bluuebunny/crossref_metadata_2025 huggingface dataset:
Cryptic proteins translated from deletion-containing viral genomes dramatically expand the influenza virus proteome
Authors: Ranum Jordan N , Ledwith Mitchell P , Alnaji Fadi G , Diefenbacher Meghan , Orton Richard , Sloan Elisabeth , Guereca Melissa , Feltman Elizabeth M , Smollett Katherine , da Silva Filipe Ana , Conley Michaela , Russell Alistair B , Brooke Christopher B , Hutchinson Edward , Mehle Andrew
Published: December 2023

Productive infections by RNA viruses require faithful replication of the entire genome. Yet many RNA viruses also produce deletion-containing viral genomes (DelVGs), aberrant replication products with large internal deletions. DelVGs interfere with the replication of wild-type virus and their presence in patients is associated with better clinical outcomes as they. The DelVG RNA itself is hypothesized to confer this interfering activity. DelVGs antagonize replication by out-competing the full-length genome and triggering innate immune responses. Here, we identify an additionally inhibitory mechanism mediated by a new class of viral proteins encoded by DelVGs. We identified hundreds of cryptic viral proteins translated from DelVGs. TheseDelVG-encodedproteins (DPRs) include canonical viral proteins with large internal deletions, as well as proteins with novel C-termini translated from alternative reading frames. Many DPRs retain functional domains shared with their full-length counterparts, suggesting they may have activity during infection. Mechanistic studies of DPRs derived from the influenza virus protein PB2 showed that they poison replication of wild-type virus by acting as dominant-negative inhibitors of the viral polymerase. These findings reveal that DelVGs have a dual inhibitory mechanism, acting at both the RNA and protein level. They further show that DPRs have the potential to dramatically expand the functional proteomes of diverse RNA viruses.
Ku-binding motifs in RAG2, XLF, PAXX and MRI support functional redundancy during V(D)J recombination
Authors: Tadi Satish K. , Gesnik Armelle , Frit Philippe , Iehl Florence , Ropars Virginie , Dingli Florent , Loew Damarys , Calsou Patrick , Callebaut Isabelle , Charbonnier Jean-Baptiste , de Villartay Jean-Pierre
Published: December 2023

The interaction of several partners with Ku through Ku-binding motifs (KBMs) in their sequences governs their enrolment in NHEJ repair complexes. Here, we first established more specifically the function of KBMs in V(D)J recombination as the molecular basis of functional redundancy between XLF and the NHEJ proteins MRI and PAXX. Then, given the functional redundancy between RAG2 and XLF, we explored the hypothesis of a KBM-mediated interaction between RAG2 and Ku. Through sequence alignment and biophysical methods, we identified a KBM at the C-terminus of RAG2 (R2CT) that mediates its interaction with Ku bothin vitroandin cellulo. Notably, we showed that R2CT/Ku interaction is independent of the RAG nuclease activity. Finally, we demonstrated that the respective KBMs of RAG2 and XLF support their functional redundancy for V(D)J recombination.
Involvement of FKBP5, but not of stress, in alcohol memory reconsolidation
Authors: Rahamim Nofar , Aronovici Coral , Liran Mirit , Goltseker Koral , Levin-Greenwald Matar , Heymann Tim , Hausch Felix , Barak Segev
Published: December 2023

Relapse is a fundamental challenge in drug addiction, often evoked by exposure to drug-associated cues. Upon retrieval, memories become temporarily labile before re-stabilizing in a process termed reconsolidation. Therefore, targeting the reconsolidation process offers a therapeutic approach for relapse prevention via the disruption of the drug-cue memories. We recently demonstrated that retrieval of contextual alcohol memories increased the expression of the mRNA encoding for FK506 binding protein 51 (FKBP51), a regulator of the hypothalamic-pituitary-adrenal (HPA) axis. Here, we explored the role of the HPA axis, and FKBP5/FKBP51 in particular, in the reconsolidation of alcohol memories. We found that the FKBP51 inhibitor SAFit2 given before alcohol-memory retrieval using contextual cues prevented the extinction of alcohol place preference behavior in female mice, suggesting that this protein may play a role in cognitive flexibility in a sex-dependent manner. Conversely, the retrieval of alcohol memories using an odor-taste cue did not affectFkbp5expression in rats with a history of chronic alcohol consumption, suggesting that FKBP5 may play a differential role in different alcohol-associated memories. In addition, we provide evidence for HPA axis activation following alcohol memory retrieval, by showing that exposure to an alcohol-associated context led to elevated corticosterone secretion. However, we found that the reconsolidation process was unaffected by HPA axis-related manipulations, namely stress exposure, and administration of corticosterone or the glucocorticoid receptors inhibitor, mifepristone. Our results suggest that although FKBP5 can affect cognitive flexibility, and thereby impact the reconsolidation of alcohol memories, this effect is not likely mediated by HPA axis-related mechanisms.
Exosome derived multi-gene biomarker panel identifies the risk of liver metastasis in lung cancer patients
Authors: Shah Kanisha A , Rawal Rakesh M
Published: December 2023

Background

The lack of non-invasive methods for detection of early metastasis is a crucial reason for the poor prognosis of lung cancer (LC) liver metastasis (LM) patients. In this study, the goal was to identify circulating biomarkers based on a biomarker model for the early diagnosis and monitoring of patients with LCLM.

Methods

An 8-gene panel identified in our previous study was validated in CTC, cfRNA and exosomes isolated from primary lung cancer with & without metastasis. Further multivariate analysis including PCA & ROC was performed to determine the sensitivity and specificity of the biomarker panel. Model validation cohort (n= 79) was used to verify the stability of the constructed predictive model. Further, clinic-pathological factors, survival analysis and immune infiltration correlations were also performed.

Results

In comparison to our previous tissue data, exosomes demonstrated a good discriminative value with an AUC of 0.7247, specificity (72.48 %) and sensitivity (96.87%) for the 8-gene panel. Further individual gene patterns led us to a 5-gene panel that showed an AUC of 0.9488 (p = <0.001) and 0.9924 (p = <0.001) respectively for tissue and exosomes. Additionally, on validating the model in a larger cohort a risk score was obtained (RS >0.2) for prediction of liver metastasis with an accuracy of 95%. Survival analysis and immune filtration markers suggested that four exosomal markers were independently associated with poor overall survival.

Conclusion

We report a novel blood-based exosomal biomarker panel for early diagnosis, monitoring of therapeutic response, and prognostic evaluation of patients with LCLM.
Can calmodulin bind to lipids of the cytosolic leaflet of plasma membranes?
Authors: Scollo Federica , Tempra Carmelo , Evci Hüseyin , Riopedre-Fernandez Miguel , Olżyńska Agnieszka , Javanainen Matti , Uday Arunima , Cebecauer Marek , Cwiklik Lukasz , Martinez-Seara Hector , Jungwirth Pavel , Jurkiewicz Piotr , Hof Martin
Published: December 2023

Calmodulin (CaM) is a ubiquitous calcium-sensitive messenger in eukaryotic cells. It was previously shown that CaM possesses an affinity for diverse lipid moieties, including those found on CaM-binding proteins. These facts together with our observation that CaM accumulates in membrane-rich protrusions of HeLa cells upon increased cytosolic calcium, motivated us to perform a systematic search for unmediated CaM interactions with model lipid membranes mimicking the cytosolic leaflet of plasma membranes. A range of experimental techniques and Molecular Dynamics simulations proves unambiguously that CaM interacts with lipid bilayers in the presence of calcium ions. Lipids phosphatidylserine (PS) and phosphatidylethanolamine (PE) hold the key to CaM-membrane interactions. Calcium induces an essential conformational rearrangement of CaM, but its binding to the headgroup of PS also neutralizes the membrane negative surface charge. More intriguingly, PE plays a dual role - it forms hydrogen bonds with CaM, but also destabilizes the lipid bilayer to increase exposure of hydrophobic acyl chains to the interacting proteins. Our findings suggest that upon increased intracellular calcium concentration, CaM and the cytosolic leaflet of cellular membranes can be functionally connected.
VirtuousPocketome: A Computational Tool for Screening Protein-ligand Complexes to Identify Similar Binding Sites
Authors: Pallante Lorenzo , Cannariato Marco , Androutsos Lampros , Zizzi Eric A. , Bompotas Agorakis , Hada Xhesika , Grasso Gianvito , Kalogeras Athanasios , Mavroudi Seferina , di Benedetto Giacomo , Theofilatos Konstantinos , Deriu Marco A.
Published: December 2023

Protein residues within binding pockets play a critical role in determining the range of ligands that can interact with a protein, influencing its structure and function. Identifying structural similarities in proteins offers valuable insights into their function and activation mechanisms, aiding in predicting protein-ligand interactions, anticipating off-target effects, and facilitating the development of therapeutic agents. Numerous computational methods assessing global or local similarity in protein cavities have emerged, but their utilization is impeded by complexity, impractical automation for amino acid pattern searches, and an inability to evaluate the dynamics of scrutinized protein-ligand systems. Here, we present a general, automatic and unbiased computational pipeline, namedVirtuousPocketome, aimed at screening huge databases of proteins for similar binding pockets starting from an interested protein-ligand complex. We demonstrate the pipeline’s potential by exploring a recently-solved human bitter taste receptor, i.e. the TAS2R46, complexed with strychnine. We pinpointed 145 proteins sharing similar binding sites compared to the analysed bitter taste receptor and the enrichment analysis highlighted the related biological processes, molecular functions and cellular components. This work represents the foundation for future studies aimed at understanding the effective role of tastants outside the gustatory system: this could pave the way towards the rationalization of the diet as a supplement to standard pharmacological treatments and the design of novel tastants-inspired compounds to target other proteins involved in specific diseases or disorders. The proposed pipeline is publicly accessible, can be applied to any protein-ligand complex, and could be expanded to screen any database of protein structures.
A cyclic peptide toolkit reveals mechanistic principles of peptidylarginine deiminase IV (PADI4) regulation
Authors: Bertran M. T. , Walmsley R. , Cummings T. , Valle Aramburu I. , Benton D. J. , Assalaarachchi J. , Chasampalioti M. , Swanton T. , Joshi D. , Federico S. , Okkenhaug H. , Yu L. , Oxley D. , Walker S. , Papayannopoulos V. , Suga H. , Christophorou M. A. , Walport L. J.
Published: December 2023

Peptidylarginine deiminase IV (PADI4) deregulation promotes the development of autoimmunity, cancer, atherosclerosis and age-related tissue fibrosis. Genetic or pharmacological PADI4 inhibition is therapeutically efficacious in mice, but no clinically relevant inhibitors currently exist. PADI4 additionally mediates immune responses and cellular reprogramming, although the full extent of its physiological roles is unexplored. Despite detailed molecular knowledge of PADI4 activationin vitro, we lack understanding of its regulation within cells, largely due to lack of appropriate systems and tools. Here, we developed and applied a set of potent and selective PADI4 modulators. Using the mRNA- display-based RaPID system, we screened >1012cyclic peptides for high-affinity, conformation-selective binders. We report PADI4_3, an inhibitor specific for the active conformation of PADI4; PADI4_7, an inert binder, which we functionalised for the isolation and study of cellular PADI4; and PADI4_11, a first-in-class activator. Using a newly developed method for the quantification of cellular PADI4 activity, we show that PADI4_3 and PADI4_11 are effective in cells. Structural studies with PADI4_11 reveal an allosteric binding mode that may reflect the mechanism that promotes cellular PADI4 activation. This work offers new understanding of PADI4 regulation and a toolkit for the study and modulation of PADI4 across physiological and pathophysiological contexts.
Fixed-target time-resolved crystallography at XFELs: the scourge of light contamination but reduced sample consumption
Authors: Gotthard Guillaume , Flores-Ibarra Andrea , Carrillo Melissa , Kepa Michal W , Mason Thomas J , Stegmann Dennis P. , Olasz Bence , Pachota Magdalena , Dworkowski Florian , Ozerov Dmitry , Pedrini Bill F. , Padeste Celestino , Beale John H , Nogly Przemyslaw
Published: December 2023

X-ray free electron laser (XFEL) light sources have allowed for the rapid growth of time-resolved structural experiments, which provide crucial information on the function of biological machines and their mechanisms. We set out to commission the SwissMX fixed-target sample delivery system at the SwissFEL Cristallina experimental station using the PSI developed MISP-chip for pump-probe time-resolved experiments. To characterise the system, we used the light-sensitive protein crystals of the Light-Oxygen-Voltage domain 1 (LOV1) fromChlamydomonas reinhardtii. Using different experimental settings, the adjacent-well light contamination was carefully assessed, indicating that it is crucial to control the light scattering from solid supports otherwise significant contamination can occur. However, our results show that, after the initial experiments and parameter refinement, the opaque MISP-chips are suitable for pump-probing a light-sensitive protein. This crystallographic experiment also probed the sub-millisecond structural dynamics of the LOV1 and indicated that at Δt=10 μs the covalent thioether bond is already established between the reactive Cys57 and FMN cofactor. This experiment validated the crystals to be suitable for in-depth follow up studies of the still poorly understood signal transduction mechanism. Importantly, the fixed-target delivery system also permitted a tenfold reduction in protein sample consumption compared to the most successful system used at XFEL, the high-viscosity extruder. This development creates the prospect of an exciting increase in XFEL project throughput for the field.
Mucosal washes are useful for sampling intestinal mucus-associated microbiota despite low biomass
Authors: Martinez-Medina Jennifer N , Ghazisaeedi Fereshteh , Kramer Catharina , Ziegler Jörn F , McParland Victoria , Siegmund Britta , Jarquín-Díaz Víctor Hugo , Fulde Marcus , Forslund Sofia K
Published: December 2023

Exploring the dynamic relationship between mucus-associated microbiota and host health is pivotal, yet prevalent studies using stool samples may not accurately represent these bacteria. Here, we explored mucus-associated microbiota in the gastrointestinal tract of mice and the terminal ileum in humans, using three different sample types: mucosal washes, scraping, and intestinal content in mice and biopsies and mucosal washes in humans. We employed DNA quantification and 16S rRNA sequencing to assess how comparable the information yielded from different sample types, evaluating findings relative to expectations from state-of-the-art and under controlled benchmarks.

Mucosal washes in mice exhibited higher bacterial DNA and lower host DNA contamination than scraping samples. Similarly, in humans, washes surpassed biopsies in bacterial yield. Despite variations in read counts, microbiota diversity and composition remained remarkably similar between methods in both species, faithfully reflecting expected genotypic and phenotypic differences.

We conclude that washes reduce host contamination without inducing substantial compositional bias when sampling mucosal microbiota. Our findings emphasize mucosal washes as alternatives to biopsies in humans and scrapings in mice, providing insights for improving result transferability across hosts. Our research underscores the importance of considering the mucus-associated microbiota to track host-microbiome interactions closer to their actual interface surface.
Myrmecophytism as a driver of macroevolutionary patterns: perspectives from the Southeast AsianMacarangaant-plant symbiosis
Authors: Dixit Nadi M , Guicking Daniela
Published: December 2023

Myrmecophytes utilise defensive services offered by obligate ant partners in a novel means of survival in tropical habitats. Although much is known about the ecology of myrmecophytism, there aren’t enough empirical examples to demonstrate whether it substantially influences evolutionary patterns in host plant lineages. In this study, we make use of the species-richMacaranga(Euphorbiaceae) ant-plant symbiosis distributed in Sundaland to delve into the evolutionary dynamics of myrmecophytism in host plants. We generated the most comprehensive dated phylogeny of myrmecophyticMacarangatill date using sequences derived from genotyping-by-sequencing (GBS), a next-generation sequencing (NGS) technique. With this in hand, we traced the evolutionary history of myrmecophytism inMacarangausing parametric biogeography and ancestral state reconstruction. Diversification rate analysis methods were employed to determine if myrmecophytism enhanced diversification rates in the genus. Our results demonstrate that myrmecophytism is plastic and easily lost unless it is overly specialised. Ancestral state reconstruction supported a single origin of myrmecophytism inMacaranga∼18 mya on Borneo followed by multiple losses. Diversification rate analysis methods did not yield sufficient evidence to support the hypothesis that myrmecophytism enhanced diversification rates inMacaranga; we found that topographical features on Borneo may have played a more direct role in the divergence of clades instead. Through this comprehensive investigation of the evolution of myrmecophytism inMacaranga, our study also provides evidence that a key innovation may not necessarily enhance diversification rates. In fact, we hypothesise that overly specialised cases of myrmecophytism may even be an evolutionary dead end.
Aberrant Wnt activation in recurrent genetically variant human pluripotent stem cells impairs cardiomyocyte differentiation and phenotype
Authors: Wing Theodore , Price Christopher J. , Stavish Dylan , Laing Owen , Riley Jack J. , Lam Alan , Oh Steve , Atlasi Yaser , Barbaric Ivana
Published: December 2023

Human pluripotent stem cell (hPSC)-derived cardiomyocytes have emerged as powerful tools for disease modelling and cell therapy. The production of cardiomyocytes from hPSCs typically requires expanding large numbers of hPSCs and maintaining them in culture for extended periods of time. This in turn predisposes hPSCs to the acquisition of non-random genetic changes, including recurrent gains of chromosome 1q. Here, we show that gain of chromosome 1q in hPSCs affects both the efficiency of differentiation to cardiomyocytes and phenotype of the differentiated cells. Mechanistically, we show that aberrant activation of the Wnt signalling pathway underpins the skewed differentiation of variant 1q hPSCs. Collectively, our data demonstrates that the presence of genetically variant cells in cultures is a significant concern for production of hPSC-derived cardiomyocytes for research or clinical applications. Further, our results suggest new approaches for removing genetically variant cells for future clinical applications.
The impact of PCR duplication on RNAseq data generated using NovaSeq 6000, NovaSeq X, AVITI and G4 sequencers
Authors: Zajac Natalia , Vlachos Ioannis S , Sajibu Sija , Opitz Lennart , Wang Shuoshuo , Chittur Sridar V , Mason Christopher E. , Knudtson Kevin L , Ashton John M , Rehrauer Hubert , Aquino Catharine
Published: December 2023

RNA sequencing (RNA-seq) is a powerful technology for gene expression and functional genomics profiling. Expression profiles generated using this approach can be impacted by the methods utilised for cDNA library generation. Selection of the optimal parameters for each step during the protocol are crucial for acquisition of high-quality data. Polymerase chain reaction (PCR) amplification of transcripts is a common step in many RNA-seq protocols and, if not optimised, high PCR duplicate proportions can be generated, resulting in the inflation of transcript counts and introduction of bias. In this study, we investigate the impact of input amount and PCR cycle number on the PCR duplication rate and on the RNA-seq data quality using a broad range of inputs (1 ng -1,000 ng) for RNA-seq library preparation with unique molecular identifiers (UMIs) and sequencing the data on four different short-read sequencing platforms: Illumina NovaSeq 6000, Illumina NovaSeq X, Element Biosciences AVITI, and Singular Genomics G4. Across all platforms, samples of input amounts greater than 125 ng had a negligible PCR duplication rate and the number of PCR cycles did not have a significant effect on data quality. However, for input amounts lower than 125ng we observed a strong negative correlation between input amount and the proportion of PCR duplicates; between 34% and 96% of reads were discarded via deduplication. Fortunately, UMIs were effective for removingin silicoPCR duplicates without removing valuable biological information. Removal of PCR duplicates resulted in more comparable gene expression obtained from the different PCR cycles. Data generated with each of the four sequencing platforms presented similar associations between starting material amount and the number of PCR cycles on PCR duplicates, a similar number of genes detected, and comparable gene expression profiles. However, the sequencers using conversion kits for Illumina libraries (AVITI, G4) exhibited lower adapter dimer abundance across all input amounts, but also a higher PCR duplication rate in very low input amounts (<15ng). Overall, this study showed that the choice of input amount and number of PCR cycles are important parameters for obtaining high-quality RNA-seq data across all sequencing platforms. UMI deduplication is an effective way to remove PCR duplicates, improving the data quality and removing any variation caused by the conversion kits.
A Sensitivity Analysis of Methodological Variables Associated with Microbiome Measurements
Authors: Forry Samuel P. , Servetas Stephanie L. , Dootz Jennifer N. , Hunter Monique E. , Kralj Jason G. , Filliben James J. , Jackson Scott A.
Published: December 2023

The experimental methods employed during metagenomic sequencing analyses of microbiome samples significantly impact the resulting data and typically vary substantially between laboratories. In this study, a full factorial experimental design was used to compare the effects of a select set of methodological choices (sample, operator, lot, extraction kit, variable region, reference database) on the analysis of biologically diverse stool samples. For each parameter investigated, a main effect was calculated that allowed direct comparison both between methodological choices (bias effects) and between samples (real biological differences). Overall, methodological bias was found to be similar in magnitude to real biological differences, while also exhibiting significant variations between individual taxa, even between closely related genera. The quantified method biases were then used to computationally improve the comparability of datasets collected under substantially different protocols. This investigation demonstrates a framework for quantitatively assessing methodological choices that could be routinely performed by individual laboratories to better understand their metagenomic sequencing workflows and to improve the scope of the datasets they produce.
Mechanism of Dimer Selectivity and Binding Cooperativity of BRAF Inhibitors
Authors: Clayton Joseph , Romany Aarion , Matenoglou Evangelia , Gavathiotis Evripidis , Poulikakos Poulikos I. , Shen Jana
Published: December 2023

Aberrant signaling of BRAFV600Eis a major cancer driver. Current FDA-approved RAF inhibitors selectively inhibit the monomeric BRAFV600Eand suffer from tumor resistance. Recently, dimer-selective and equipotent RAF inhibitors have been developed; however, the mechanism of dimer selectivity is poorly understood. Here, we report extensive molecular dynamics (MD) simulations of the monomeric and dimeric BRAFV600Ein the apo form or in complex with one or two dimer-selective (PHI1) or equipotent (LY3009120) inhibitor(s). The simulations uncovered the unprecedented details of the remarkable allostery in BRAFV600Edimerization and inhibitor binding. Specifically, dimerization retrains and shifts the αC helix inward and increases the flexibility of the DFG motif; dimer compatibility is due to the promotion of the αC-in conformation, which is stabilized by a hydrogen bond formation between the inhibitor and the αC Glu501. A more stable hydrogen bond further restrains and shifts the αC helix inward, which incurs a larger entropic penalty that disfavors monomer binding. This mechanism led us to propose an empirical way based on the co-crystal structure to assess the dimer selectivity of a BRAFV600Einhibitor. Simulations also revealed that the positive cooperativity of PHI1 is due to its ability to preorganize the αC and DFG conformation in the opposite protomer, priming it for binding the second inhibitor. The atomically detailed view of the interplay between BRAF dimerization and inhibitor allostery as well as cooperativity has implications for understanding kinase signaling and contributes to the design of protomer selective RAF inhibitors.
INTEGRATED GLOBAL CHICKEN REFERENCE PANEL FROM 13,187 CHICKEN GENOMES
Authors: Zhu Di , Wang Yuzhan , Qu Hao , Feng Chugang , Zhang Hui , Sheng Zheya , Jiang Yuliang , Nie Qinghua , Chu Suqiao , Shu Dingming , Zhang Dexiang , Fang Lingzhao , Zhao Yiqiang , Wang Yuzhe , Hu Xiaoxiang
Published: December 2023

Chickens are a crucial source of protein for humans and a popular model animal for bird research. Despite the emergence of imputation as a reliable genotyping strategy for large populations, the lack of a high-quality chicken reference panel has hindered progress in chicken genome research. To address this issue, here we introduce the first phase of the 100 K Global Chicken Reference Panel Project (100 K GCRPP). The project includes 13,187 samples and provides services for varied applications on its website (http://farmrefpanel.com/GCRP/). Currently, two panels are available: a Comprehensive Mix Panel (CMP) for domestication diversity research and a Commercial Breed Panel (CBP) for breeding broilers specifically. Evaluation of genotype imputation quality showed that CMP had the highest imputation accuracy compared to imputation using existing chicken panel in animal SNPAtlas, whereas CBP performed stably in the imputation of commercial populations. Additionally, we found that genome-wide association studies using GCRP-imputed data, whether on simulated or real phenotypes, exhibited greater statistical power. In conclusion, our study indicates that the GCRP effectively fills the gap in high-quality reference panels for chickens, providing an effective imputation platform for future genetic and breeding research.
Adipose Tissue Analysis Toolkit (ATAT) for Automated Analysis of Adipocyte Size and Extracellular Matrix in White Adipose Tissue
Authors: Robino Jacob J. , Plekhanov Alexander P. , Zhu Qingzhang , Jensen Michael D. , Scherer Philipp E. , Roberts Charles T. , Varlamov Oleg
Published: December 2023

Objective

The pathological expansion of white adipose tissue (WAT) in obesity involves adipocyte hypertrophy accompanied by expansion of collagen-rich pericellular extracellular matrix (ECM) and the development of crown-like structures (CLS). Traditionally, WAT morphology is assessed through immunohistochemical analysis of WAT sections. However, manual analysis of large histological sections is time-consuming, and available digital tools for analyzing adipocyte size and pericellular ECM are limited. To address this gap, we developed the Adipose Tissue Analysis Toolkit (ATAT), an ImageJ plugin facilitating analysis of adipocyte size, WAT ECM and CLS.

Methods and Results

ATAT utilizes local and image-level differentials in pixel intensity to independently threshold background, distinguishing adipocyte-free tissue without user input. It accurately captures adipocytes in histological sections stained with common dyes and automates the analysis of adipocyte cross-sectional area, total-field, and localized region-of-interest ECM. ATAT allows fully automated batch analysis of histological images using default or user-defined adipocyte detection parameters.

Conclusions

ATAT provides several advantages over existing WAT image analysis tools, enabling high-throughput analyses of adipocyte-specific parameters and facilitating the assessment of ECM changes associated with WAT remodeling due to weight changes and other pathophysiological alterations that affect WAT function.

Study Importance Questions

What is already known about this subject?

The manual analysis of large WAT histological sections is very time-consuming, while digital tools for the analysis of WAT are limited.

What are the new findings in your manuscript?

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ATAT enables fully automated analysis of batches of histological images using either default or user-defined adipocyte detection parameters

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ATAT allows high-throughput analyses of adipocyte-specific parameters and pericellular extracellular matrix

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ATAT enables the assessment of fibrotic changes associated with WAT remodeling and crown-like structures

How might your results change the direction of research or the focus of clinical practice?

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ATAT is designed to work with histological sections and digital images obtained using a slide scanner or a microscope.

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This tool will help basic and clinical researchers to conduct automated analyses of adipose tissue histological sections.
Cysteine String Protein alpha in Extracellular Vesicle Subtypes: a Proteomic Analysis
Authors: Nogueira de Almeida Luiz Gustavo , Armstrong Victoria , Dufour Antoine , Braun Janice E.A.
Published: December 2023

Cysteine string protein (CSPα /DnaJC5) is a presynaptic J-domain protein (JDP) that prevents neurodegeneration. CSPα/DnaJC5 is reported to facilitate export of distinct, highly oligomeric, disease-causing proteins in addition to wild-type TDP-43, tau and α-synuclein. Yet, detailed mechanistic knowledge of the full CSPα/DnaJC5 secreted proteome is lacking. Understanding the CSPα/DnaJC5 export pathway has implications for a growing number of neurodegenerative diseases. In humans, Leu115Arg or Leu116deletion mutations cause adult-onset neuronal ceroid lipofusinosis (ANCL), a rare neurodegenerative disorder. In the present study, we examined extracelular vesicles (EVs) released from CSPα/DnaJC5 expressing cells. Cells are known to secrete many types of EVs of different sizes and origins into the extracellular space. EV subpopulations were separated by their sedimentation speed and subjected to proteomic analysis. We find that CSPα/DnaJC5 and the CSPα/DnaJC5 mutants, Leu115Arg or Leu116del are enriched in multiple EV subpopulations. The exported protein profile is determined by proteomics. We report that several other J-domain proteins (JDPs), such as DnaJC7, DnaJA1 and DnaJA2 are exported and speculate that export of JDPs may facilitate the secretion of diverse client proteins. Our work provides a platform for further inquiry into the role of secreted CSPα/DnaJC5 and other JDPs in proteostasis.
LINE-1 retrotransposition and its deregulation in cancers: implications for therapeutic opportunities
Authors: Mendez-Dorantes Carlos , Burns Kathleen H.
Published: December 2023

Long interspersed element 1 (LINE-1) is the only protein-coding transposon that is active in humans. LINE-1 propagates in the genome using RNA intermediates via retrotransposition. This activity has resulted in LINE-1 sequences occupying approximately one-fifth of our genome. Although most copies of LINE-1 are immobile, ∼100 copies are retrotransposition-competent. Retrotransposition is normally limited via epigenetic silencing, DNA repair, and other host defense mechanisms. In contrast, LINE-1 overexpression and retrotransposition are hallmarks of cancers. Here, we review mechanisms of LINE-1 regulation and how LINE-1 may promote genetic heterogeneity in tumors. Finally, we discuss therapeutic strategies to exploit LINE-1 biology in cancers.
AI-assisted proofreading of RNA splicing
Authors: Guerra-Moreno Ángel , Valcárcel Juan
Published: December 2023

RNA helicases orchestrate proofreading mechanisms that facilitate accurate intron removal from pre-mRNAs. How these activities are recruited to spliceosome/pre-mRNA complexes remains poorly understood. In this issue ofGenes & Development, Zhang and colleagues (pp. 968–983) combine biochemical experiments with AI-based structure prediction methods to generate a model for the interaction between SF3B1, a core splicing factor essential for the recognition of the intron branchpoint, and SUGP1, a protein that bridges SF3B1 with the helicase DHX15. Interaction with SF3B1 exposes the G-patch domain of SUGP1, facilitating binding to and activation of DHX15. The model can explain the activation of cryptic 3′ splice sites induced by mutations in SF3B1 or SUGP1 frequently found in cancer.
Customer incivility: cause and effect in the food and beverage industry in Vietnam
Authors: Nguyen-Viet Bang , Phuc Nguyen My
Published: December 2023

Purpose

Customer incivility is a key phenomenon with various harmful consequences for businesses, particularly in the food and beverage industry. This study investigated the antecedents of this issue and explored its outcomes for frontline employees in Vietnam.

Design/methodology/approach

This study used quantitative methodology to survey 780 participants who frequently experienced customer incivility in cafés and bubble tea shops. Structural equation modeling was used to examine the data.

Findings

The results revealed three antecedents of customer incivility – employee incivility, selling and customer orientation – as well as outcomes such as revenge motivation, emotional exhaustion, service sabotage and job performance, along with two mediating effects.

Practical implications

Managers can create and enhance additional training classes with varied curricula for different staff groups to foster their perspectives and understand an organization's customer orientation, eliminating vengeance motives, emotional strain, service sabotage and workplace performance.

Originality/value

This study emphasizes the importance of customer incivility and how it can be minimized by examining its causes and consequences in Vietnamese cafés and bubble tea shops.
The mechanical deformation characteristics of the internal structure of large diameter shield tunnel in different construction stages
Authors: Zhang Xiwen , Zhang Zhen , Sun Wenhao , Hu Jilei , Zhang Liangliang , Zhu Weidong
Published: December 2023

Purpose

Under the repeated action of the construction load, opening deformation and disturbed deformation occurred at the precast box culvert joints of the shield tunnel. The objective of this paper is to investigate the effect of construction vehicle loading on the mechanical deformation characteristics of the internal structure of a large-diameter shield tunnel during the entire construction period.

Design/methodology/approach

The structural response of the prefabricated internal structure under heavy construction vehicle loads at four different construction stages (prefabricated box culvert installation, curved lining cast-in-place, lane slab installation and pavement structure casting) was analyzed through field tests and ABAQUS (finite element analysis software) numerical simulation.

Findings

Heavy construction vehicles can cause significant mechanical impacts on the internal structure, as the construction phase progresses, the integrity of the internal structure with the tunnel section increases. The vertical and horizontal deformation of the internal structure is significantly reduced, and the overall stress level of the internal structure is reduced. The bolts connecting the precast box culvert have the maximum stress at the initial stage of construction, as the construction proceeds the stress distribution among the bolts gradually becomes uniform.

Originality/value

This study can provide a reference for the design model, theoretical analysis and construction technology of the internal structure during the construction of large-diameter tunnel projects.
Investigation of the lattice Boltzmann method to resolve combined radiation-conduction heat transfer in participating media with curved boundaries
Authors: Sharifi Marjan , Siavashi Majid , Hosseini Milad
Published: December 2023

Purpose

Present study aims to extend the lattice Boltzmann method (LBM) to simulate radiation in geometries with curved boundaries, as the first step to simulate radiation in complex porous media. In recent years, researchers have increasingly explored the use of porous media to improve the heat transfer processes. The lattice Boltzmann method (LBM) is one of the most effective techniques for simulating heat transfer in such media. However, the application of the LBM to study radiation in complex geometries that contain curved boundaries, as found in many porous media, has been limited.

Design/methodology/approach

The numerical evaluation of the effect of the radiation-conduction parameter and extinction coefficient on temperature and incident radiation distributions demonstrates that the proposed LBM algorithm provides highly accurate results across all cases, compared to those found in the literature or those obtained using the finite volume method (FVM) with the discrete ordinates method (DOM) for radiative information.

Findings

For the case with a conduction-radiation parameter equal to 0.01, the maximum relative error is 1.9% in predicting temperature along vertical central line. The accuracy improves with an increase in the conduction-radiation parameter. Furthermore, the comparison between computational performances of two approaches reveals that the LBM-LBM approach performs significantly faster than the FVM-DOM solver.

Originality/value

The difficulty of radiative modeling in combined problems involving irregular boundaries has led to alternative approaches that generally increase the computational expense to obtain necessary radiative details. To address the limitations of existing methods, this study presents a new approach involving a coupled lattice Boltzmann and first-order blocked-off technique to efficiently model conductive-radiative heat transfer in complex geometries with participating media. This algorithm has been developed using the parallel lattice Boltzmann solver.
Numerical simulation of pulsatile blood flow through eccentric double stenosed carotid artery
Authors: Rajmane Swapnil Narayan , Tiwari Shaligram
Published: December 2023

Purpose

This study aims to perform three-dimensional numerical computations for blood flow through a double stenosed carotid artery. Pulsatile flow with Womersley number (Wo) of 4.65 and Reynolds number (Re) of 425, based on the diameter of normal artery and average velocity of inlet pulse, was considered.

Design/methodology/approach

Finite volume method based ANSYS Fluent 20.1 was used for solving the governing equations of three-dimensional, laminar, incompressible and non-Newtonian blood flow. A high-quality grid with sufficient refinement was generated using ICEM CFD 20.1. The time-averaged flow field was captured to investigate the effect of severity and eccentricity on the lumen flow characteristics.

Findings

The results show that an increase in interspacing between blockages brings shear layer instability within the region between two blockages. The velocity profile and wall shear stress distribution are found to be majorly influenced by eccentricity. On the other hand, their peak magnitude is found to be primarily influenced by severity. Results have also demonstrated that the presence of eccentricity in stenosis would assist in flow development.

Originality/value

Variation in severity and interspacing was considered with a provision of eccentricity equal to 10% of diameter. Eccentricity refers to the offset between the centreline of stenosis and the centreline of normal artery. For the two blockages, severity values of 40% and 60% based on diameter reduction were permuted, giving rise to four combinations. For each combination, three values of interspacing in the multiples of normal artery diameter (D), viz. 4D, 6D and 8D were considered.
Situational selections of design methods for digital innovation processes
Authors: Liu Xuanhui , Werder Karl , Maedche Alexander , Sun Lingyun
Published: December 2023

Purpose

Numerous design methods are available to facilitate digital innovation processes in user interface design. Nonetheless, little guidance exists on their appropriate selection within the design process based on specific situations. Consequently, design novices with limited design knowledge face challenges when determining suitable methods. Thus, this paper aims to support design novices by guiding the situational selection of design methods.

Design/methodology/approach

Our research approach includes two phases: i) we adopted a taxonomy development method to identify dimensions of design methods by reviewing 292 potential design methods and interviewing 15 experts; ii) we conducted focus groups with 25 design novices and applied fuzzy-set qualitative comparative analysis to describe the relations between the taxonomy's dimensions.

Findings

We developed a novel taxonomy that presents a comprehensive overview of design conditions and their associated design methods in innovation processes. Thus, the taxonomy enables design novices to navigate the complexities of design methods needed to design digital innovation. We also identify configurations of these conditions that support the situational selections of design methods in digital innovation processes of user interface design.

Originality/value

The study’s contribution to the literature lies in the identification of both similarities and differences among design methods, as well as the investigation of sufficient condition configurations within the digital innovation processes of user interface design. The taxonomy helps design novices to navigate the design space by providing an overview of design conditions and the associations between methods and these conditions. By using the developed taxonomy, design novices can narrow down their options when selecting design methods for their specific situations.
Blockchain-based governance implications for ecologically sustainable supply chain management
Authors: Jimenez-Castillo Luis , Sarkis Joseph , Saberi Sara , Yao Tianchi
Published: December 2023

Purpose

The authors explore the impact of an emerging technology, blockchain technology, on diverse governance mechanisms and sustainable supply chain practices and how its relationships with the linkage of these elements.

Design/methodology/approach

The methodology incorporates a literature review and a qualitative empirical analysis of the Electronic Product Environmental Assessment Tool (EPEAT) standards. Expert opinions from various firms and organizations within the electronics sector are assessed. Through a thematic analysis, the relationships are identified and examined.

Findings

Data immutability, transparency and traceability capabilities of blockchain technology enhance the relationship between environmental standards and ecological supply chain sustainability practices. Although immature, the blockchain can influence the governance of supply chain sustainability practices. Immaturity of technology, lack of expertise, sharing information and trust have delayed adoption.

Originality/value

There is limited empirical evidence regarding blockchain's impact on governance mechanisms, specifically hybrid public-private mechanisms and sustainable supply chain practices. The study further evaluates how particular blockchain features may exert varying influences on these aspects and different sustainable supply chain traits. As an exploratory study, it proposes new areas for further research, including how blockchain's traceability function can improve sustainability standard adoption. Additionally, there is a call for integrating blockchain with technologies like IoT and sensors which may influence supply chain governance mechanisms, standards and sustainability practices.
Proactive personality, transformational leadership and ethical standards: influences on radical creativity
Authors: Zhang Wengang , Xu Feng
Published: December 2023

Purpose

This study aims to investigates the influence of proactive personality on employee radical creativity through transformational leadership, professional ethical standards and creative self-efficacy.

Design/methodology/approach

The data were collected from 343 superior–subordinate dyads in China. A confirmatory factor analysis was performed to measure the validity of the variables. A regression analysis was performed to assess the relationship between model assumptions.

Findings

The results showed that: (1) Proactive personality was positively related to employee radical creativity. (2) Transformational leadership and professional ethical standards moderated the relationship between proactive personality and radical creativity. Specifically, the relationship between proactive personality and employee radical creativity was strong, as expected. It was the strongest in the presence of high transformational leadership and high professional ethical standards. (3) Creative self-efficacy acted as a mediator in this interaction.

Originality/value

This study is a pioneering investigation in the Chinese context. It empirically examines the interactive relationship between proactive personality and radical creativity through transformational leadership and professional ethical standards. Additionally, it substantiates creative self-efficacy as the psychological mechanism behind this interaction. Consequently, this study offers a comprehensive framework with potential implications for personality assessments in the workplace, leadership training, criteria formulation and enhancement of radical creativity.
Revealing human impact on natural ecosystems through soil bacterial DNA sampled from an archaeological site
Authors: Boivin Stéphane , Bourceret Amélia , Maurice Kenji , Laurent‐Webb Liam , Figura Tomáš , Bourillon Julie , Nespoulous Jérôme , Domergue Odile , Chaintreuil Clémence , Boukcim Hassan , Selosse Marc‐André , Fiema Zbigniew , Botte Emmanuel , Nehme Laila , Ducousso Marc
Published: December 2023

Human activities have affected the surrounding natural ecosystems, including belowground microorganisms, for millennia. Their short‐ and medium‐term effects on the diversity and the composition of soil microbial communities are well‐documented, but their lasting effects remain unknown. When unoccupied for centuries, archaeological sites are appropriate for studying the long‐term effects of past human occupancy on natural ecosystems, including the soil compartment. In this work, the soil chemical and bacterial compositions were compared between the Roman fort of Hegra (Saudi Arabia) abandoned for 1500 years, and a preserved area located at 120 m of the southern wall of the Roman fort where no human occupancy was detected. We show that the four centuries of human occupancy have deeply and lastingly modified both the soil chemical and bacterial compositions inside the Roman fort. We also highlight different bacterial putative functions between the two areas, notably associated with human occupancy. Finally, this work shows that the use of soils from archaeological sites causes little disruption and can bring relevant information, at a large scale, during the initial surveys of archaeological sites.