bluuebunny/crossref_metadata_2025_split huggingface dataset:
Urine-based detection of biomarkers indicative of chronic kidney disease in a patient cohort from Ghana
Authors: Wruck Wasco , Boima Vincent , Erichsen Lars , Thimm Chantelle , Koranteng Theresa , Kwakyi Edward , Antwi Sampson , Adu Dwomoa , Adjaye James 
Published: October 2022

AbstractChronic kidney disease (CKD) is a global health burden with a continuously increasing prevalence associated with an increasing incidence of diabetes and hypertension in aging populations. The CKD definition of a more than three months lasting low glomerular filtration rate (GFR) or other renal impairments including proteinuria implies that multiple factors may contribute to the disease. While there are indications of ethnic differences it is hard to disentangle these from confounding social factors. Usually, CKD is detected in later stages of the disease when irreversible renal damage has already occurred, thus suggesting a need for early non-invasive diagnostic markers.In this study, we explored the urine secretome of a CKD patient cohort from Ghana employing a kidney-injury and a more general cytokine assay.We identified panels of kidney-specific cytokine markers which were also gender-specific and a panel of gender-independent cytokine markers. The gender-specific markers are IL10 and MME for male and CLU, RETN, AGER, EGFR and VEGFA for female. The gender-independent cytokine markers were APOA1, ANGPT2, C5, CFD, GH1, ICAM1, IGFBP2, IL8, KLK4, MMP9 and SPP1 (up-regulated) and FLT3LG, CSF1, PDGFA, RETN and VEGFA (down-regulated).APOA1 – the major component of HDL particles – was up-regulated in Ghanaian CKD patients and its co-occurrence with APOL1 in a subpopulation of HDL particles may point to specific CKD-predisposing APOL1 haplotypes in patients of African descent – this however needs further investigation. The identified panels may lay down the foundation for CKD-biomarker assays to be confirmed in further studies with a larger cohort of patients.
The functional and structural characterization ofXanthomonas campestrispv.campestriscore effector XopP revealed a new kinase activity
Authors: Kotsaridis Konstantinos , Michalopoulou Vassiliki A. , Tsakiri Dimitra , Kotsifaki Dina , Kefala Aikaterini , Koundourakis Nikolaos , Celie Patrick H.N. , Kokkinidis Michael , Sarris Panagiotis F. 
Published: October 2022

SummaryThe exocyst complex subunit protein Exo70B1 plays a crucial role in a variety of cell mechanisms including immune responses against pathogens. The calcium dependent kinase 5 (CPK5) ofArapidopsis thaliana, phosphorylatesAtExo70B1 upon functional disruption. We previously reported that, theXanthomonas campestrispv.campestiseffector XopP, compromises Exo70B1 and bypasses the host’s hypersensitive response (HR), in a way that is still unclear.Herein we designed an experimental approach based on biophysical, biochemical and molecular assays, based on structural and functional predictions, as well as, utilizing Aplhafold and DALI online servers respectively, in order to characterize thein vivo XccXopP function.The interaction betweenAtExo70B1 andXccXopP is very stable in high temperatures, while theAtExo70B1 appeared to be phosphorylated atXccXopP expressing transgenicArabidopsis.XccXopP reveals similarities with known mammalian kinases, and phosphorylatesAtExo70B1 at Ser107, Ser111, Ser248, Thr309 and Thr364. Furthermore,XccXopP protectsAtExo70B1 from AtCPK5 phosphorylation.Together these findings show that,XccXopP is an effector, which not only functions as a novel serine/threonine kinase upon its host’s protein targetAtExo70B1, but also protects the latter from the innate AtCPK5 phosphorylation, to bypass the host’s immune responses.
Induction of telomerase in p21-positive cells counteracts capillaries rarefaction in aging mice lung
Authors: Lipskaia Larissa , Breau Marielle , Cayrou Christelle , Churikov Dmitri , Braud Laura , Fouillade Charles , Curras-Alonso Sandra , Bauwens Serge , Jourquin Frederic , Fiore Frederic , Castellano Rémy , Josselin Emmanuelle , Sánchez-Ferrer Carlota , Giovinazzo Giovanna , Gilson Eric , Flores Ignacio , Londono-Vallejo Arturo , Adnot Serge , Géli Vincent 
Published: October 2022

ABSTRACTTelomerase is required for long-term cell proliferation and linked to stem cells. This is evident in the lung where short telomeres are associated with lung dysfunction. We constructed a mouse model in which the telomerase (Tert) is expressed from the p21Cdkn1apromoter. We found that this peculiar Tert expression curb age-related emphysema and pulmonary perivascular fibrosis in old mice. In old mice lungs, such Tert expression preferentially occurs in endothelial cells where it reduces the number of senescent endothelial cells. Remarkably, we report that Tert counteracts the age-related decline in capillary density. This was associated with an increased number of Cd34+ cells identified as a subclass of capillary cells with proliferative capacity. Expression of catalytically inactiveTertneither prevents the decline of capillary density in old mice nor protects against age-related emphysema and fibrosis. These findings reveal that telomerase decreases age-decline of pulmonary functions by sustaining microvasculature regeneration and outgrowth.
EEG mismatch responses in a multi-modal roving stimulus paradigm provide evidence for probabilistic inference across audition, somatosensation and vision
Authors: Grundei Miro , Schröder Pia , Gijsen Sam , Blankenburg Felix 
Published: October 2022

AbstractThe human brain is constantly subjected to a multi-modal stream of probabilistic sensory inputs. EEG signatures, such as the mismatch negativity (MMN) and the P3, can give valuable insight into neuronal probabilistic inference. Although reported for different modalities, mismatch responses have largely been studied in isolation, with a strong focus on the auditory MMN. To investigate the extent to which early and late mismatch responses across modalities represent comparable signatures of uni- and cross-modal probabilistic inference in the hierarchically structured cortex, we recorded EEG from 32 participants undergoing a novel tri-modal roving stimulus paradigm. The employed sequences consisted of high and low intensity stimuli in the auditory, somatosensory and visual modalities and were governed by uni-modal transition probabilities and cross-modal conditional dependencies. We found modality specific signatures of MMN (∼100-200ms) in all three modalities, which were source localized to the respective sensory cortices and shared right lateralized pre-frontal sources. Additionally, we identified a cross-modal signature of mismatch processing in the P3a time range (∼300-350ms), for which a common network with frontal dominance was found. Across modalities, the mismatch responses showed highly comparable parametric effects of stimulus train length, which were driven by standard and deviant response modulations in opposite directions. Strikingly, the P3a responses across modalities were increased for mispredicted compared to predicted and unpredictable stimuli, suggesting sensitivity to cross-modal predictive information. Finally, model comparisons indicated that the observed single trial dynamics were best captured by Bayesian learning models tracking uni-modal stimulus transitions as well as cross-modal conditional dependencies.
Cell-intrinsic and -extrinsic functions of the ESCRT-III component Shrub in cytokinetic abscission ofDrosophilaSensory Organ precursor
Authors: Bruelle Céline , Pinot Mathieu , Daniel Emeline , Daudé Marion , Mathieu Juliette , Borgne Roland Le 
Published: October 2022

AbstractWhile the molecular mechanisms underlying the abscission of isolated cells are largely decrypted, those of fast-cycling, epithelial progenitors surrounded by epidermal cells (ECs) connected by junctions remain largely unexplored. Here, we investigated the remodeling of the permeability barrier ensured by septate junctions (SJs) during cytokinesis of Drosophila sensory organ precursor (SOP). We report that SOP cytokinesis involves the coordinated polarized assembly and remodeling of SJs in the dividing cell and its neighbors, which remained connected via membrane protrusions pointing toward the SOP midbody. SJs assembly and midbody basal displacement occur more rapidly in SOP than in ECs, leading to a faster disentanglement of the protrusions that precedes midbody release. As reported in isolated cells, the endosomal sorting complex required for transport-III component Shrub/CHMP4B is recruited at the midbody and cell-autonomously regulates abscission. In addition, we found that Shrub is recruited to membrane protrusions, is required for SJ integrity, and that alteration of SJ integrity leads to premature abscission. Our study uncovers cell-intrinsic and -extrinsic functions of Shrub in epithelial abscission to support the coordination of permeability barrier maintenance and abscission in SOPs.
Overruled by nature: A plastic response to an ecological regime shift disconnects a gene and its trait
Authors: Besnier F. , Skaala Ø. , Wennevik V. , Ayllon F. , Utne K.R. , Fjeldheim P.T. , Andersen-Fjeldheim K. , Knutar S. , Glover K.A. 
Published: October 2022

AbstractIn Atlantic salmon, age at maturation is a life history trait ruled by a sex-specific trade-off between reproductive success and survival. Following an ecological regime shift in 2005, many North Atlantic salmon populations currently display smaller size at age and delayed age at maturation. However, whether this change reflects rapid evolution or plastic response is unknown. Some 1500 historical and contemporary salmon from river Etne (Western Norway) genotyped at 50k SNPs revealed three loci significantly associated with age at maturation. These includedvgll3andsix6, which collectively explained 36 to 50% of the age at maturation variation in the 1983-1984 period. Strikingly, the combined influence of these genes was nearly absent in all samples from 2013-2016, despite allelic frequencies atvgll3remaining unchanged. We conclude that the regime shift has led to the sudden bypassing of the influence ofvgll3andsix6on maturation through growth-driven plasticity.
SalienceNet: an unsupervised Image-to-Image translation method for nuclei saliency enhancement in microscopy images
Authors: Emmanuel Bouilhol , Lefevre Edgar , Barry Thierno , Levet Florian , Beghin Anne , Viasnoff Virgile , Galindo Xareni , Galland Rémi , Sibarita Jean-Baptiste , Nikolski Macha 
Published: October 2022

AbstractAutomatic segmentation of nuclei in low-light microscopy images remains a difficult task, especially for high-throughput experiments where need for automation is strong. Low saliency of nuclei with respect to the background, variability of their intensity together with low signal-to-noise ratio in these images constitute a major challenge for mainstream algorithms of nuclei segmentation. In this work we introduce SalienceNet, an unsupervised deep learning-based method that uses the style transfer properties of cycleGAN to transform low saliency images into high saliency images, thus enabling accurate segmentation by downstream analysis methods, and that without need for any parameter tuning. We have acquired a novel dataset of organoid images with soSPIM, a microscopy technique that enables the acquisition of images in low-light conditions. Our experiments show that SalienceNet increased the saliency of these images up to the desired level. Moreover, we evaluated the impact of SalienceNet on segmentation for both Otsu thresholding and StarDist and have shown that enhancing nuclei with SalienceNet improved segmentation results using Otsu thresholding by 30% and using StarDist by 26% in terms of IOU when compared to segmentation of non-enhanced images. Together these results show that SalienceNet can be used as a common preprocessing step to automate nuclei segmentation pipelines for low-light microscopy images.
Structural Maintenance of Chromosome 3 interacts with the Topoisomerase VI complex and contributes to the oxidative stress response inArabidopsis thaliana
Authors: Velay Florent , Abdallah Dina , Lecampion Cécile , Kbiri Nadia , D’Alessandro Stefano , Field Benjamin , Laloi Christophe 
Published: October 2022

SummaryIn plants adverse environmental conditions can induce the accumulation of reactive oxygen species, such as singlet oxygen or hydrogen peroxide, at the level of the photosynthetic apparatus. The coordinated action of nucleus-encoded genes is required for containing the deleterious effects of reactive oxygen species. The regulation of such genes follows a molecular signalling process between the chloroplast and the nucleus called retrograde signalling. Previously, we proposed that the Topoisomerase VI (Topo VI) complex participates in the singlet oxygen stress response by regulating the expression of specific subsets of nuclear genes. However, the underlying molecular mechanisms remain unresolved. In this study, we demonstrate that the Topo VI subunit BIN4 interacts with the cohesin subunit AtSMC3. We also show that, similarly to Topo VI mutants, a line suppressing AtSMC3 shows constitutive activation of singlet oxygen response genes and enhanced tolerance to photooxidative stress. Together, these results suggest that Topo VI and AtSMC3 control the expression of singlet oxygen response genes and are possibly involved in the acclimation of plants to photooxidative stress conditions.
Integration and segregation in the brain as a cognitive flexibility during tasks and rest
Authors: Capouskova Katerina , Zamora-López Gorka , Kringelbach Morten L , Deco Gustavo 
Published: October 2022

AbstractTo flexibly respond to a continuously changing environment, the human brain must be able to flexibly switch amongst many demanding cognitive tasks. The flexibility inside the brain is enabled by integrating and segregating information in large-scale functional networks over time. In this study, we used graph theory metrics prior to clustering to identify two brain states, segregated and integrated, in 100 healthy adults selected from the Human Connectome Project (HCP) dataset at rest and during six cognitive tasks. Furthermore, we explored two-dimensional (2D) latent space revealed by a deep autoencoder. In the latent space, the integrated state occupied less space compared with the segregated state. After binning the latent space, we obtained entropy from the probability for each data point of being in the bin. The integrated state showed lower entropy than the segregated state, and the rest modality showed higher entropy in both states compared with tasks. We also found that modularity and global efficiency are good measures for distinguishing between tasks and rest in both states. Overall, the study shows that integration and segregation are present in rest and in task modalities, while integration serves as information compression and segregation as information specialisation. These characteristics ensure the necessary cognitive flexibility to learn new tasks with deep proficiency.
VSV-based vaccine provides species-specific protection against Sudan virus challenge in macaques
Authors: Marzi Andrea , Fletcher Paige , Feldmann Friederike , Saturday Greg , Hanley Patrick W. , Feldmann Heinz 
Published: October 2022

AbstractThe ongoing Sudan virus (SUDV) outbreak in Uganda highlights the need for rapid response capabilities against emerging viruses with high public health impact. While such countermeasures have been established for Ebola virus (EBOV), they unfortunately do not exist for SUDV or any other human-pathogenic filovirus.Here, we describe the generation and characterization of the vesicular stomatitis virus (VSV)-based vaccine VSV-SUDV and demonstrate the protective efficacy following a single-dose vaccination against lethal SUDV infection in nonhuman primates (NHPs). As we repurposed NHPs from a successful VSV-EBOV vaccine efficacy study, we further demonstrate that VSV-SUDV can be used effectively in individuals previously vaccinated against EBOV. While the NHPs developed cross-reactive humoral responses to SUDV after VSV-EBOV vaccination and EBOV challenge, cross-protection was limited emphasizing the need for the development of specific countermeasures for each human-pathogenic ebolavirus. Additionally, our data provides evidence that while previous VSV-EBOV immunity is boosted after VSV-SUDV vaccination, it has only limited impact on the immunogenicity and protective efficacy of VSV-SUDV vaccination important for frontline outbreak workers.
A new gene encoding a cytosolic glutamine synthetase in pine is linked to developing tissues
Authors: Valderrama-Martín José Miguel , Ortigosa Francisco , Aledo Juan Carlos , Ávila Concepción , Cánovas Francisco M. , Cañas Rafael A. 
Published: October 2022

SUMMARYThe enzyme glutamine synthetase (EC 6.3.1.2) is mainly responsible for the incorporation of inorganic nitrogen into organic molecules in plants. In the present work, a new pineGS1(PpGS1b.2) gene was identified, showing a high sequence identity with theGS1b.1gene previously characterized in conifers. Phylogenetic analysis revealed that the presence ofPpGS1b.2is restricted to the generaPinusandPiceaand is not found in other conifers. Gene expression data suggest a putative role ofPpGS1b.2in plant development, similar to otherGS1bgenes from angiosperms, suggesting evolutionary convergence. The characterization of GS1b.1 and GS1b.2 at the structural, physicochemical, and kinetic levels has shown differences even though they have high sequence homology. Alterations in the kinetic characteristics produced by the site-directed mutagenesis approach carried out in this work strongly suggest an implication of amino acids at positions 264 and 267 in the active center of pine GS1b.1 and GS1b.2. Therefore, the amino acid differences between GS1b.1 and GS1b.2 would support the functioning of both enzymes to meet distinct plant needs.
uORF4u: a tool for annotation of conserved upstream open reading frames
Authors: Egorov Artyom A. , Atkinson Gemma C. 
Published: October 2022

AbstractSummaryUpstream open reading frames (uORFs, encoding so-called leader peptides) can regulate translation and transcription of downstream main ORFs (mORFs) in prokaryotes and eukaryotes. However, annotation of novel functional uORFs is challenging due their short size of usually less than 100 codons. While transcription- and translation-level next generation sequencing (NGS) methods can be used for genome-wide uORF identification, this data is not available for the vast majority of species with sequenced genomes. At the same time, the exponentially increasing amount of genome assemblies gives us the opportunity to take advantage of evolutionary conservation in our predictions of ORFs.Here we present a tool for conserved uORF annotation in 5′ upstream sequences of a user-defined protein of interest or a set of protein homologues. It can also be used to find small ORFs within a set of nucleotide sequences. The output includes publication-quality figures with multiple sequence alignments, sequence logos and locus annotation of the predicted uORFs in graphical vector format.Availability and ImplementationuORF4u is written in Python3 and runs on Linux and MacOS. The command-line interface covers most practical use cases, while the provided Python API allows usage within a Python program and additional customisation. Source code is available from the GitHub page:https://github.com/art-egorov/uorf4u. Detailed documentation that includes an example-driven guide available at the software home page:https://art-egorov.github.io/uorf4u.
The boosting of the total quality management on corporate green growth in emerging markets: the mediating roles of corporate social responsibility and customer loyalty
Authors: Le Thanh Tiep 
Published: October 2022

PurposeThe primary purpose of this research is to examine how total quality management (TQM) boosts corporate green growth (CGG) with the involvement of corporate social responsibility (CSR) and customer loyalty (CL) as mediators in the relationship between TQM and CGG for small- and medium-sized enterprises (SMEs) in an emerging economy.Design/methodology/approachThis research adopts a quantitative approach. According to the scope of this study, constructs of TQM, CSR, CL and CGG and the conceptual relationships between them are established using a systematic literature review. This study uses enterprise-level primary data collected from a questionnaire-based survey. The respondents are those holding managerial positions in their enterprises. There were 424 valid responses obtained following the necessary screening steps to ensure the eligibility of the collected data for analysis using AMOS version 20.FindingsThis study reveals that TQM has a positive and significant relationship with CSR, CL and CGG. Amongst these direct connections, TQM has the most substantial influence on CGG, followed by CL and CSR. Furthermore, the findings assert that CSR positively and significantly affects CGG and CL. When comparing the weighting of these effects, the results show that the impact of CSR on CGG is stronger than that on CL. Furthermore, the results confirm that CSR and CL partially mediate the relationship between TQM and CGG, both independently and simultaneously. The article also discusses the theoretical and managerial implications based on the stated findings.Originality/valueThe originality of this study stems from its contribution to enriching the body of the current literature on TQM and its combined influence on corporate performance. In this respect, this study adds to the existing literature by providing additional empirical evidence on the mechanism by which TQM boosts CGG with the involvement of CSR and CL in mediating the stated relationship between TQM and CGG for SMEs in an emerging economy. To the best of the author’s knowledge, such holistic incorporation is rare in the current literature. Furthermore, this study sheds light on the TQM enabling factors that are extended beyond the quality or technical scope as previously assumed. The stated contributions deserve to be originally derived from the attempt of this scientific work that may be of interest to academics, professionals and business practitioners.
Two decades of research on halal hospitality and tourism: a review and research agenda
Authors: Al-Ansi Amr , Olya Hossein , Han Heesup 
Published: October 2022

Purpose
This study aims to conduct a synopsis and overview of past research that discussed halal hospitality development and the halal travel market.

Design/methodology/approach
An extensive systematic review of 108 articles within the hospitality and tourism domain from 2000 to 2021 that were extracted from the Web of Science and Scopus databases was exhaustively assessed.

Findings
The results are visualised to determine the most thematic domains, contexts and concepts previously discussed. It also computed the contribution of journals, authors and affiliations in fostering the mobility of halal tourism studies. The study attempted to chart new directions and insights for future scholars and academics to expand the scope of halal literature in two ways. It articulated the implications and guidance themes emphasised in previous studies and identified new paths to abreast the contemporary issues of the hospitality and tourism industry, including sustainable consumption trends, community development, technology and smart practises, as well as potential threats and challenges such as islamophobia.

Originality/value
In view of the fast growth of halal market studies, the direction and contribution of the previous literature produced limited discussions with certain theoretical concepts. This study advises new pathways in which halal tourism development can respond to contemporary issues in hospitality and tourism.