bluuebunny/crossref_metadata_2025_split huggingface dataset:
imageseg: an R package for deep learning-based image segmentation
Authors: Niedballa Jürgen , Axtner Jan , Döbert Timm Fabian , Tilker Andrew , Nguyen An , Wong Seth T. , Fiderer Christian , Heurich Marco , Wilting Andreas 
Published: December 2021

AbstractConvolutional neural networks (CNNs) and deep learning are powerful and robust tools for ecological applications. CNNs can perform very well in various tasks, especially for visual tasks and image data. Image segmentation (the classification of all pixels in images) is one such task and can for example be used to assess forest vertical and horizontal structure. While such methods have been suggested, widespread adoption in ecological research has been slow, likely due to technical difficulties in implementation of CNNs and lack of toolboxes for ecologists.Here, we present R package imageseg which implements a workflow for general-purpose image segmentation using CNNs and the U-Net architecture in R. The workflow covers data (pre)processing, model training, and predictions. We illustrate the utility of the package with two models for forest structural metrics: tree canopy density and understory vegetation density. We trained the models using large and diverse training data sets from a variety of forest types and biomes, consisting of 3288 canopy images (both canopy cover and hemispherical canopy closure photographs) and 1468 understory vegetation images.Overall classification accuracy of the models was high with a Dice score of 0.91 for the canopy model and 0.89 for the understory vegetation model (assessed with 821 and 367 images, respectively), indicating robustness to variation in input images and good generalization strength across forest types and biomes.The package and its workflow allow simple yet powerful assessments of forest structural metrics using pre-trained models. Furthermore, the package facilitates custom image segmentation with multiple classes and based on color or grayscale images, e.g. in cell biology or for medical images. Our package is free, open source, and available from CRAN. It will enable easier and faster implementation of deep learning-based image segmentation within R for ecological applications and beyond.
Interest of phenomic prediction as an alternative to genomic prediction in grapevine
Authors: Brault Charlotte , Lazerges Juliette , Doligez Agnès , Thomas Miguel , Ecarnot Martin , Roumet Pierre , Bertrand Yves , Berger Gilles , Pons Thierry , François Pierre , Le Cunff Loïc , This Patrice , Segura Vincent 
Published: December 2021

AbstractPhenomic prediction has been defined as an alternative to genomic prediction by using spectra instead of molecular markers. A reflectance spectrum reflects the biochemical composition within a tissue, under genetic determinism. Thus, a relationship matrix built from spectra could potentially capture genetic signal. This new methodology has been successfully applied in several cereal species but little is known so far about its interest in perennial species. Besides, phenomic prediction has only been tested for a restricted set of traits, mainly related to yield or phenology. This study aims at applying phenomic prediction for the first time in grapevine, using spectra collected on two tissues and over two consecutive years, on two populations and for 15 traits. First, we characterized the genetic signal in spectra and under which condition it could be maximized, then phenomic predictive ability was compared to genomic predictive ability. We found that the co-inertia between spectra and genomic data was stable across tissues or years, but variable across populations, with co-inertia around 0.3 and 0.6 for diversity panel and half-diallel populations, respectively. Differences between populations were also observed for predictive ability of phenomic prediction, with an average of 0.27 for the diversity panel and 0.35 for the half-diallel. For both populations, there was a correlation across traits between predictive ability of genomic and phenomic prediction, with a slope around 1 and an intercept of −0.2, thus suggesting that phenomic prediction could be applied for any trait.
The 677C>T variant in methylenetetrahydrofolate reductase causes morphological and functional cerebrovascular deficits in mice
Authors: Reagan Alaina M. , Christensen Karen E. , Graham Leah C. , Bedwell Amanda A. , Eldridge Kierra , Speedy Rachael , Figueiredo Lucas L. , Persohn Scott C. , Bottiglieri Teodoro , Sasner Michael , Territo Paul R. , Rozen Rima , Howell Gareth R. 
Published: December 2021

AbstractVascular contributions to cognitive impairment and dementia (VCID) particularly Alzheimer’s disease and related dementias (ADRDs) are increasing; however, mechanisms driving cerebrovascular decline are poorly understood. Methylenetetrahydrofolate reductase (MTHFR) is a critical enzyme in the folate and methionine cycles. Variants in MTHFR, notably 677C>T, are associated with dementias, but no mouse model existed to identify mechanisms by which MTHFR677C>T increases risk. Therefore, MODEL-AD created a novel knock-in (KI) strain carrying the Mthfr677C>T allele on the C57BL/6J background (Mthfr677C>T) to characterize morphology and function perturbed by the variant. Consistent with human clinical data, Mthfr677C>T mice have reduced enzyme activity in the liver and elevated plasma homocysteine levels. MTHFR enzyme activity as well as critical metabolites in the folate and methionine cycles are reduced in the Mthfr677C>T brain. Mice showed reduced tissue perfusion in numerous brain regions by PET/CT as well as significantly reduced vascular density and increased GFAP-expressing astrocytes in frontal cortex. Electron microscopy revealed cerebrovascular damage including endothelial and pericyte apoptosis, reduced luminal size, and increased astrocyte and microglial presence in the microenvironment. Collectively, these data suggest critical perturbations to cerebrovascular function in Mthfr677C>T mice supporting its use as a model for preclinical studies of VCID.
A practical guide for generating unsupervised, spectrogram-based latent space representations of animal vocalizations
Authors: Thomas Mara , Jensen Frants H. , Averly Baptiste , Demartsev Vlad , Manser Marta B. , Sainburg Tim , Roch Marie A. , Strandburg-Peshkin Ariana 
Published: December 2021

ABSTRACTThe manual detection, analysis, and classification of animal vocalizations in acoustic recordings is laborious and requires expert knowledge. Hence, there is a need for objective, generalizable methods that detect underlying patterns in these data, categorize sounds into distinct groups, and quantify similarities between them. Among all computational methods that have been proposed to accomplish this, neighborhood-based dimensionality reduction of spectrograms to produce a latent-space representation of calls stands out for its conceptual simplicity and effectiveness. Using a dataset of manually annotated meerkat (Suricata suricatta) vocalizations, we demonstrate how this method can be used to obtain meaningful latent space representations that reflect the established taxonomy of call types. We analyze strengths and weaknesses of the proposed approach, give recommendations for its usage and show application examples, such as the classification of ambiguous calls and the detection of mislabeled calls. All analyses are accompanied by example code to help researchers realize the potential of this method for the study of animal vocalizations.
Specific vulnerability of long telomeres to undergo end fusions revealed by mutational analysis of Rap1
Authors: Pan Lili , Tormey Duncan , Bobon Nadine , Baumann Peter 
Published: December 2021

AbstractThe conserved Rap1 protein is part of the shelterin complex that plays critical roles in chromosome end protection and telomere length homeostasis. Previous studies addressed how fission yeast Rap1 contributes to telomere length maintenance, but the mechanism by which the protein inhibits end fusions has remained elusive. Here, we use a genetic screen in combination with high throughput sequencing to identify several amino acid positions in Rap1 that have a key role in end protection. Interestingly, mutations at these sites render cells susceptible to genome instability in a conditional manner with longer telomeres being prone to undergoing end fusions, while short telomeres are sufficiently protected. The protection of long telomeres requires their nuclear envelope attachment mediated by the Rap1-Bqt4 interaction. Our data demonstrates that longer telomeres pose an additional challenge for the maintenance of genome integrity and provides an explanation for a species-specific upper limit in telomere length.
Bioinformatics analysis of differentially expressed genes in non alcoholic fatty liver disease using next generation sequencing data
Authors: Vastrad Basavaraj , Vastrad Chanabasayya 
Published: December 2021

AbstractNon alcoholic fatty liver disease (NAFLD) is the most common metabolic disease in humans, affecting the majority of individuals. In the current investigation, we aim to identify potential key genes linked with NAFLD through bioinformatics analyses of next generation sequencing (NGS) dataset. NGS dataset of GSE135251 from the Gene Expression Omnibus (GEO) database were retrieved. Differentially expressed genes (DEGs) were obtained by DESeq2 package. g:Profiler database was further used to identify the potential gene ontology (GO) and REACTOME pathways. Protein-protein interaction (PPI) network was constructed using the Hippie interactome database. miRNet and NetworkAnalyst databases were used to establish a miRNA-hub gene regulatory network and TF-hub gene regulatory network for the hub genes. Hub genes were verified based on receiver operating characteristic curve (ROC) analysis. Totally, 951 DEGs were identified including 476 up regulated genes and 475 down regulated genes screened in NAFLD and normal control. GO showed that DEGs were significantly enhanced for signaling and regulation of biological quality. REACTOME pathway analysis revealed that DEGs were enriched in signaling by interleukins and extracellular matrix organization. ESR2, JUN, PTN, PTGER3, CEBPB, IKBKG, HSPA8, SFN, CDKN1A and E2F1 were indicated as hub genes from PPI network, miRNA-hub gene regulatory network and TF-hub gene regulatory network. Furthermore, ROC analysis revealed that ESR2, JUN, PTN, PTGER3, CEBPB, IKBKG, HSPA8, SFN, CDKN1A and E2F1 might serve as diagnostic biomarkers in NAFLD. The current investigation provided insights into the molecular mechanism of NAFLD that might be useful in further investigations.
Distinct N and C cross-feeding networks in a synthetic mouse gut consortium
Authors: Escriva Pau Perez , Fuhrer Tobias , Sauer Uwe 
Published: December 2021

AbstractThe complex interactions between gut microbiome and host or pathogen colonization resistance cannot solely be understood from community composition. Missing are causal relationships such as metabolic interactions among species to better understand what shapes the microbiome. Here, we focused on metabolic niches generated and occupied by the Oligo-Mouse-Microbiota consortium, a synthetic community composed of 12 members that is increasingly used as a model for the mouse gut microbiome. Combining mono-cultures and spent medium experiments with untargeted metabolomics uncovered broad metabolic diversity in the consortium, constituting a dense cross-feeding network with more than 100 pairwise interactions. Quantitative analysis of the cross-feeding network revealed distinct C and N food webs that highlight the two Bacteroidetes consortium members B. caecimuris and M. intestinale as primary suppliers of carbon, and a more diverse group as nitrogen providers. Cross-fed metabolites were mainly carboxylic acids, amino acids, and the so far not reported nucleobases. In particular the dicarboxylic acids malate and fumarate provided a strong physiological benefit to consumers, presumably as anaerobic electron acceptors. Isotopic tracer experiments validated the fate of a subset of cross-fed metabolites, in particular the conversion of the most abundant cross-fed compound succinate to butyrate. Thus, we show that this consortium is tailored to produce the anti-inflammatory metabolite butyrate. Overall, we provide evidence for metabolic niches generated and occupied by OMM members that lays a metabolic foundation to facilitate understanding of the more complex in vivo behavior of this consortium in the mouse gut.ImportanceThis article maps out the cross-feeding network amongst 10 members of a synthetic consortium that is increasingly used as the model mouse gut microbiota. Combining metabolomics with in vitro cultivations, two dense networks of carbon and nitrogen exchange are described. The vast majority of the about 100 interactions are synergistic in nature, in several cases providing distinct physiological benefits to the recipient species. These networks lay the ground work towards understanding gut community dynamics and host-gut microbe interactions.
Changes in blood cell deformability in Chorea-Acanthocytosis and effects of treatment with dasatinib or lithium
Authors: Reichel Felix , Kräter Martin , Peikert Kevin , Glaß Hannes , Rosendahl Philipp , Herbig Maik , Prieto Alejandro Rivera , Kihm Alexander , Bosman Giel , Kaestner Lars , Hermann Andreas , Guck Jochen 
Published: December 2021

AbstractMisshaped red blood cells (RBCs), characterized by thorn-like protrusions known as acanthocytes, are a key diagnostic feature in Chorea-Acanthocytosis (ChAc), a rare neurodegenerative disorder. The altered RBC morphology likely influences their biomechanical properties which are crucial for the cells to pass the microvasculature. Here, we investigated blood cell deformability of 5 ChAc patients compared to healthy controls during up to one-year individual off-label treatment with the tyrosine kinases inhibitor dasatinib or several weeks with lithium. Measurements with two microfluidic techniques allowed us to assess RBC deformability under different shear stresses. Furthermore, we characterized leukocyte stiffness at high shear stresses. The results show that blood cell deformability – including both RBCs and leukocytes - in general is altered in ChAc patients compared to healthy donors. Therefore, this study shows for the first time an impairment of leukocyte properties in ChAc. During treatment with dasatinib or lithium, we observe alterations in RBC deformability and a stiffness increase for leukocytes. The hematological phenotype of ChAc patients hints at a reorganization of the cytoskeleton in blood cells which partly explains the altered mechanical properties observed here. These findings highlight the need for a systematic assessment of the contribution of impaired blood cell mechanics to the clinical manifestation of ChAc.
The p97 cofactor Ubxn7 facilitates replisome disassembly during S-phase
Authors: Tarcan Zeynep , Poovathumkadavil Divyasree , Skagia Aggeliki , Gambus Agnieszka 
Published: December 2021

AbstractComplex cellular processes are driven by the regulated assembly and disassembly of large multi-protein complexes. In eukaryotic DNA replication, whilst we are beginning to understand the molecular mechanism for assembly of the replication machinery (replisome), we still know relatively little about the regulation of its disassembly at replication termination. Over recent years, the first elements of this process have emerged, revealing that the replicative helicase, at the heart of the replisome, is polyubiquitylated prior to unloading and that this unloading requires p97 segregase activity. Two different E3 ubiquitin ligases are now known to ubiquitylate the helicase under different conditions: Cul2Lrr1and TRAIP. Here we have found two p97 cofactors, Ubxn7 and Faf1, which can interact with p97 during replisome disassembly in S-phase. Only Ubxn7 however facilitates efficient replisome disassembly through its interaction with both Cul2Lrr1and p97. Our data therefore characterise Ubxn7 as the first substrate-specific p97 cofactor regulating replisome disassembly in vertebrates.
Real-time imaging of Arc/Arg3.1 transcription ex vivo reveals input-specific immediate early gene dynamics
Authors: Lituma Pablo J. , Singer Robert H. , Das Sulagna , Castillo Pablo E. 
Published: December 2021

AbstractThe ability of neurons to process and store salient environmental features underlies information processing in the brain. Long-term information storage requires synaptic plasticity and regulation of gene expression. While distinct patterns of activity have been linked to synaptic plasticity, their impact on immediate early gene (IEG) expression remains poorly understood. The activity regulated cytoskeleton associated (Arc) gene has received wide attention as an IEG implicated in synaptic plasticity and memory. Yet, to date, the transcriptional dynamics of Arc in response to compartment and input-specific activity is unclear. By developing a knock-in mouse to fluorescently tag Arc alleles, we studied real-time transcription dynamics after stimulation of dentate granule cells (GCs) in acute hippocampal slices. To our surprise, we found that Arc transcription displayed distinct temporal kinetics depending on the activation of excitatory inputs that convey functionally distinct information, i.e. medial and lateral perforant paths (MPP and LPP, respectively). Moreover, the transcriptional dynamics of Arc after synaptic stimulation was similar to direct activation of GCs, although the contribution of ionotropic glutamate receptors, L-type voltage gated calcium channel, and the endoplasmic reticulum (ER) differed. Specifically, we observed an ER-mediated synapse-to-nucleus signal that supported elevations in nuclear calcium, and rapid induction of Arc transcription following MPP stimulation. However, activation of LPP inputs displayed lower nuclear calcium rise, which could underlie the delayed transcriptional onset of Arc. Our findings highlight how input-specific activity distinctly impacts transcriptional dynamics of an IEG linked to learning and memory.Significance statementEnvironmental experiences trigger neuronal activity that elicits gene expression in the nervous system. Rapid induction of specific genes known as immediate early genes (IEGs) supports activity-dependent changes of neuronal circuits to ultimately influence animal behavior. However, the cellular and molecular mechanisms controlling how distinct forms of neuronal activity modulate IEG expression remains unclear. The activity regulated cytoskeleton associated (Arc) gene is a critical IEG linked to memory. By imaging Arc transcription in real-time after neuronal activity, we identified how different receptors and signaling pathways influence transcriptional induction and dynamics of an IEG. Our findings provide insights into how information received by distinct synaptic inputs could be encoded by modulating IEG dynamics.
The histone methyltransferase NSD3 contributes to sister chromatid cohesion and to cohesin loading at mitotic exit
Authors: Eot-Houllier Grégory , Magnaghi-Jaulin Laura , Bourgine Gaëlle , Smagulova Fatima , Giet Régis , Watrin Erwan , Jaulin Christian 
Published: December 2021

AbstractSister chromatid cohesion guarantees the correct transmission of chromosomes to daughter cells, and this multi-step process occurs throughout the cell cycle. Loading of the core cohesin complex onto chromatin takes place during mitotic exit, cohesion establishment happens during DNA replication, and the timely removal of cohesin occurs during mitosis. While cohesion establishment and mitotic cohesion dissolution have already been explored, the regulation of cohesin loading is not as well understood. Here, we report that the histone-lysine N-methyltransferase NSD3 is an essential factor in sister chromatid cohesion and mitotic progression, and that this occurs before and not after entry into mitosis. We establish that NSD3 interacts with the cohesin loader complex kollerin (NIPBL/MAU2), and that at mitotic exit it ensures proper levels of both MAU2 and cohesin itself on chromatin. In accordance with this newly described function in cohesin loading, we also show that NSD3 associates with chromatin in early anaphase, prior to the loading recruitment of MAU2 and RAD21, and that it then dissociates from chromatin when prophase begins. Going further, we also demonstrate that of the two NSD3 variants existing in somatic cells, it is the long isoform that is responsible for regulating kollerin and cohesin chromatin-loading, and that this isoform’s methyltransferase activity is required for efficient sister chromatid cohesion. Based on these observations, we propose that NSD3-dependent methylation contributes to sister chromatid cohesion by ensuring the proper recruitment of kollerin and thus loading of cohesin.
The pervasive role of accounting and accountability during the COVID-19 emergency
Authors: Leoni Giulia , Lai Alessandro , Stacchezzini Riccardo , Steccolini Ileana , Brammer Stephen , Linnenluecke Martina , Demirag Istemi 
Published: December 2021

PurposeThis paper introduces the second part of a AAAJ special issue on accounting, accountability and management during the COVID-19 emergency. The authors analyse the themes that emerge from the second part of the special issue, which allows us to identify the diverse accounting and accountability practices across different geographical and organisational contexts. The authors also provide an overall picture of the contributions of the special issue, with insights into avenues of future research.Design/methodology/approachBuilding on the first part of the AAAJ special issue, the paper draws together and identifies additional emerging themes related to research into the COVID-19 pandemic and how it impacts accounting, accountability and management practices. The authors reflect on the contributions of the special issue to the interdisciplinary accounting research project.FindingsThe authors identify two macro-themes and outline their contributions to the accounting literature. The first deals with the changes and dangers of accounting and accountability practices during the pandemic. The second considers accountability practices in a broader sense, including reporting, disclosure and rhetorical practices in the management of COVID-19.Practical implicationsThe paper shows the pervasive role of accounting and accountability in the unprecedented and indiscriminate health crisis of COVID-19. It highlights the important role of special issues in producing timely research that responds to unfolding events.Originality/valueThis paper contributes to current debates on the roles of accounting and accountability during COVID-19 by drawing together the themes of the special issue and identifying future interdisciplinary accounting research on the pandemic's aftermath.