bluuebunny/crossref_metadata_2025 huggingface dataset:
Increased mitochondrial surface area and cristae density in the skeletal muscle of strength athletes
Authors: Botella Javier , Schytz Camilla T. , Pehrson Thomas F. , Hokken Rune , Laugesen Simon , Aagaard Per , Suetta Charlotte , Christensen Britt , Ørtenblad Niels , Nielsen Joachim
Published: January 2023

Mitochondria are the cellular organelles responsible for resynthesising the majority of ATP. In skeletal muscle, there is an increased ATP turnover during resistance exercise to sustain the energetic demands of muscle contraction. Despite this, little is known regarding the mitochondrial characteristics of chronically strength-trained individuals and any potential pathways regulating the strength-specific mitochondrial remodelling. Here, we investigated the mitochondrial structural characteristics in skeletal muscle of strength athletes and age-matched untrained controls. The mitochondrial pool in strength athletes was characterised by increased mitochondrial cristae density, decreased mitochondrial size, and increased surface-to-volume ratio, despite similar mitochondrial volume density. We also provide a fibre-type and compartment specific assessment of mitochondria morphology in human skeletal muscle, which reveals across groups a compartment-specific influence on mitochondrial morphology that is largely independent of fibre-type. Furthermore, we show that resistance exercise leads to signs of mild mitochondrial stress, without an increase in the number of damaged mitochondria. Using publicly available transcriptomic data we show that acute resistance exercise increases the expression of markers of mitochondrial biogenesis, fission, and mitochondrial unfolded protein responses (UPRmt). Further, we observed an enrichment of the UPRmtin the basal transcriptome of strength-trained individuals. Together, these findings show that strength athletes possess a unique mitochondrial remodelling, which minimises the space required for mitochondria. We propose that the concurrent activation of markers of mitochondrial biogenesis and mitochondrial remodelling pathways (fission and UPRmt) with resistance exercise may be partially responsible for the observed mitochondrial phenotype of strength athletes.
Analysis of cell death induction by the barley NLR immune receptor PBR1
Authors: Jaiswal Namrata , Myers Ariana , Weese Terri L. , Carter Morgan E. , Scofield Steven R. , Helm Matthew
Published: January 2023

The barley (Hordeum vulgaresubsp.vulgare) disease resistance proteinAvrPphB Response 1(PBR1) mediates recognition of thePseudomonas syringaeeffector, AvrPphB. PBR1 belongs to the coiled-coil nucleotide-binding leucine-rich repeat (CNL) family. However, little is known about the molecular mechanisms that lead to PBR1-dependent cell death (hypersensitive reaction; HR) in response to AvrPphB. Here, we investigated PBR1 immune signaling afterAgrobacterium-mediated transient expression inNicotiana benthamiana. We found that co-expression of PBR1 with AvrPphB resulted in robust cell death, confirming previous observations that PBR1 is indeed the cognate NLR that recognizes AvrPphB. The N-terminal tagging of PBR1 with super Yellow Fluorescent Protein (sYFP) abolished PBR1-mediated cell death, demonstrating that an N-terminal epitope tag disrupts PBR1-mediated immune signaling. Furthermore, none of the individual protein domains or truncations of PBR1 induced a HR-like cell death response as strong as full-length PBR1 when co-expressed with AvrPphB, indicating that the individual domains and fragments of PBR1 are insufficient to trigger HR. Intriguingly, introducing the typically auto-activating D496V mutation within NB-ARC-containing fragments of PBR1 does not activate immune signaling revealing PBR1-mediated immune signaling requires cooperation of all domainsin cis. Using co-immunoprecipitation and split-luciferase assays, we also show full-length PBR1 self-associates in the absence of AvrPphB and such self-association is not dependent on a functional P-loop/Walker A motif. Collectively, these findings provide valuable insights into PBR1-mediated disease resistance and extends upon our understanding of NLR-mediated immune signaling.
PeruNPDB: The Peruvian Natural Products Database for in silico drug screening
Authors: Barazorda-Ccahuana Haruna Luz , Ranilla Lena Gálvez , Candia-Puma Mayron Antonio , Cárcamo-Rodriguez Eymi Gladys , Centeno-Lopez Angela Emperatriz , Del-Carpio Gonzalo Davila , Medina-Franco José L. , Chávez-Fumagalli Miguel Angel
Published: January 2023

Since the number of drugs based on natural products (NPs) represents a large source of novel pharmacological entities, NPs have acquired significance in drug discovery. Peru is considered a megadiverse country with many endemic species of plants, terrestrial, and marine animals, and microorganisms. NPs databases have a major impact on drug discovery development. For this reason, several countries such as Mexico, Brazil, India, and China have initiatives to assemble and maintain NPs databases that are representative of their diversity and ethnopharmacological usage. We describe the assembly, curation, and full chemoinformatic evaluation of the content and coverage in chemical space, as well as the physicochemical attributes and chemical diversity of the initial version of the Peruvian Natural Products Database (PeruNPDB), which contains 280 compounds. Access to PeruNPDB is available for free (https://perunpdb.com.pe/). The PeruNPDB’s collection is intended to be used in a variety of tasks, such as virtual screening campaigns against various disease targets or biological endpoints. This emphasizes the significance of biodiversity protection both directly and indirectly on human health.
Serum protein N-glycome patterns reveal alterations associated with endometrial cancer and its phenotypes of differentiation
Authors: Zhang Zejian , Cao Zhen , Wang Jinhui , Li Zepeng , Wang Tao , Xiang Yang
Published: January 2023

Background and aims

Aberrant N-glycosylation and its involvement in pathogenesis have been reported in endometrial cancer (EC). Nevertheless, the serum N-glycomic signature of EC remains unknown. Here, we investigated serum N-glycome patterns of EC to identify candidate biomarkers.

Materials and methods

This study enrolled 34 untreated EC patients and 34 matched healthy controls (HC) from Peking Union Medical College Hospital. State-of-the-art MS-based methods were employed for N-glycans profiling. Multivariate and univariate statistical analyses were used to identify discriminative N-glycans driving classification. Receiver operating characteristic analyses were performed to evaluate classification accuracy.

Results

EC patients displayed distinct differences in serum N-glycome and had abnormal high-mannose and hybrid-type N-glycans, fucosylation, galactosylation, and linkage□specific sialylation compared with HC. The glycan panel built with the four most discriminative and biologically important derived N-glycan traits could accurately identify EC (random forest model, the area under the curve [AUC]=0.993 [95%CI 0.955-1]). The performance was validated by two other models. Total hybrid-type N-glycans significantly associated with the differentiation types of EC could effectively stratify EC into well- or poorly-differentiated subgroups (AUC>0.8).

Conclusion

This study to the best of our knowledge provides the initial evidence supporting the utility of serum N-glycomic signature as potential markers for the diagnosis and phenotyping of EC.
Cryo-EM reveals the mechanism of DNA compaction byMycobacterium smegmatisDps2
Authors: Garg Priyanka , Satheesh Thejas , Ganji Mahipal , Dutta Somnath
Published: January 2023

DNA-binding protein under starvation (Dps), is a miniature ferritin complex which plays a vital role in protecting bacterial DNA during starvation for maintaining the integrity of bacteria from hostile conditions.Mycobacterium smegmatisis one such bacteria that express MsDps2, which binds DNA to protect it under oxidative and nutritional stress conditions. Several approaches, including cryo-electron tomography (Cryo-ET), were implemented to identify the structure of the Dps protein that is bound to DNA. However, none of the structures of the Dps-DNA complex was resolved to high resolution to be able to identify the DNA binding residues. In this study, we implemented various biochemical and biophysical studies to characterize the DNA protein interactions of Dps protein. We employed single-particle cryo-EM-based structural analysis of MsDps2-DNA and identify that the region close to N-terminal confers the DNA binding property. Based on cryo-EM data, we performed mutations of several arginine residues proximal to DNA binding region, which dramatically reduced the MsDps2-DNA interaction. In addition, we demonstrated the proposed model for DNA compaction during lattice formation. We also pinpointed arginine residues, which are responsible for DNA binding in lattice arrangement of MsDps2. We performed single-molecule imaging experiments of MsDps2-DNA interactions that corroborate well with our structural studies.
Deadenylation rate is not a major determinant of RNA degradation in yeast
Authors: Audebert Léna , Feuerbach Frank , Decourty Laurence , Namane Abdelkader , Permal Emmanuelle , Badis Gwenaël , Saveanu Cosmin
Published: January 2023

Gene expression and its regulation depend on mRNA degradation. In eukaryotes, degradation is controlled by deadenylation rates, since a short poly(A) tail is considered to be the signal that activates decapping and triggers mRNA degradation. In contrast to this view, we show that global stability of mRNAs can be explained by variations in decapping speed alone. Rapid decapping of unstable mRNAs, for example, allows little time for deadenylation, which explains their longer than average poly(A) tails. As predicted by modeling of RNA degradation kinetics, mRNA stabilization in the absence of decapping led to a decrease in the length of the poly(A) tail, while depletion of deadenylases only increased the tail length. Our results suggest that decapping activation dictates mRNA stability independent of the deadenylation speed.

One-Sentence Summary

Unstable mRNAs are characterized by rapid 5’ cap removal, independent of a prior shortening of the poly(A) tail.
The emergence of goblet inflammatory or ITGB6hinasal progenitor cells determines age-associated SARS-CoV-2 pathogenesis
Authors: Woodall Maximillian , Cujba Ana-Maria , Worlock Kaylee B. , Case Katie-Marie , Masonou Tereza , Yoshida Masahiro , Polanski Krzysztof , Huang Ni , Lindeboom Rik G. H. , Mamanova Lira , Bolt Liam , Richardson Laura , Ellis Samuel , Palor Machaela , Burgoyne Thomas , Pinto Andreia , Moulding Dale , McHugh Timothy D. , Saleh Aarash , Kilich Eliz , Mehta Puja , O’Callaghan Chris , Zhou Jie , Barclay Wendy , Coppi Paolo De , Butler Colin R. , Vinette Heloise , Roy Sunando , Breuer Judith , Chambers Rachel C. , Heywood Wendy E. , Mills Kevin , Hynds Robert E. , Teichmann Sarah A. , Meyer Kerstin B. , Nikolić Marko Z. , Smith Claire M.
Published: January 2023

Children infected with SARS-CoV-2 rarely progress to respiratory failure, but the risk of mortality in infected people over 85 years of age remains high, despite vaccination and improving treatment options. Here, we take a comprehensive, multidisciplinary approach to investigate differences in the cellular landscape and function of paediatric (<11y), adult (30- 50y) and elderly (>70y) nasal epithelial cells experimentally infected with SARS-CoV-2. Our data reveal that nasal epithelial cell subtypes show different tropism to SARS-CoV-2, correlating with age, ACE2 and TMPRSS2 expression. Ciliated cells are a viral replication centre across all age groups, but a distinct goblet inflammatory subtype emerges in infected paediatric cultures, identifiable by high expression of interferon stimulated genes and truncated viral genomes. In contrast, infected elderly cultures show a proportional increase in ITGB6hiprogenitors, which facilitate viral spread and are associated with dysfunctional epithelial repair pathways.

Graphical Abstract
The impact of modern admixture on archaic human ancestry in human populations
Authors: Witt Kelsey E. , Funk Alyssa , Fang Lesly Lopez , Huerta-Sanchez Emilia
Published: January 2023

Admixture, the genetic merging of parental populations resulting in mixed ancestry, has occurred frequently throughout the course of human history. Numerous admixture events have occurred between human populations across the world, as well as introgression between humans and archaic humans, Neanderthals and Denisovans. One example are genomes from populations in the Americas, as these are often mosaics of different ancestries due to recent admixture events as part of European colonization. In this study, we analyzed admixed populations from the Americas to assess whether the proportion and location of admixed segments due to recent admixture impact an individual’s archaic ancestry. We identified a positive correlation between non-African ancestry and archaic alleles, as well as a slight enrichment of Denisovan alleles in Indigenous American segments relative to European segments in admixed genomes. We also identify several genes as candidates for adaptive introgression, based on archaic alleles present at high frequency in admixed American populations but low frequency in East Asian populations. These results provide insights into how recent admixture events between modern humans redistributed archaic ancestry in admixed genomes.
Extraordinary Evasion of Neutralizing Antibody Response by Omicron XBB.1.5, CH.1.1 and CA.3.1 Variants
Authors: Qu Panke , Faraone Julia N. , Evans John P. , Zheng Yi-Min , Carlin Claire , Anghelina Mirela , Stevens Patrick , Fernandez Soledad , Jones Daniel , Panchal Ashish , Saif Linda J. , Oltz Eugene M. , Xu Kai , Gumina Richard J. , Liu Shan-Lu
Published: January 2023

Newly emerging Omicron subvariants continue to emerge around the world, presenting potential challenges to current vaccination strategies. This study investigates the extent of neutralizing antibody escape by new subvariants XBB.1.5, CH.1.1, and CA.3.1, as well as their impacts on spike protein biology. Our results demonstrated a nearly complete escape of these variants from neutralizing antibodies stimulated by three doses of mRNA vaccine, but neutralization was rescued by a bivalent booster. However, CH.1.1 and CA.3.1 variants were highly resistant to both monovalent and bivalent mRNA vaccinations. We also assessed neutralization by sera from individuals infected during the BA.4/5 wave of infection and observed similar trends of immune escape. In these cohorts, XBB.1.5 did not exhibit enhanced neutralization resistance over the recently dominant BQ.1.1 variant. Notably, the spike proteins of XBB.1.5, CH.1.1, and CA.3.1 all exhibited increased fusogenicity compared to BA.2, correlating with enhanced S processing. Overall, our results support the administration of new bivalent mRNA vaccines, especially in fighting against newly emerged Omicron subvariants, as well as the need for continued surveillance of Omicron subvariants.
Ribosome rescue factor PELOTA modulates translation start site choice and protein isoform levels of transcription factor C/EBPα
Authors: Fernandez Samantha G. , Ferguson Lucas , Ingolia Nicholas T.
Published: January 2023

Translation initiation at alternative start sites can dynamically control the synthesis of two or more functionally distinct protein isoforms from a single mRNA. Alternate isoforms of the hematopoietic transcription factor CCAAT-enhancer binding proteinα(C/EBPα) produced from different start sites exert opposing effects during myeloid cell development. This alternative initiation depends on sequence features of theCEBPAtranscript, including a regulatory upstream open reading frame (uORF), but the molecular basis is not fully understood. Here we identifytrans-acting factors that affect C/EBPαisoform choice using a sensitive and quantitative two-color fluorescence reporter coupled with CRISPRi screening. Our screen uncovered a role for the ribosome rescue factor PELOTA (PELO) in promoting expression of the longer C/EBPαisoform, by directly removing inhibitory unrecycled ribosomes and through indirect effects mediated by the mechanistic target of rapamycin (mTOR) kinase. Our work provides further mechanistic insights into coupling between ribosome recycling and translation reinitiation in regulation of a key transcription factor, with implications for normal hematopoiesis and leukemiagenesis.
Synovial Monocytes Drive the Pathogenesis in Oligoarticular Juvenile Idiopathic Arthritis via IL-6/JAK/STAT Signalling and Cell-Cell Interactions
Authors: Schmidt Tobias , Dahlberg Alma , Berthold Elisabet , Król Petra , Arve-Butler Sabine , Rydén Emilia , Najibi Seyed Morteza , Mossberg Anki , Bengtsson Anders , Kahn Fredrik , Månsson Bengt , Kahn Robin
Published: January 2023

Objectives

Synovial monocytes in oligoarticular juvenile idiopathic arthritis (oJIA) are polarized, but little is known of how they contribute to disease and attain their pathogenic features. The aim of this study was to investigate the role of monocytes in the pathogenesis of oJIA.

Methods

The function of synovial monocytes was analysed by several assays believed to reflect key pathogenic events, such as T-cell activation-, efferocytosis- and cytokine production assays through flow cytometry in untreated oJIA patients (n=33). The effect of synovial fluid on healthy monocytes was investigated through mass spectrometry, broad-spectrum phosphorylation assays and functional assays. Additional effects on monocytes were studied through co-cultures with primary fibroblast-like synoviocytes.

Results

The results demonstrate that synovial monocytes display functional alterations, e.g., increased ability to induce T-cell activation, increased efferocytosis and resistance to cytokine production following activation with LPS.In vitro, synovial fluid induced regulatory features in healthy monocytes through an IL-6/JAK/STAT mechanism. The magnitude of synovial IL-6 driven activation in monocytes was reflected in circulating cytokine levels. An increased ability to induce T-cell activation and markers of antigen presentation could be induced by co-culture with fibroblast-like synoviocytes.

Conclusions

Synovial monocytes in oJIA are functionally affected, drive chronic inflammation, and promote adaptive immune responses. This phenotype can be replicatedin vitrothrough a combination of synovial fluid (through IL-6/JAK/STAT) and cell-cell interactions. These data support a role of monocytes in the pathogenesis of oJIA and highlight a group of patients more likely to benefit from targeting the IL-6/JAK/STAT axis to restore synovial homeostasis.

Key messages

What is already known on this topic

Monocytes infiltrate the joint in oligoarticular juvenile idiopathic arthritis (JIA), where they display a pathogenic phenotype and signs of activation

What this study adds

The results of this study demonstrate functional alterations of synovial monocytes in driving chronic inflammation in oligoarticular JIA

Synovial monocytes acquire their regulatory properties through the IL-6/JAK/STAT pathway in synovial fluid and their inflammatory properties through cell-cell interactions

In patients with high IL-6/JAK/STAT involvement, this is reflected in elevated circulating cytokine levels

How this study might affect research, practice or policy

This study describes the mechanisms controlling the function of synovial monocytes in oligoarticular JIA and identifies patients likely to respond to IL-6/JAK/STAT inhibition, which should be further explored to facilitate personalized medicine.
Therapeutic and vaccine-induced cross-reactive antibodies with effector function against emerging Omicron variants
Authors: Addetia Amin , Piccoli Luca , Case James Brett , Park Young-Jun , Beltramello Martina , Guarino Barbara , Dang Ha , Pinto Dora , Scheaffer Suzanne M. , Sprouse Kaitlin , Bassi Jessica , Silacci-Fregni Chiara , Muoio Francesco , Dini Marco , Vincenzetti Lucia , Acosta Rima , Johnson Daisy , Subramanian Sambhavi , Saliba Christian , Giurdanella Martina , Lombardo Gloria , Leoni Giada , Culap Katja , McAlister Carley , Rajesh Anushka , Dellota Exequiel , Zhou Jiayi , Farhat Nisar , Bohan Dana , Noack Julia , Lempp Florian A. , Cameroni Elisabetta , Whitener Bradley , Giannini Olivier , Ceschi Alessandro , Ferrari Paolo , Franzetti-Pellanda Alessandra , Biggiogero Maira , Garzoni Christian , Zappi Stephanie , Bernasconi Luca , Kim Min Jeong , Schnell Gretja , Czudnochowski Nadine , Franko Nicholas , Logue Jennifer K. , Yoshiyama Courtney , Stewart Cameron , Chu Helen , Schmid Michael A. , Purcell Lisa A. , Snell Gyorgy , Lanzavecchia Antonio , Diamond Michael S. , Corti Davide , Veesler David
Published: January 2023

Currently circulating SARS-CoV-2 variants acquired convergent mutations at receptor-binding domain (RBD) hot spots1. Their impact on viral infection, transmission, and efficacy of vaccines and therapeutics remains poorly understood. Here, we demonstrate that recently emerged BQ.1.1. and XBB.1 variants bind ACE2 with high affinity and promote membrane fusion more efficiently than earlier Omicron variants. Structures of the BQ.1.1 and XBB.1 RBDs bound to human ACE2 and S309 Fab (sotrovimab parent) explain the altered ACE2 recognition and preserved antibody binding through conformational selection. We show that sotrovimab binds avidly to all Omicron variants, promotes Fc-dependent effector functions and protects mice challenged with BQ.1.1, the variant displaying the greatest loss of neutralization. Moreover, in several donors vaccine-elicited plasma antibodies cross-react with and trigger effector functions against Omicron variants despite reduced neutralizing activity. Cross-reactive RBD-directed human memory B cells remained dominant even after two exposures to Omicron spikes, underscoring persistent immune imprinting. Our findings suggest that this previously overlooked class of cross-reactive antibodies, exemplified by S309, may contribute to protection against disease caused by emerging variants through elicitation of effector functions.
Aqueous Spice Extracts as Alternative Antimycotics to Control Highly Drug Resistant Extensive Biofilm Forming Clinical Isolates ofCandida albicans
Authors: Sadanandan Bindu , Vijayalakshmi Vaniyamparambath , Ashrit Priya , Babu U V , Kumar L M Sharath , Sampath V , Shetty Kalidas , Joglekar Amruta Purushottam , Awaknavar Rashmi
Published: January 2023

Candida albicansforms biofilm by associating with biotic and abiotic surfaces. Biofilm formation byC. albicansis relevant and significant as the organisms residing within, gain resistance to conventional antimycotics and are therefore difficult to treat. This study targeted the potential of spice-based antimycotics to controlC. albicansbiofilms. Ten clinical isolates ofC. albicansalong with a standard culture MTCC-3017 (ATCC-90028) were screened for their biofilm-forming ability.C. albicansM-207 andC. albicansS-470 were identified as high biofilm formers by point inoculation on TSA medium as they formed a lawn within 16 h and exhibited resistance to fluconazole and caspofungin at 25 mcg and 8 mcg respectively. Aqueous and organic spice extracts were screened for their antimycotic activity againstC. albicansM-207 and S-470 by agar and disc diffusion and Zone of Inhibition was observed. Minimal Inhibitory Concentration was determined based on growth absorbance and cell viability measurements. The whole aqueous extract of garlic inhibited biofilms ofC. albicansM-207, whereas whole aqueous extracts of garlic, clove, and Indian gooseberry were effective in controllingC. albicansS-470 biofilm within 12 h of incubation. The presence of allicin, ellagic acid, and gallic acid as dominant compounds in the aqueous extracts of garlic, clove, and Indian gooseberry respectively was determined by High-Performance Thin Layer Chromatography and Liquid Chromatography-Mass Spectrometry. The morphology ofC. albicansbiofilm at different growth periods was also determined through bright field microscopy, phase contrast microscopy, and fluorescence microscopy. The results of this study indicated that the alternate approach in controlling high biofilm-forming, multi-drug resistant clinical isolates ofC. albicansM-207 and S-470 using whole aqueous extracts of garlic, clove, and Indian gooseberry is a safe, potential, and cost-effective one that can benefit the health care needs with additional effective therapeutics to treat biofilm infections.
Quorum sensing inhibits Type III-A CRISPR-Cas system activity through repressing positive regulators SarA and ArcR inStaphylococcus aureus
Authors: Li Yang , Tang Yuanyue , Li Xiaofei , Høyland-Kroghsbo Nina Molin , Ingmer Hanne , Jiao Xinan , Li Qiuchun
Published: January 2023

CRISPR-Cas is an adaptive immune system that protects prokaryotes from the invasion of foreign genetic elements. The components and immunity mechanisms of CRISPR-Cas have been extensively studied, but the regulation of this system inStaphylococciremains unclear. Here, we show that in theS. aureusType III-A CRISPR-Cas system, the Pcasof 300 bp located incas1displays as a critical regulatory node that initiates the transcription ofcasgene clusters. We discovered two transcriptional regulators, SarA and CRP-like ArcR, promote the expression and activity of the CRISPR-Cas system by directly binding to the novel promoter Pcas. Furthermore, we demonstrated that the cell-cell communication, known as quorum sensing (QS), inhibits the activity of CRISPR-Cas system by repressing the positive regulators SarA and ArcR. Bioinformatic analyses suggest that Pcasis conserved in many Type II and III CRISPR-Cas systems in Firmicutes. Our data reveal a new regulatory mechanism for QS-mediated repression of the Type III-A CRISPR-Cas system, which may allowS. aureusto acquire foreign genetic elements encoding antibiotic resistance or virulence factors specifically at high cell density.
Cell division tracing combined with single-cell transcriptomics reveals new cell types and differentiation paths in the regenerating mouse lung
Authors: Martins Leila R. , Sieverling Lina , Michelhans Michelle , Schiller Chiara , Erkut Cihan , Triana Sergio , Fröhling Stefan , Velten Lars , Glimm Hanno , Scholl Claudia
Published: January 2023

Understanding the molecular and cellular processes involved in lung epithelial regeneration may fuel the development of new therapeutic approaches for lung diseases. We combined new mouse models that allow diphtheria toxin (DTA)-mediated depletion of specific epithelial cell types and GFP-labeling of dividing cells with single-cell transcriptomics to characterize the regeneration of the distal lung. We uncovered new cell types, some of which likely represent epithelial precursors, propose goblet cells as progenitor cells, and provide evidence that adventitial fibroblasts act as supporting cells in epithelial regeneration. We also found that DTA-expressing cells can persist in the lung, express specific inflammatory factors, and resemble a previously undescribed population in the lungs of COVID-19 patients. Our study provides a comprehensive single-cell atlas of the distal lung that characterizes early transcriptional and cellular responses to defined epithelial injury, encompassing proliferation, differentiation, and cell-to-cell interactions.
Benchmarking of analytical combinations for COVID-19 outcome prediction using single-cell RNA sequencing data
Authors: Cao Yue , Ghazanfar Shila , Yang Pengyi , Yang Jean
Published: January 2023

The advances of single-cell transcriptomic technologies have led to increasing use of single-cell RNA sequencing (scRNA-seq) data in large-scale patient cohort studies. The resulting high-dimensional data can be summarised and incorporated into patient outcome prediction models in several ways, however, there is a pressing need to understand the impact of analytical decisions on such model quality. In this study, we evaluate the impact of analytical choices on model choices, ensemble learning strategies and integration approaches on patient outcome prediction using five scRNA-seq COVID-19 datasets. First, we examine the difference in performance between using each single-view feature space versus multi-view feature space. Next, we survey multiple learning platforms from classical machine learning to modern deep learning methods. Lastly, we compare different integration approaches when combining datasets is necessary. Through benchmarking such analytical combinations, our study highlights the power of ensemble learning, consistency among different learning methods and robustness to dataset normalisation when using multiple datasets as the model input.

Summary key points

This work assesses and compares the performance of three categories of workflow consisting of 350 analytical combinations for outcome prediction using multi-sample, multi-conditions single-cell studies.

We observed that using ensemble of feature types performs better than using individual feature type

We found that in the current data, all learning approaches including deep learning exhibit similar predictive performance. When combining multiple datasets as the input, our study found that integrating multiple datasets at the cell level performs similarly to simply concatenating the patient representation without modification.
High-resolution structural study on pyridin-3-yl ebselen and its N-methylated tosylate and iodide derivatives
Authors: Xu Ruyi , Fellowes Thomas , White Jonathan M.
Published: January 2023

The crystal structure of the pyridine-substituted benzisoselenazolinone 2-(pyridin-3-yl)-2,3-dihydro-1,2-benzoselenazol-3-one (C12H8N2OSe, 2), related to the antioxidant ebselen [systematic name: 2-phenyl-1,2-benzoselenazol-3(2H)-one, 1], is characterized by strong intermolecular N...Se(—N) chalcogen bonding, where the N...Se distance of 2.3831 (6) Å is well within the sum of the van der Waals radii for N and Se (3.34 Å). This strong interaction results in significant lengthening of the internal N—Se distance, consistent with significant population of the Se—N σ* antibonding orbital. Much weaker intermolecular O...Se chalcogen bonding occurs between the amide-like O atom in 2 and the less polarized C—Se bond in this structure. Charge density analysis of 2 using multipole refinement of high-resolution data allowed the electrostatic surface potential for 2 to be mapped, and clearly reveals the σ-hole at the extension of the Se—N bond as an area of positive electrostatic potential. Topological analysis of the electron-density distribution in 2 was carried out within the Quantum Theory of Atoms in Molecules (QTAIM) framework and revealed bond paths and (3,−1) bond critical points (BCPs) for the N...Se—N moiety consistent with a closed-shell interaction; however, the potential energy term is suggestive of electron sharing. Analysis of the electron localization function (ELF) for the strong N...Se and the weak O...Se chalcogen-bonding interactions in the structure of 2 suggest significant electron sharing in the former interaction, and a largely electrostatic interaction in the latter. Conversion of 2 to its N-methylated derivatives by reaction with methyl iodide [1-methyl-3-(3-oxo-2,3-dihydro-1,2-benzoselenazol-2-yl)pyridin-1-ium iodide, C13H11N2OSe+·I−] and methyl tosylate [1-methyl-3-(3-oxo-2,3-dihydro-1,2-benzoselenazol-2-yl)pyridin-1-ium toluenesulfonate trihydrate, C13H11N2OSe+·C7H7O3S−·3H2O] removes the possibility of N...Se chalcogen bonding and instead structures are obtained where the iodide and tosylate counter-ions fulfill the role of chalcogen-bond acceptors, with a strong I−...Se interaction in the iodide salt and a weaker p-Tol-SO3
−...Se interaction in the tosylate salt.
Social work in alcohol and other drug service navigation: supporting social complexity in dual diagnosis
Authors: Thomas Sally , Cotroneo Sophia , Pham Daniel , Kalogeropoulos Rosemary , Tyler Jonathan , Arunogiri Shalini
Published: January 2023

Purpose

Many people with dual diagnosis present with social complexity that impedes service access. The role of social work support in such service navigation is poorly understood. This study aims to characterise client presentations to an Australian telephone-based social work alcohol and other drug (AOD) service navigation and linkage program, with consideration of presentation complexity compared between those clients who present with or without self-reported mental health (MH) concerns and a history of MH diagnoses, to identify differences in baseline characteristics, and linkage outcomes.

Design/methodology/approach

A retrospective audit was conducted of routinely collected clinical information from a six-month period, selected to capture the social and health challenges experienced during the mid-pandemic period (mid-2021) in Victoria, Australia, during which a number of lockdowns resulted in a reliance on telephone-based services. The audit focused on client and presentation characteristics, and compared clients with and without a history of co-occurring MH and AOD concerns.

Findings

It was found that three in four people accessing an Australian telephone-based AOD service navigation and linkage program presented with dual diagnosis. Individuals with dual diagnosis required more support from the service compared to those without a co-occurring MH disorder; but overall, were just as likely to achieve a successful linkage to services, when offered holistic, long-term social work support.

Originality/value

This study focused on the role of social workers in this service navigation program in supporting individuals with complexity. It also highlights the challenges in operationalising social complexity factors alongside clinical MH and AOD diagnoses, and points to the need for further research to guide future service development for this vulnerable client group.
Social support on Reddit for antiretroviral therapy
Authors: Ming Yue
Published: January 2023

Purpose

Social media platforms such as Reddit can be used as a place for people with shared health problems to share knowledge and support. Previous studies have focused on the overall picture of how much social support people who live with HIV/AIDS (PLWHA) receive from online interactions. Yet, only few studies have examined the impact of social support from social media platforms on antiretroviral therapy (ART), which is a necessary lifelong therapy for PLWHA. This study used social support theory to examine related Reddit posts.

Design/methodology/approach

This study used content analysis to analyze ART-related Reddit posts. Each Reddit post was manually coded by two coders for social support type. A computational text analysis tool, Linguistic Inquiry and Word Count, was used to generate linguistic features. ANOVA analyses were conducted to compare differences in user engagement and well-being across the types of social support.

Findings

Results suggest that most of the posts were informational support posts, followed by emotional support posts and instrumental support posts. Results indicate that there are no significant differences within user engagement variables, but there are significant differences within several well-being variables including analytic score, clout score, health words usage and negative emotional words usage among social support types.

Originality/value

This study contributes to further understanding of social support theory in an online context used predominantly by a younger generation. Practical advice for public health researchers and practitioners is discussed.
Consumer psychology for food choices: a systematic review and research directions
Authors: Khan Abdul Wahid , Pandey Jatin
Published: January 2023

Purpose

Consumer food behavior has received considerable attention from marketers, researchers and regulators. With the rising obesity epidemic worldwide, the existing literature and previous reviews provide a limited understanding of consumers’ unhealthy food choices. To address this gap, this study aims to investigate consumer psychology for food choices in terms of mental processes and behavior.

Design/methodology/approach

This systematic literature review analyzed 84 research papers accessed from the Web of Science database and selected high-quality marketing journals. A detailed analysis identified themes arranged in an organizing framework. Gaps, limitations, convergence and ambivalent findings were noted to derive future research directions.

Findings

Major themes in the literature include food marketers’ actions (food stimuli and context), environmental influence (micro and macro) and consumer psychology and personal factors, leading to food choice related decisions. The antecedents and consequences of food choice healthiness are summarized. Several studies converged on the benefits of health motivations and goals, food literacy and customizing meals bottom-up on food choice healthiness.

Research limitations/implications

This review helps researchers gain state-of-the-art understanding on consumer psychology for food choices. It presents ambivalent and converging findings, gaps and limitations of extant research to inform researchers about issues that need to be addressed in the literature. This review presents future research questions to guide research on critical issues. This literature review contributes to marketing domain literature on consumer’s food well-being and overall well-being.

Practical implications

This review offers actionable insights for food marketers, policymakers and nongovernmental organizations to drive consumer demand for healthier foods, focusing on food labeling, food environment, message framing and raising consumer awareness.

Originality/value

This review offers current understanding of consumer psychology for food choices focusing on healthiness, an aspect lacking in previous literature reviews.
Analyzing hospitality leader–follower dyads with polynomial regression: a critical reflection
Authors: Shi Xiaolin (Crystal)
Published: January 2023

Purpose

Congruence serves as a key framework in many leader–follower dyad theories. This paper aims to introduce polynomial regression analysis with response surface methodology (PRA with RSM) as a statistical technique for investigating research questions concerning leader–follower dyadic relationships in the hospitality context.

Design/methodology/approach

First, this paper illustrates the necessity of applying PRA with RSM to more effectively address the research issues related to leader–follower dyadic relationships. Next, this paper presents an overview and the key concepts of PRA with RSM. Critical issues that need to be noted and two recent hospitality leadership studies that have used PRA with RSM are discussed. Third, an empirical example in the hotel context is provided to illustrate the application of PRA with RSM.

Findings

By applying this methodology to the study of hospitality leader–follower dyadic relationships, researchers will be able to address a range of topics related to dyadic theory, such as leader–member exchange and value congruence.

Practical implications

PRA with RSM reveals that congruence effects vary within leader–follower dyads. Industry professionals can promote a better leader–follower fit by incorporating dyadic surveys to understand mutual agreement and perceptions regarding same-workplace phenomena.

Originality/value

The paper addresses the misalignment between leader–follower dyadic theory and the methodology used in hospitality leadership studies.
Will consumers give us another chance to bounce back? Effects of precrisis commitments to social and product responsibility on brand resilience
Authors: Kang Jiyun , Faria Amy A. , Lee Judy , Choi Woo Jin
Published: January 2023

Purpose

Merely being known as a highly ethical or strong performer cannot shield a company from every kind of crisis. From product failures to environmental and social issues, a brand’s ability to manage crises and rapidly regain consumer trust is essential. This study aims to explore whether consumer perceptions of a brands’ prior commitments to two different areas of corporate responsibility (social and product responsibility) alleviate the postcrisis attribution of accountability and further build brand resilience, examining differences between two types of crisis situations – values versus performance crises.

Design/methodology/approach

A scenario-based online survey on product versus ethical labor issues was conducted. The data were collected from a highly valid, nationwide sample set of more than a thousand US consumers. Multigroup structural equation modeling was used as the primary data analysis method.

Findings

A brand’s precrisis commitment to social responsibility was found to decrease attribution of accountability across both types of crises. It also strengthened brand resilience, but this effect was more prevalent in a performance than a values crisis. The effects of precrisis commitment to product responsibility on brand resilience were minimal or insignificant across crisis types.

Originality/value

Previous research underexplores which types of corporate responsibility commitments provide a firm with a better protection against crises. This study significantly advances the knowledge regarding the type of commitments that can substantially increase brand resilience, which supports the rationale of making stronger commitments to social responsibility than to product responsibility. Practical insights are provided into how investments in corporate social responsibility help alleviate consumers’ negative perceptions during the outbreak of a brand crisis and build more brand muscle that enables resilience against future crises.
Banking service quality literature: a bibliometric review and future research agenda
Authors: Patel Ritesh J. , Siddiqui Aaliyah
Published: January 2023

Purpose

The purpose of this paper is to perform a meta-bibliometric analysis of the banking service quality and to provide various research streams. Another goal is to provide future research questions to explore these areas in more detail.

Design/methodology/approach

The authors used three major academic databases (Scopus, ProQuest and EBSCO) from 1980–2021 and found 226 papers, where they performed the meta-bibliometric analysis by performing co-citation analysis, co-authorship analysis, cartographic analysis and content analysis.

Findings

The SERVQUAL model is the most used conceptual framework and model to study banking service quality. Structural equation modeling (SEM), followed by partial least squares SEM, is a majorly used method. There are three research streams in the literature: retail banking service quality, internet banking service quality and mobile banking service quality. Retail banking is the most studied stream, whereas mobile banking is the least studied stream. The study on banking service quality was initially conducted in developed markets, and later in emerging markets. All three streams have scope for further exploration, and hence, 44 future research questions have also been proposed.

Research limitations/implications

This study has implications for bank managers, academicians and future researchers.

Originality/value

This study is unique in that it examines the meta-bibliometric dimensions of banking service quality and provides directions for future research for academicians and researchers.
A ‘Get‐Save‐Return’ process continuum runs on phosphorus economy among subtropical tree species
Authors: Jiang Lei , Wang Huimin , Li Shenggong , Dai Xiaoqin , Meng Shengwang , Fu Xiaoli , Yan Han , Zheng Jiajia , Ma Ning , Kou Liang
Published: January 2023

Plants allocate nutrients to new leaves via making a cost–benefit trade‐off between root nutrient absorption (‘get’) and leaf nutrient resorption (‘save’). This active trade‐off in nutrient acquisition pathways may cause a passive trade‐off between resorption and decomposition (‘return’). However, whether these nutrient‐associated processes are linked and form a ‘get‐save‐return’ (GSR) continuum, and its linkages with the above‐ground leaf economics spectrum (LES) and the below‐ground mycorrhizal association remain unclear.

Here, we present the first empirical evidence of a direct link among multiple nutrient‐associated processes and tested this continuum hypothesis by synchronously integrating root nutrient absorption, leaf nutrient resorption and leaf litter decomposition of 15 co‐occurring tree species hosting either arbuscular mycorrhizal or ectomycorrhizal fungi in subtropical forests of China.

Across species, there was an active trade‐off between phosphorus (P) absorption and resorption, which further caused a passive trade‐off between P resorption and leaf litter decomposition, indicating that the GSR continuum exists and runs on P economy. However, these processes associated with nitrogen economy were not well linked. Interestingly, the loading scores of species on the LES were positively correlated with root P absorption, negatively with leaf P resorption and positively with leaf litter decomposition. These linkages indicate that species running in the ‘fast lane’ had greater root P absorption, lower leaf P resorption and faster leaf litter decomposition than species running in the ‘slow lane’, and that the process‐based GSR continuum follows the trait‐based ‘fast‐slow’ LES. Furthermore, the continuum on P economy emerged evidently in the ectomycorrhizal tree species rather than in the arbuscular mycorrhizal tree species, indicating critical control of mycorrhizal association over the continuum.

Synthesis. Overall, these results demonstrate the existence of the GSR continuum on tree P economy, which conforms to the economics spectrum theory but varies with mycorrhizal association type. Our findings provide a process‐based framework for mechanistic understanding of the whole plant nutrient economy and ecosystem nutrient cycling, and facilitate improved predictions of biogeochemical models.
A long entanglement with nature: Flyfishers in the wild
Authors: Adedokun Busola Christianah , McHenry Melinda Therese , Kirkpatrick James Barrie
Published: January 2023

Large wild areas are important for both nature conservation and nature‐based recreation. Information on the reciprocal relationships between recreators and the environments in which they recreate can help both conservation and recreation management. We considered motivations, perceptions, environmental concerns, and social concerns among flyfishers who recreate within the Tasmanian Wilderness World Heritage Area on the Central Plateau of Tasmania, Australia. Using semi‐structured interviews with 27 participants, we established that they were motivated by a love of nature, desire for experience, escapism, connection, and challenge. On the basis of motivations and attitudes, we discriminated four groups of flyfishers: “social” (those who fish with friends), “trophy” (lone fishers who are goal‐oriented), “outdoor enthusiast” (those who enjoy the outdoor experience, fishing optional), and “hunter‐gatherer” (those prepared to travel long distances for catch). Nonetheless, all groups perceived environmental and social problems related to fishing and visitation behaviours, from littering to climate change. Fishers perceived environmental problems included identifying exotic weeds and pests but did not specifically include trout as a pest, despite their exotic status and adverse effects on native ecosystems. However, flyfishers were aware of most of their impacts and were willing to help mitigate them. Such insight is significant for geographers and those in associated disciplines and professions seeking to manage wild protected areas.