bluuebunny/crossref_metadata_2025 huggingface dataset:
Spatio-temporal variation of bacterial community structure in two intertidal sediment types of Jiaozhou Bay
Authors: Chen Xuechao , Zhang Xinran , Yu Hao , Han Meiaoxue , Sun Jianhua , Liu Gang , Ji Yan , Zhai Chuan , Zhu Liyan , Shao Hongbing , Liang Yantao , McMinn Andrew , Wang Min
Published: May 2023

The intertidal sediment environment is dynamic and the biofilm bacterial community within it must constantly adjust, but an understanding of the differences in the biofilm bacterial community within sediments of different types is still relatively limited. In this study, the structure of the bacterial community in Jiaozhou Bay sediment biofilms are described using high-throughput 16S rRNA gene sequencing and the effects of temporal change and different sediment environment types are discussed. The Shannon index was significantly higher in sandy samples than in muddy samples. The co-occurrence network was tighter and more species were involved in community building in sandy samples. The principal coordinates analysis identified a significant separation between different sediment types and between stations (LiCun estuary, LC and ZhanQiao Pier, ZQ). Proteobacteria, which had a relative abundance of approximately 50% at all phylum levels, was significantly more abundant at ZQ, while Campilobacterota and Firmicutes were significantly more abundant at LC. The relative abundances of Bacteroidetes, Campilobacterota, Firmicutes, and Chloroflexi were significantly higher in the muddy samples, while Actinobacteria and Proteobacteria were higher in the sandy samples. There were different phylum-level biomarkers between sediment types at different stations. There were also different patterns of functional enrichment in biogeochemical cycles between sediment types and stations with the former having more gene families that differed significantly, highlighting their greater role in determining bacterial function. The RDA results, where each month’s samples were concentrated individually, showed reduced variation between months when the amplicon sequence variant was replaced by KEGG orthologs, presumably the temporal change had an impact on shaping the intertidal sediment bacterial community, although this was less clear at the gene family level. Random forest prediction yielded a combination of 43 family-level features that responded well to temporal change, reflecting the influence of temporal change on sediment biofilm bacteria.

Highlights

Sandy sediments have more bacterial species involved in community building.

Different substrates from different stations have their own phylum biomarkers.

Substrates have a greater influence on shaping bacterial function.

Temporal changes have a greater shaping power on bacteria than on gene families.

Graphic abstract
Mitochondrial temperature homeostasis resists external metabolic stresses
Authors: Terzioglu Mügen , Veeroja Kristo , Montonen Toni , Ihalainen Teemu O. , Salminen Tiina S. , Bénit Paule , Rustin Pierre , Chang Young-Tae , Nagai Takeharu , Jacobs Howard T.
Published: May 2023

Based on studies with a fluorescent reporter dye, Mito Thermo Yellow, and the genetically encoded gTEMP ratiometric fluorescent temperature indicator targeted to mitochondria, the temperature of active mitochondria in four mammalian and one insect cell-line was estimated to be up to 15 °C above that of the external environment to which the cells were exposed. High mitochondrial temperature was maintained in the face of a variety of metabolic stresses, including substrate starvation or modification, decreased ATP demand due to inhibition of cytosolic protein synthesis, inhibition of the mitochondrial adenine nucleotide transporter and, if an auxiliary pathway for electron transfer was available via the alternative oxidase, even respiratory poisons acting downstream of OXPHOS complex I. We propose that the high temperature of active mitochondria is an inescapable consequence of the biochemistry of oxidative phosphorylation and is homeostatically maintained as a primary feature of mitochondrial metabolism.

IMPACT STATEMENT

Mitochondria are up to 15 °C hotter than their external environment in living cells. In response to diverse metabolic stresses, mitochondrial temperature re-adjusts to this value whenever possible.
Creating, curating and querying computer models of biological pathways for Inherited Metabolic Disorders
Authors: Slenter Denise N. , Willighagen Egon L.
Published: May 2023

Collecting knowledge about Inherited Metabolic Disorders (IMDs) has the potential to support early diagnosis as well as foster research into treatment options. Biological pathway databases can be used to create an overview of relevant articles and books describing IMDs and collect, curate, and summarize knowledge about these disorders. Reuse of the information captured in these databases in research requires the knowledge to be accurate but also machine-readable. WikiPathways is a community-driven project to establish a machinereadable knowledge base of biological processes. We here describe how pathways models from WikiPathways were used to represent the underlying biological mechanisms of many IMDs collected by domain experts over a period of six years. This paper describes a standardized approach to depict IMDs in WikiPathways, shows the current limitations in creating machine-readable disease information, and introduces an approach to support data curation based on these machine-readable biological pathways. Furthermore, several SPARQL-queries were developed to analyze the biological content created in these models. Using this approach, 47 pathways were collected about 345 diseases, involving 877 metabolites, 421 annotated metabolic interactions, 262 genes, and 587 proteins related to these disorders.
A Generative Model for Creating Path Delineated Helical Proteins
Authors: Kibler Ryan D. , Wicky Basile , Coventry Brian , Woodall Nicholas B.
Published: May 2023

Engineered proteins with precisely defined shapes can scaffold functional protein domains in 3D space to fine-tune their functions, such as the regulation of cellular signaling by ligand positioning or the design of self-assembling protein materials with specific forms. Methods for simply and efficiently generating the protein backbones to initiate these design processes remain limited. In this work, we develop a lightweight neural network to guide helix fragment assembly along a guideline using a GAN architecture and show that this approach can rapidly generate viable samples while being computationally inexpensive. Key to our approach is the transformation of the input structural data used for training into a parametric representation of helices to reduce the generator network size, which in turn facilitates rapid backpropagation to find specific helical arrangements during generation. This approach provides a method to quickly generate helical protein scaffolds.
ROCCO: A Robust Method for Detection of Open Chromatin via Convex Optimization
Authors: Hamilton Nolan H. , Furey Terrence S.
Published: May 2023

Motivation

Analysis of open chromatin regions across multiple samples from two or more distinct conditions can determine altered gene regulatory patterns associated with biological phenotypes and complex traits. The ATAC-seq assay allows for tractable genome-wide open chromatin profiling of large numbers of samples. Stable, broadly applicable genomic annotations of open chromatin regions are not available. Thus, most studies first identify open regions using peak calling methods for each sample independently. These are then heuristically combined to obtain a consensus peak set. Reconciling sample-specific peak resultspost hocfrom larger cohorts is particularly challenging, and informative spatial features specific to open chromatin signals are not leveraged effectively.

Results

We propose a novel method,ROCCO, that determines consensus open chromatin regions across multiple samples simultaneously.ROCCOemploys robust summary statistics and solves a constrained optimization problem formulated to account for both enrichment and spatial dependence of open chromatin signal data. We show this formulation admits attractive theoretical and conceptual properties as well as superior empirical performance compared to current methodology.

Availability and Implementation

Source code, documentation, and usage demos forROCCOare available on GitHub at:https://github.com/nolan-h-hamilton/ROCCO.ROCCOcan also be installed as a standalone binary utility usingpip/PyPI.

Contact

nolanh@email.unc.eduortsfurey@email.unc.edu.

Supplementary Information

Supplementary material is available with this submission. Additional resources that may aid readers are available in theROCCOGitHubrepository.
Improving the study of RNA dynamics through advances in RNA-seq with metabolic labeling and nucleotide-recoding chemistry
Authors: Zimmer Joshua T. , Vock Isaac W. , Schofield Jeremy A. , Kiefer Lea , Moon Michelle H. , Simon Matthew D.
Published: May 2023

RNA metabolic labeling using 4-thiouridine (s4U) captures the dynamics of RNA synthesis and decay. The power of this approach is dependent on appropriate quantification of labeled and unlabeled sequencing reads, which can be compromised by the apparent loss of s4U-labeled reads in a process we refer to as dropout. Here we show that s4U-containing transcripts can be selectively lost when RNA samples are handled under sub-optimal conditions, but that this loss can be minimized using an optimized protocol. We demonstrate a second cause of dropout in nucleotide recoding and RNA sequencing (NR-seq) experiments that is computational and downstream of library preparation. NR-seq experiments involve chemically converting s4U from a uridine analog to a cytidine analog and using the apparent T-to-C mutations to identify the populations of newly synthesized RNA. We show that high levels of T-to-C mutations can prevent read alignment with some computational pipelines, but that this bias can be overcome using improved alignment pipelines. Importantly, kinetic parameter estimates are affected by dropout independent of the NR chemistry employed, and all chemistries are practically indistinguishable in bulk, short-read RNA-seq experiments. Dropout is an avoidable problem that can be identified by including unlabeled controls, and mitigated through improved sample handing and read alignment that together improve the robustness and reproducibility of NR-seq experiments.
Tumor-resident regulatory T cells in pancreatic cancer express the αvβ5 integrin as a targetable activation marker
Authors: Suzuki Kodai , Kunisada Yuki , Miyamura Norio , Eikawa Shingo , Hurtado de Mendoza Tatiana , Mose Evangeline S. , Lu Caisheng , Kuroda Yukihito , Ruoslahti Erkki , Lowy Andrew M. , Sugahara Kazuki N.
Published: May 2023

Pancreatic ductal adenocarcinoma (PDAC) has abundant immunosuppressive regulatory T cells (Tregs), which contribute to a microenvironment resistant to immunotherapy. Here, we report that Tregs in the PDAC tissue, but not those in the spleen, express the αvβ5 integrin in addition to neuropilin-1 (NRP-1), which makes them susceptible to the iRGD tumor-penetrating peptide, which targets cells positive for αv integrin- and NRP-1. As a result, long-term treatment of PDAC mice with iRGD leads to tumor-specific depletion of Tregs and improved efficacy of immune checkpoint blockade. αvβ5 integrin+Tregs are induced from both naïve CD4+T cells and natural Tregs upon T cell receptor stimulation, and represent a highly immunosuppressive subpopulation of CCR8+Tregs. This study identifies the αvβ5 integrin as a marker for activated tumor-resident Tregs, which can be targeted to achieve tumor-specific Treg depletion and thereby augment anti-tumor immunity for PDAC therapy.
A novel approach to modeling side chain ensembles of the bifunctional spin label RX
Authors: Tessmer Maxx H. , Stoll Stefan
Published: May 2023

We introduce a novel approach to modeling side chain ensembles of bifunctional spin labels. This approach utilizes rotamer libraries to generate side chain conformational ensembles. Because the bifunctional label is constrained by two attachment sites, the label is split into two monofunctional rotamers which are first attached to their respective sites, then rejoined by a local optimization in dihedral space. We validate this method against a set of previously published experimental data using the bifunctional spin label, RX. This method is relatively fast and can readily be used for both experimental analysis and protein modeling, providing significant advantages over modeling bifunctional labels with molecular dynamics simulations. Use of bifunctional labels for site directed spin labeling (SDSL) electron paramagnetic resonance (EPR) spectroscopy dramatically reduces label mobility, which can significantly improve resolution of small changes in protein backbone structure and dynamics. Coupling the use of bifunctional labels with side chain modeling methods allows for improved quantitative application of experimental SDSL EPR data to protein modeling.

Statements and Declarations

The authors declare no competing interests.
Oxic microbial electrosynthesis can be more energy efficient for biomass production than knallgas or photosynthesis based processes
Authors: Rominger Leonie , Hackbarth Max , Jung Tobias , Scherzinger Marvin , Horn Harald , Kaltschmitt Martin , Gescher Johannes
Published: May 2023

Data on the efficiency and development of continuous processes are scarce in the emerging field of oxic microbial electrosynthesis (OMES). Therefore, the recently isolated knallgas bacteriumKyrpidia spormanniiwas observed in a bioelectrochemical flow cell setup to study biomass formation and energy efficiency of cathode dependent growth. The study revealed that a potential of -500 mV vs. the standard hydrogen electrode (SHE) caused differences in the structure of the biofilm developing on the cathode, but had almost no impact on biomass growth behavior compared to -375 mV vs. SHE. No growth was observed at 0 mV vs SHE. Coulombic efficiency (CE) was calculated for the cultivation at -500 mV vs. SHE. The process can be conducted with the same electron efficiency as traditional gas fermentation. The solar energy demand with 67.89 kWh kg-1dry biomass is highly competitive to alternative and already established processes for converting (solar) energy to biomass. Additionally, with suggestions for a biomass harvesting method and subsequent recultivation, proof of principle for a continuously operable process was provided. The results pave the way for a new concept in carbon dioxide-based biotechnology.

Significance statement

To mitigate global climate change, it is imperative to transition the human economy to a different resource foundation, moving away from fossil fuels and reducing atmospheric carbon dioxide levels. Biotechnological production based on CO2necessitates a supply of energy and electrons. This study reveals that an oxic process, wherein bacteria are directly cultivated as a biofilm on the cathode surface of a bioelectrochemical system, can exhibit higher energy efficiency than plant-based systems or systems reliant on hydrogen generated through water electrolysis. This technology could be instrumental in establishing carbon dioxide and renewable energy as the foundation for feed, food, and platform chemical production.
Cell type deconvolution of bulk blood RNA-Seq to reveal biological insights of neuropsychiatric disorders
Authors: Boltz Toni , Schwarz Tommer , Bot Merel , Hou Kangcheng , Caggiano Christa , Lapinska Sandra , Duan Chenda , Boks Marco P. , Kahn Rene S. , Zaitlen Noah , Pasaniuc Bogdan , Ophoff Roel
Published: May 2023

Genome-wide association studies (GWAS) have uncovered susceptibility loci associated with psychiatric disorders like bipolar disorder (BP) and schizophrenia (SCZ). However, most of these loci are in non-coding regions of the genome with unknown causal mechanisms of the link between genetic variation and disease risk. Expression quantitative trait loci (eQTL) analysis of bulk tissue is a common approach to decipher underlying mechanisms, though this can obscure cell-type specific signals thus masking trait-relevant mechanisms. While single-cell sequencing can be prohibitively expensive in large cohorts, computationally inferred cell type proportions and cell type gene expression estimates have the potential to overcome these problems and advance mechanistic studies. Using bulk RNA-Seq from 1,730 samples derived from whole blood in a cohort ascertained for individuals with BP and SCZ this study estimated cell type proportions and their relation with disease status and medication. We found between 2,875 and 4,629 eGenes for each cell type, including 1,211 eGenes that are not found using bulk expression alone. We performed a colocalization test between cell type eQTLs and various traits and identified hundreds of associations between cell type eQTLs and GWAS loci that are not detected in bulk eQTLs. Finally, we investigated the effects of lithium use on cell type expression regulation and found examples of genes that are differentially regulated dependent on lithium use. Our study suggests that computational methods can be applied to large bulk RNA-Seq datasets of non-brain tissue to identify disease-relevant, cell type specific biology of psychiatric disorders and psychiatric medication.
NSC95397 is a Novel HIV-1 Latency Reversing Agent
Authors: Nichols Doyle Randilea , Yang Vivian , Kayode Yetunde I. , Damoiseaux Robert , Taylor Harry E. , Fregoso Oliver I.
Published: May 2023

The latent viral reservoir represents one of the major barriers of curing HIV-1. Focus on the “kick and kill” approach, in which virus expression is reactivated then cells producing virus are selectively depleted, has led to the discovery of many latency reversing agents (LRAs) that have furthered our understanding of the mechanisms driving HIV-1 latency and latency reversal. Thus far, individual compounds have yet to be robust enough to work as a therapy, highlighting the importance of identifying new compounds that target novel pathways and synergize with known LRAs. In this study, we identified a promising LRA, NSC95397, from a screen of ∼4250 compounds. We validated that NSC95397 reactivates latent viral transcription and protein expression from cells with unique integration events and across different latency models. Co-treating cells with NSC95397 and known LRAs demonstrated that NSC95397 synergizes with different drugs under both standard normoxic and physiological hypoxic conditions. NSC95397 does not globally increase open chromatin, and bulk RNA sequencing revealed NSC95397 does not greatly increase cellular transcription. Instead, NSC95397 downregulates pathways key to metabolism, cell growth, and DNA repair – highlighting the potential of these pathways in regulating HIV-1 latency. Overall, we identified NSC95397 as a novel LRA that does not largely alter global transcription, that shows potential for synergy with known LRAs, and that may act through novel pathways not previously recognized for their ability to modulate HIV-1 latency.

Importance

One of the largest barriers to curing HIV-1 is the latent viral reservoir – this is when the virus incorporates itself into long-lived cells in the body, ready to reactivate and re-seed infection. Destroying dormant HIV-1 is one potential pathway to a cure, yet no therapeutics have been discovered to work well in patients. In our study, we identified a compound, NSC95397, that can awaken dormant HIV-1 on its own through novel mechanisms not previously linked to HIV-1 latency. Moreover, NSC95397 improves the abilities of previously identified compounds to reactivate latent HIV-1. Thus, our study has identified a compound that can help towards the better understanding of an HIV-1 cure.
The Australian Eye and Ear Health Survey (AEEHS): study protocol for a population-based cross-sectional study
Authors: Kha Richard , Macken Oonagh , Mitchell Paul , Liew Gerald , Keay Lisa , Waddell Colina , Yang Eleanor , Do Vu , Fricke Tim , Newall John , Gopinath Bamini
Published: May 2023

Introduction

Vision and hearing impairments are highly prevalent and have a significant impact on physical, psychological and social wellbeing. There is a need for accurate, contemporary national data on the prevalence, risk factors and impacts of vision and hearing loss in Australian adults.

Objectives

The Australian Eye and Ear Health Survey (AEEHS) aims to determine the prevalence, risk factors and impacts of vision and hearing loss in both Aboriginal and Torres Strait Islander and non-Indigenous older adults.

Methods and analysis

The AEEHS is a population-based cross-sectional survey which will include 5,000 participants (3250 non-Indigenous aged 50 years or older and 1750 Aboriginal and Torres Strait Islander people aged 40 years or older) from 30 sites covering urban and rural/regional geographic areas, selected using a multi-stage, random cluster sampling strategy. Questionnaires will be administered to collect data on socio-demographic, medical, ocular and otological history. The testing battery includes assessment of blood pressure, blood sugar, anthropometry, visual acuity (presenting, unaided, pinhole and best-corrected), refraction, tonometry, slit lamp and dilated eye examination, ocular imaging including optical coherence tomography (OCT), OCT-angiography and retinal photography, and automated visual fields. Audiometry, tympanometry and video otoscopy will also be performed. The primary outcomes are age-standardised prevalence of cause-specific vision and hearing impairment. Secondary outcomes are prevalence of non-blinding eye diseases (including dry eye disease), patterns in health service utilisation, universal health coverage metrics, risk factors for vision and hearing impairment, and impact on quality of life.

Ethics

The protocol for this study was approved by the University of Sydney Human Research Ethics Committee (HREC-2020/818) and Australian Institute of Aboriginal and Torres Strait Islander Studies (AIATSIS) Research Ethics Committee (HREC-EO303-20211008).

Dissemination of results

Our findings will be disseminated through presentation at meetings and peer-reviewed publications. Findings will also be widely disseminated by project partners with the aim of improving public health policy directives and equitable service delivery to prevent avoidable vision and hearing impairment in Australia.
IAMSAM : Image-based Analysis of Molecular signatures using the Segment-Anything Model
Authors: Lee Dongjoo , Park Jeongbin , Cook Seungho , Yoo Seongjin , Lee Daeseung , Choi Hongyoon
Published: May 2023

Spatial transcriptomics is a cutting-edge technique that combines gene expression data with spatial information, allowing researchers to study gene expression patterns within tissue architecture. Here, we present IAMSAM, a user-friendly web-based tool for analyzing spatial transcriptomics data focusing on morphological features. IAMSAM accurately segments tissue images using the Segment-anything model, allowing for the semi-automatic selection of regions of interest based on morphological signatures. Furthermore, IAMSAM provides downstream analysis, such as identifying differentially expressed genes, enrichment analysis, and cell type prediction within the selected regions. With its simple interface, IAMSAM empowers researchers to explore and interpret heterogeneous tissues in a streamlined manner.
Characterizing physical interactions between male and female mosquitoes (Aedes aegypti) in relation to female receptivity and insemination outcomes using a hydrophobic fluorescent dye
Authors: Cramer Monica M. , Gabel Thomas M. , Duvall Laura B.
Published: May 2023

Aedes aegypti, the yellow fever mosquito, presents a major threat to human health across the globe as a vector of disease-causing pathogens. Females of this species generally mate only once. From this single mating event, the female stores sufficient sperm to fertilize the multiple clutches of eggs produced during her lifetime. Mating causes dramatic changes in the female’s behavior and physiology, including a lifetime suppression of her mating receptivity. Female rejection behaviors include male avoidance, abdominal twisting, wing-flicking, kicking, and not opening vaginal plates or extruding the ovipositor. Many of these events occur on a scale that is too miniscule or fast to see by eye, so high-resolution videography has been used to observe these behaviors instead. However, videography can be labor intensive, require specialized equipment, and often requires restrained animals. We used an efficient, low-cost method to record physical contact between males and females during attempted and successful mating, determined by recording spermathecal filling after dissection. A hydrophobic oil-based fluorescent dye can be applied to the abdominal tip of one animal and can be subsequently transferred to the genitalia of animals of the opposite sex when genital contact occurs. Our data indicate that male mosquitoes make high levels of contact with both receptive and unreceptive females and that males attempt to mate with more females than they successfully inseminate. Female mosquitoes with disrupted remating suppression mate with and produce offspring from multiple males, transferring dye to each. These data suggest that physical copulatory interactions occur independently of the female’s receptivity to mate and that many of these interactions represent unsuccessful mating attempts that do not result in insemination.
Comprehensive map of ribosomal 2′-O-methylation and C/D box snoRNAs inDrosophila melanogaster
Authors: Sklias Athena , Cruciani Sonia , Marchand Virginie , Spagnuolo Mariangela , Lavergne Guillaume , Bourguignon Valérie , Dreos René , Novoa Eva Maria , Motorin Yuri , Roignant Jean-Yves
Published: May 2023

During their maturation, ribosomal RNAs (rRNAs) are decorated by hundreds of chemical modifications that participate in proper folding of rRNA secondary structures and therefore in ribosomal function. Along with pseudouridine, methylation of the 2′-hydroxyl ribose moiety (Nm) is the most abundant modification of rRNAs. The majority of Nm modifications in eukaryotes are placed by Fibrillarin, a conserved methyltransferase belonging to a ribonucleoprotein complex guided by C/D box small nucleolar RNAs (C/D box snoRNAs). These modifications impact interactions between rRNAs, tRNAs and mRNAs, and some are known to fine tune translation rates and efficiency. In this study, we built the first comprehensive map of Nm sites inDrosophila melanogasterrRNAs using two complementary approaches (RiboMethSeq and Nanopore direct RNA sequencing) and identified their corresponding C/D box snoRNAs by whole-transcriptome sequencing. Wede novoidentified 61 Nm sites, from which 55 are supported by both sequencing methods, we validated the expression of 106 C/D box snoRNAs and we predicted new or alternative rRNA Nm targets for 31 of them. Comparison of methylation level upon different stresses show only slight but specific variations, indicating that this modification is relatively stable inD. melanogaster. This study paves the way to investigate the impact of snoRNA-mediated 2′-O-methylation on translation and proteostasis in a whole organism.
Tyramine promotes colon cancer risk and development by inducing DNA damage and inflammation
Authors: Glymenaki Maria , Curio Sophie , Shrestha Smeeta , El-Bahrawy Mona , Wang Yulan , Gooderham Nigel J. , Guerra Nadia , Li Jia V.
Published: May 2023

High dietary consumption of processed meat is associated with increased colorectal cancer (CRC) risk, but mechanistic links remain largely unknown. Tyramine is a biogenic amine found in processed food and a gut bacterial product from tyrosine. However, the impact of tyramine on gut health has not been studied. We found that tyramine induced necrosis and promoted cell proliferation and DNA damage in HCT116 cells. Ingestion of tyramine increased colonic tumor size, intestinal cell proliferation and inflammation (e.g., increased mRNA expression of IL-17A and a higher number of Ly6G+ neutrophils) inApcMin/+mice. Furthermore, tyramine-treated wild-type mice exhibited visible adenomas and significantly enhanced intestinal tissue DNA damage, together with altered gene pathways involved in epithelial barrier function. In addition, natural killer cell numbers were lower and polymorphonuclear-myeloid derived suppressor cells were higher in tumors from tyramine-treatedApcMin/+mice, suggesting a suppressive anti-tumor immune response. Thus, tyramine not only increases CRC risk, but also facilitates tumor development. Modulating the levels of tyramine in food and monitoring high-risk individuals could aid in better prognosis and management of CRC.
Roles of Lipopolysaccharide Glycosyltransferases in Maintenance ofHelicobacter pyloriMorphology, Cell Wall Permeability, and Antimicrobial Susceptibilities
Authors: Tang Xiaoqiong , Yang Tiankuo , Shen Yalin , Song Xiaona , Benghezal Mohammed , Marshall Barry J. , Tang Hong , Li Hong
Published: May 2023

Helicobacter pyloriunique lipopolysaccharide structure is essential in maintaining the cell envelop integrity and renders the bacterium natural resistance to cationic antimicrobial peptides (CAMPs). Our group has recently elucidated the complete set of LPS glycosyltransferase genes inH. pylorireference strain G27. Here, with a series of 8 systematically constructed LPS glycosyltransferase gene mutants (G27ΔHP1578, G27ΔHP1283, G27ΔHP0159, G27ΔHP0479, G27ΔHP0102, G27ΔwecA, G27ΔHP1284and G27ΔHP1191), we investigated the roles ofH. pyloriLPS glycosyltransferases in maintenance of cell morphology, cell wall permeability, and antimicrobial susceptibilities. We demonstrated that deletion of these LPS glycosyltransferase genes did not interfere with bacterial cell wall permeability, but resulted in significant morphological changes (coccoid, coiled “c”-shape, and irregular shapes) after 48 h growth as compared to the rod-like cell shape of the wild-type strain. Moreover, as compared with the wild-type, none of the LPS mutants had altered susceptibility against clarithromycin, levofloxacin, amoxicillin, tetracycline, and metronidazole. However, the deletion of the conserved LPS glycosyltransferases, especially the O-antigen initiating enzyme WecA displayed a dramatic increase in susceptibility to the CAMP polymyxin B and rifampicin. Taken together, our findings suggest that the LPS glycosyltransferases play critical roles in the maintenance of the typical spiral morphology ofH. pylori, as well as resistance to CAMPs and rifampicin. The LPS glycosyltransferases could be promising targets for developing novel anti-H. pyloridrugs.

Importance

H. pyloritypical helical morphology, cell wall integrity, as well as resistance to cationic CAMPs and antimicrobials are significant factors for its long-term colonization and persistent infection in human gastric mucosa. Our results show that each of the 8 LPS glycosyltransferase genes (HP1578,HP1283,HP0159,HP0479,HP0102,wecA,HP1284andHP1191) deletion did not interfere with bacterial cell wall permeability, but resulted in significant loss ofH. pyloritypical helical shape. Furthermore, deletion of the conserved LPS glycosyltransferases, especially the O-antigen initiating enzyme WecA displayed a dramatic increase in susceptibility to the CAMP polymyxin B and rifampicin. Taken together, we believe that the LPS glycosyltransferases are good targets for developing novel anti-H. pyloridrugs.
Inclusion of “managing flexibility” valuations in the pricing of PPP projects: a multi-objective decision-making method
Authors: Guo Yubo , Su Yangyang , Chen Chuan , Martek Igor
Published: May 2023

Purpose

The Public–Private Partnership (PPP) modality plays an important role in the procurement of global infrastructure projects. Regarding PPP's complex transaction structure, pricing of a PPP project is critical to both parties where the government pursues a high value for money (VFM) and the investor strives to maximize its financial gains. Despite the straightforward win–win principle, a formidable compromise is often the case to end up with a fairly acceptable price, subject to many determinants such as the risk profile, expected return, technological innovation and capacities of both parties. Among them, this study chooses to examine the “managing flexibility” (MF) capacity of investors in pricing of a PPP project, in light of the widely recognized importance of a real-option perspective toward the long term, complex and uncertain PPP arrangement. This study addresses two major questions: (1) how is MF in PPP projects to be valued and (2) how are PPP projects to be priced when considering a project's MF value.

Design/methodology/approach

A binomial tree model is used to evaluate the MF value in PPP projects. Based on the developed MF pricing model, net present value (NPV) and adjusted VFM value are then calculated. Finally, a multi-objective decision-making method (MODM) was adopted to determine the optimal level of returns based on invested capital (ROIC), return on operation maintenance (ROOM) and concession period.

Findings

The applicability and functionality of the proposed model is investigated using a real project case. For a given return, extended NPV and adjusted VFM value were calculated and analyzed using sensitivity analysis. Factor influence is shown by the model to be dependent on factor impact on cash flow. Subsequently, a multi-objective decision-making (MODM) model was adopted to determine the optimal level of returns, where the solution approximates the real-world bidding price. Results confirm that the pricing model provides a reliable and practical PPP proposal pricing tool.

Originality/value

This study proposes an integrated framework for valuing MF in PPP projects and thus more accurately determine optimal pricing of PPP projects than revealed in extant research. The model offers a practical tool to aid in the valuation of PPP projects.
Configuration analysis of the innovation pathway of gerontechnological enterprises under the market-organization-technology perspective
Authors: Zheng Supeng , Appolloni Andrea , Lin Haifen , Ding Xiangan
Published: May 2023

Purpose

This paper aims to investigate the innovation pathway of gerontechnological enterprises under the market-organization-technology (MOT) perspective through configuration analysis.

Design/methodology/approach

Based on the analytical framework of technology, organization and market, this paper conducts configuration analysis on the cases of 55 elderly-friendly enterprises in China combined with fuzzy-set qualitative comparative analysis (fsQCA).

Findings

First, this study identifies the three first-level preconditions affecting innovation performance: organization's architectural innovation, technology adapting to aging and market environment attention on the innovation pathway of gerontechnological enterprises. These three first-level conditions include six sub-conditions. Second, this study investigates three innovation pathways by analyzing the configuration effects of preconditions: Configuration 1, technology-balanced type; Configuration 2, organization-market linkage type and Configuration, 3 balanced type. Third, there are differences in the distribution of different configuration types in subdivided industries. The technology-balanced configuration is mainly concentrated in design-driven innovative enterprises, the organization-market linkage configuration is mainly concentrated in medical auxiliary equipment enterprises and the balanced configuration is mainly concentrated in smart elderly care service platform enterprises empowered by digital technology. Fourth, there are differences in the innovation impact paths of the same configuration type. However, the essence lies in the high-level innovation performance formed by the coordinated evolution of technology, organization and market factors, reflecting the characteristics of the same goal through different routes.

Research limitations/implications

The authors' study generates new insights for innovation managers of gerontechnological enterprises about the innovation pathway.

Originality/value

This research enriches innovation management by integrating the linkage adaptation relationship among market, organization and technology factors; further research studies on the different configuration types suitable for different types of enterprises, as well as differentiated innovation pathways under the same configuration type, could contribute to the study on the innovation pathway under a premise of MOT.
Provisions for people living with dementia in housing with care settings in England
Authors: Barrett Julia
Published: May 2023

Purpose

This paper aims to describe a literature review and online survey to explore the provisions and support for people living with dementia in housing with care (HwC) settings within England.

Design/methodology/approach

An initial scoping literature review was conducted to synthesise the evidence relating to residents living with dementia in HwC settings and informed the development of an online survey distributed to HwC housing managers to explore the provisions, policies, procedures and support services relating to people living with dementia in HwC settings.

Findings

The findings provided a picture of HwC settings in England and the residents, particularly those living with dementia, in terms of policies and procedures, reasons for moving into HwC, reasons for denying entry, reasons for leaving, positive outcomes, staff knowledge and training, environmental design, challenges and successes.

Research limitations/implications

The survey responses were from a self-selected sample of HwC providers and scheme/village managers; thus, it may be the case that the settings involved were doing more to support residents living with dementia. It should also be appreciated that the responses were based on the perceptions of the individual staff members completing the survey, not those of the HwC residents.

Originality/value

This study presented a picture of the current state of provisions and support for people with dementia within HwC settings in England, providing an essential platform from which to undertake targeted research to help shape future provision and enabling housing providers to assess their current schemes within the wider context.
Hotel management schemes: liminal protean pathways derived from acting as lifeguards in Gulf luxury resorts
Authors: Dutt Christopher S. , Ryan Chris
Published: May 2023

Purpose

This paper examines why individuals start their hospitality careers by becoming temporary lifeguards while aspiring to later promotion. It reports data from young people working in one major upmarket hotel chain that operates in the Gulf but has a global reach. This study aims to address issues regarding this often-overlooked career path for young staff.

Design/methodology/approach

A qualitative questionnaire was distributed to lifeguards working in a luxury hotel chain in a Gulf country to explore their reasons for working as a lifeguard and their experiences in this role. Data were analysed using QDA Miner and WordStat to generate coherence and similarity indices.

Findings

It is found that the attractions include good training with a well-established company operating in an upmarket location, but other important factors include career prospects, skill enhancement, self-development, monetary savings and experience working in one of the world’s most exciting tourist locations.

Practical implications

The results offer implications for management looking to recruit expatriate labour without considering long-term employment or residence. Nonetheless, while this offers opportunities to assess many potential long-term employees, there are costs to the practice.

Originality/value

Little research has been conducted on lifeguards and how employment in such roles can develop careers in hospitality. The study contributes to understanding motives and career development and conceptually suggests that liminal status complements those drawn to protean career development. The results shed light on how new employees, including management trainees, undertake liminal, protean careers, to care for family, develop their careers and enter markets that may otherwise be difficult to enter.
Social media analytics and product innovation: mediating effects of knowledge exploration and exploitation competences
Authors: Cheng Colin C.J. , Sheu Chwen
Published: May 2023

Purpose

Prior research on business analytics has advanced substantially our understanding of how social media analytics affect business performance. However, the specific value of social media analytics to product innovation has not been fully explored and appreciated. To address this important issue, the present study draws on the resource-based view and the knowledge-based view to examine (1) whether the use of social media analytics strengthens radical product innovation to a greater extent than it does incremental product innovation and (2) how knowledge-exploration competence and knowledge-exploitation competence mediate the influence of social media analytics on radical and incremental product innovation.

Design/methodology/approach

This study tested the proposed model using data collected from 205 manufacturing firms. Structural equation modeling was applied to test the research hypotheses using LISREL 8.80 software program.

Findings

The statistical findings provide compelling evidence that the use of social media analytics is more likely to lead to radical product innovation than to incremental product innovation. In addition, knowledge-exploration competence only partially mediates the relationship between social media analytics and radical product innovation. Knowledge-exploitation competence not only partially mediates such a relationship, but also fully mediates the link between social media analytics and incremental product innovation.

Originality/value

This study contributes to the social media analytics and innovation literature by offering novel theoretical and empirical insights into how firms can leverage the value of social media analytics to create superior product innovation.
Predicting the intention to use Paytech services by Islamic banking users
Authors: Irimia-Diéguez Ana , Albort-Morant Gema , Oliver-Alfonso Maria Dolores , Ullah Shakir
Published: May 2023

Purpose

This study aims to identify the factors that could explain the intention to use Paytech services within an Islamic banking context. The authors use an extended version of the technology acceptance model to develop a causal–predictive analysis.

Design/methodology/approach

The research model and hypotheses were tested by applying partial least square-structured equation modeling to data collected from 214 users of Islamic banking in Saudi Arabia.

Findings

The results show that perceived trust has a highly significant direct effect on the intention to use Islamic Paytech services, whereas perceived risk has a significant indirect effect on IU.

Research limitations/implications

Internet banking behavior may not be static. In technology acceptance, during the various phases from introduction to the maturity phase, the respondent’s perceptions tend to change

Practical implications

From the point of view of Fintech services providers, the knowledge of the factors fostering the adoption of Fintech services would allow an international expansion without the inconvenience of establishing offices or companies in countries whose legislation does not favor the operations carried out by Islamic banks.

Social implications

These digital payment services would allow access to financial services to the entire Muslim population regardless of their location (Islamic and non-Islamic nations) and will also reach out to the next generation of young Muslims as a majority are “digital natives” ready for digital Islamic financial solutions.

Originality/value

This study is the first to explore the intention to use Paytech services by Islamic banking users in Saudi Arabia. From a theoretical perspective, this work contributes to the academic literature by analyzing the intention to use Paytech services in an Islamic banking context. On the practical front, the study identifies the crucial factors that industry players can use to design their Paytech applications and services to increase financial inclusion in Saudi Arabia and other countries with similar cultures as well as to design an international expansion without the inconvenience of establishing offices or companies in countries whose legislation does not favor the operations carried out by Islamic banks.
The effect of the motion attributes of spokes-characters on app launch pages on brand memory
Authors: Zhang Ning , Liya Zhu
Published: May 2023

Purpose

The use of brand slogans that represent brand concepts on app launch pages can improve user brand impressions. The purpose of this paper is to investigate the impact of using animated or static spokes-characters with brand slogans on app launch pages.

Design/methodology/approach

Using the theory of attention selection, the authors conducted two experiments to study the boundary and mediation path of the influence of the motion attributes of spokes-characters (static vs animated) on brand memory based on app launch time (3 s vs 5 s), user engagement with spokes-characters and the level of attention to brand slogans.

Findings

Study 1 explores the effect of the interaction between launch time and the motion attributes of spokes-characters on brand memory. The results show that when the launch time of the app is 3 s, the advertisement memory effect of using a static spokes-character is better than that of using an animated spokes-character; when the launch time of the app is 5 s, the advertisement memory effect of using an animated spokes-character is better than that of using a static spokes-character. Study 2 shows that user engagement with spokes-characters and the level of attention given to brand slogans play a continuous mediating role in the effect of the interaction between launch time and the motion attributes of spokes-characters on brand memory.

Originality/value

This paper contributes to the marketing literature by expanding the knowledge of spokes-characters and animated visual images, providing new insights for future research.
Artificial intelligence in personalised learning: a bibliometric analysis
Authors: Li Kam Cheong , Wong Billy Tak-Ming
Published: May 2023

Purpose

This paper aims to present a comprehensive overview of the patterns and trends of publications on artificial intelligence (AI) in personalised learning. It addresses the need to investigate the intellectual structure and development of this area in view of the growing amount of related research and practices.

Design/methodology/approach

A bibliometric analysis was conducted to cover publications on AI in personalised learning published from 2000 to 2022, including a total of 1,005 publications collected from the Web of Science and Scopus. The patterns and trends in terms of sources of publications, intellectual structure and major topics were analysed.

Findings

Research on AI in personalised learning has been widely published in various sources. The intellectual bases of related work were mostly on studies on the application of AI technologies in education and personalised learning. The relevant research covered mainly AI technologies and techniques, as well as the design and development of AI systems to support personalised learning. The emerging topics have addressed areas such as big data, learning analytics and deep learning.

Originality/value

This study depicted the research hotspots of personalisation in learning with the support of AI and illustrated the evolution and emerging trends in the field. The results highlight its latest developments and the need for future work on diverse means to support personalised learning with AI, the pedagogical issues, as well as teachers’ roles and teaching strategies.