse L. , Cole Stephanie J. , Carter Jared A. , Belew Ashton T. , El-Sayed Najib , Lee Vincent T. 
Published: November 2023

AbstractPseudomonas aeruginosais an opportunistic nosocomial pathogen responsible for catheter-associated urinary tract infections (CAUTI). In a murine model ofP. aeruginosaCAUTI, we previously demonstrated that urea within urine suppresses quorum sensing and induces the Entner-Douderoff (E-D) pathway. The E-D pathway consists of the geneszwf, pgl, edd, andeda. Zwf and Pgl convert glucose-6-phosphate into 6-phosphogluconate. Edd hydrolyzes 6-phosphogluconate to 2-keto-3-deoxy-6-phosphogluconate (KDPG). Finally, Eda cleaves KDPG to glyceraldehyde-3-phosphate and pyruvate, which enters the citric acid cycle. Here, we generated in-frame E-D mutants in strain PA14 and assessed their growth phenotypes on chemically defined media. These E-D mutants have a growth defect when grown on glucose or gluconate as sole carbon source which are similar to results previously reported for PAO1 mutants lacking E-D genes. RNA-sequencing following short exposure to urine revealed minimal gene regulation differences compared to the wild type. In a murine CAUTI model, virulence testing of E-D mutants revealed that two mutants lackingzwfandpglshowed minor fitness defects. Infection with the Δpglstrain exhibited a 20% increase in host survival, and the Δzwfstrain displayed decreased colonization of the catheter and kidneys. Consequently, our findings suggest that the E-D pathway inP. aeruginosais dispensable in this model of CAUTI.ImportancePrior studies have shown that the Entner-Douderoff pathway is up-regulated whenPseudomonas aeruginosais grown in urine. Pseudomonads use the Entner-Douderoff pathway to metabolize glucose instead of glycolysis which led us to ask whether this pathway is required for urinary tract infection. Here, single-deletion mutants of each gene in the pathway were tested for growth on chemically defined media with single-carbon sources as well as complex media. The effect of each mutant on global gene expression in laboratory media and urine was characterized. The virulence of these mutants in a murine model of catheter-associated urinary tract infection revealed that these mutants had similar levels of colonization indicating that glucose is not the primary carbon source utilized in the urinary tract.
Genomic islands of speciation harbor genes underlying coloration differences in a pair of Neotropical seedeaters
Authors: Nguyen Tram N. , Repenning Márcio , Suertegaray Fontana Carla , Campagna Leonardo 
Published: November 2023

AbstractIncomplete speciation can be leveraged to associate phenotypes with genotypes, thus providing insights into the traits relevant to the reproductive isolation of diverging taxa. We investigate the genetic underpinnings of the phenotypic differences betweenSporophila plumbeaandS. beltoni.S. beltonihas only recently been described based, most notably, on differences in bill coloration (yellow vs. black inS. plumbea). Both species are indistinguishable through mtDNA or reduced-representation genomic data, and even whole-genome sequencing revealed low genetic differentiation. Demographic reconstructions attribute this genetic homogeneity to gene flow, despite divergence in the order of millions of generations. We found a narrow hybrid zone in southern Brazil where genetically, yet not phenotypically, admixed individuals appear to be prevalent. Despite the overall low genetic differentiation, we identified three narrow peaks along the genome with highly differentiated SNPs. These regions harbor six genes, one of which is involved in pigmentation (EDN3) and is a candidate for controlling bill color. Within the outlier peaks we found signatures of resistance to gene flow, as expected for islands of speciation. Our study shows how genes related to coloration traits are likely involved in generating prezygotic isolation and establishing species boundaries early in speciation.
Circadian Control of Histone Turnover During Cardiac Development and Growth
Authors: Arrieta Adrian , Chapski Douglas J. , Reese Anna , Kimball Todd , Song Kunhua , Rosa-Garrido Manuel , Vondriska Thomas M. 
Published: November 2023

AbstractRationale:During postnatal cardiac hypertrophy, cardiomyocytes undergo mitotic exit, relying on DNA replication-independent mechanisms of histone turnover to maintain chromatin organization and gene transcription. In other tissues, circadian oscillations in nucleosome occupancy influence clock-controlled gene expression, suggesting an unrecognized role for the circadian clock in temporal control of histone turnover and coordinate cardiomyocyte gene expression.Objective:To elucidate roles for the master circadian transcription factor, Bmal1, in histone turnover, chromatin organization, and myocyte-specific gene expression and cell growth in the neonatal period.Methods and Results:Bmal1 knockdown in neonatal rat ventricular myocytes (NRVM) decreased myocyte size, total cellular protein, and transcription of the fetal hypertrophic gene Nppb following treatment with increasing serum concentrations or the α-adrenergic agonist phenylephrine (PE). Bmal1 knockdown decreased expression of clock-controlled genes Per2 and Tcap, and salt-inducible kinase 1 (Sik1) which was identified via gene ontology analysis of Bmal1 targets upregulated in adult versus embryonic hearts. Epigenomic analyses revealed co-localized chromatin accessibility and Bmal1 localization in the Sik1 promoter. Bmal1 knockdown impaired Per2 and Sik1 promoter accessibility as measured by MNase-qPCR and impaired histone turnover indicated by metabolic labeling of acid-soluble chromatin fractions and immunoblots of total and chromatin-associated core histones. Sik1 knockdown basally increased myocyte size, while simultaneously impairing and driving Nppb and Per2 transcription, respectively.Conclusions:Bmal1 is required for neonatal myocyte growth, replication-independent histone turnover, and chromatin organization at the Sik1 promoter. Sik1 represents a novel clock-controlled gene that coordinates myocyte growth with hypertrophic and clock-controlled gene transcription.
Genetically dissecting the electron transport chain of a soil bacterium reveals a generalizable mechanism for biological phenazine-1-carboxylic acid oxidation
Authors: Tsypin Lev M.Z. , Saunders Scott H. , Chen Allen W. , Newman Dianne K. 
Published: November 2023

AbstractThe capacity for bacterial extracellular electron transfer via secreted metabolites is widespread in natural, clinical, and industrial environments. Recently, we discovered biological oxidation of phenazine-1-carboxylic acid (PCA), the first example of biological regeneration of a naturally produced extracellular electron shuttle. However, it remained unclear how PCA oxidation was catalyzed. Here, we report the mechanism, which we uncovered by genetically perturbing the branched electron transport chain (ETC) of the soil isolateCitrobacter portucalensisMBL. Biological PCA oxidation is coupled to anaerobic respiration with nitrate, fumarate, dimethyl sulfoxide, or trimethylamine-N-oxide as terminal electron acceptors. Genetically inactivating the catalytic subunits for all redundant complexes for a given terminal electron acceptor abolishes PCA oxidation. In the absence of quinones, PCA can still donate electrons to certain terminal reductases, albeit much less efficiently. InC. portucalensisMBL, PCA oxidation is largely driven by flux through the ETC, which suggests a generalizable mechanism that may be employed by any anaerobically respiring bacterium with an accessible cytoplasmic membrane. This model is supported by analogous genetic experiments during nitrate respiration byPseudomonas aeruginosa.Author summaryMany bacteria have extremely flexible metabolisms, and we are only beginning to understand how they manifest in the environment. Our study focuses on the role of phenazine-1-carboxylic acid (PCA), a molecule that some bacteria synthesize and secrete into their surroundings. PCA is an “extracellular electron shuttle,” a molecule that readily transfers electrons between cells and oxidizing/reducing compounds or other cells. Until our investigation, the role of PCA electron-shuttling had only been studied in one direction: how it takes electrons away from cells, and the effect this has on their viability. Here we present a detailed account of the opposite process and its mechanism: what happens when PCA delivers electrons to cells? Our findings indicate that this previously underappreciated process is generalizable to any anaerobically respiring bacterium. Consequently, we expect that electron donation by PCA is widespread in environments where PCA is plentiful and oxygen is sparse, such as in some agricultural soils. The universality of the extracellular electron shuttle oxidation mechanism we describe for PCA suggests that it should also occur with similar small molecules, of which there are thousands, deepening the implication that this is a significant process in the environment and motivating further research into its consequences.
The heparin-binding domain of VEGF165 directly binds to integrin αvβ3 and plays a critical role in signaling
Authors: Takada Yoko K. , Yu Jessica , Ye Xiaojin , Wu Chun-Yi , Felding Brunie H. , Fujita Masaaki , Takada Yoshikazu 
Published: November 2023

AbstractVEGF-A is a key cytokine in tumor angiogenesis and a major therapeutic target for cancer. VEGF165 is the predominant isoform and is the most potent angiogenesis stimulant. VEGFR2/KDR domains 2 and 3 (D2D3) bind to the N-terminal domain (NTD, residues 1-110) of VEGF165. Since removal of the heparin-binding domain (HBD, residues 111-165) markedly reduced the mitogenic activity of VEGF165, it has been proposed that the HBD plays a critical role in the mitogenicity of VEGF165. Integrin αvβ3 has been shown to bind to VEGF165, but the role of integrin αvβ3 in VEGF165 signaling are unclear. Here we describe that αvβ3 specifically bound to the isolated HBD, but not to the NTD. We identified several critical amino acid residues in HBD for integrin binding (Arg-123, Arg-124, Lys-125, Lys-140, Arg-145, and Arg-149) by docking simulation and mutagenesis, and generated full-length VEGF165 that is defective in integrin binding by including mutations in the HBD. The full-length VEGF165 mutant defective in integrin binding (R123A/R124A/K125A/K140A/R145A/R149A) was defective in ERK1/2 phosphorylation, integrin β3 phosphorylation, and KDR phosphorylation, although the mutation did not affect KDR binding to VEGF165. We propose a model in which VEGF165 induces KDR (through NTD)-VEGF165 (through HBD)-integrin αvβ3 ternary complex formation on the cell surface and this process is critically involved in potent mitogenicity of VEGF165.
Meiotic drive, postzygotic isolation, and the Snowball Effect
Authors: Unckless Robert L. 
Published: November 2023

AbstractAs populations diverge, they accumulate incompatibilities which reduce gene flow and facilitate the formation of new species. Simple models suggest that the genes that cause Dobzhansky-Muller incompatibilities should accumulate at least as fast as the square of the number of substitutions between taxa, the so-called snowball effect. We show, however, that in the special— but possibly common— case in which hybrid sterility is due primarily to cryptic meiotic (gametic) drive, the number of genes that cause postzygotic isolation may increase nearly linearly with the number of substitutions between species.
Multi-Modality Machine Learning Models to Predict Stroke and Atrial Fibrillation in Patients with Heart Failure
Authors: Zhou Jiandong , Murugappan Lakshmi , Lu Lei , Chou Oscar Hou In , Cheung Bernard Man Yung , Tse Gary , Zhu Tingting 
Published: November 2023

AbstractIntroductionAtrial fibrillation (AF) and stroke are leading causes of death of heart failure patients. Several ML models have been built using electrocardiography (ECG)-only data, or lab test data or health record data to predict these outcomes. However, a multi-modal approach using wearable ECG data integrated with lab tests and electronic health records (EHRs) data has not been developed.ObjectiveThe aim of this study was to apply machine learning techniques to predict stroke and AF amongst heart failure patients from a multi-modal dataset.MethodsThis study analysed hospitalised patients with heart failure in Hong Kong between 1 January 2010 and 31 December 2016, with the last follow-up of 31 December 2019. The primary outcomes were AF and stroke. The secondary outcomes were all-cause and cardiovascular mortality. ECG-only, non-ECG-only and multimodal models were built to assess feature importance. Four machine learning classifiers and seven performance measures were used to evaluate the performance.ResultsThere are in total 2,868 subjects with heart failure upon admission, among them 1,150 (40.10%) had new onset AF, 668 (23.29%) had new onset stroke/TIA. It was found that accurate and sensitive machine learning models can be created to predict stroke and AF from multimodal data. XGBoost, which was the best algorithm tested, achieved a mean (over 10 iterations) accuracy, AUROC, AUPRC, positive predictive value and negative predictive value of 0.89, 0.80, 0.74, 0.99 and 0.88, respectively, for stroke and 0.78, 0.82, 0.77, 0.77 and 0.79, respectively, for AF. The predictive models, built using multimodal data, were easy to use and had high accuracy.ConclusionMulti-modal machine learning models could be used to predict future stroke and AF occurrences in patients hospitalised for heart failure.
Does knowledge collecting and donating enhance a bank's salesperson performance?
Authors: Herjanto Halimin , Amin Muslim , Fatimah Cut Erika 
Published: November 2023

PurposeThis study investigates the role of knowledge collecting and donating in enhancing relationship proneness and intimacy and improving a bank's salesperson satisfaction and performance.Design/methodology/approachUsing the snowball technique, 315 online questionnaires were collected from commercial banks. A total of 300 useable questionnaires were included for further analysis.FindingsThe findings demonstrated that knowledge collecting affects relationship proneness and salesperson performance, while knowledge donating affects relationship proneness but not satisfaction. The results also suggested that relationship proneness is responsible for salesperson intimacy. Furthermore, intimacy was found to affect salesperson performance and satisfaction. Finally, salesperson satisfaction was found to affect salesperson performance positively.Practical implicationsThe findings help bankers understand and utilize the power of their knowledge management in improving their sales performance and developing suitable training and strategies to strengthen salesperson intimacy.Originality/valueThis study incorporated knowledge management, relationship proneness and intimacy to enhance a better understanding of how these indicators will affect the salesperson's satisfaction and performance.
Study on mechanical properties of corrugated steel support tunnel under fault sliding
Authors: Zhang Hong-tao , Liu Shan , Sun Lan-xi , Zhao Yu-fei 
Published: November 2023

PurposeThere have been limited investigations on the mechanical characteristics of tunnels supported by corrugated plate structures during fault dislocation. The authors obtained circumferential and axial deformations of the spiral corrugated pipe at various fault displacements. Lastly, the authors examined the impact of reinforced spiral stiffness and soil constraints on the support performance of corrugated plate tunnels under fault displacement.Design/methodology/approachBy employing the theory of similarity ratios, the authors conducted model tests on spiral corrugated plate support using loose sand and PVC (polyvinyl chloride) spiral corrugated PE pipes for cross-fault tunnels. Subsequently, the soil spring coefficient for tunnel–soil interaction was determined in accordance with ASCE (American Society of Civil Engineers) specifications. Numerical simulations were performed on spiral corrugated pipes with fault dislocation, and the results were compared with the experimental data, enabling the determination of the variation pattern of the soil spring coefficient.FindingsThe findings indicate that the maximum axial tensile and compressive strains occur on both sides of the fault. As the reinforced spiral stiffness reaches a certain threshold, the deformation of the corrugated plate tunnel and the maximum fault displacement stabilize. Furthermore, a stronger soil constraint leads to a lower maximum fault displacement that the tunnel can withstand.Research limitations/implicationsIn this study, the calculation formula for density similarity ratio cannot be taken into account due to the limitations of the helical corrugated tube process and the focus on the deformation pattern of helical corrugated tubes under fault action.Originality/valueThis study provides a basis for the mechanical properties of helical corrugated tube tunnels under fault misalignment and offers optimization solutions.
An analysis of users’ continuous use intention of academic library social media using the WeChat public platform as an example
Authors: Meng Yuan , Lin Hongwei , Gong Weijing , Guan Rui , Dong Li 
Published: November 2023

Purpose
This study aims to discover the factors which influence user satisfaction levels and their continuous use intention (CUI) of academic library social media, and then considers how to promote and improve further work on library social media to reduce user churn and increase user satisfaction.

Design/methodology/approach
An updated DeLone and McLean information systems success (D&M ISS) model and the expectation confirmation model for information systems continuance (ECM-ISC) with new variables of emotions are used to examine the factors which influence user satisfaction levels and CUI of academic library social media through 445 questionnaires. Partial least squares structural equation modelling was used to analyse the data and presented in tables.

Findings
The results show that information quality, system quality and emotions affect user satisfaction and CUI, and reveal that emotions can affect that most obviously.

Research limitations/implications
The WeChat public platform is mainly used in China, so the study only focuses on Chinese academic libraries. There are still limitations on the settings of observed variables which cannot cover all the causes of users’ positive and negative emotions. In addition, although the respondents of this questionnaire can represent academic library users, 445 samples are still fairly low in contrast to the great number of academic library WeChat public platform users.

Originality/value
This study integrates ECM-ISC and D&M ISS models, adds positive and negative emotions as new variables, to broaden the application scope of these models, and demonstrates the applicability of these two models in the fields of researching academic library social media, expanding and deepening related theories above. This also provides practical reference for academic libraries on how to improve user satisfaction and CUI of academic library social media and academic library WeChat public platforms, promoting the development of academic library social media.
Impact of employee well-being on performance in the context of crisis-induced remote work: role of boundary control and professional isolation
Authors: Jaiswal Akanksha , Prabhakaran Neethu 
Published: November 2023

PurposeCOVID-19 forced employees to work remotely. Since this shift from physical to remote working was sudden and unprecedented, the authors aimed to examine the impact of employee well-being on performance in the context of remote work. Further, the authors explored how feelings of professional isolation and employees' control over their personal and professional boundaries (i.e. boundary control) moderated the well-being and performance link. The authors invoke the equity theory and boundary theory to augment their hypotheses.Design/methodology/approachWith 218 full-time employees representing large information technology organisations in India, the authors tested the hypothesised relationships using regression and double moderation in the PROCESS macro.FindingsResults indicate that well-being has a significant positive impact on employee performance as they worked remotely. Further, the authors found that professional isolation and boundary control moderated the link between well-being and performance such that when boundary control is high and professional isolation is low, the aforementioned relationship strengthened and vice versa.Research limitations/implicationsThe authors extend the boundary theory as the crisis-induced remote work highlighted the employees' need for deploying alternating boundary management styles to balance their personal and professional lives.Practical implicationsOrganisations must develop flexible work policies to facilitate remote work and managers must efficiently craft the overall management of professional isolation and employees' boundaries to boost their well-being and performance.Originality/valueThe authors not only examine the impact of employee well-being on performance in the context of remote work but also, in a first, examine the role of boundary control and professional isolation in this relationship.