bluuebunny/crossref_metadata_2025 huggingface dataset:
TCR transgenic clone selection guided by immune receptor analysis and single cell RNA expression of polyclonal responders
Authors: Debeuf Nincy , Lameire Sahine , Vanheerswynghels Manon , Deckers Julie , De Wolf Caroline , Toussaint Wendy , Verbeke Rein , Verstaen Kevin , Hammad Hamida , Vanhee Stijn , Lambrecht Bart N.
Published: March 2024

Since the precursor frequency of naïve T cells is extremely low, investigating the early steps of antigen-specific T cell activation is challenging. To overcome this detection problem, adoptive transfer of a cohort of T cells purified from T cell receptor (TCR) transgenic donors has been extensively used but is not readily available for emerging pathogens. Constructing TCR transgenic mice from T cell hybridomas is a labor-intensive and sometimes erratic process, since the best clones are selected based on antigen-induced CD69 upregulation or IL-2 productionin vitro, and TCR chains are PCR-cloned into expression vectors. Here, we exploited the rapid advances in single cell sequencing and TCR repertoire analysis to select the best clones without hybridoma selection, and generated CORSET8 mice (CORonaSpikeEpitope specific CD8Tcell), carrying a TCR specific for the Spike protein of SARS-CoV-2. Implementing newly created DALI software for TCR repertoire analysis in single cell analysis enabled the rapid selection of the ideal responder CD8 T cell clone, based on antigen reactivity, proliferation and immunophenotypein vivo.Identified TCR sequences were inserted as synthetic DNA into an expression vector and transgenic CORSET8 donor mice were created. After immunization with Spike/CpG-motifs, mRNA vaccination or SARS-CoV2 infection, CORSET8 T cells strongly proliferated and showed signs of T cell activation. Thus, a combination of TCR repertoire analysis and scRNA immunophenotyping allowed rapid selection of antigen-specific TCR sequences that can be used to generate TCR transgenic mice.
Absolute quantification of rare gene targets in limited samples using crude lysate and ddPCR
Authors: Kaur Charandeep , Adams Stuart , Kibirige Catherine N , Asquith Becca
Published: March 2024

Background

Accurate quantification of rare genes from limited clinical samples is crucial for research purposes but is technically challenging. In particular, nucleic acid extraction for quantification of gene targets may lead to target loss. Here, we report the development and validation of a novel crude lysate ddPCR assay for the absolute quantification of rare genes, TRECs in our case, from infrequent cells, that removes the need for DNA extraction, hence minimizing the target loss.

Methods

The analytical validation was performed on PBMCs extracted from the blood of healthy donors. Standard ddPCR was first optimized to detect TREC copies/cell and then applied to a crude lysate ddPCR assay. The assay was optimized by varying several steps. The optimised assay was directly compared to standard ddPCR and the performance of the assay quantified.

Results

The newly developed assay showed good agreement with the standard ddPCR assay in the range from 0.0003 to 0.01 TRECs/cell. The assay had a limit of quantification of <0.0003 TRECs/cell and a limit of detection of <0.0001 TRECs/cell; this performance is favourable compared to standard ddPCR. The intra-assay variation was low. This method can also be applied to fixed and permeabilized cells.

Conclusions

The newly developed crude lysate ddPCR assay for quantifying rare targets from limited samples has high accuracy, specificity, and reproducibility; additionally, it eliminates the need for DNA extraction for absolute quantification. The assay has the potential to be used for quantification of other trace targets from small samples.
Genome-wide association study elucidates the genetic architecture of manganese tolerance inBrassica napus
Authors: Raman Harsh , Bai Zetao , McVittie Brett , Mukherjee Sourav , Goold Hugh D , Zhang Yuanyuan , Khin Nay Chi , Qiu Yu , Liu Shengyi , Delourme Regine , Pogson Barry , Balasubramanian Sureshkumar , Raman Rosy
Published: March 2024

Brassica napus(canola) is a significant contributor to the world’s oil production and is cultivated across continents, yet acidic soils with Al3+and Mn2+toxicities limit its production. The genetic determinants underlying acidic soil tolerance in canola are unknown and require to be uncovered for canola breeding and production. Here, through comprehensive phenotyping, whole genome resequencing, and genome-wide association analysis, we identified three QTLs for tolerance to Mn2+toxicity on chromosomes A09, C03, and C09. Allelism tests between four tolerance sources confirmed that at least one locus on A09 controls Mn2+tolerance inB. napus. Integrated analysis of genomic and expression QTL and Mn2+tolerance data reveals thatBnMTP8.A09,in conjunction withBnMATE.C03,BnMTP8.C04andBnMTP8.C08, play a central role in conferring Mn2+tolerance inB. napus. Gene expression analysis revealed a high correlation (R2= 0.74) between Mn2+tolerance and theBnMTP8.A09expression. Yeast complementation assays show thatBnMTP8.A09can complement manganese-hypersensitive yeast mutant strainPMR1Δ and restore Mn2+tolerance to wild-type levels. Inductively coupled plasma mass spectrometry revealed that Mn2+tolerant accessions accumulate less Mn in the shoots compared to Mn2+sensitives, suggesting that theBnMTP8.A09transporter likely sequesters Mn2+into the tonoplast. Taken together, our research unveils the genetic architecture of Mn2+tolerance and identifiesBnMTP8.A09as a major gene imparting tolerance to Mn2+toxicity inB. napus.
Targeted proteomics addresses selectivity and complexity of protein degradation by autophagy
Authors: Leytens Alexandre , Benítez-Fernández Rocío , Jiménez-García Carlos , Roubaty Carole , Stumpe Michael , Boya Patricia , Dengjel Jörn
Published: March 2024

Autophagy is a constitutively active catabolic lysosomal degradation pathway, often found dysregulated in human diseases. It is often considered to act in a cytoprotective manner and is commonly upregulated in cells undergoing stress. Its initiation is regulated at the protein level and does not requirede novoprotein synthesis. Historically, autophagy has been regarded as non-selective; however, it is now clear that different stimuli can lead to the selective degradation of cellular components via selective autophagy receptors (SARs). Due to its selective nature and the existence of multiple degradation pathways potentially acting in concert, monitoring of autophagy flux,i.e.selective autophagy-dependent protein degradation, should address this complexity. Here, we introduce a targeted proteomics approach monitoring abundance changes of 37 autophagy-relevant proteins covering process-relevant proteins such as the initiation complex and the ATG8 lipidation machinery, as well as most known SARs. We show that proteins involved in autophagosome biogenesis are upregulated and spared from degradation under autophagy inducing conditions in contrast to SARs. Classical bulk stimuli such as nutrient starvation mainly induce degradation of ubiquitin-dependent soluble SARs and not of ubiquitin-independent, membrane-bound SARs. In contrast, treatment with the iron chelator deferiprone leads to the degradation of ubiquitin-dependent and - independent SARs linked to mitophagy and reticulophagy/ER-phagy. Our approach is automatable and supports large-scale screening assays paving the way to (pre)clinical applications and monitoring of specific autophagy fluxes.
A Novel Dual Probe-based Method for Mutation Detection using Isothermal Amplification
Authors: Nandu Nidhi , Miller Michael , Tong Yanhong , Lu Zhi-xiang
Published: March 2024

Cost efficient and rapid detection tools to detect mutations especially those linked to drug-resistance are important to address concerns of the rising multi-drug resistance infections. Here we integrated dual probes, namely a calibrator probe and an indicator probe, into isothermal amplification detection system. These two probes are designed to bind distinct regions on the same amplicon to determine the presence or absence of mutation. The calibrator probe signal is used as an internal signal calibrator for indicator probe which detects the presence or absence of the mutation. As an illustrative example, we evaluated the applicability of this dual probe method for detecting mutations associated with rifampicin (RIF) drug resistance at codons 516, 526 and 531 of the rpoB gene inMycobacterium tuberculosis. In this assessment, we examined 127 artificial samples comprising wild type and mutant target sequences with single or multiple mutations. Our results demonstrated 100% accuracy of both wild type and mutant samples for mutations at codons 526 and 531. As regards to mutations at codon 516, the wild type was identified with 100% accuracy, while the mutant type was identified with 95% accuracy. Moreover, when we extended our evaluation using the Zeptometrix MTB Verification panel, our dual probe method correctly differentiated between the wild type and mutant, and identified the RIF-mutant strain which harbors mutations at codon 531 of the rpoB gene. Our isothermal mutation detection system, relying on dual probes exhibits a versatile approach. With the capability to identify mutations without prior knowledge of their specific mutation direction, our dual-probe method shows significant promise for applications in drug resistance nucleic acid testing, particularly in resource-limited settings.
Molecular basis for condensin enrichment at pericentromeres
Authors: Wang Menglu , Zou Juan , Spanos Christos , Rappsilber Juri , Marston Adele L.
Published: March 2024

Faithful chromosome segregation requires packaging of the genome on both global and local scales. Condensin plays a crucial role at pericentromeres to resist spindle forces and ensure the bioriented attachment of kinetochores to microtubules in mitosis. Here we demonstrate that budding yeast condensin is recruited to pericentromeres through a direct interaction between its Ycg1 subunit and the pericentromeric adaptor protein, shugoshin (Sgo1). We identify a Short Linear Motif (SLiM), termed CR1, within the C-terminal region of Sgo1 which inserts into a conserved pocket on Ycg1. Disruption of this interface abolishes the Sgo1-condensin interaction, prevents condensin recruitment to pericentromeres and results in defective sister kinetochore biorientation in mitosis. Similar motifs to CR1 are found in known and potential condensin binding partners and the Ycg1 binding pocket is broadly conserved, including in the mammalian homolog CAP-G. Overall, we uncover the molecular mechanism that targets condensin to define a specialized chromosomal domain.
Membrane vesicles can contribute to cellulose degradation byTeredinibacter turnerae,a cultivable intracellular endosymbiont of shipworms
Authors: Gasser Mark T. , Liu Annie , Altamia Marvin , Brensinger Bryan R. , Brewer Sarah L. , Flatau Ron , Hancock Eric R. , Preheim Sarah P. , Filone Claire Marie , Distel Dan L.
Published: March 2024

Teredinibacter turneraeis a cultivable cellulolytic Gammaproteobacterium (Cellvibrionaceae) that commonly occurs as an intracellular endosymbiont in the gills of wood-eating bivalves of the family Teredinidae (shipworms). The genome ofT. turneraeencodes a broad range of enzymes that deconstruct cellulose, hemicellulose, and pectin and contribute to wood (lignocellulose) digestion in the shipworm gut. However, the mechanisms by whichT. turneraesecretes lignocellulolytic enzymes are incompletely understood. Here, we show thatT. turneraecultures grown on carboxymethyl cellulose (CMC) produce membrane vesicles (MVs) that include a variety of proteins identified by LC-MS/MS as carbohydrate-active enzymes (CAZymes) with predicted activities against cellulose, hemicellulose, and pectin. Reducing sugar assays and zymography confirm that these MVs exhibit cellulolytic activity, as evidenced by the hydrolysis of CMC. Additionally, these MVs were enriched withTonB-dependent receptors, which are essential to carbohydrate and iron acquisition by free-living bacteria. These observations indicate a potential role for MVs in lignocellulose utilization byT. turneraein the free-living state, suggest possible mechanisms for host-symbiont interaction, and may be informative for commercial applications such as enzyme production and lignocellulosic biomass conversion.
Membrane curvature association of amphipathic helix 8 drives constitutive endocytosis of GPCRs
Authors: Schmidt Jan Hendrik , Herlo Rasmus , Rombach Joscha , Larsen Andreas Haahr , Stoklund Mikkel , Perslev Mathias , Nielsen Tommas Theiss Ehlers , Andersen Keenie Ayla , Herenbrink Carmen Klein , Lycas Matthew D. , Ejdrup Aske Lykke , Christensen Nikolaj Riis , Christensen Jan P. , Salman Mootaz , Herborg Freja , Gether Ulrik , Hauser Alexander Sebastian , Bassereau Patricia , Perrais David , Madsen Kenneth Lindegaard
Published: March 2024

Cellular signaling relies on the activity of transmembrane receptors and their presentation on the cellular surface. Their continuous insertion in the plasma membrane is balanced by constitutive and activity dependent internalization, which is orchestrated by adaptor proteins recognizing semi-specific motifs within the receptors’ intracellular regions. Here we describe a complementary and evolutionary conserved and refined trafficking mechanism for G-protein coupled receptors (GPCR). This mechanism relies on the insertion of their amphipathic helix 8 into the inner leaflet of lipid membranes, orthogonal to the transmembrane helices. These amphipathic helices dictate subcellular localization of the receptors and autonomously drive their endocytosis by cooperative assembly and association with areas of high membrane curvature. The strength of helix 8 membrane insertion propensity quantitatively predicts the rate of constitutive internalization of GPCRs. This discovery advances our understanding of membrane protein trafficking and highlights a new principle of receptor-lipid interactions that may have broader implications for cellular signaling and therapeutic targeting.

One-Sentence Summary

Receptor proteins navigate cellular membranes by interacting with their curvature using an evolutionary conserved mechanism that relies on amphipathic helices and complements direct coupling to the endocytic protein machinery.
Calculating Structure Factors of Protein Solutions by Atomistic Modeling of Protein-Protein Interactions
Authors: Qin Sanbo , Zhou Huan-Xiang
Published: March 2024

We present a method, FMAPS(q), for calculating the structure factor,S(q), of a protein solution, by extending ourfast Fourier transform-basedmodeling ofatomisticprotein-protein interactions (FMAP) approach. The interaction energy consists of steric, nonpolar attractive, and electrostatic terms that are additive among all pairs of atoms between two protein molecules. In the present version, we invoke the free-rotation approximation, such that the structure factor is given by the Fourier transform of the protein center-center distribution functiongC(R). At low protein concentrations,gC(R) can be approximated ase−βW(R), whereW(R) is the potential of mean force along the center-center distanceR. We calculateW(R) using FMAPB2, a member of the FMAP class of methods that is specialized for the second virial coefficient [Qin and Zhou, J Phys Chem B 123 (2019) 8203-8215]. For higher protein concentrations, we obtainS(q) by a modified random-phase approximation, which is a perturbation around the steric-only energy function. Without adjusting any parameters, the calculated structure factors for lysozyme and bovine serum albumin at various ionic strengths, temperatures, and protein concentrations are all in reasonable agreement with those measured by small-angle X-ray or neutron scattering. This initial success motivates further developments, including removing approximations and parameterizing the interaction energy function.
Molecular Basis for RNA Cytidine Acetylation by NAT10
Authors: Zhou Mingyang , Gamage Supuni Thalalla , Tran Khoa A. , Bartee David , Wei Xuepeng , Yin Boyu , Berger Shelley , Meier Jordan L. , Marmorstein Ronen
Published: March 2024

Human NAT10 acetylates the N4 position of cytidine in RNA, predominantly on rRNA and tRNA, to facilitate ribosome biogenesis and protein translation. NAT10 has been proposed as a therapeutic target in cancers as well as aging-associated pathologies such as Hutchinson-Gilford Progeria Syndrome (HGPS). The ∼120 kDa NAT10 protein uses its acetyl-CoA-dependent acetyltransferase, ATP-dependent helicase, and RNA binding domains in concert to mediate RNA-specific N4-cytidine acetylation. While the biochemical activity of NAT10 is well known, the molecular basis for catalysis of eukaryotic RNA acetylation remains relatively undefined. To provide molecular insights into the RNA-specific acetylation by NAT10, we determined the single particle cryo-EM structures ofChaetomium thermophilumNAT10 (CtNAT10) bound to a bisubstrate cytidine-CoA probe with and without ADP. The structures reveal that NAT10 forms a symmetrical heart-shaped dimer with conserved functional domains surrounding the acetyltransferase active sites harboring the cytidine-CoA probe. Structure-based mutagenesis with analysis of mutantsin vitrosupports the catalytic role of two conserved active site residues (His548 and Tyr549 inCtNAT10), and two basic patches, both proximal and distal to the active site for RNA-specific acetylation. Yeast complementation analyses and senescence assays in human cells also implicates NAT10 catalytic activity in yeast thermoadaptation and cellular senescence. Comparison of the NAT10 structure to protein lysine and N-terminal acetyltransferase enzymes reveals an unusually open active site suggesting that these enzymes have been evolutionarily tailored for RNA recognition and cytidine-specific acetylation.
Extracellular biosynthesis of silver nanoparticles using cell suspension ofRhodococcus fascians
Authors: Ghadamgahi Farideh , Konakalla Naga Charan , Sang Atash Masome Mehraban , Ortiz Rodomiro , Vetukuri Ramesh
Published: March 2024

Biosynthesis of metallic nanoparticles using biological systems such as bacteria has become an important nanobiotechnology area. In this report, we present the first extracellular biosynthesis of silver nanoparticles (AgNPs) using the gram-positive bacteriumRhodococcus fascians. The AgNPs underwent characterization through various analytical techniques, encompassing UV–visible spectroscopy, X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), Transmission electron microscopy (TEM) and Scanning electron microscopy (SEM). UV-visible spectroscopy revealed the emergence of an absorbance peak at 430 nm due to the synthesis of AgNPs.R. fasciansstarted producing AgNPs after 12 h of incubation, with the highest yield after 48 h. The extent of synthesis was higher when cultures were grown in the dark than in the light. According to TEM and SEM, the AgNPs had a uniform spherical morphology of diameter 10–80 nm. The AgNPs exhibited antifungal efficacy against the virulent filamentous fungiRhizoctonia solani, Botrytis cinerea, andFusarium graminearum, which cause root rot, soft rot and head blight on plants, respectively. This research provides evidence on the ability ofR. fasciansto generate AgNPs from silver nitrate, as well as their subsequent assembly and potential for controlling vascular wilt disease.
Assembling bacterial puzzles: piecing together functions into microbial pathways
Authors: Chung Henri , Friedberg Iddo , Bromberg Yana
Published: March 2024

Functional metagenomics enables the study of unexplored bacterial diversity, gene families, and pathways essential to microbial communities. However, discovering biological insights with these data is impeded by the scarcity of quality annotations. Here, we use a co-occurrence-based analysis of predicted microbial protein functions to uncover pathways in genomic and metagenomic biological systems. Our approach, based on phylogenetic profiles, improves the identification of functional relationships, or participation in the same biochemical pathway, between enzymes over a comparable homology-based approach. We optimized the design of our profiles to identify potential pathways using minimal data, clustered functionally related enzyme pairs into multi-enzymatic pathways, and evaluated our predictions against reference pathways in KEGG. We then demonstrated a novel extension of this approach to predict inter-bacterial protein interactions amongst members of a marine microbiome. Most significantly, we show our method predicts emergent biochemical pathways between known and unknown functions. Thus, our work establishes a basis for identifying the potential functional capacities of the entire metagenome, capturing previously unknown and abstract functions into discrete putative pathways.
The Molecular Architecture of the Nuclear Basket
Authors: Singh Digvijay , Soni Neelesh , Hutchings Joshua , Echeverria Ignacia , Shaikh Farhaz , Duquette Madeleine , Suslov Sergey , Li Zhixun , van Eeuwen Trevor , Molloy Kelly , Shi Yi , Wang Junjie , Guo Qiang , Chait Brian T. , Fernandez-Martinez Javier , Rout Michael P. , Sali Andrej , Villa Elizabeth
Published: March 2024

The nuclear pore complex (NPC) is the sole mediator of nucle-ocytoplasmic transport. Despite great advances in understanding its conserved core architecture, the peripheral regions can exhibit considerable variation within and between species. One such structure is the cage-like nuclear basket. Despite its crucial roles in mRNA surveillance and chromatin organization, an architectural understanding has remained elusive. Using in-cell cryo-electron tomography and subtomogram analysis, we explored the NPC’s structural variations and the nuclear basket across fungi (yeast;S. cerevisiae), mammals (mouse;M. musculus), and protozoa (T. gondii). Using integrative structural modeling, we computed a model of the basket in yeast and mammals that revealed how a hub of Nups in the nuclear ring binds to basket-forming Mlp/Tpr proteins: the coiled-coil domains of Mlp/Tpr form the struts of the basket, while their unstructured termini constitute the basket distal densities, which potentially serve as a docking site for mRNA preprocessing before nucleocytoplasmic transport
Effects of iron on cardiovascular, kidney and safety outcomes in patients with chronic kidney disease: a systematic review and meta-analysis
Authors: Chan Bernard , Varghese Amanda , Badve Sunil V , Pecoits-Filho Roberto , Guedes Murilo , Arnott Clare , Kozor Rebecca , O’Lone Emma , Jun Min , Kotwal Sradha , Block Geoffrey A , Chertow Glenn M. , Solomon Scott D , Vaduganathan Muthiah , Neuen Brendon L.
Published: March 2024

Background and aims

Heart failure and chronic kidney disease (CKD) are closely linked, with iron deficiency being highly prevalent in both conditions. Yet, major cardiovascular and nephrology guidelines offer contrasting recommendations on the use of iron. We evaluated the effects of iron versus usual care/placebo on clinical outcomes in patients with CKD.

Methods

We conducted a systematic review and meta-analysis of randomised trials of intravenous or oral iron in CKD (PROSPERO CRD42023453468). We searched Medline, Embase and the Cochrane Register from database inception until February 1, 2024 to identify eligible trials. We determined results overall and stratified by dialysis- and non-dialysis-requiring CKD using random effects models, with certainty of evidence assessed using the Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach. The primary composite endpoint was heart failure hospitalisation or cardiovascular death.

Results

We identified 45 trials that met our inclusion criteria. Compared to usual care/placebo, iron reduced the risk of the primary composite endpoint (1659 events; RR 0.84, 95% CI 0.75-0.94; moderate certainty) an effect consistent across dialysis and non-dialysis requiring CKD (P-heterogeneity=0.70). The effect on the primary endpoint appeared driven by both components of hospitalisation for heart failure (RR 0.77; 95% CI 0.61-0.96; moderate certainty) and cardiovascular death (RR 0.81; 95% CI 0.65-1.02; low certainty). The incidence of serious adverse events was lower for iron compared to usual care/placebo (RR 0.90, 95% CI 0.82-0.98; moderate certainty; P-heterogeneity=0.09).

Conclusion

Iron therapies may reduce the risk of heart failure or cardiovascular death in patients with CKD. Randomised rials evaluating effects of iron on clinical outcomes are needed, especially in non-dialysis CKD, with or without anaemia.
Associations of employment status, working time and job satisfaction with sleep duration and sleep quality among the Japanese 50+ population
Authors: Wels Jacques , Fu Rong
Published: March 2024

Background

Few studies have captured the relationship between employment status, working time and job satisfaction and sleep duration and quality in Japan where poor sleep quality and low sleep duration are major public health concerns.

Methods

We use four waves from the Japan Study of Aging and Retirement (JSTAR) to assess the relationship between employment status and self-reported job satisfaction and sleep duration and self-reported sleep quality. We control for socio-demographic characteristics, working time and self-reported measures of health. The initial sample includes 7,082 respondents. We use mixed effects modified Poisson regression for binary outcomes for sleep quality and linear mixed effects for sleep duration and multiple imputations to correct for sample attrition.

Results

No major difference is observed between employment status and poor sleep quality except for housekeepers (0.123 [ 95%CI: 0.041; 0.205]) in comparison with full-time employed workers. All categories of workers tend to report sleeping longer than full-time employees with higher hours among those who retired (0.339 [95%CI: 0.218; 0.460]). Poor job satisfaction is associated with higher risks of self-reported poor sleep quality (0.230 [95%CI: 0.040, 0.421]) and waking up at night (0.362 [95%CI: 0.025, 0.699]) but the associations fade away when controlling for other health measurements (respectively, −0.137 [95%CI: −0.328, 0.054] and 0.092 [95%CI: −0.248; 0.432]).

Conclusion

Retirement increases sleep duration without improving sleep quality and housekeepers sleep longer but with poorer sleep quality. Job satisfaction is a major cofounder of sleep quality among the workforce but the effect is mediated by physical and mental health levels.
Mitochondrial genome variation affects humoral and cell-mediated innate immune responses and infection outcomes
Authors: Salminen Tiina S. , Vesala Laura , Basikhina Yuliya , Kutzer Megan , Tuomela Tea , Lucas Ryan , Monteith Katy , Prakash Arun , Tietz Tilman , Vale Pedro F.
Published: March 2024

The role of mitochondria in both adaptive and innate immune responses is increasingly recognized, but the role of mitochondrial DNA (mtDNA) variation as an immunomodulatory factor has received less attention. One reason for this is the difficulty of separating the effect of mtDNA from that of the nuclear genome. By utilizing the fruit flyDrosophila melanogaster, a powerful model system, we created cytoplasmic hybrids, aka. cybrid lines, where unique mtDNAs (mitotypes) were introgressed into a controlled isogenic nuclear background. We harnessed a panel of cybrid lines to study the effect of mtDNA variation on humoral and cell-mediated innate immune responses. Mitotypes exhibited heterogeneity in infection outcomes upon bacterial, viral and parasitoid infections. One mitotype of note (mtKSA2) was more immunocompetent when compared to other mitotypes. We performed transcriptomic profiling of uninfected and infected flies to find the mechanistic basis of the immunocompetence of the mtKSA2 line. We found that in uninfected flies mtKSA2 caused an upregulation of oxidative phosphorylation (OXPHOS) and tricarboxylic acid cycle (TCA) related genes and a downregulation of a set of antimicrobial peptides (AMPs). Upon infection, mtKSA2 flies produced transcriptomic changes that were infection type and duration specific. When we examined immune cells (hemocytes) in mtKSA2 larvae, we noted an increase in hemocyte numbers. These hemocytes were activated in the absence of infection, increased their production of ROS, and showed evidence of increased encapsulation efficiency upon parasitoid wasp infection. Overall, our results show that mtDNA variation acts as an immunomodulatory factor in both humoral and cell-mediated innate immunity and that specific mitotypes can provide enhanced protection against various infections.
Updated analyses of gluon distribution functions for the pion and kaon from the gauge-invariant nonlocal chiral quark model
Authors: Hutauruk Parada. T. P. , Nam Seung-il
Published: March 2024

In this work, we investigate the gluon distribution functions for the pion and kaon, in addition to the improved result of the valence-quark ones, in the gauge-invariant nonlocal chiral-quark model, in which the momentum dependence of the quark interactions is properly taken into account. We then analyze the gluon distribution functions, generated dynamically through the splitting functions in the Dokshitzer-Gribov-Lipatov-Altarelli-Parisi QCD evolution. By comparing with the recent lattice QCD results and Jefferson Lab angular momentum global analyses, it is found that the present numerical results for the gluon parton distribution functions for the pion exhibit a good agreement and the valence up-quark distribution results for the pion by reproducing the reanalyzed experimental data with a remarkable agreement. Our prediction on the gluon distribution functions for the kaon is also consistent with the recent lattice data for the kaon within the errors.

Published by the American Physical Society
2024
Effect of micro-particles on cavitation erosion behavior of 2Cr3WMoV steel
Authors: Zhao Han , Ding Qingmiao , Li Yaozhi , Cui Yanyu , Luo Junjie
Published: March 2024

Purpose

This paper aims to study the influence of microparticles on the surface cavitation behavior of 2Cr3WMoV steel; microparticle suspensions of different concentration, particle size, material and shape were prepared based on ultrasonic vibration cavitation experimental device.

Design/methodology/approach

2Cr3WMoV steel was taken as the research object for ultrasonic cavitation experiment. The morphology, quantity and distribution of cavitation pits were observed and analyzed by metallographic microscope and scanning electron microscope.

Findings

The study findings showed that the surface cavitation process produced pinhole cavitation pits on the surface of 2Cr3WMoV steel. High temperature in the process led to oxidation and carbon precipitation on the material surface, resulting in the “rainbow ring” cavitation morphology. Both the concentration and size of microparticles affected the number of pits on the material surface. When the concentration of microparticles was 1 g/L, the number of pits reached the maximum, and when the size of microparticles was 20 µm, the number of pits reached the minimum. The microparticles of Fe3O4, Al2O3, SiC and SiO2 all increased the number of pits on the surface of 2Cr3WMoV steel. In addition, the distribution of pits of spherical microparticles was more concentrated than that of irregularly shaped microparticles in turbidity.

Originality/value

Most of the current studies have not systematically focused on the effect of each factor of microparticles on the cavitation behavior when they act separately, and the results of the studies are more scattered and varied. At the same time, it has not been found to carry out the study of microparticle cavitation with 2Cr3WMoV steel as the research material, and there is a lack of relevant cavitation morphology and experimental data.
Assessing the asymmetric cost behavior in China
Authors: Shan Yuxin , Richardson Vernon J. , Cheng Peng
Published: March 2024

Purpose

A country’s institutional environment influences every facet of its business. This paper aims to identify institutional factors (state ownership, government attention on employment and employees’ educational background) that affect the asymmetric cost behavior in China.

Design/methodology/approach

Using 2,570 listed firms’ data between 2002 and 2015, we use empirical models to explore the effects of state ownership, government attention on employment and employees’ educational background on the asymmetric cost behavior in China.

Findings

This study found that the asymmetric cost behavior of central state-owned enterprises (CSOEs) is greater than local state-owned enterprises (LSOEs). Meanwhile, the empirical results show that government attention on employment is reflected in five-year government plans, and employees’ educational backgrounds are positively associated with asymmetric cost behavior.

Originality/value

This study contributes to the economic theory of sticky costs, institutional theory and asymmetric cost behavior literature by providing evidence that shows how government intervention and employee educational background limit the flexibility of corporate cost adjustments. Additionally, this study provides guidance to policymakers by showing how government long-term plans affect firm-level resource adjustment decisions.
Investigating the effect of augmented reality packaging on behavioral intentions in traditional Iranian nougat GAZ packaging
Authors: Tabaeeian Reihaneh Alsadat , Hossieni Farzaneh Alsadat , Fatehi Maedeh , Forghani Tehrani Alireza
Published: March 2024

Purpose

The purpose of the study is to investigate the effect of augmented reality (AR) characteristics in packaging on perceived value and consumer behavioral intentions such as purchase intention and pay more in traditional Iranian nougat GAZ packaging.

Design/methodology/approach

The statistical population was the 550 customers bought traditional Iranian nougat GAZ. Sampling method was simple random sampling. Questionnaire had been chosen for collecting data. In total, 236 customers filled in questionnaires. Research model tested by structural equation modeling method and by using SPSS and PLS software.

Findings

The finding considered the characteristics of AR packaging which include interactivity, informativeness, enjoyment and usefulness have a positive effect on the dimensions of the perceived value, hedonic and utilitarian value. In the same way hedonic and utilitarian value had positive effects on the consumer behavior, purchase intention and willingness to pay more.

Originality/value

These results help managers to use AR characteristics to improve the interaction between customers and product and sell their products.
Mixed ownership reform and non-state-owned enterprise innovation: Evidence from China
Authors: Ling Runze , Pan Ailing , Xu Lei
Published: March 2024

Purpose

This study examines the impact of China’s mixed-ownership reform on the innovation of non-state-owned acquirers, with a particular focus on the impact on firms with high financing constraints, low-quality accounting information or less tangible assets.

Design/methodology/approach

We use a proprietary dataset of firms listed on the Shanghai and Shenzhen Stock Exchanges to investigate the impact of mixed ownership reform on non-state-owned enterprise (non-SOE) innovation. We employ regression analysis to examine the association between mixed ownership reform and firm innovation.

Findings

The study finds that non-state-owned firms can improve innovation by acquiring equity in state-owned enterprises (SOEs) under the reform. Eased financing constraints, lowered financing costs, better access to tax incentives or government subsidies, lowered agency costs, better accounting information quality and more credit loans are underlying the impact. Additionally, cross-ownership connections amongst non-SOE executives and government intervention strengthen the impact, whilst regional marketisation weakens it.

Originality/value

This study adds to the literature on the association between mixed ownership reform and firm innovation by focussing on the conditions under which this impact is stronger. It also sheds light on the policy implications for SOE reforms in emerging economies.
Does supply chain concentration promote or inhibit corporate R&D investment?
Authors: Zhao Shukuan , Fan Xueyuan , Shao Dong , Wang Shuang
Published: March 2024

Purpose

This study aims to investigate the impact of supply chain concentration (SCC) on corporate research and development (R&D) investment and determine the moderating roles of industry concentration and financing constraints on the relationship between SCC and R&D investment.

Design/methodology/approach

The study collected data from Chinese listed companies, used the fixed effects model to test the research hypotheses and further used the two-stage Heckman test and propensity score matching (PSM) to address potential endogeneity issues.

Findings

The result reveals a negative impact of SCC on corporate R&D investment. In addition, industry concentration mitigates the negative impact of SCC on corporate R&D investment, but financing constraints strengthen the negative impact.

Originality/value

This study introduces the concept of SCC and empirically tests its effect on R&D investment, further explaining the lack of corporate innovation. This study inspires companies to strengthen SC management and weigh the level of SCC with environmental factors.
Navigating multiple institutional environments: institutional quality and the role of Belt and Road Initiative on location choice of Chinese MNEs
Authors: Zhang Ya’nan , Li Xuxu , Su Yiyi
Published: March 2024

Purpose

This study aims to explore the extent to which Chinese multinational enterprises (MNEs) rely on supranational institution – the Belt and Road Initiative (BRI) – versus host country institutional quality to navigate their foreign location choice.

Design/methodology/approach

This study uses a conditional logit regression model using a sample of 1,302 greenfield investments by Chinese MNEs in 54 BRI participating countries during the period 2011–2018.

Findings

The results indicate that as a supranational institution, the BRI serves as a substitution mechanism to address the deficiencies in institutional quality in BRI participating countries, thereby attracting Chinese MNEs to invest in those countries. In addition, the BRI’s substitution effect on host country institutional quality is more pronounced for large MNEs, MNEs in the manufacturing industry and MNEs in inland regions.

Originality/value

This study expands the understanding of the BRI as a supranational institution for MNEs from emerging markets and reveals its substitution effect on the host country institutional quality. Furthermore, it highlights that MNEs with diverse characteristics gain varying degrees of benefits from the BRI.
Understanding the manufacturing reshoring decision-making content through the lens of the Eclectic Paradigm: a systematic literature review
Authors: Li Haihan , Hilletofth Per , Eriksson David , Tate Wendy
Published: March 2024

Purpose

This study aims to investigate the manufacturing reshoring decision-making content from an Eclectic Paradigm perspective.

Design/methodology/approach

Data were collected through a six-step systematic literature review on factors influencing manufacturing reshoring decision-making. The review is based on 100 peer-reviewed journal papers discussing reshoring decision-making contents published from 2009 to 2022.

Findings

In total, 80 decision factors were extracted and then categorized into resource-seeking (8%), market-seeking (11%), efficiency-seeking (41%) and strategic asset-seeking (16%) advantages. Additionally, 24% of these were identified as hybrid, which means that they were classified into multiple categories. Some decision factors were further identified as reshoring influencing factors (i.e. drivers, enablers and barriers).

Research limitations/implications

Scholars need to consider what other theories can be used or developed to identify and evaluate the decision factors (determinants) of manufacturing reshoring as well as how currently adopted theory can be further advanced to create clearer and comprehensive theoretical frameworks.

Practical implications

This research underscores the importance of developing clearer and more comprehensive theoretical frameworks. For practitioners, understanding the multifaceted nature of decision factors could enhance strategic decision-making regarding reshoring initiatives.

Originality/value

To the best of the authors’ knowledge, this is the first study to investigate the value and practicality of the Eclectic Paradigm in categorizing factors in manufacturing reshoring decision-making content and presents in-depth theoretical classifications. In addition, it bridges the gap between decision factors and influencing factors in the decision-making content research realm.
Automated compliance checking for BIM models based on Chinese-NLP and knowledge graph: an integrative conceptual framework
Authors: Li Sihao , Wang Jiali , Xu Zhao
Published: March 2024

Purpose

The compliance checking of Building Information Modeling (BIM) models is crucial throughout the lifecycle of construction. The increasing amount and complexity of information carried by BIM models have made compliance checking more challenging, and manual methods are prone to errors. Therefore, this study aims to propose an integrative conceptual framework for automated compliance checking of BIM models, allowing for the identification of errors within BIM models.

Design/methodology/approach

This study first analyzed the typical building standards in the field of architecture and fire protection, and then the ontology of these elements is developed. Based on this, a building standard corpus is built, and deep learning models are trained to automatically label the building standard texts. The Neo4j is utilized for knowledge graph construction and storage, and a data extraction method based on the Dynamo is designed to obtain checking data files. After that, a matching algorithm is devised to express the logical rules of knowledge graph triples, resulting in automated compliance checking for BIM models.

Findings

Case validation results showed that this theoretical framework can achieve the automatic construction of domain knowledge graphs and automatic checking of BIM model compliance. Compared with traditional methods, this method has a higher degree of automation and portability.

Originality/value

This study introduces knowledge graphs and natural language processing technology into the field of BIM model checking and completes the automated process of constructing domain knowledge graphs and checking BIM model data. The validation of its functionality and usability through two case studies on a self-developed BIM checking platform.
Investigation of the effect of laser technology on the color of polyester fabrics
Authors: Atav Rıza , Çolakoğlu Özge
Published: March 2024

Purpose

The purpose of this study is to determine the effect of laser treatment on disperse dye-uptake and fastness values of polyester fabrics. Furthermore, it was aimed to evaluate colors directly over the photos of fabric samples instead of color measuring with spectrophotometer which is thought to be useful in terms of online digital color assessment.

Design/methodology/approach

In this study, 100% polyester (150 denier) single jersey knitted fabrics (weight: 145 g/m2, course density: 15 loops/cm, wale density: 24 loops/cm) were used in the trials. The effect of laser treatments before and after dyeing on color was investigated. Laser treatments were applied to fabrics at different resolutions (20, 25 and 30 dpi) and pixel times (60, 80 and 100 µs) before dyeing. The power of the laser beam was 210 W and the wavelength was 10.6 µm. In order to determine the effect of laser treatment on polyester; FTIR analysis, SEM-EDX analysis and bursting strength tests were applied to untreated and treated fabric samples.

Findings

It was found that treatments with laser have a significant effect on disperse dye-uptake of polyester fibers, and for this reason laser-treated fabrics were dyed in darker shade. Furthermore, it was determined that the samples treated at 30 dpi started to melt and the fabric was damaged considerably, but the fabrics treated at 20 and 25 dpi were not affected at all. Another result obtained regarding the use of laser technology in polyester fabrics is that if some areas of fabrics are not treated with laser and some other areas are treated with laser at 20 dpi 60 µs and 25 dpi 60 µs, it will be possible to obtain patterns containing three different shades of the same color on the fabric.

Originality/value

When the literature is examined, it is seen that there are various studies on the dyeability and patterning of polyester fabrics with disperse dyes by laser technology. As it is known, today color measurement is done digitally using a spectrophotometer. However, when we look at a photograph on computer screens, the colors we see are defined by RGB (red-green-blue) values, while in the spectrophotometer they are defined by L*a*b* (L*: lightness-darkness, a*: redness-greenness, b*: yellowness-blueness) values. Especially when it is desired to produce various design products by creating patterns with laser technology, it would be more useful to show the color directly to the customer on the computer screen and to be able to speak over the same values on the color. For this reason, in this study, the color measurement of the fabric samples was not made with a spectrophotometer, instead, the RGB values obtained from the photographs of the samples were converted into L*a*b* values with MATLAB and interpreted, that is, a digital color evaluation was made on the photographs. Therefore, it is believed that this study will contribute to the literature.
Socioeconomic indicators and their influence on the adoption of renewable energy technologies in rural Malawi
Authors: Nkhoma Richard , Mwale Vincent Dodoma , Ngonda Tiyamike
Published: March 2024

Purpose

This study aims to examine the impact of socioeconomic factors on electricity usage and assess the feasibility of implementing a mini-grid system in Kasangazi, Malawi. The primary aim is to understand the community’s current and potential utilisation of electrical equipment.

Design/methodology/approach

A mixed-methods approach was used to collect quantitative and qualitative data. Information was gathered through structured questionnaires, and energy audits were conducted among 87 randomly selected households from 28 Kasangazi communities. Data analysis relied on descriptive statistics using IBM SPSS version 28.

Findings

The study indicates that every household in Kasangazi uses non-renewable energy sources: 60 households use disposable batteries for lighting, 20 for radios and all use firewood, freely sourced from local forests, for cooking and heating water. The study shows that firewood is the community’s preferred energy source, illustrating the challenges faced in the fight against deforestation. Most household income comes from farming, with smaller contributions from businesses, employment and family remittances. Access to higher education is scarce, with only one out of 349 family members receiving tertiary education. Despite the constraints of low education levels and income, there is a demand for larger electrical appliances such as stoves and refrigerators. This underscores the need for mini-grid solutions, even in less technologically advanced, agriculture-dependent communities.

Originality/value

This study underscores that in Sub-Saharan Africa, factors like household size, income and education levels do not significantly influence the electricity demand but should be taken as part of the fundamental human rights. Rural populations express a desire for electricity due to the convenience it offers, particularly for appliances like refrigerators and stoves. Mini-grids emerge as a viable alternative in regions where grid electricity provision is challenging. It is concluded from this paper that the issue of using renewable energy should not only be taken for environmental preservation but also to promote energy access, augmenting efforts in supplying electricity to the remotest parts of the country.