bluuebunny/crossref_metadata_2025_split huggingface dataset:
CD56-mediated activation of human natural killer cells is triggered byAspergillus fumigatusgalactosaminogalactan
Authors: Heilig Linda , Natasha Fariha , Trinks Nora , Aimanianda Vishukumar , Sze Wah Wong Sarah , Fontaine Thierry , Terpitz Ulrich , Strobel Lea , Le Mauff François , Sheppard Donald C. , Schäuble Sascha , Kurzai Oliver , Hünniger Kerstin , Weiss Esther , Vargas Mario , Howell P. Lynne , Panagiotou Gianni , Wurster Sebastian , Einsele Hermann , Löffler Jürgen 
Published: August 2023

AbstractInvasive aspergillosis causes significant morbidity and mortality in immunocompromised patients. Natural killer (NK) cells are pivotal for antifungal defense. Thus far, CD56 is the only knownpathogen recognition receptoron NK cells triggering potent antifungal activity againstAspergillus fumigatus. However, the underlying cellular mechanisms and the fungal ligand of CD56 have remained unknown. Using purified cell wall components, biochemical treatments, andA. fumigatusmutants with altered cell wall composition, we herein found that CD56 interacts with theA. fumigatuscell wall carbohydrate galactosaminogalactan (GAG). This interaction induced NK cell activation, degranulation, and secretion of immune-enhancing chemokines and cytotoxic effectors. Supernatants from GAG-stimulated NK cells elicited antifungal activity and enhanced antifungal effector responses of polymorphonuclear cells. In conclusion, we identifiedA. fumigatusGAG as a ligand of CD56 on human primary NK cells, stimulating potent antifungal effector responses and activating other immune cells.
Identification and mapping of human lymph node stromal cell subsets by combining single-cell RNA sequencing with spatial transcriptomics
Authors: Grasso Cristoforo , Roet Janna , Gago de Graça Catarina , Semmelink Johanna F. , Remmerswaal Ester , Jongejan Aldo , Moerland Perry D. , Mebius Reina E. , van Baarsen Lisa G. M. 
Published: August 2023

SummaryLymph node stromal cells (LNSCs) have a crucial immunomodulatory function, but their heterogeneity in human is incompletely understood. Here, we report the single cell RNA sequencing (scRNA-seq) of 12’000 LNSCs isolated from a human lymph node (LN). This study comprehensively defines the gene signatures of 10 fibroblast subtypes: CCL21+SC, CCL19+SC, CD34+CXCL14+SC, pericytes, DES+SC, LAMP5+SC, NR4A1+BCAM+SC, HLA-DR+SC, SEPT4+SC and GLDN+SC. To explore the heterogeneous stromal compartment within the complex LN tissue architecture, we integrated the scRNA-seq profiles of the identified LNSC subsets with a publicly available human spatial transcriptomic LN dataset and predicted their location within the complex LN tissue architecture. Each LNSC subtype was spatially restricted to specific LN regions, indicating different LNSC-lymphocyte interactions which was further investigated using NicheNet. The positioning of distinct LNSC subtypes in different LN regions sets the stage for future research on the relationship between LNSC-specific niches and immunomodulatory function during health and disease.
‘Radical’ differences between two FLIM microscopes affect interpretation of cell signaling dynamics
Authors: Mukherjee Sravasti , Klarenbeek Jeffrey , Oualid Farid El , Broek Bram van den , Jalink Kees 
Published: August 2023

ABSTRACTEmerging evidence suggests that cell signaling outcomes depend not only on the signal strength but also on its temporal progression. Our lab employs Fluorescence Lifetime Imaging of Resonance Energy Transfer (FLIM/FRET) biosensors to study intracellular signaling dynamics. We studied activation of β1 receptors by Isoproterenol, which triggers cAMP signaling via the G protein Gαs, using two different FLIM microscopes: a widefield frequency domain FLIM (fdFLIM) setup and a fast confocal Time Correlated Single Photon Counting (TCSPC) setup.When comparing results from each FLIM setup, unexpectedly we obtained distinctively different cAMP kinetics: fdFLIM recording of cAMP in HeLa and Cos7 cells yielded transient responses, reminiscent of rapid receptor desensitization, while TCSPC recordings exhibited sustained responses lasting over 30 minutes. We initially suspected phototoxicity due to the intense light locally in the laser focus spot in confocal microscopy to interfere with normal termination of signal transduction and set out to map photosensitive steps in the signaling cascade in detail. We find no evidence for light-sensitivity in either generation or breakdown of cAMP, but rather, our findings show that the kinetic differences are due to selective degradation of β1 agonists on the fdFLIM setup. Agonist degradation appeared due to the commercial FluoroBrite medium, even though this has been specifically advertised to lower phototoxicity and reduce autofluorescence. Mass spectrometry identified Folic acid, an undisclosed constituent of FluoroBrite, as the culprit leading to artifacts in fdFLIM measurements.In all, our study underscores the impact of subtle phototoxicity effects on experimental outcome, and it shows that in this case confocal TCSPC provides the more reliable data needed to study response kinetics. This work also emphasizes the it is crucial that scientific vendors fully disclose chemical formulations.
Endothelial Lipase Variant, T111I, Does Not Alter Inhibition by Angiopoietin-like Proteins
Authors: Sylvers-Davie Kelli L. , Bierstedt Kaleb C. , Schnieders Michael J. , Davies Brandon S. J. 
Published: August 2023

ABSTRACTHigh levels of HDL-C are correlated with a decreased risk of cardiovascular disease. HDL-C levels are modulated in part by the secreted phospholipase, endothelial lipase (EL), which hydrolyzes the phospholipids of HDL and decreases circulating HDL-C concentrations. A 584C/T polymorphism inLIPG, the gene which encodes EL, was first identified in individuals with increased HDL levels. This polymorphism results in a T111I point mutation the EL protein. The association between this variant, HDL levels, and the risk of coronary artery disease (CAD) in humans has been extensively studied, but the findings have been inconsistent. In this study, we took a biochemical approach, investigating how the T111I variant affected EL activity, structure, and stability. Moreover, we tested whether the T111I variant altered the inhibition of phospholipase activity by angiopoietin-like 3 (ANGPTL3) and angiopoietin-like 4 (ANGPTL4), two known EL inhibitors. We found that neither the stability nor enzymatic activity of EL was altered by the T111I variant. Moreover, we found no difference between wild-type and T111I EL in their ability to be inhibited by ANGPTL proteins. These data suggest that any effect this variant may have on HDL-C levels or cardiovascular disease are not mediated through alterations in these functions.
Membrane binding and pore formation is Ca2+-dependent for theClostridioides difficilebinary toxin
Authors: Abeyawardhane Dinendra L. , Sevdalis Spiridon E. , Adipietro Kaylin A. , Godoy-Ruiz Raquel , Varney Kristen M. , Nawaz Izza F. , Spittel Alejandro X. , Rustandi Richard R. , Silin Vitalii I. , des Georges Amedee , Cook Mary E. , Pozharski Edwin , Weber David J. 
Published: August 2023

AbstractTheC. difficilebinary toxin (CDT) enters host cells via endosomal delivery like many other ‘AB’-type binary toxins. In this study, the cell-binding component of CDT, termed CDTb, was found to bind and form pores in lipid bilayers upon depleting free Ca2+ion concentrations, and not by lowering pH, as found for other binary toxins (i.e., anthrax). Cryoelectron microscopy, nuclear magnetic resonance spectroscopy, surface plasmon resonance, electrochemical impedance spectroscopy, CDT toxicity studies, and site directed mutagenesis show that dissociation of Ca2+from a single site in receptor binding domain 1 (RBD1) of CDTb is consistent with a molecular mechanism in which Ca2+dissociation from RBD1 induces a “trigger” via conformational exchange that enables CDTb to bind and form pores in endosomal membrane bilayers as free Ca2+concentrations decrease during CDT endosomal delivery.One-Sentence SummaryCa2+dissociation and unfolding of a receptor binding domain in CDTb activates pore-formation by theC. difficilebinary toxin.
Causal role of the angular gyrus in insight-driven memory reconfiguration
Authors: Grob Anna-Maria , Heinbockel Hendrik , Milivojevic Branka , Doeller Christian F. , Schwabe Lars 
Published: August 2023

AbstractMaintaining an accurate model of the world relies on our ability to update memory representations in light of new information. Previous research on the integration of new information into memory mainly focused on the hippocampus. Here, we hypothesized that the angular gyrus, known to be involved in episodic memory and imagination, plays a pivotal role in the insight-driven reconfiguration of memory representations. To test this hypothesis, participants received continuous theta burst stimulation (cTBS) over the left angular gyrus or sham stimulation before gaining insight into the relationship between previously separate life-like animated events in a narrative-insight task. During this task, participants also underwent EEG recording and their memory for linked and non-linked events was assessed shortly thereafter. Our results show that cTBS to the angular gyrus decreased memory for the linking events and reduced the memory advantage for linked relative to non-linked events. At the neural level, cTBS targeting the angular gyrus reduced centro-temporal coupling with frontal regions and abolished insight-induced neural representational changes for events linked via imagination, indicating impaired memory reconfiguration. Further, the cTBS group showed representational changes for non-linked events that resembled the patterns observed in the sham group for the linked events, suggesting failed pruning of the narrative in memory. Together, our findings demonstrate a causal role of the left angular gyrus in insight-related memory reconfigurations.
Comprehensive Interrogation of Synthetic Relationships in the Human DNA Damage Response
Authors: Fielden John , Siegner Sebastian M , Gallagher Danielle N , Schröder Markus S , Dello Stritto Maria Rosaria , Kobel Lena , Schlapansky Moritz F , Cejka Petr , Jost Marco , Corn Jacob E 
Published: August 2023

AbstractThe DNA damage response (DDR) is a multi-faceted network of pathways that preserves genome stability. Unraveling the complementary interplay between these pathways remains a challenge. Here, we comprehensively mapped genetic interactions for all core DDR genes using combinatorial CRISPRi screening. We discovered myriad new connections, including interactions between cancer genes and small molecule targets. We focused on two of the strongest interactions:FEN1/LIG1:WDR48andFANCM:SMARCAL1. First, we found that WDR48 works with USP1 to restrain overactive translesion synthesis in FEN1/LIG1-deficient cells, and that a preclinical inhibitor of USP1 specifically kills FEN1-deficient cells. Second, we found that SMARCAL1 and FANCM suppress DNA double-strand break (DSB) formation at TA-rich repeats in late replicating regions that otherwise escape into mitosis and cause nuclear fragmentation. We present fundamental insights into genome maintenance processes and our dataset provides a springboard for mechanistic investigations into connections between DDR factors and suggests multiple interactions that could be exploited in cancer therapy.
Endogenous BAX and BAK form mosaic rings of variable size and composition on apoptotic mitochondria
Authors: Schweighofer Sarah Vanessa , Jans Daniel C. , Keller-Findeisen Jan , Folmeg Anne , Bates Mark , Jakobs Stefan 
Published: August 2023

AbstractOne hallmark of apoptosis is the oligomerization of BAX and BAK to form a pore in the mitochondrial outer membrane, which mediates the release of pro-apoptotic intermembrane space proteins into the cytosol. Cells overexpressing BAX or BAK fusion proteins are a powerful model system to study the dynamics and localization of these proteins in cells. However, it is unclear whether overexpressed BAX and BAK form the same ultrastructural assemblies following the same temporal hierarchy as endogenously expressed proteins. Combining live– and fixed-cell STED super-resolution microscopy, we show that overexpression of BAK results in novel BAK structures, which are virtually absent in non-overexpressing apoptotic cells. We further demonstrate that in wildtype cells, BAK is recruited to apoptotic pores before BAX. Both proteins together form unordered, mosaic rings on apoptotic mitochondria in immortalized cell culture models as well as in human primary cells. In BAX– or BAK-single-knockout cells, the remaining protein is able to form rings independently. The heterogeneous nature of these rings corroborates the toroidal apoptotic pore model.
LiaX is a surrogate marker for cell-envelope stress and daptomycin non-susceptibility inEnterococcus faecium
Authors: Axell-House Dierdre B. , Simar Shelby R. , Panesso Diana , Rincon Sandra , Miller William R. , Khan Ayesha , Pemberton Orville A. , Valdez Lizbet , Nguyen April H. , Hood Kara S. , Rydell Kirsten , DeTranaltes Andrea M. , Jones Mary N. , Atterstrom Rachel , Reyes Jinnethe , Sahasrabhojane Pranoti V , Suleyman Geehan , Zervos Marcus , Shelburne Samuel A. , Singh Kavindra V. , Shamoo Yousif , Hanson Blake M. , Tran Truc T. , Arias Cesar A. 
Published: August 2023

ABSTRACTDaptomycin (DAP) is often used as a first line therapy to treat vancomycin-resistantEnterococcus faecium(VREfm) infections but emergence of DAP non-susceptibility threatens the effectiveness of this antibiotic. Moreover, current methods to determine DAP MICs have poor reproducibility and accuracy. In enterococci, DAP resistance is mediated by the LiaFSR cell membrane stress response system and deletion ofliaRencoding the response regulator results in hypersusceptibility to DAP and antimicrobial peptides. The main genes regulated by LiaR are a cluster of three genes, designatedliaXYZ. InEnterococcus faecalis, LiaX is surface exposed with a C-terminus that functions as a negative regulator of cell membrane remodeling and an N-terminal domain that is released to the extracellular medium where it binds DAP. Thus, inE. faecalis, LiaX functions as a sentinel molecule recognizing DAP and controlling the cell membrane response, but less is known about LiaX inE. faecium. Here, we found thatliaXis essential inE. faecium(Efm) with an activated LiaFSR system. UnlikeE. faecalis,EfmLiaX is not detected in the extracellular milieu and does not appear to alter phospholipid architecture. We further postulated that LiaX could be used as a surrogate marker for cell envelope activation and non-susceptibility to DAP. For this purpose, we developed and optimized a LiaX ELISA. We then assessed 86 clinicalE. faeciumBSI isolates for DAP MICs and used whole genome sequencing to assess for substitutions in LiaX. All DAP-R clinical strains ofE. faeciumexhibited elevated LiaX levels. Strikingly, 73% of DAP-S isolates by standard MIC determination had elevated LiaX ELISAs above the established cut-off. Phylogenetic analyses of predicted amino acid substitutions showed 12 different variants of LiaX without a specific association with DAP MIC or LiaX ELISA values. Our findings also suggest that manyEfmisolates that test DAP susceptible by standard MIC determination are likely to have an activated cell stress response that may predispose to DAP failure. As LiaX appears to be essential for the cell envelope response to DAP, its detection could prove useful to improve the accuracy of susceptibility testing by anticipating therapeutic failure.
Cis-regulatory modes ofUltrabithoraxinactivation in butterfly forewings
Authors: Tendolkar Amruta , Mazo-Vargas Anyi , Livraghi Luca , Hanly Joseph J. , Van Horne Kelsey C. , Gilbert Lawrence E. , Martin Arnaud 
Published: August 2023

ABSTRACTHoxgene clusters encode transcription factors that drive regional specialization during animal development:e.g.the Hox factor Ubx is expressed in the insect metathoracic (T3) wing appendages and differentiates them from T2 mesothoracic identities.Hoxtranscriptional regulation requires silencing activities that prevent spurious activation and regulatory crosstalks in the wrong tissues, but this has seldom been studied in insects other thanDrosophila, which shows a derivedHoxdislocation into two genomic clusters that disjoinedAntennapedia(Antp) andUltrabithorax(Ubx). Here we investigated howUbxis restricted to the hindwing in butterflies, amidst a contiguousHoxcluster. By analysing Hi-C and ATAC-seq data in the butterflyJunonia coenia, we show that a Topologically Associated Domain (TAD) maintains a hindwing-enriched profile of chromatin opening aroundUbx. This TAD is bordered by a Boundary Element (BE) that separates it from a region of joined wing activity around theAntplocus. CRISPR mutational perturbation of this BE releases ectopicUbxexpression in forewings, inducing homeotic clones with hindwing identities. Further mutational interrogation of two non-coding RNA encoding regions and one putativecis-regulatory module within theUbxTAD cause rare homeotic transformations in both directions, indicating the presence of both activating and repressing chromatin features. We also describe a series of spontaneous forewing homeotic phenotypes obtained inHeliconiusbutterflies, and discuss their possible mutational basis. By leveraging the extensive wing specialization found in butterflies, our initial exploration ofUbxregulation demonstrates the existence of silencing and insulating sequences that prevent its spurious expression in forewings.
Investments, subsidies and financial constraints in Estonian agriculture
Authors: Aleksandrova Olha , Fertő Imre , Viira Ants-Hannes 
Published: August 2023

PurposeThe purpose of this study is to explore the determinants of investment decisions of Estonian farms after the transition to market economy and accession to the European Union (EU), in the period 2006–2019.Design/methodology/approachThe paper employs Estonian Farm Accountancy Data Network (FADN) individual farm-level data from the period 2006–2019, and standard and augmented accelerator investment models. Generalised methods of moments (GMM) and bias-corrected least-squares dummy variables (LSDVC) regressions were used to estimate parameters of these models.FindingsIn the considered period, farm investments were positively affected by sales growth, investment subsidies and the cash flow. Decomposition of cash flow into volatile, market income related part, and more stable, farm subsidies related part indicated that investments do not depend on market income part of cash flow. Instead, the stable part of the cash flow (farm subsidies) had a significant and positive effect on investments. This suggests that credit rationing could be present in the EU agriculture, and it depends on the farm subsidies not market income of farms.Originality/valueDespite the wealth of literature on the investment behaviour of farmers, this article is the first attempt to decompose farm cash flow into stable (farm subsidies) and volatile (market income) parts to explain the role of subsidies as a part of cash flow in credit rationing.
Packaging of ready-to-eat products: a mix research approach for exploring aesthetic element influence on brand preference
Authors: Dave Anupama Chirag 
Published: August 2023

PurposePackaging design has the power to convey persuasive and functional benefits, thereby inducing the brand preference as per empirical studies, but not much has been studied in detail about aesthetic aspects of packaging. This study is a careful attempt to understanding the influence of aesthetic elements—colour, illustrations/images/pictures and information representation’s influence on consumer brand preference for ready-to-eat (RTE) product category of pav bhaji.Design/methodology/approachThe data for this study have been collected in two phases; phase 1 was a quantitative research where structure Google form was used while in order to elite consumer responses regarding their preferences structured interview was conducted in phase 2. Twenty-five respondents were selected using snowball sampling, who were approached for understanding how aesthetic element influenced their brand preference.FindingsThis research could help in identifying various underlying subthemes within the three major themes of aesthetic element in packaging. By utilising these, packaging modifications could be made to increase brand preference.Originality/valueIn case of RTE segment, in-store decisions are mostly take in spurn of minutes, hence making it one of essential topics of research. The findings of this research can contribute in placement of correct element in appropriate position to grab consumers’ interest leading to brand preference.
Incentive contract design and selection for inhibiting unethical collusion in construction projects
Authors: Cui Lei 
Published: August 2023

Purpose The construction industry has long been criticized for unethical conduct. The owner usually manages the contractor's opportunistic behaviors by employing a professional supervisor, but there is a risk of covert collusion between the supervisor and contractor. Based on the principal–agent theory and collusion theory, this paper aims to investigate optimal collusion-proof incentive contracts.Design/methodology/approachThis paper presents a game-theoretic framework comprising an owner, supervisor and contractor, who interact and pursue maximized self-profits. Built upon the fixed-price incentive contract, cost-reimbursement contract, and revenue-sharing contract, different collusion-proof incentive contracts are investigated. A real project case is used to validate the developed model and derived results.FindingsThis paper shows that the presence of unethical collusion undermines the owner's interests. Especially, the possibility of agent collusion may induce the owner to abandon extracting quality information from the supervisor. Furthermore, information asymmetry significantly affects the construction contract selection, and the application conditions for different incentive contracts are provided.Research limitations/implicationsThis study still has some limitations that deserve further exploration. First, this study explores contractor–supervisor collusion but ignores the possibility of the supervisor abusing authority to extort the contractor. Second, to focus on collusion, this paper ignores the supervision costs. What's the optimal supervision effort that the owner should induce the supervisor to exert? Finally, this paper assumes that the colluders involved always keep their promises. However, what if the colluders may break their promises?Practical implicationsSeveral collusion-proof incentive contracts are explored in a project management setting. The proposed incentive contracts can provide the project owner with effective and practical tools to inhibit covert collusion in construction management and thus safeguard construction project quality.Originality/valueThis study expands the organization collusion theory to the field of construction management and investigates the optimal collusion-proof incentive contracts. In addition, this study is the first to investigate the effects of information asymmetry on contract selection.