bluuebunny/crossref_metadata_2025 huggingface dataset:
The Effects of Sodium Fructose Diphosphate on BLood Coagulation Reaction Time and Plasma Coagulation Factor Activity Tests in vitro
Authors: Zhang Yalong , Zhong Xingguo , Zhou Lin , He Ning , Fang Yuan , Chen Tongqing
Published: February 2025

Objective To investigate the effects of sodium fructose diphosphate (FDP) on blood coagulation reaction time and plasma coagulation factor activity in vitro. Method The thromboelastogram detection system provided by three different manufacturers (Maiketian, Lepu, and Dingrun) was used to determine the blood coagulation reaction time (R), clotting time (K), α-angle, and maximal amplitude (MA) of blood samples mixed with different concentrations FDP and the samples before dosing.The activities of coagulation factors for plasma mixed with FDP were determined by automatic hemagglutination analysis system. New Zealand white rabbits were selected for the experiment on the effect of the drug on blood coagulation in vivo. Result The results of thrombologram provided by three different manufacturers showed that the R value of blood sample was significantly correlated with the blood FDP concentration (P<0.000). The results of in vitro experiments showed that plasma coagulation factor V, VII, IX, XI and XII activities were significantly negatively correlated with plasma FDP concentrations (P<0.000). In vivo experiments of New Zealand white rabbits, blood clotting reaction time was also prolonged to varying degrees. Conclusion  FDP can affect the results of blood coagulation test in vivo and vitro. It may really affect the function of our coagulation system.
Framework for precision medicine in focal segmental glomerulosclerosis: Translation of sparsentan-responsive genes in a rat model to kidney disease associated proteins in biofluids
Authors: Eddy Sean , Nair Viji , Hartman John R. , Fermin Damian , Eichinger Felix , Godfrey Bradley , Ju Wenjun , Hodgin Jeffrey B , Mariani Laura H. , Bedard Patricia W. , Jenkinson Celia P. , Hendry Bruce , Komers Radko , Inrig Jula , Kretzler Matthias
Published: February 2025

Sparsentan, a dual endothelin receptor A inhibitor and angiotensin blocker, reduced proteinuria in patients with focal segmental glomerulosclerosis (FSGS) in Phase II and Phase III studies. However, the estimated glomerular filtration rate (eGFR) endpoint was not achieved, partially attributed to disease heterogeneity among participants. Sparsentan reversed the molecular fingerprint in kidneys of an adriamycin-challenged rat model of chronic kidney disease, consistent with the phenotypic data. Transcriptomic profiles from this model were used to identify differentially expressed genes, 388 of which had reversed directionality, and networks responsive to sparsentan. These included disease networks relevant to FSGS, including suppression of cytokine signaling, immune and inflammatory pathways as well as inhibition of networks downstream of endothelin and angiotensin activation. Human orthologs of genes upregulated and reversed by sparsentan in the rat model were elevated in glomerular (p<0.001) and tubulointerstitial (p<0.0001) profiles of participants with FSGS in the Nephrotic Syndrome Study Network (NEPTUNE) compared to healthy living donors, pointing to a likely anti-inflammatory action of sparsentan on kidneys. The gene signature in both compartments was negatively correlated with eGFR (p<0.005) and positively correlated with UPCR (p<0.005) and the response profile was elevated in a molecular subgroup of patients with greater disease severity. Several urine proteins were associated with the sparsentan response score highlighting opportunities for the development of non-invasive surrogates of sparsentan response to enable a precision medicine approach for treatment with dual endothelin angiotensin receptor antagonists.
GLYCO-2: a Tool to Quantify Glycan Shielding of Glycosylated Proteins with Improved Data Processing and Computation Speed
Authors: Reveiz Mateo , Lee Myungjin , Kwong Peter D. , Zhou Tongqing , Rawi Reda
Published: February 2025

Motivation: Glycans bound to glycoproteins mediate immune response, including antibody recognition and immune evasion. Previously, we developed an in silico tool GLYCO (GLYcan COverage) to quantify the glycan shielding of a protein surface, applying it to various studies. However, GLYCO lacks sufficient computational efficiency when analyzing larger datasets. Results: Here we introduce GLYCO-2 which improves the computational speed by ~4-fold compared to GLYCO by adopting a new analytical cylinder method with k-d trees. GLYCO-2 can calculate glycan shielding from a single coordinate file or from multiple frames derived from molecular dynamics simulations accounting for the inherent flexibility of oligosaccharides. We applied GLYCO-2 to quantify glycan shielding of influenza hemagglutinin (HA) proteins across diverse subtypes that infect humans, revealing an increasing trend in glycan shielding over time within each subtype, likely contributing to immune evasion. Overall, the enhanced computational efficiency of GLYCO-2 allows for faster and easier quantification of glycans, which contributes to the understand of glycan shielding effects in fields such as immunology and vaccine design.
Flow similarity model predicts allometric relationships among Acer platanoides branches
Authors: Price Charles , Dahle Gregory A , Grabosky Jason C
Published: February 2025

Using physical models to predict patterns of plant growth has been a long-standing goal for biologists. Most approaches invoke either biomechanical or hydraulic principles and assume the mechanism of interest applies similarly throughout the plant branching architecture. A recent effort, the flow similarity model, predicts numerous aspects of branching physiology and morphology and argues that the physiological constraints experienced by plants change as a function of branch order and size, with more basal portions satisfying more biomechanical constraints, and more distal portions, hydraulic ones. Distal branches are expected to have a strong influence on allometric relationships within plants due to their numerical abundance. Here we evaluate the predictions of the flow similarity model and a well-known alternative fractal branching model, using data on the dimensions of 3,484 individual stem internodes across four individual Acer platanoides trees. Overall, we find strong agreement between model predictions and the allometric exponents describing tree branch allometry. Further the predicted curvature in allometric relationships is found in all 24 cases examined and the frequency distributions of branch lengths and diameters are consistent with model expectations in 6/8 cases. We also find the area ratios are consistent with the model assumption of area-preserving branching. Collectively, our data and analysis provides strong support for the flow similarity model, and identifies several areas in need of subsequent inquiry.
Ca2+increases cardiac muscle viscoelasticity independent of active force development
Authors: Baker Anthony J. , Li On Yeung , Ježek Filip , Simpson Paul C. , Chesler Naomi C. , Beard Daniel A
Published: February 2025

In addition to activation of muscle contraction by Ca2+, recent studies suggest that Ca2+also affects muscle passive mechanical properties. The goal of this study was to determine if Ca2+regulates the stiffness of cardiac muscle, independent of active contraction. The mechanical response to stretch for mouse demembranated cardiac trabeculae was probed at different Ca2+levels after eliminating active contraction using a combination of two myosin ATPase inhibitors: para-nitroblebbistatin (PNB, 50 μM), plus mavacampten (Mava, 50 μM). Myocardial force level was assessed during large stretches (≈ 20% initial muscle length) with a range of stretch velocities. For relaxed muscle, in response to stretch, muscle force rose to a peak and then decayed toward a lower steady-state level, consistent with the viscoelastic nature of cardiac muscle. Peak force was higher with faster stretch velocity, but the steady-state force was independent of stretch velocity, consistent with the presence of both apparent viscous and elastic components of the stretch response. In the presence of the inhibitors PNB plus Mava, when Ca2+level was increased, active contraction was completely prevented. However, the viscoelastic force response to stretch was markedly increased by high Ca2+and was > 6-fold higher than at low Ca2+level. The relationship of viscous force to Ca2+level had a similar form to the relationship of active force to Ca2+(measured in the absence of inhibitors), suggesting a common regulatory mechanism is involved. As expected, Ca2+-activated contraction was inhibited by lowering the temperature from 21°C to 10°C. In contrast, the Ca2+-activated viscous property was not inhibited at lower temperature, further suggesting that active contraction and the viscous property involve distinct mechanisms. This study demonstrates that in addition to triggering activation of contraction, Ca2+also increases the apparent viscous property of cardiac muscle.
Structural basis for anomalous cellular trafficking behavior of glaucoma-associated A427T mutant myocilin
Authors: Hill Kamisha R , Scelsi Hailee F , Youngblood Hannah A , Farali Jennifer A , Itakura Tatsuo , Fini M Elizabeth , Peters Donna M , Lieberman Raquel L
Published: February 2025

Familial mutations in myocilin cause vision loss in glaucoma due to misfolding and a toxic gain of function in a senescent cell type in the anterior eye. Here we characterize the cellular behavior and structure of the myocilin (myocilin A427T) mutant, of uncertain pathogenicity. Our characterization of A427T demonstrates that even mutations that minimally perturb myocilin structure and stability can present challenges for protein quality control clearance pathways. Namely, when expressed in an inducible immortalized trabecular meshwork cell line, inhibition of the proteasome reroutes wild-type myocilin, but not myocilin A427T, from endoplasmic reticulum associated degradation to lysosomal degradation. Yet, the crystal structure of the A427T myocilin olfactomedin domain shows modest perturbations largely confined to the mutation site. The previously unappreciated range of mutant myocilin behavior correlating with variable stability and structure provides a rationale for why it is challenging to predict causal pathogenicity of a given myocilin mutation, even in the presence of clinical data for members of an affected family. Comprehending the continuum of mutant myocilin behavior in the laboratory supports emerging efforts to use genetics to assess glaucoma risk in the clinic. In addition, the study supports a therapeutic strategy aimed at enhancing autophagic clearance of mutant myocilin.
Stenotrophomonas maltophilia promotes wheat growth by enhancing nutrient assimilation and rhizosphere microbiota modulation
Authors: Sharma Pinki , Pandey Rajesh S , Chauhan Nar S
Published: February 2025

Background: Stenotrophomonas maltophilia has gained considerable attention for its biocontrol and biofertilizer potential in promoting plant growth. It could be employed to enhance wheat yield to ensure food security for the growing population. However, its biofertilizer potential in field conditions and its impact on wheat rhizosphere microbiota must be assessed before its employment in agriculture practices to increase wheat production. Methods: We have assessed the role of Stenotrophomonas maltophilia on wheat seed germination, plant growth parameters, and crop yield in the field conditions. Additionally, wheat rhizosphere microbiota was explored to assess the impact of seed pretreatment with Stenotrophomonas maltophilia on the wheat rhizosphere microbiota. Results and Discussion: Stenotrophomonas maltophilia strains BCM and BCM_F demonstrated superior antifungal activity, indicating their biocontrol potential. Seed pretreatment with these strains promoted nitrogen fixation and phosphate solubilization in the wheat rhizosphere showcasing biofertilizer potential. Uniquely identified OTUs in the rhizosphere microbiota of treated groups and microbial community dynamics, particularly at Feeks 3.0 and 6, indicated Stenotrophomonas maltophilia-induced microbiota restructuring. The abundance of Stenotrophomonas maltophilia 16S rRNA gene sequences at different Feeks treated with microbial indicates its stability across different plant growth stages. Their rhizospheric presence also impacted plant health indicators, including improved sugar and nitrite concentrations and significantly enhanced crop yield (P>0.05). Enhanced growth parameters and better crop yield in Stenotrophomonas maltophilia pre-inoculated seeds in field conditions indicated their potential to offer a sustainable alternative to enhance wheat production. Conclusion: The present study highlighted the biofertilizer and biocontrol potential of Stenotrophomonas maltophilia strains BCM and BCM_F in supporting sustainable agricultural practices.
The development of a multidisciplinary care pathway for patients with inflammatory bowel disease before, during and after pregnancy
Authors: De Dycker Els , Lenie Sien , Ceulemans Michael , Geens Patricia , Lambrechts Tessy , Loddewijckx Elien , Paps Ariane , Degry Justien , D'Hondt Caroline , Matthijs Annelies , Vermeire Severine , Sabino Joao , Verstockt Bram , Lannoo Lore , Van Calsteren Kristel , Ferrante Marc
Published: February 2025

Background: Recent advancements have significantly enhanced our understanding of the interplay between inflammatory bowel disease (IBD) and reproductive health. While international organizations provide guidelines for best practices, translating them into actionable strategies is crucial. Aim: This study aimed to develop a comprehensive care pathway to enhance preconception counselling and support for IBD patients in the perinatal period, ensuring they receive optimal expert care. Methods: We used the 7-phase model for the development of the care pathway. Findings: The resulting care pathway, structured as a time-task matrix, outlines the required actions at preconception, during pregnancy, and in the postpartum period for women with IBD. Discussion: The pathway provides a structured and multidisciplinary approach that addresses the unique needs of IBD patients of childbearing age. It emphasizes holistic and personalized support throughout the preconception, pregnancy, and postpartum period. Conclusion: The development of this care pathway represents a significant advancement in the perinatal management of IBD. By offering multidisciplinary and individualized care, optimal maternal and infant outcomes are pursued, while establishing a new global standard for reproductive health and perinatal management.
Identification of claudin-3 as an entry factor for rat hepacivirus
Authors: Tanaka Tomohisa , Akaike Yasunori , Kasai HIrotake , Yamashita Atsuya , Matsuura Yoshiharu , Moriishi Kohji
Published: February 2025

Approximately 58 million people worldwide are believed to be infected with hepatitis C virus (HCV), a major causative agent of chronic liver diseases. Hepacivirus ratti strain rn-1, which was discovered from Rattus norvegicus (Norway rat) and designated Norway rat hepacivirus 1 (NRHV1), shares similar properties with HCV in terms of genetic homology, target cell tropism, pathogenicity and the immune response. In vivo infection systems for NRHV1 will help overcome the challenges in HCV research for vaccine development. However, the virological characteristics of NRHV1, such as the mechanisms of cell entry, remain largely unexplored, in part owing to a paucity of cell culture systems for NRHV1. Here, we identified the host factors that facilitate NRHV1 entry by profiling the gene expression of two cell lines with different susceptibilities to NRHV1 infection. NRHV1 employs rodent orthologues of HCV entry factors, including scavenger receptor class BI, CD81, and occludin, and utilizes claudin-3 (CLDN3) but not claudin-1. The expression of rat and mouse, but not human, CLDN3 facilitates the entry of NRHV1 into murine cell lines that are insusceptible to NRHV1 infection. The host-specific cell entry of CLDN3 is determined by two amino acid residues, Ile44 and Trp46, in extracellular loop 1. These findings suggest that some hepacivirus species share an HCV-like entry mechanism but show evidence of adaptive evolution of their virus-specific entry factors to host animals.
Structural implications of glycosylation on the voltage-gated sodium channel β3-subunit
Authors: Beaudoin Christopher A. , Hayes Jerrard , Liu Hengrui , Namadurai Sivakumar , Deery Michael J. , August Ethan A. , Krasner Samuel , Hamaia Samir W. , Salvage Samantha C. , Huang Christopher L.-H. , Jackson Antony P.
Published: February 2025

Voltage-gated sodium (NaV) channel α-subunits are modulated by associated β-subunits that affect their localization, trafficking and gating behaviour. The β-subunits are members of the immunoglobulin (Ig) domain family of cell-adhesion molecules and the interactions between their extracellular Ig-domains may modify channel clustering. The full-length β3-subunit can form cis trimers on the plasma membrane. The atomic resolution structure of a deglycosylated trimeric β3-subunit Ig-domain has been solved by X-ray crystallography. However, it is not clear whether this particular trimeric Ig-domain structure is plausible for cell-expressed, glycosylated β3-subunits. Here we use glycan profiling to confirm an extensive and heterogeneous pattern of β3-subunit glycosylation, with the majority of glycans being bi- and tri-antennary structures with one or two terminal sialic acids. Two tryptic peptides of the β3 Ig-domain are predicted to contain potential N-linked glycosylation sites. When the isolated, glycosylated full-length β3-subunit was trypsin-digested and analysed by LC-MS/MS, only one of these peptides - containing an N-linked glycosylation site at residue N95 and located close to the trimer interface - was identified in its unmodified form, suggesting that residue N95 is under-glycosylated. All-atom molecular dynamics simulations of the glycosylated, membrane-bound full-length β3 trimer confirmed that glycans can be accommodated with the Ig-domain trimer and indeed, may contribute to protein-membrane and inter-protomer interactions within the full-length, membrane-embedded trimer. Further biochemical studies are warranted to explore the interactions between oligomeric β-subunits with corresponding α-subunit sodium channels.
Can Plitidepsin Be Used as an Antiviral Against RSV?
Authors: Estampes Charlotte , Fix Jenna , Sourimant Julien , Sutto-Ortiz Priscila , Richard Charles-Adrien , Decroly Etienne , Galloux Marie , Eleouet Jean-Francois
Published: February 2025

Human respiratory syncytial virus (HRSV) is a main cause of acute lower respiratory tract infections in infants, the elderly and the immunocompromised patients. Although vaccines have recently been approved for the elderly and for pregnant women, there is no curative treatment for HRSV. HRSV replicates in the cytoplasm of infected cells, and transcription and replication of the viral genome depend on the viral RNA polymerase complex, which recruits cellular factors for RNA synthesis. Among them, the eucaryotic translation elongation factor 1A (eEF1A) was previously shown to be critical for HRSV replication. eEF1A activity can be inhibited by plitidepsin (Aplidin), a cyclopeptide extracted from ascidian Aplidium albicans, which was shown highly potent against SARS-CoV-2, with a 50% inhibitory concentration (IC90) of 0.70 to 1.62 nM depending on the cell line. Here, we investigated whether plitidepsin could also inhibit HRSV replication. We found that plitidepsin inhibited HRSV replication with an IC50 of ≈3 nM in cell cultures. However, further investigation revealed that plitidepsin has pleiotropic effects, affecting the translation of both cellular and viral proteins in a similar manner. Overall, our results show that plitidepsin blocks cellular translation and indicate that plitidepsin induces a proteasome-mediated degradation of eEF1A, also showing the dependance of HRSV replication to cellular factors such as eEF1A. These results thus highlight an original mechanism of action of plitidepsin on eEF1A, which render the use of this compound for antiviral therapy very risky.
Structure and dynamics of a multidomain ligand-gated ion channel revealed under acidic conditions
Authors: Andén Olivia , Rovšnik Urška , Lycksell Marie , Delarue Marc , Howard Rebecca J , Lindahl Erik
Published: February 2025

Ligand-gated ion channels are critical mediators of electrochemical signal transduction across evolution. The bacterial channel DeCLIC constitutes a provocative model system for structure, function, and dynamics in this family, including a modulatory N-terminal domain (NTD). Previous closed structures of DeCLIC support a rationale for its inhibition by calcium; however, properties of its open state remain unclear. Here we used cryogenic electron microscopy under acidic conditions to determine a previously unreported conformation of DeCLIC with an expanded pore. This structure was relatively stable and permeable in simulations, and agreed with the average low-pH solution structure by small-angle neutron scattering. In the absence of calcium, an alternative closed class exhibited dynamic rearrangements in the NTD. We propose that our expanded-pore structure corresponds to a functional open state of DeCLIC, while calcium-site and NTD dynamics drive channel closure, providing a detailed template for modulatory mechanisms in the larger channel family.
"Paraxenoviridae", a putative family of ubiquitous marine bacteriophages with double-stranded RNA genomes
Authors: Yoshida Mitsuhiro , Medvedeva Sofia , Fukudome Akihito , Wolf Yuri I. , Urayama Syun-ichi , Nishimura Yosuke , Takaki Yoshihiro , Koonin Eugene V. , Krupovic Mart , Nunoura Takuro
Published: February 2025

Fragmented and primer Ligated DsRNA Sequencing (FLDS) was used to reconstruct five complete, bisegmented RNA genomes of paraxenoviruses, a group of viruses that was previously identified in the ocean and that based on the analysis of partial genomes was proposed to represent a putative new phylum within the kingdom Orthornavirae of the realm Riboviria. Phylogenetic analysis of the RNA-directed RNA polymerases of paraxenoviruses demonstrated their affinity with the ribovirus order Durnavirales within the class Duplopiviricetes of the phylum Pisuviricota. The order Durnavirales includes families Cystoviridae that consists of well-characterized dsRNA bacteriophages and less thoroughly studied Picobirnaviridae that are also suspected to infect bacteria. Consistently, modeling and analysis of the structure of the predicted capsid protein (CP) of several paraxenoviruses revealed similarity to picobirnavirus CP although the paraxenovirus CP is much larger and contains unique structural elaborations. Taken together, these affinities suggest that paraxenoviruses represent a distinct family within Durnavirales, which we provisionally name "Paraxenoviridae". Both genomic segments in Picobirnaviridae and "Paraxenoviridae" encompass multiple open reading frames, each preceded by a typical bacterial ribosomebinding site, strongly suggesting that these families consist of bacterial viruses. Search for homologs of paraxenovirus genes shows widespread distribution of this virus group in the global ocean, suggesting a potential important contribution to marine microbial ecosystems. Our findings further expand the diversity and ecological role of the bacterial RNA virome, reveal extensive structural variability of RNA viral capsid proteins, and demonstrate the common ancestry of several distinct families of bacterial viruses with dsRNA genomes.
A myofilament lattice model of Drosophila flight muscle sarcomeres based on multiscale morphometric analysis during development
Authors: Görög Péter , Tibor Novák , Polgár Tamás Ferenc , Bíró Péter , Gutheil Adél , Kozma Csaba , Gajdos Tamás , Tóth Krisztina , Alexandra Tóth Vivien , Erdélyi Miklós , József Mihály , Szikora Szilárd
Published: February 2025

The indirect flight muscle is a widely used model for studying sarcomere structure and muscle development due to its extremely regular architecture. Nevertheless, precise measurement of the basic sarcomeric parameters remains a challenge even in this greatly ordered tissue. In this study, we identified several factors affecting measurement reliability and developed a software tool for precise, high-throughput measurement of sarcomere length and myofibril width. The accuracy of this new tool was validated against simulated images and blinded manual measurements. To extend the scope of this morphometric analysis to the sub-sarcomeric scale, we used electron and super-resolution microscopy to quantify myofilament number and filament length during myofibrillogenesis. These results provided novel insights into the dynamics of sarcomere growth, and enabled us to construct a refined model of sarcomere growth reaching to the level of individual myofilaments and providing a spatial framework for interpreting molecular localization data. These findings enhance our understanding of sarcomere assembly and offer a foundation for future studies of muscle development and function.
INFLUENCE OF LIFESTYLE ON BRAIN SENSITIVITY TO CIRCULATING INSULIN-LIKE GROWTH FACTOR 1
Authors: Zegarra-Valdivia Jonathan A , Khan Mohammed Zahid , Putzolu Aurora , Cipriani Raffaela , Pignatelli Jaime , Torres Aleman Ignacio
Published: February 2025

Life style conditions such as social relationships and diet impinge on mood homeostasis, a mechanism that becomes dysregulated in high-incidence mental illnesses such as depression or Alzheimer dementia (AD). Since insulin-like growth factor 1 (IGF-1) modulates mood and its blood levels are altered both in AD and in affective disorders, we investigated whether its activity was altered in the brain of mice submitted to isolation or fed with a high-fat diet (HFD). As in humans, both life style conditions increased anxiety and depression-like behavior. Significantly, both life style conditions abrogated neuronal responses to systemic IGF-1. Thus, enhanced neuronal activity in response to intraperitoneal IGF-1, as determined by Ca++ fiber-photometry in the prefrontal cortex, was lost in isolated or HFD-fed mice. However, only the latter had elevated serum IGF-1 levels. These findings suggest that loss of brain IGF-1 input may contribute to mood disturbances observed in lonely and obese subjects. Furthermore, they provide additional insight into the heightened risk of depression and Alzheimer's disease associated with these conditions. Importantly, since the reduction of IGF-1 activity in the brain is not consistently mirrored by its serum levels, serum measurements do not reliably reflect brain IGF-1 activity.
MYB59 is linked to natural variation of water use associated with warmer temperatures in Arabidopsis thaliana
Authors: Ferguson John Nicholas , Brendel Oliver , Bechtold Ulrike
Published: February 2025

Water-use contributes significantly to plant growth and productivity, yet the extent to which variation in water-use is a function of adaptive differentiation is unknown. Here, we studied natural variation of water use in Arabidopsis thaliana to understand how climatic history impacts water use strategies. We performed a survey of vegetative water use (VWU) and life history traits across A. thaliana ecotypes in controlled and outdoor settings. Performance of select ecotypes in controlled experiments was reflective of performance in outdoor conditions. Through trait-climate and genome-wide association (GWAS) analyses, we tested for signals 39 of environmental adaption in water use. Ecotypes from warmer environments were noted in displaying enhanced water use, independent of precipitation. GWAS identified MYB59 as a determiner of VWU. Functionally significant MYB59 SNPs showed associations with temperature, but not precipitation, and myb59 mutants demonstrated reduced water use under high temperatures. Our study suggests infraspecific variation in water-use can be explained in part by climatic history, where temperature is the most significant driver. MYB59 appears involved in this association and holds promise for study in crops.
Strain-level and phenotypic stability contrasts with plasmid and phage variability in water kefir communities
Authors: Somerville Vincent , Sarton-Loheac Garance , de Bakker Vincent , El Chazli Yassine , Kesner Lucie , Ndiaye Malick , Garrido-Sanz Daniel , Prasad Aiswarya , Bonilla-Rosso German , Mazel Florent , Sentchilo Vladimir , Moineau Sylvain , Maurice Corinne F , Tamarelle Jeanne , Ulrich Eric , Engel Philipp
Published: February 2025

Microbial communities can change in response to top-down factors, such as phages, and bottom-up factors, such as nutrient availability. Previous studies have successfully investigated bacterial species-level dynamics, but diversity and interactions beyond the species-level is usually lacking. Traditional fermented foods, such as water kefir, provide ideal systems to study ecological and evolutionary dynamics beyond the species-level, as they are simple and trackable systems that are cultivated in non-sterile, nutrient-rich environments which foster microbial growth and invasion. Despite the central role of only a few lactic acid bacteria for fermentation, little is known about the genomic diversity and dynamics of these community members over time. Within the framework of a graduate course, 35 students propagated water kefir across several generations under different nutrient conditions and in different households to study microbial responses over time. We found that water kefir communities were generally stable at the species-level, with only rare bacterial species replaced over long timescales (more than 2 years). While we observed little strain-level diversity with few strain replacements over long timescales, closely related strains exhibited variation in accessory gene content, often encoded on plasmids, particularly those involved in ecologically meaningful functions such as sugar utilization pathways and phage defense systems. We hypothesise that these genomic variations could reflect the adaptations of strains to different sugars and phages. Consistent with this, we observed a diverse array of phages, many likely originating from the unique household environments. By documenting the genomic landscape of microbial species, strains, plasmids, and phages, this study advances our understanding of the diversity and dynamics of microbial communities in fermented foods. Furthermore, our course material is publicly available and offers a blueprint for bridging the gap between teaching and research, inspiring the next generation of scientists to unravel the complexities of microbial ecosystems.
A novel vimentin variant from tumor-associated macrophages directs cancer metastasis by engaging IGF-1R
Authors: Jiu Yaming , Miao Chenglin
Published: February 2025

Tumor-associated macrophages (TAMs) are recognized for their role in promoting malignancy. However, the specific mechanisms by which they drive cancer cell migration remain largely unexplored. Here, we identified a novel N-terminal-less variant of vimentin, a cytoskeletal intermediate filament protein, that is selectively secreted by TAMs through a type I unconventional secretion pathway following caspase cleavage of its N-terminus. The macrophage-secreted short vimentin (mssVIM) enhances tumor migration, as demonstrated in breast cancer cell lines, patient-derived cancer cells, mammospheres, and in vivo mouse xenograft models. Mechanistically, mssVIM binds and activates the insulin-like growth factor 1 receptor (IGF-1R) on the cancer cell surface, by exposing binding sites that are otherwise masked in full-length vimentin. Unlike the canonical IGF-1-IGF-1R signaling pathway that promotes cell proliferation, mssVIM-activated IGF-1R triggers ribosomal S6 kinase (RSK) activation, which increases integrin αVβ6 expression, ultimately facilitating tumor cell migration. Analysis of tissue samples from a cohort of breast cancer patients showed that mssVIM levels positively correlate with tumor malignancy and lymph node metastasis, suggesting its potential as a prognostic biomarker.
ASEAN, gender equality and women’s empowerment in STEM
Authors: Lemus-Delgado Daniel , Cerda Carlos
Published: February 2025

Purpose

A paradigm shift is essential to achieving gender equality, including participation in science, technology, engineering and mathematics (STEM). This article aims to analyze how the involvement of international organizations in this task is essential to succeeding beyond the actions of local and national governments.

Design/methodology/approach

Based on the case study of ASEAN, we examine official documents of the ASEAN Secretariat to analyze the relationship between Innovation, Science and Technology for ASEAN countries and action plans to advance women’s participation in STEM.

Findings

The article evidences the scope, limits, contributions and challenges of ASEAN as a promotor of gender equality in STEM.

Research limitations/implications

This case study explores how the official position of the ASEAN Secretariat can contribute to advancing gender equity in STEM. Subsequent studies based on other qualitative methodologies, considering decision-makers from the ASEAN countries, will enrich the findings.

Originality/value

The traditional focus of analyzing how women can participate more in STEM has been regional or national approaches. Academic literature often considers the role of provincial or national governments as the most decisive influence on correcting inequalities of opportunities between men and women. However, this research takes a different approach, discussing the few explored roles of international organizations, both global and regional, in this critical task. The potential contribution of international organizations on this issue, despite their non-binding recommendations and resolutions, can contribute to impulse a change in the gender gap in STEM as the ASEAN case evidences.
Staff bonding and accounting fraud tendency: does cost of living matter?
Authors: Seudib Ezekiel Nibenong , Oppong Clement
Published: February 2025

Purpose

The paper explores the ramifications of rising costs of living on accounting fraud (ACF) as well as how it disrupts the effect of staff bonding (SB) on ACF tendencies.

Design/methodology/approach

Data were collected from 310 respondents using a structured questionnaire and analysed using the partial least squares structural equation model.

Findings

The study reveals that rising costs of living increase ACF tendencies, while SB reduces it. However, the study also shows that costs of living decrease the effectiveness of SB as a corporate governance measure, aligning with the Stimulus, Capability, Opportunity, Rationalisation, and Ego (S.C.O.R.E.) theory.

Originality/value

The paper’s theoretical contribution is consistent with the S.C.O.R.E. theory. The study concluded that working with hungry employees, whose disposable incomes are further worsened by rising costs of living, is not only an anticipatory accident but also a timed bomb waiting to explode. Hence, as the leading study on the intricate relationships, one takeaway from the study is that strengthening SB conditions and maintaining salary parity with rising costs of living are two excellent strategies for mitigating ACF.
Revitalizing old low-rise residential environments by focusing on communities: case studies in Seoul, Korea
Authors: Kim Young Ju , Kim Mi Jeong , Jun Han Jong
Published: February 2025

Purpose

Apartments have become a representative urban housing type for mass housing construction; therefore, interest in low-rise residential areas has decreased. Low-rise residential areas have proved to be a poor residential environment for all aspects of life because of the density of the old buildings. Using the Moa Towns project as a case study, this research explores the steps for revitalizing low-rise residential environments, emphasizing communities.

Design/methodology/approach

The study first investigated the historical changes in urban housing types in Korea. Through a review of the related literature, a systematic analysis framework was developed. The residential environments of the case study and the questionnaire survey were analyzed through the framework, with a focus on the quality of housing.

Findings

To improve the quality of housing for residents, a housing plan is needed to ensure safety and comfort. To establish an accessible residential environment infrastructure, improve the quality of housing, and encourage social relationships between neighbors, community facilities within a 15-min walk should be installed. To increase interaction between neighbors, a circular pedestrian system can be created by establishing a community street.

Originality/value

This study is significant in that it focuses on people in revitalizing the community; identifies factors for physical improvement, exchange activities, and facility support; and presents a conceptual framework for building a residential environment in low-rise residential areas. The results are critical to the quality of housing and community facilities for low-rise residential development.
Tax losses and bankruptcy emergence: evidence from US firms filing under Chapter 11
Authors: Gabrielli Alessandro , Greco Giulio
Published: February 2025

Purpose

This study aims to investigate the relationship between tax losses and the likelihood of emerging from bankruptcy procedures as reorganized entities, exploiting the exogenous shock provided by the 1997 Taxpayer Relief Act (TRA) in the USA.

Design/methodology/approach

The empirical analysis uses a difference-in-differences approach and investigates a sample of US public firms filing under Chapter 11 bankruptcy procedures during the period 1984–2016. The analysis includes several robustness and endogeneity tests, including heterogeneous treatment effect analysis, entropy balancing and propensity score matching.

Findings

The findings show that filing firms with higher tax losses are more likely to emerge from the procedure as reorganized firms. Further, this paper shows that firms with high tax losses reduced their likelihood of reorganization after the enactment of the 1997 TRA, as the new regulation reduced tax benefits related to losses. Additional analyses show that tax losses contribute to the reorganization of filing firms requiring more cash resources and restructuring efforts and they increase post-bankruptcy creditors’ recovery rates.

Practical implications

This study informs policymakers, shareholders, creditors and other stakeholders that tax policy can facilitate business continuity within restructuring frameworks and preserve economic and social value.

Originality/value

This study contributes to the literature on taxation and corporate restructuring with evidence that tax-loss policies incentivize reorganization during bankruptcy procedures. To the best of the authors’ knowledge, this is the first study to empirically demonstrate that tax losses influence the form of exit from bankruptcy procedures, adding to the set of firms’ features affecting bankruptcy emergence.
Navigating the green transition: assessing the impact of Chinese green public procurement on corporate pollution emissions
Authors: Tan Weijie , Chen Xihui , Teng Mingming , An Weidong , Wu Changhua
Published: February 2025

Purpose

Green Public Procurement (GPP) is a crucial way to promote producing green products, but its relationship with corporate pollution emissions needs to be verified. This study aims to evaluate the environmental effects of the policy by analyzing how GPP influences corporate environmental pollution.

Design/methodology/approach

This study is based on extensive sample data of Chinese industrial enterprises from 2001 to 2010, using China’s first GPP list as an exogenous policy. The authors have established a differential model to explore the impact of GPP on corporate environmental pollution and its underlying mechanisms.

Findings

GPP significantly reduces the sulfur dioxide (SO2) emissions of enterprises. Verify the robustness of this conclusion by replacing variables, excluding other policy interventions that reduce selfselection bias, and conducting placebo testing. GPP encourages regulated enterprises to improve their production processes, drive clean production with green technology innovation, optimize energy structure, improve energy efficiency and reduce their emissions. The environmental cleaning effect of GPP is more significant in eastern and central China large and medium-sized urban areas. GPP has more effectively reduced SO2 emissions from private capital-intensive and heavily polluting enterprises.

Originality/value

This paper constructs a difference-in-differences model to study China’s first GPP list in 2006. It explores how GPP policies affect corporate pollution reduction. The findings enrich GPP research in China and emerging economies. Moreover, unlike existing studies on corporate pollution subject to environmental regulation, this paper focuses on how corporate pollution reduction is affected by demand-driven GPP policies, expanding the theoretical research.
Assessing student satisfaction with MOOCs: a comprehensive analysis of Coursera’s instructional design and learner experience
Authors: Le Ha Van
Published: February 2025

Purpose

The rapid expansion of online education in the 21st century, driven by technological advancements and the COVID-19 pandemic, has highlighted the critical role of massive open online courses (MOOCs) in higher education. This study aims to investigate student satisfaction with the instructional design of MOOCs at a private university in Vietnam.

Design/methodology/approach

This mixed-methods research integrates quantitative data from a survey of 225 students with qualitative insights from interviews with 10 students. The study examines key determinants of student satisfaction, including course content, instructional methodologies, assessment systems, engagement in discussion forums and the overall online learning environment.

Findings

The findings reveal high levels of student satisfaction with the quality of course materials, the flexibility of the platform and the usability of the interface. However, areas of dissatisfaction include limited interactive engagement, inadequate motivational elements, suboptimal assessment strategies and insufficient staff support. The study underscores the need for comprehensive instructor evaluations, increased student-instructor interactions, improved plagiarism detection mechanisms and timely academic support to enhance the instructional design and educational outcomes of MOOCs.

Originality/value

This study provides a nuanced understanding of student satisfaction with MOOCs, specifically within the context of a private university in Vietnam. By integrating both quantitative and qualitative data, the research offers valuable insights into specific elements that contribute to or detract from learner satisfaction. These findings can inform practical enhancements in MOOC design and delivery, ultimately aiming to improve educational outcomes in online learning environments.
The empirical and managerial landscape of workplace spirituality: a systematic literature review of studies published in ABDC list journals
Authors: Munjal Nancy , Sachdeva Geeta , Garg Naval
Published: February 2025

Purpose

The purpose of this paper is to provide a comprehensive understanding of workplace spirituality's (WPS) past, present and future by conducting a systematic literature review over the past 15 years, tracing its emergence in the managerial landscape and identifying the research gaps.

Design/methodology/approach

A PRISMA framework is used to systematically analyse 58 empirical studies categorised according to the ABDC journal quality list and published between 2009 and 2024. Furthermore, this review highlights the key trends, methodological approaches, dimensions explored, geographic distribution, research themes and the existing research gaps. Additionally, the Theory, Context, Characteristics and Methodology framework emphasises critical theoretical perspectives, contextual factors, distinguishing characteristics and methodological approaches that can shape future research in WPS.

Findings

The review revealed the global interest in WPS’s positive organisational impacts, supported by rigorous empirical studies and advanced statistical methods. Furthermore, this research highlights a significant gap in exploring WPS antecedents, suggesting a need for future studies to examine the factors contributing to WPS’s development and enhancement within organisational settings.

Research limitations/implications

This study focuses on the Scopus database and English-language papers, deliberately excluding other sources such as unpublished work, books and non-empirical articles. Consequently, this study may need to look at some relevant studies.

Originality/value

This study is original in its systematic approach to review the literature on WPS, categorising the empirical articles according to established quality lists and applying the Theory, Context, Characteristics and Methodology framework to identify future research directions. This paper offers a holistic understanding of WPS and provides valuable insights for researchers and practitioners in this evolving field.
Be cautious of your voice when boss is in shame: how manager shame shapes defensive reactions toward employee voice
Authors: Wang Xiaotian , Cai Yujie , Lin Xiaowan , Duan Jinyun
Published: February 2025

Purpose

Integrating the psychological threat perspective of voice with cognitive dissonance theory, the current research seeks to uncover how managers’ experience of shame shapes the extent to which they are threatened by and subsequently react defensively to voice(r).

Design/methodology/approach

A two (employee voice: voice condition vs no-voice condition) by two (manager shame: shame vs control) between-subjects experiment with 263 participants (i.e. front-line managers from mainland China) was conducted to test the hypotheses.

Findings

Employee voice (vs no voice) induced a higher ego threat among managers experiencing a higher than lower level of shame. The heightened ego threat, in turn, negatively affected the perceived warmth of the employee via perceived behavioral appropriateness. In a similar vein, it affected the perceived competence of the employee via perceived behavioral constructiveness.

Practical implications

Organizations and managers should be aware of the potential unfavorable effects of managers’ emotional state of shame on voice(r) evaluations and take action to improve managers’ emotional regulation skills. Employees should work on their emotional intelligence, which helps them better “read the wind” before speaking up.

Originality/value

The present work advances the understanding of managerial defensive reactions to employee voice by demonstrating that shamed managers are more likely to cognitively denigrate the voice and the voicer as an approach to defend their threatened ego.