bluuebunny/crossref_metadata_2025 huggingface dataset:
A single pathogen-secreted protein reprograms plants for drought resilience
Authors: Subieta Konrad , Weber Leonie , Lübbers Jan-Niclas , Wiesotzki Karin , Pierdzig Leon , Thurow Corinna , Schmitz Johanna , Lipka Ulrike , Heimel Kai , Schmitt Kerstin , Thürmer Andrea , Poehlein Anja , Daniel Rolf , de Vries Jan , Valerius Oliver , Braus Gerhard H. , Polle Andrea , Gatz Christiane , Teichmann Thomas , Lipka Volker
Published: January 2025

Climate change-enforced drought stress conditions and diseases caused by pathogens often co-occur and represent one of the greatest challenges in plant science1–3. Wilt pathogens that colonize water-conducting plant tissues can aggravate the problem and affect a wide range of agricultural crops4,5. However, whilst fungal infections with the vascular pathogenVerticillium dahliaeare typically associated with wilt symptoms due to occlusion of xylem tissues, the relatedV. longisporuminducesde novoformation of tracheary elements6,7. This promotes not only its virulence but also enables elevated water storage capacity of the infected host plant and resilience against drought stress conditions6,7. Here, we identified a secretedVerticilliumprotein,TRANSDIFFERENTIATIONEFFECTOR (TRADE), which triggers cell identity switches of bundle sheath cells into tracheary elements. We show that TRADE interacts with the intracellular plant protein VARICOSE (VCS), a conserved component of the mRNA turnover machinery and ortholog of the metazoan protein ENHANCER OF DECAPPING 4 (EDC4/HEDLS/Ge-1)8. The TRADE-VCS interaction induces SUCROSE NON-FERMENTING 1 (SNF1)-related protein kinase (SRK)-dependent phosphorylation and thus dysfunction of VCS. This affects the abundance of mRNAs encoding master regulators of xylem differentiation and demonstrates how a single pathogen effector protein triggers complex tissue-specific developmental reprogramming and thus promotes abiotic stress resilience.
Overcoming pride via the dorsal ACC underlies acceptance of unfair offers
Authors: Numano Shotaro , Frith Chris , Haruno Masahiko
Published: January 2025

Bargaining is a fundamental social behavior in which individuals often accept unfair offers. Traditional behavioral models, based solely on choice data, typically interpret this acceptance as simple reward-maximization. However, the suppression of emotions such as inequity aversion or pride may also play a critical role in this decision. Incorporating response time alongside choice data provides a means to quantify participants’ internal conflict in suppressing these emotions and deciding to accept unfair offers. In this study, we conducted functional magnetic resonance imaging (fMRI) of the ultimatum game, where participants decided within 10 seconds whether to accept or reject monetary distribution offers from a proposer. Using the drift diffusion model (DDM), we quantified decision-making dynamics based on both choice and response time. Participants who suppressed disadvantageous inequity (DI)-driven rejection (reflected by a lower DDM weight for DI) exhibited heightened dorsal anterior cingulate cortex (dACC) activity in response to DI. Functional connectivity analysis revealed a negative correlation between the dACC and the ventrolateral prefrontal cortex (vlPFC) when DI was large, which encoded both the rejection rates, and the response times associated with accepting DI offers. Furthermore, vlPFC activity was significantly correlated with amygdala activity during high DI conditions, specifically encoding response time for accepting DI offers but not rejection rates. Importantly, these findings could not be captured using standard value-based models that rely solely on choice data. Our results underscore the dACC’s critical role in mediating the suppression of emotional responses to DI, enabling the acceptance of unfair offers in a dynamic bargaining process.
Biomimetic hydrogel platform reveals active force transduction from retinal pigment epithelium to photoreceptors
Authors: Korpela Sanna , Kauppila Maija , Karema-Jokinen Viivi , Sukki Lassi , Kallio Pasi , Skottman Heli , Nymark Soile , Ihalainen Teemu O.
Published: January 2025

Retinal pigment epithelium (RPE) is an epithelial monolayer located at the back of the eye underneath the neural retina. RPE and retina interact closely, with RPE performing multiple tasks to ensure proper retinal physiology and forming a tight, interlocked structure with photoreceptor outer segments (POS). Essential for retinal welfare, RPE enables the daily renewal of POS by phagocytosing their aged tips. Current RPEin vitrocell culture systems lack the contact between RPE and retina, possibly limiting not only RPE maturation but also hindering the studies addressing the RPE-retina interactions. We constructed a retina-mimicking structure from a soft polyacrylamide hydrogel with Matrigel coating and introduced it to RPE cells’ apical side during culturing to model the RPE-retina interfacein vitro. RPE cells adhered to the hydrogels during culture, enabling further studies of the biophysical properties of the RPE-hydrogel interface with methods utilizing rheology and traction force microscopy. During phagocytosis, RPE cells generated considerable traction forces that were followed using a hydrogel coated with POS particles. Disruption of RPE’s actin cytoskeleton with Cytochalasin D significantly reduced the force generation. These results support the view of RPE as a mechanically active partner for retina. In addition, our retina-mimicking structure offers a tool for further biophysical modeling of the RPE-retina interface.
occumb: An R package for site occupancy modeling of eDNA metabarcoding data
Authors: Fukaya Keiichi , Hasebe Yuta
Published: January 2025

Environmental DNA (eDNA) metabarcoding has become an increasingly popular method for the rapid assessment of species distribution and diversity. However, the detection of DNA sequences of species in eDNA metabarcoding is not flawless; thus, accounting for potential false negatives (nondetection of DNA sequences of existing species) is crucial for the effective implementation of eDNA-based monitoring and research. This study introduces the occumb R package, which was developed to facilitate the easy and flexible application of community site occupancy modeling for eDNA metabarcoding that accounts for the imperfect detection of DNA sequences of species. The package provides functions for specifying models using the formula syntax, Bayesian model fitting using Markov chain Monte Carlo (MCMC), posterior inferences, and model assessments and exploring optimal study settings based on the fitted model. A case study of eDNA metabarcoding on riverine aquatic insects is illustrated using the occumb package, emphasizing the importance of ensuring biological replicates in achieving reliable species detection in eDNA metabarcoding. By making complex community site occupancy models easily accessible to users, we hope that the development of the occumb package will promote eDNA metabarcoding applications for the accurate assessment of species distribution and diversity.
Evidence for multiple independent expansions of Fox gene families within flatworms
Authors: Gąsiorowski Ludwik
Published: January 2025

Expansion and losses of gene families are important drivers of molecular evolution. A recent survey of Fox genes in flatworms revealed that this superfamily of multifunctional transcription factors, present in all animals, underwent extensive losses and expansions during platyhelminth evolution. In this paper, I analyzed Fox gene complement in four additional species of platyhelminths, that represent early-branching lineages in the flatworm phylogeny: catenulids (Stenostomum brevipharyngiumandStenostomum leucops) and macrostomorphs (Macrostomum hystrixandMacrostomum cliftonense). Phylogenetic analysis of Fox genes from this expanded set of species provided evidence for multiple independent expansions of Fox gene families within flatworms. Notably,FoxG, a panbilaterian brain-patterning gene, appears to be the least susceptible to duplication, whileFoxJ1, a conserved ciliogenesis factor, has undergone extensive expansion in various flatworm lineages. Analysis of the single-cell atlas of S.brevipharyngium, combined with RNAin situhybridization, elucidated the tissue-specific expression of the selected Fox genes:FoxGis expressed in the brain, three of the Fox genes (FoxN2/3-2, FoxO4andFoxP1) are expressed in the pharyngeal cells of likely glandular function, while one of theFoxQDparalogs is specifically expressed in the protonephridium. Overall, the evolution of Fox genes in flatworms appears to be characterized by an early contraction of the gene complement, followed by lineage-specific expansions that have enabled the co-option of newly evolved paralogs into novel physiological and developmental functions.

Statements and Declarations

The author has no competing interests to declare that are relevant to the content of this article. The research was funded by the Alexander von Humboldt Foundation (The Humboldt Research Fellowship for Postdoctoral Researchers) and The Polish National Agency for Academic Exchange (Polish Returns NAWA grant no. BPN/PPO/2023/1/00002).
Sleep increases propagation speed of physiological brain pulsations
Authors: Elabasy Ahmed , Helakari Heta , Väyrynen Tommi , Rajna Zalán , Huotari Niko , Raitamaa Lauri , Isokoski Ville , Järvelä Matti , Kaakinen Mika , Piispala Johanna , Kallio Mika , Korhonen Vesa , Seppänen Tapio , Kiviniemi Vesa
Published: January 2025

During sleep, there is an increase in the brain cerebrospinal fluid (CSF) solute convection driven by physiological pulsations. Although the main drivers of CSF flow, namely cardiac, respiratory, and vasomotor pulsations, become more powerful during sleep, there is relatively little information regarding their effects on CSF flow velocity across human brain during sleep. Here, we used functional magnetic resonance encephalography (MREG) to measure non-invasively changes in brain water flow during to sleep by tracking the propagating ultrafast signal changes induced by physiological brain pulsations. We first undertook a phantom study confirming that dense optical flow analysis of MREG data accurately detects water flow velocity, and reflects the power of the physiological pulsations. We then applied the method to quantify CSF water flow velocity in brain of healthy volunteers during EEG-verified awake and sleep recordings of ultrafast MREG data. Sleep induced an increase in CSF flow speed, as demonstrated by elevated vasomotor and respiratory pulsation speeds, while the speed of cardiovascular impulse propagation remained unchanged. The speed increases match previous findings of respective pulsation power changes, and correlated with slow delta EEG power. The sleep-induced CSF flow speed increases occurred dynamically over both pulsation cycles, without the large effects on flow directions reported previously in several neurological conditions. In conclusion, sleep increases 3D water flow speed dynamically in human brain regions showing concomitant pulse power increases, supporting a porous media model of hydrodynamics in brain cortex.
Identification of a novel GREMLIN1 uptake pathway in epithelial cells that requires BMP binding
Authors: Gao Zhichun , Gao Yuhan , Dutton Louise R. , Todd Grace , Gipson Gregory R. , Browne Connor , Kerr Emma M. , Daly Carole , Plouffe Bianca , Dunne Philip D. , Brazil Derek P.
Published: January 2025

Gremlin1 is a member of a cysteine-knot containing family of secreted antagonists of bone morphogenetic protein signaling. GREM1 binding to BMP targets prevents their engagement with cognate BMP receptors, attenuating BMP-dependent gene expression. Some evidence suggests that GREM1 can directly bind to receptor tyrosine kinases on the plasma membrane, further complicating our understanding of GREM1 biology. To attempt to clarify the modalities of GREM1 signaling, we show that GREM1 protein is produced and secreted by intestinal fibroblasts and endocytosed by neighbouring epithelial cells. GREM1 uptake is a slow process and occurs by both clathrin- and caveolin-mediated endocytosis. Cell membrane heparin sulfate proteoglycans are required for GREM1 binding and uptake, and once internalised, GREM1 appears to localise to the early endosomes. Addition of BMP2 enhanced GREM1 uptake into cells. Remarkably, generation of a BMP-resistant GREM1 mutant abolished GREM1 uptake both in the presence and absence of BMP2. These data suggest that GREM1 binding and uptake into cells requires BMP binding, a process that may contribute to the antagonism of BMP signaling by GREM1.

In this article, we demonstrate differential GREM1 mRNA versus protein expression in mouse intestine. We also identify a novel GREM1 endocytosis pathway whereby mammalian cells take up GREM1 protein in what appears to be a BMP-dependent mechanism.
Cerebral Metabolic Rate of Oxygen and Accelerometry-Based Fatigability in Community-Dwelling Older Adults
Authors: Gay Emma L. , Rosano Caterina , Coen Paul M. , Bohnen Nicholaas , Huppert Theodore , Qiao Yujia (Susanna) , Glynn Nancy W.
Published: January 2025

Alterations in energy metabolism may drive fatigue in older age, but prior research primarily focused on skeletal muscle energetics without assessing other systems, and utilized self-reported measures of fatigue. We tested the association between energy metabolism in the brain and an objective measure of fatigability in the Study of Muscle, Mobility and Aging (N=119, age 76.8±4.0 years, 59.7% women). Total brain cerebral metabolic rate of oxygen (CMRO2) was measured using arterial spin labeling and T2-relaxation under spin tagging MRI protocols. Accelerometry-based fatigability status during a fast-paced 400m walk was determined using the Pittsburgh Fatigability Index (PPFI, higher=worse). Confounders included skeletal muscle energetics, measured in vivo using spectroscopy and ex vivo using respirometry, cardiorespiratory fitness (VO2peak), weight, medication count, and multimorbidity.

Multivariable logistic regression models were used to estimate the association (odds ratio (OR)) of CMRO2with PPFI>0 compared to the referent group PPFI=0. Models were first adjusted for age and sex, and further adjusted for confounders. In this sample, 41.2% had PPFI>0 (median 3.3% [0.4-8.0%]). CMRO2was positively associated with PPFI>0 (age and sex adjusted OR=1.61, 95% CI: 1.06, 2.45, p=0.03); adjustment for confounders attenuated the association. The positive association of brain energetics and fatigability warrants further study in older adults.
Survival-Inferred Fragility of Statistical Significance in Phase III Oncology Trials
Authors: Sherry Alexander D. , Liu Yufei , Msaouel Pavlos , Lin Timothy A. , Koong Alex , Lin Christine , Abi Jaoude Joseph , Patel Roshal R. , Kouzy Ramez , El-Alam Molly B. , Miller Avital M. , Owiwi Mohannad , Ofer Jonathan , Bomze David , McCaw Zachary R. , Meirson Tomer , Ludmir Ethan B.
Published: January 2025

Background

Statistical significance currently defines superiority in phase III oncology trials. However, this practice is increasingly questioned. Here, we estimated the fragility of phase III oncology trials.

Methods

Using Kaplan-Meier curves for the primary endpoints of 230 two-arm superiority phase III oncology trials, we reconstructed data for individual patients. We estimated the survival-inferred fragility index (SIFI) by iteratively flipping the best responder from the experimental arm to the control arm (SIFIB) until the interpretation was changed according to the significance threshold of each trial. Severe fragility was defined by SIFI≤1%.

Results

This study included 230 trials enrolling 184,752 patients. The median number of patients required to change trial interpretation was 8 (interquartile range, 4 to 19) or 1.4% (interquartile range, 0.7% to 3%) per SIFIB. Estimations of SIFI by multiple methods were largely consistent. For trials with an overall survival primary endpoint, the median SIFIBwas 1% (IQR, 0.5% to 1.9%). Severe fragility was found in 87 trials (38%). As a continuous statistic, the originalPvalue—but not its binary significance interpretation—was associated with fragility and severe fragility. Trials with subsequent FDA approval had lower odds of severe fragility. Lastly, the underlying survival model had differential effects on SIFI estimation.

Conclusions

Even among phase III oncology trials, which directly inform patient care, changes in the outcomes of few patients are often sufficient to change statistical significance and trial interpretation. These findings imply that current definitions of statistical significance used in phase III oncology are inadequate to identify replicable findings.
Systematic characterization of zinc in a series of breast cancer cell lines reveals significant changes in zinc homeostasis
Authors: Woyciehowsky Mena , Larson Portia , Stephan Annika R. , Dandridge Sharee L. , Idonije Doreen , Berg Kylie A. , Lanthier Alyx , Acuna Stephanie Araiza , Stites Saskia W. , Gebhardt Waverly J. , Holtzen Samuel E. , Rakshit Ananya , Palmer Amy E.
Published: January 2025

An optimal amount of labile zinc (Zn2+) is essential for proliferation of human cells, where Zn2+levels that are too high or too low cause cell cycle exit. Tumors of the breast have been characterized by high levels of total Zn2+. Given the role of Zn2+in proliferation of human cells and elevation of zinc in breast cancer tumors, we examined the concentration of total and labile Zn2+across a panel of 5 breast cancer cell lines, compared to the normal MCF10A cell line. We found that three cell lines (MDA-MB-231, MDA-MB-157, and SK-Br-3) showed elevated labile Zn2+in the cytosol, while T-47D showed significantly lower Zn2+, and MCF7 showed no change compared to MCF10A cells. There was no change in total Zn2+across the cell lines, as measured by ICP-MS, but we did observe a difference in the cells ability to accumulate Zn2+when Zn2+in the media was elevated. Therefore, we examined how proliferation of each cell line was affected by increases and decreases in the media. We found striking differences, where three cancer cell lines (MDA-MB-231, MDA-MB-157, and MCF7) showed robust proliferation in high Zn2+at concentrations that killed MCF10A, T-47D, and SK-Br-3 cells. We also discovered that 4 of the 5 cancer cell lines demonstrate compromised proliferation and increased cell death in low Zn2+, suggesting these cells may be addicted to Zn2+. Overall, our study suggests significant differences in Zn2+homeostasis and regulation in different types of breast cancer cells, with consequences for both proliferation and cell viability.
Abdominal myosteatosis is associated with lower processing speed in a multiethnic cohort of older adults
Authors: McNeish Brendan L. , Miljkovic Iva , Allison Matthew A. , Hughes Timothy , Nasrallah Ilya , Terkpertey Eric , Rosano Caterina
Published: January 2025

Background

Prior research linking myosteatosis with cognition in older adults has been conducted in relatively homogenous populations with narrow age ranges. We evaluated if abdominal myosteatosis was associated with processing speed in a multiethnic cohort of middle aged and older adults.

Methods

The analytical sample included 1,268 adults (46-86 years old, mean 63±9 years, 53% female of 41% White, 20% Black, 14% Chinese, and 25% Hispanic), a subset from the Multi-Ethnic Study of Atherosclerosis (MESA). Bivariate analyses were performed between abdominal computed tomography derived muscle densities (a myosteatosis measure) at year 3 with Digit Symbol Coding (DSC) with cytokines. Multivariable models were first adjusted for demographics, education, and general cognition, and further adjusted for other known predictors of dementia:APOE-4, physical activity, diabetes, cholesterol, smoking, and blood pressure. We further assessed whether central adiposity, general adiposity, and cytokines modified this association. We tested interactions by ethnicity, sex, and age.

Results

Rectus abdominis myosteatosis was significantly associated with worse DSC (B= −0.247, 95% CI: 0.098,0.396, p=0.001) independent of demographics, education, general cognition, and dementia risk factors. Adjustment for central adiposity, and cytokines did not attenuate the associations. Tests for interactions by ethnicity, sex, and age were not statistically significant.

Conclusions

Rectus abdominis myosteatosis is associated with worse processing speed in this middle and older aged multiethnic population of men and women, independent of other known predictors of cognition. Longitudinal studies should assess the interplay of myosteatosis with other markers of adiposity, inflammation, and circulating mediators and their combined impact on processing speed.

Highlights

Abdominal myosteatosis correlated with lower cognitive processing speed in older adults.

Myosteatosis links muscle density to cognitive function beyond dementia risk factors.

Pro-inflammatory cytokines do not mediate the muscle-cognition association.

Ethnicity, sex, and adiposity measures do not modify myosteatosis-cognition links.

Abdominal CT scans could serve as diagnostic tools for cognitive health insights
Real-world datasets for the International Registry for Alzheimer’s Disease and Other Dementias (InRAD) and other registries: an international consensus
Authors: Perneczky Robert , Darby David , Frisoni Giovanni B. , Hyde Robert , Iwatsubo Takeshi , Mummery Catherine J. , Park Kee Hyung , van Beek Johan , van der Flier Wiesje M. , Jessen Frank
Published: January 2025

BACKGROUND

Many dementia and Alzheimer’s disease (AD) registries operate at local or national levels without standardization or comprehensive real-world data (RWD) collection. This initiative sought to achieve consensus among experts on priority outcomes and measures for clinical practice in caring for patients with symptomatic AD, particularly in the mild cognitive impairment and mild to moderate dementia stages.

OBJECTIVE

The primary aim was to define a minimum dataset (MDS) and extended dataset (EDS) to collect RWD in the new International Registry for AD and Other Dementias (InRAD) and other AD registries. The MDS and EDS focus on informing routine clinical practice, covering relevant comorbidities and safety, and are designed to be easily integrated into existing data capture systems.

METHODS AND RESULTS

An international steering committee (ISC) of AD clinician experts lead the initiative. The first drafts of the MDS and EDS were developed based on a previous global inter-societal Delphi consensus on outcome measures for AD. Based on the ISC discussions, a survey was devised and sent to a wider stakeholder group. The ISC discussed the survey results, resulting in a consensus MDS and EDS covering: patient profile and demographics; lifestyle and anthropometrics; co-morbidities and diagnostics; imaging; treatment; clinical characterization; safety; discontinuation; laboratory tests; patient and care partner outcomes; and interface functionality.

CONCLUSION

By learning from successful examples in other clinical areas, addressing current limitations, and proactively enhancing data quality and analytical rigor, the InRAD registry will be a foundation to contribute to improving patient care and outcomes in neurodegenerative diseases.
Extracellular stiffness regulates site-specific lung development
Authors: Liao Zhiying , Lv Junjie , Wang Dong , Chen Xuepeng , Zhao Jincun , Xu Tao , Meng Hao , Liu Huisheng
Published: January 2025

Extracellular matrix (ECM) stiffness plays a crucial role in regulating cell fate and maturation, but its influence on lung development is limited known. Here we utilized stiffness-tunable gelatin methacryloyl (GelMA) hydrogels to investigate how ECM stiffness influences site-specific lung development in a stem cell-derived lung organoid model. We found increased stiffness promoted NKX2-1+ lung progenitor cells (LPCs) generation. In airway organoids (hAWOs), stiff hydrogels directed proximal airway differentiation enriched with goblet, ciliated, and basal cells; whereas the decreased stiffness favored emergence of secretory cells in the proximal-distal transition zone and distal airway. In alveolar organoids (hALOs), increased stiffness enhanced AT2 and AT1 cells transition. Moreover, infection assays with Omicron BA.1.1 and Delta variants recapitulated the proximal-to-distal tropism of SARS-CoV-2 in the lung. Transcriptomic sequencing revealed ECM stiffness regulates lung development via Hippo, TGF-β, HIF and Wnt pathways. These findings advance mechanism understanding of ECM stiffness on lung development and provide a novel mechanical regulation for generating site-specific lung organoids.
Structural basis of K11/K48-branched ubiquitin chain recognition by the human 26S proteasome
Authors: Draczkowski Piotr , Chen Szu-Ni , Chen Ting , Wang Yong-Sheng , Huang Jessica Y.C. , Tsai Ming-Chieh , Lin Shu-Yu , Viner Rosa , Chang Yuan-Chih , Wu Kuen-Phon , Hsu Shang-Te Danny
Published: January 2025

Beyond the canonical K48-linked homotypic polyubiquitination for proteasome-targeted proteolysis, K11/K48-branched ubiquitin (Ub) chains are involved in fast-tracking protein turnover during cell cycle progression and proteotoxic stress. Here, we report cryo-EM structures of human 26S proteasome in a complex with a K11/K48-branched Ub chain. The structures revealed a multivalent substrate recognition mechanism involving a hitherto unknown K11-linked Ub binding site at the groove formed by RPN2 and RPN10 in addition to the canonical K48-linkage binding site formed by RPN10 and RPT4/5 coiled-coil. Additionally, RPN2 recognizes an alternating K11-K48 linkage through a conserved motif similar to the K48-specific T1 binding site of RPN1. The insights gleaned from these structures explain the molecular mechanism underlying the recognition of the K11/K48 branched Ub as a priority signal in the ubiquitin-mediated proteasomal degradation.
Characterization of the role of spatial proximity of DNA double-strand breaks in the formation of CRISPR-Cas9-induced large structural variations
Authors: Dahl-Jessen Mikkel , Terkelsen Thorkild , Bak Rasmus O. , Jensen Uffe Birk
Published: January 2025

Structural variations (SVs) play important roles in genetic diversity, evolution, and carcinogenesis and are, as such, important for human health. However, it remains unclear how spatial proximity of double-strand breaks (DSBs) affects the formation of SVs. To investigate if spatial proximity between two DSBs affects DNA repair, we used data from 3C experiments (Hi-C, ChIA-PET, and ChIP-seq) to identify highly interacting loci on six different chromosomes. The target regions correlate with the borders of megabase-sized topologically associated domains (TADs), and we used CRISPR-Cas9 nuclease and pairs of single guide RNAs (sgRNAs) against these targets to generate DSBs in both K562 cells and H9 human embryonic stem cells (hESCs). Droplet digital PCR (ddPCR) was used to quantify the resulting recombination events, and high-throughput sequencing was used to analyze the chimeric junctions created between the two DSBs. We observe a significantly higher formation frequency of deletions and inversions with DSBs in proximity compared with deletions and inversions with DSBs not in proximity in K562 cells. Additionally, our results suggest that DSB proximity may affect the ligation of chimeric deletion junctions. Taken together, spatial proximity between DSBs is a significant predictor of large-scale deletion and inversion frequency induced by CRISPR-Cas9 in K562 cells. This finding has implications for understanding SVs in the human genome and for the future application of CRISPR-Cas9 in gene editing and the modeling of rare SVs.
Influence of hydrogen on the electronic structure in the transition metallic glass
V80Zr20
Authors: Bylin Johan , Lindblad Rebecka , Spode Lennart , Scheicher Ralph H. , Pálsson Gunnar K.
Published: January 2025

We investigate the influence of hydrogen on the electronic structure of a binary transition metallic glass of V80Zr20. We examine the hybridization between the hydrogen and metal atoms with the aid of hard x-ray photoelectron spectroscopy. Combined with density functional theory, we are able to show and predict the formation of s−d hybridized energy states. With optical transmission and resistivity measurements, we investigate the emergent electronic properties formed out of those altered energy states, and together with the theoretical calculations of the frequency-dependent conductivity tensor, we qualitatively support the observed strong wavelength-dependency of the hydrogen-induced changes on the optical absorption and a positive parabolic change in resistivity with hydrogen concentration.

Published by the American Physical Society
2025
Ionization calculations using classical molecular dynamics
Authors: Plummer Daniel , Svensson Pontus , Gericke Dirk O. , Hollebon Patrick , Vinko Sam M. , Gregori Gianluca
Published: January 2025

By performing an ensemble of molecular dynamics simulations, the model-dependent ionization state is computed for strongly interacting systems self-consistently. This is accomplished through a free energy minimization framework based on the technique of thermodynamic integration. To illustrate the method, two simple models applicable to partially ionized hydrogen plasma are presented in which pair potentials are employed between ions and neutral particles. Within the models, electrons are either bound in the hydrogen ground state or distributed in a uniform charge-neutralizing background. Particular attention is given to the transition between atomic gas and ionized plasma, where the effect of neutral interactions is explored beyond commonly used models in the chemical picture. Furthermore, pressure ionization is observed when short-range repulsion effects are included between neutrals. The developed technique is general, and we discuss the applicability to a variety of molecular dynamics models for partially ionized warm dense matter.

Published by the American Physical Society
2025
Employee personal hygiene, visible cleanliness and microbial contamination of beverages at coffee outlets in Busan: a pilot study
Authors: Choe Yunseon , Lee Seungjun , Yeo Sohyun , Choi Jinkyung
Published: January 2025

Purpose

The study objective was to investigate the microbial status of the coffee, ice and cups used in coffee outlets. This study compared food safety practices and microbial status between franchised and single-unit outlets.

Design/methodology/approach

The study subjects included franchised and single-unit coffee outlets. This study adopted two different methods: self-answered checklists and microbial laboratory tests. We compared the two datasets by operation type (franchised vs single-unit). We analysed the data using independent t-test and chi-square tests.

Findings

Franchised outlets were more likely to apply food safety practices than single-unit outlets; however, microbial testing showed that franchised outlets had a worse microbial status than single-unit outlets. A restaurant sanitation certificate did not influence microbial status. In addition, an analysis of food safety practice checklist items and microbial status showed that the checklist items did not impact food safety.

Originality/value

These study results suggest that regular employee training programmes are needed for food safety and sanitation. Current inspection items should be revised and new items added for target operations (outlets that make and serve beverages). The current restaurant certification system should be revised, and certified food service outlets should be inspected regularly.
It’s not all fun and games: gamification in e-commerce on consumers’ impulse buying of retail food products
Authors: Lim Song-Yik , Tan Yiqi , Loh Xiu-Ming , Cham Tat-Huei , Ooi Mun-Yee , Tan Garry Wei-Han
Published: January 2025

Purpose

This study aims to look into the role of gamification as an effective marketing tool to engage with consumers and influence purchase behaviours. As there are a plethora of gamified elements, it is crucial to determine which of them can significantly facilitate consumer purchase behaviour. Therefore, a unique stimulus–organism–response (SOR) framework which encompasses four popular gamified elements (i.e. fun, rewards, competition and badges) was employed to investigate consumers’ engagement.

Design/methodology/approach

An online survey was utilized to collect the data which yielded 307 responses. Subsequently, partial least squares-structural equation modeling (PLS-SEM) was used to analyse the data.

Findings

Among the gamification elements assessed in this study, fun was revealed to be the strongest facilitating antecedent of shopping engagement. However, reward was revealed to have an insignificant effect on shopping engagement. In addition, it was found that consumers undergo a processual development with regard to their impulse buying of retail food products. More precisely, shopping engagement is a significant facilitator of customer satisfaction which subsequently motivates impulse buying.

Originality/value

This is among the pioneering studies to provide detailed insights into the effect of different gamified elements on consumer engagement. Furthermore, a number of practical and theoretical implications for the relevant stakeholders were discussed.
Fukushima twelve years after the nuclear accident
Authors: Kawasaki Kota
Published: January 2025

Purpose

This paper analyzes the structure of recovery policies in Fukushima, discusses the current situation of the affected areas and the affected people of Fukushima 12 years after the Fukushima nuclear accident occurred and points out issues concerning revitalization of Fukushima based on the results of field surveys of the affected areas, as well as interviews and questionnaires of the affected people and literature reviews.

Design/methodology/approach

After the Fukushima nuclear accident occurred in March 2011, what policies have been implemented? To what extent have the affected areas of Fukushima been regenerated? To what extent have the affected people of Fukushima rebuilt their lives? What are the issues that need to be addressed for the revitalization of Fukushima? Since the Fukushima nuclear accident occurred, the author has continued to conduct field surveys of the affected areas, as well as interviews and questionnaires of the affected people, and literature review. This paper aims to answer three questions based on the results of these surveys and reviews.

Findings

First, the nuclear disaster is characterized by its wide-area and long-term nature. Second, recovery of the affected areas by public projects do not have sufficient effect on rebuilding of the lives of the affected people since most of the affected people do not return to the affected areas. Third, it is necessary to establish a legal system for disaster prevention, recovery and revitalization suited to the characteristics of the nuclear disaster in order to promote rebuilding of the lives of the affected people and for the recovery of the affected areas.

Originality/value

There is little literature that has been systematically examined regarding the recovery from the Fukushima nuclear accident. This paper discusses the current status and issues of recovery from nuclear disaster 12 years after the nuclear accident, based on my experiences as the chairperson of the Fukushima Prefecture Recovery Planning Committee and the chairperson of the Recovery Planning Committee in several municipalities where evacuation orders were issued after the Fukushima nuclear accident occurred.
Adapting to change: redefining employee utilization in construction projects through lessons learnt from COVID-19
Authors: Arshad Muneeb , Sumbal Muhammad Saleem , Akhtar Muhammad Naseer , Nauman Shazia
Published: January 2025

Purpose

The study aims to understand the challenges of effective employee utilization in construction projects during the coronavirus disease 2019 (COVID-19) pandemic in a developing country and to develop mitigation strategies for post-pandemic workforce management.

Design/methodology/approach

We used a qualitative research design to conduct semi-structured interviews with elite informants of various construction firms and analyze the data using thematic analysis.

Findings

The results showed that numerous factors, including supply chain issues, inadequate worker healthcare, ineffective knowledge management and job losses, have negatively impacted the construction industry. The prominent outcomes of the study are a conceptual framework for effective workforce management post-pandemic and beyond, including recommendations for managers and executives and future research.

Originality/value

The workforce management framework with knowledge management developed in this study provides a new theoretical view of post-pandemic mitigation strategies through the theoretical lens of dynamics capabilities and knowledge management. The findings cover industrial insights, particularly from the stakeholders’ perspective, and provide a solid foundation for future research in this domain.
Film festivals and social inclusion: the Ciputra Film Festival’s collaborative spirit
Authors: Haryono Cosmas Gatot , Pamungkas Thomas Bambang , Hartanto Louisa
Published: January 2025

Purpose

The purpose of this study is to investigate the strategies used by Ciputra Film Festival organizers to package the festival as an inclusive festival. It will be revealed how film festivals serve as a means of collaboration for various Indonesian film communities.

Design/methodology/approach

This study was carried out using an exploratory method, a qualitative approach and an interpretive paradigm, in which researchers put themselves in the shoes of the participants.

Findings

According to the findings of the thematic analysis, the strategy for organizing the Ciputra Film Festival (from the beginning of planning to the end of the festival) promotes the values of diversity from each community. They promote the festival as a celebration of diversity as well as a collaboration among local film communities that reflect the characteristics of the Indonesian nation, which is indeed very diverse in terms of ethnicity, culture, social and political preferences. The local film community is active in all aspects of the festival, including consumption, production, political participation and social interaction.

Practical implications

The organization of the Ciputra Film Festival has attempted to be inclusive by uniting the interests of the local film community, local culture and the film business. However, some community aspirations and the existence of local cultural elements must continue to be prioritized so that participants and visitors get the best experience.

Originality/value

This study advances a discussion of inclusive film festival events that collaborate with as many local film communities as possible, with the goal of identifying specific practices of engaging local film communities that contribute to inclusivity.
Employee disputes and innovation performance: evidence from the pharmaceutical industry
Authors: Rayfield Blake , Unsal Omer
Published: January 2025

Purpose

This study aims to explore the impact of employee litigation on the innovation output of firms, specifically within the pharmaceutical sector, by examining the relationship between employee lawsuits and Food and Drug Administration (FDA) product approvals.

Design/methodology/approach

Utilizing a hand-collected dataset comprising 2,293 employee disputes, this research conducts an empirical analysis to test how litigation involving employees influences the rate of FDA approvals for new pharmaceutical products.

Findings

The analysis reveals that employee disputes are negatively associated with the number of FDA-approved products, indicating that firms facing frequent employee allegations tend to exhibit lower innovation outcomes. Further, the study identifies case characteristics, such as the involvement of labor unions and the duration of cases, as significant determinants that delay the FDA approval process, thereby adversely affecting innovation performance.

Research limitations/implications

While the study provides novel insights into the relationship between employee litigation and innovation in the pharmaceutical industry, the findings are contingent upon the accuracy of the dataset and may not be universally applicable across all sectors.

Practical implications

The results underscore the critical importance of maintaining a positive workplace environment and treating employees fairly to foster innovation performance. Firms are encouraged to adopt strategies that mitigate the risk of litigation to enhance their innovation capabilities.

Originality/value

This research contributes to the literature by offering empirical evidence on the detrimental effects of employee litigation on firms’ ability to innovate, particularly in the highly regulated pharmaceutical industry. It highlights the significance of workplace relations in influencing a firm’s innovation outcomes.
Catalytic role of Islam’s social well-being and economic justice as determinants of peaceful coexistence: a systematic literature review using PRISMA
Authors: Ashafa Saheed Afolabi , Raimi Lukman , Bamiro Nurudeen Babatunde
Published: January 2025

Purpose

The contributions of Islam to human civilization, spanning theology, philosophy, politics, economy, sociology and science, find ample documentation in several historical records. This paper aims to critically examine the catalytic role played by Islam’s social well-being and economic justice in advancing peaceful coexistence.

Design/methodology/approach

This exploration is carried out through a systematic literature review using the PRISMA framework. The paper addresses three core thematic research questions, with the intent of offering a comprehensive contribution to both the theory and application of Islamic Studies. To acquire essential data, a qualitative research approach focused on documentation, particularly the collection of non-numerical data from secondary sources, including the Qur’an, Hadith and scholarly articles, was used.

Findings

The systematic literature review led to three notable insights. Firstly, the promotion of social well-being by Islam contributes positively to peaceful coexistence across various global regions. Secondly, Islam’s emphasis on economic justice also plays a constructive role in nurturing peaceful coexistence in diverse geographical areas. Thirdly, the alignment between Islam’s promotion of social well-being and economic justice, following the principles of Maqasid al-Shari’ah and the five international principles of peaceful coexistence, lays the groundwork for prospective theoretical inquiries.

Originality/value

This study provides a pioneering perspective by systematically integrating Islamic principles with international frameworks for peaceful coexistence through the Preferred Reporting Items for Systematic Reviews and Meta Analysis (PRISMA) methodology. It offers a unique contribution by presenting how Islam’s intrinsic values of social well-being and economic justice using Maqasidul Shari’ah indicators serve as catalysts for promoting global harmony and social stability. By bridging religious tenets with universal coexistence principles, the study sets a foundational framework for interdisciplinary and policy-driven discourse on achieving sustainable peace through faith-based social and economic structures.
High-performance and promising biolubricants from agro-waste cashew nut shell liquid
Authors: Li Tianjiao , Ma Jing , Li Guangwen , Chen Xiaowei
Published: January 2025

Purpose

This study aims to replace petroleum-based lubricating oils with sustainable biomaterials, addressing issues associated with existing alternatives, such as poor performance, high cost and limited availability.

Design/methodology/approach

The transformation of agricultural waste cardanol, a nonedible vegetable oil that is abundantly available, into green cardanyl acetate (CA) biolubricating ester oil. The potential of CA as a base stock for lubricants is validated by assessing its lubrication performance.

Findings

CA exhibited a higher viscosity index, flash point and thermal stability than commercially available mineral-based (CTL3, coal-to-liquid) and synthetic (PAO2, poly-alpha-olefin) lubricant base stocks. Moreover, CA exhibits excellent anticorrosivity properties as well as PAO2 and CTL3. The tribological properties of CA were evaluated, and the results show that CA exhibits a smaller average wear scar diameter (WSD) of 0.54 mm than that of PAO2 (0.85 mm) and CTL3 (0.90 mm). In extreme pressure tests, acylated CA demonstrated the highest last nonseizure load capacity at 510 N, outperforming commercial CTL3 (491 N) and PAO2 (412 N). All results demonstrate that CA displays an excellent series of base stock properties.

Originality/value

The novelty of this work lies in the utilization of renewable agricultural waste, cashew nut shell liquid, to produce a high-value biolubricant as an alternative to commercial fossil-based lubricants. The renewable nature, low cost, and large-scale availability of raw materials pave a new path for the production and application of biolubricants, showcasing the immense potential of converting agricultural waste into high-value products.

Peer review

The peer review history for this article is available at: https://publons.com/publon/10.1108/ILT-03-2024-0064/
Institutional logics, social interactions and management of tensions in public-private partnership organizations
Authors: Danışman Ali , Özseven Mustafa
Published: January 2025

Purpose

We aim to understand the link between field-level institutional logics and practice-level social interactions and relationships between public and private actors and their influences on the responses and resolutions to the issues causing tensions.

Design/methodology/approach

Adopting a multiple logics perspective with a focus on social interactions and relationships between public and private actors, we conducted a multiple case study in five city hospitals recently established under a public-private partnership model in the Turkish healthcare field.

Findings

We found that the state and market logics that predominantly characterize the Turkish healthcare field were enacted in each of the five hospitals in different manners and constitute three different configurations as compatible, complementary and contradictory. The social interactions and relationships developed between the public and private actors occur based on these configurations, and they all together shape the responses and resolutions to the issues causing tensions.

Research limitations/implications

Since we did all analyses between the organizational actors at the partnership level, we did not consider possible differences arising from individual and positional roles in each partnership. It is therefore important to acknowledge that the interviews, which are central to the research results, might be influenced by the motivation and power dynamics of the participants in terms of their positions, roles and responsibilities. Thus, much work must be done to understand the management of tensions in public-private partnership organizations (PPPOs) influenced by institutional logics with a greater focus on individual, partnership, organizational and field-level interactions.

Practical implications

Tensions arising between public and private actors in PPPOs can be understood better and managed more effectively when the enactment of institutional logics is considered together with their social interactions and relationships.

Originality/value

The novelty of our study is that we advance the knowledge on the management of tensions in PPPOs by empirically showing the link between field-level institutional logics and practice-level social interactions and relationships and their influences on the responses and resolutions to the issues causing tensions. Our results indicate that tensions arising between public and private actors in PPPOs are primarily responded to by private actors mainly with avoidance, defiance or decoupling and subsequently resolved by their joint efforts through informal collaboration, formalization, formalized collaboration, enforcement or coercive pressure, depending on how the state and market logics are enacted within the hospitals and how social interactions and relationships between public and private side actors are formed accordingly.