bluuebunny/crossref_metadata_2025_split huggingface dataset:
Aryl hydrocarbon receptor utilises cellular zinc signals to maintain the gut epithelial barrier
Authors: Hu Xiuchuan , Xiao Wenfeng , Lei Yuxian , Green Adam , Lee Xinyi , Maradana Muralidhara Rao , Gao Yajing , Xie Xueru , Wang Rui , Chennell George , Basson M. Albert , Kille Pete , Maret Wolfgang , Bewick Gavin A. , Zhou Yufeng , Hogstrand Christer 
Published: November 2022

AbstractBoth zinc and plant-derived ligands of the aryl hydrocarbon receptor (AHR) are dietary components which regulate intestinal epithelial barrier function and protect against Inflammatory Bowel Disease (IBD)1,2. Here, we explore whether zinc and AHR pathway are linked using a mouse IBD model with follow-on studies on human and mouse ileum organoids. Our data demonstrate that AHR regulates cellular zinc uptake, and that zinc is an integral part of AHR signalling processes. We show that dietary supplementation in mice with the plant-derived AHR ligand precursor, indole-3-carbinol (I3C), offers a high level of protection against dextran sulfate sodium induced IBD while protection fails in mice with AHR deleted in the intestinal epithelium. AHR agonist treatment is also ineffective in mice with a nutritional zinc deficiency. Experiments in the human Caco-2 cell line and ileum organoids showed that AHR activation increases total cellular zinc and cytosolic free Zn2+concentrations through transcriptional upregulation of severalSLC39zinc importers. As a consequence, genes for tight junction (TJ) proteins were upregulated in a zinc-dependent manner involving zinc inhibition of signalling to NF-κB and attenuated degradation of TJ proteins through zinc inhibition of calpain activity. Thus, our data indicate that AHR activation by plant-derived dietary ligands improves gut barrier function via zinc-dependent cellular pathways, suggesting that combined dietary supplementation with AHR ligands and zinc might be effective in preventing and treating inflammatory gut disorders.
Host-driven temperature dependence of viral infection in honey bees
Authors: Palmer-Young Evan C , Ryabov Eugene V , Markowitz Lindsey , Boncristiani Dawn L , Grubbs Kyle , Pawar Asha , Peterson Raymond , Evans Jay D 
Published: November 2022

ABSTRACTThe temperature dependence of infection reflects changes in the performance of parasites and hosts. High temperatures (i.e., fever) often mitigate infection by favoring heat-tolerant hosts over heat-sensitive parasites. Honey bees exhibit an endothermic, colony-level temperature regulation that is exceptional among insects and favors resistance to several parasites. However, proliferation of viruses is heavily host-dependent, suggesting that viral infection could be linked to—not threatened by—optimum host function. To understand how temperature-driven changes in performance of viruses and hosts shape virus proliferation, we compared the temperature dependence of isolated viral enzyme activity, three honey bee traits, and infection of honey bee pupae.Viral enzyme activity varied by <2-fold over a >30 °C interval that spanned the temperatures typical of ectothermic insects and honey bees. In contrast, metrics of honey bee performance peaked at high (≥ 35 °C) temperatures and were highly temperature-sensitive, with respiration varying 8-fold over a 20 °C interval and successful development requiring a narrow 8 °C temperature range. Although these results suggested that hosts would gain a relative advantage over viruses with increasing temperature, the temperature dependence of pupal infection matched that of pupal development, falling only near pupae’s upper thermal limits. Our results reflect the host-dependent nature of virus proliferation, suggesting that infection is accelerated—not curtailed—by optimum host function, contradicting predictions of infection based on the relative performance of parasites and hosts, and suggesting tradeoffs between infection resistance and host survival. Despite a 98% reduction in infection at the upper end of the colony temperature range, the narrow thermal safety margin for honey bee development might preclude the effectiveness of ‘fever’ for controlling viruses.
RADICAL CATION SCAVENGING ACTIVITY OF BERBERINE BRIDGE ENZYME-LIKE OLIGOSACCHARIDE OXIDASES ACTING ON SHORT CELL WALL FRAGMENTS
Authors: Scortica Anna , Scafati Valentina , Giovannoni Moira , Benedetti Manuel , Mattei Benedetta 
Published: November 2022

ABSTRACTOligogalacturonide-oxidases (OGOXs) and cellodextrin-oxidase (CELLOX) are plant berberine bridge enzyme-like oligosaccharide-oxidases (OSOXs) that oxidize, respectively, oligogalacturonides (OGs) and cellodextrins (CDs), thereby inactivating their elicitor nature and concomitantly releasing H2O2. Little is known about the physiological role of OSOX activity. By using an ABTS•+-reduction assay, we identified a novel reaction mechanism through which the activity of OSOXs on cell wall oligosaccharides scavenged the radical cation ABTS•+with an efficiency dependent on the type and length of the oxidized oligosaccharide. In contrast to the oxidation of longer oligomers such as OGs (degree of polymerization from 10 to 15), the activity of OSOXs on short galacturonan- and cellulose-oligomers (degree of polymerization ≤ 4) successfully counteracted the radical cation-generating activity of a fungal laccase, suggesting that OSOXs can generate radical cation scavenging activity in the apoplast with a power proportional to the extent of degradation of plant cell wall, with possible implications for redox homeostasis and defense against oxidative stress.
Astrocyte-like CEPsh glia respond to stress
Authors: Chien Evangeline , Garcia Angel J. , L’Etoile Noelle D. , Chandra Rashmi 
Published: November 2022

AbstractWhile astrocytes are known to be important for development and nourishment of the nervous system, the field is just beginning to explore how astrocytes respond to environmental stimuli. UsingCaenorhabditis elegansand their astrocyte-equivalent, CEPsh, we asked whether astrocyte-like glia respond to odor exposure. We found one day-old adultC. elegansdecreasehlh-17promoter (CEPsh glia marker) mediated fluorescent expression when trained with an innately attractive odor butanone. Moreover, the olfactory training paradigm itself affects phlh-17expression, but in a different way. This suggests astrocyte-like CEPsh glia can integrate environmental information to respond to changes in the environment, which enhances survival.
Modeling the iron storage protein ferritin reveals how residual ferrihydrite iron determines initial ferritin iron sequestration kinetics
Authors: Masison Joseph , Mendes Pedro 
Published: November 2022

AbstractFerritin is the primary iron storage protein in mammalian cells and is necessary for cellular iron homeostasis. Its ability to sequester iron protects cells from rising concentrations of ferrous iron limiting oxidative cell damage. The dynamics of its sequestration behavior have been studied extensively experimentally, but mostlyin vitro, rather than within mammalian cells, computational modeling efforts are lacking, and several open questions remain. The importance of FT modeling is driven by the idea that understanding the kinetics of ferritin iron sequestration and how it impacts the regulation of iron metabolism in the cells that compose the main iron regulatory tissues (eg. Kupffer cells, splenic macrophages, enterocytes, erythroblasts, etc.) is central to understanding systemic iron control. The focus of the work here is establishing a model that tractably simulates the ferritin iron sequestration kinetics in a mechanistic way for incorporation into larger cell models, in addition to contributing to the understanding of ferritin iron sequestration dynamics within cells. The model’s parameter values were determined from published kinetic and binding experiments and the model was validated against independent data not used in its construction. Simulation results indicate that FT concentration is the most impactful on overall sequestration dynamics, while the FT iron saturation (number of iron atoms sequestered per FT cage) fine tunes the initial rates. Finally, because this model has a small number of reactions and species, was built to represent important mechanistic details of FT kinetics, and has flexibility to include subtle changes in subunit composition, we propose this model to be used as a building block for models of iron metabolism in a variety of specific cell types.
Synonymous and non-synonymous transitions/transversions vividly disclose purifying selection inEscherichia colicoding sequences
Authors: Beura Pratyush Kumar , Aziz Ruksana , Sen Piyali , Das Saurav , Namsa Nima Dondu , Feil Edward J , Satapathy Siddharatha Sankar , Ray Suvendra Kumar 
Published: November 2022

AbstractTransition (ti) and transversion (tv) are the major causes for genome variation. The accurate estimation oftitotvratioin genomes is crucial for understanding of mutational and selection processes in organisms as it is influenced by both codon degeneracy and pretermination codons (PTC). Therefore, we developed a method (accessible athttps://github.com/CBBILAB/CBBI.git) to estimateratio by accounting codon degeneracy as well as PTC in protein coding sequences. Our findings revealed a distinct impact of codon degeneracy and PTC on theratio in theEscherichia coligenome. We observed a decreasing order among the frequencies of different base substitutions such as synonymous transition (Sti) > synonymous transversion (Stv) > non-synonymous transition (Nti) > non-synonymous transversion (Ntv) inE. coligenome. The correlation was strong betweenStiandStvvalues (Pearsonrvalue 0.795) whereas the correlation was weak betweenStiandNti(Pearsonrvalue 0.192). Coding sequences with similarStivalues exhibited a wide range ofNtivalues. This indicated the varying strength of purifying selection acting on the coding sequences. In concordance with the assumption, the genes having higherNtivalues were observed with lower codon adaptation index (CAI) values than that of the genes having lowerNtivalues. Our approach is convenient to visualize the frequency of base substitution variation as well as selection in protein coding sequences. The proposed method is useful to estimate differentratios accurately in coding sequences and is insightful from an evolutionary perspective.Article SummaryGenetic diversity is pivotal in evolution, with base substitution as a key driver. Transition (ti) frequency surpasses transversion (tv) frequency in genomes, makingratios a valuable metric for studying mutation bias. Our improved estimator forcalculation accounts for codon degeneracy and nonsense substitutions in pretermination codons. Additionally, we unveil insights into the frequency of different substitutions such asSti, Stv, Nti, andNtvand demonstrate the impact of selection on protein coding sequences.
Age and lead configuration matter: A comparative study of RF-induced heating of epicardial and endocardial electronic devices in adult and pediatric anthropomorphic phantoms in 1.5 T MR
Authors: Jiang Fuchang , Henry Kaylee R. , Bhusal Bhumi , Sanpitak Pia , Webster Gregory , Popescu Andrada , Bonmassar Giorgio , Laternser Christina , Kim Daniel , Golestanirad Laleh 
Published: November 2022

AbstractBackgroundChildren with congenital heart defects often have life-sustaining indications for a cardiac implantable electronic device (CIED). In children, these devices are typically sewn to the heart epicardium, but the FDA has never licensed an epicardial system as MR-Conditional due to limited data. Children’s hospitals default to either refusing MRI service to a vast majority of pediatric CIED patients or adopting a scan-all strategy based on results from adult studies. We argue that both approaches are flawed, and the risk-benefit decisions should be made on an individual basis.PurposeTo provide evidence-based knowledge on RF-induced heating of CIEDs in children and adults with epicardial and endocardial leads of different lengths.Study TypePhantomField Strength/Sequence1.5 T.Assessment120 clinically relevant epicardial and endocardial device configurations were implemented in adult and pediatric anthropomorphic phantoms. Temperature rise was recorded during RF exposure at 1.5 T.Statistical TestsMeans comparisons were implemented using two-sample t-tests, reliability analysis using interclass correlation coefficient based on a single rating, absolute-agreement, 2-way mixed-effects model.ResultsThere was significantly higher RF heating of epicardial leads compared to endocardial leads in the pediatric phantom (3.4 ± 3.0 vs. 0.6 ± 0.4 °C, p<0.001); however, there was no significant difference in the adult phantom (3.0 ± 3.2 vs. 2.0 ± 1.8, p=0.16). Endocardial leads in the pediatric phantom generated significantly less RF heating than in the adult phantom (0.6 ± 0.4 °C vs. 2.0 ± 1.8 °C, p<0.001).Data ConclusionBody size and lead length significantly affected RF heating. For models based on younger children with short epicardial leads (e.g., 25cm), RF heating up to 12 °C was observed, delivering a cumulative thermal dose previously associated with tissue necrosis. In contrast, RF heating in model based on children with endocardial leads was well below the heating expected from physiologic fever (3 °C).
First reported detection of the mobile colistin resistance genes,mcr-8 andmcr-9, in the Irish environment
Authors: Cahill Niamh , Hooban Brigid , Fitzhenry Kelly , Joyce Aoife , O’Connor Louise , Miliotis Georgios , McDonagh Francesca , Burke Liam , Chueiri Alexandra , Farrell Maeve Louise , Bray James E. , Delappe Niall , Brennan Wendy , Prendergast Deirdre , Gutierrez Montserrat , Burgess Catherine , Cormican Martin , Morris Dearbháile 
Published: November 2022

AbstractThe emergence and dissemination of mobile colistin resistance (mcr) genes across the globe poses a significant threat to public health, as colistin remains one of the last line treatment options for multi-drug resistant infections. Environmental samples (157 water and 157 wastewater) were collected in Ireland between 2018 and 2020. Samples collected were assessed for the presence of antimicrobial resistant bacteria using Brilliance ESBL, Brilliance CRE, mSuperCARBA and McConkey agar containing a ciprofloxacin disc. All water and integrated constructed wetland influent and effluent samples were filtered and enriched in buffered peptone water prior to culture, while wastewater samples were cultured directly. Isolates collected were identified via MALDI-TOF, were tested for susceptibility to 16 antimicrobials, including colistin, and subsequently underwent whole genome sequencing. Overall, eightmcrpositive Enterobacterales (onemcr-8 and sevenmcr-9) were recovered from six samples (freshwater (n=2), healthcare facility wastewater (n=2), wastewater treatment plant influent (n=1) and integrated constructed wetland influent (piggery farm waste) (n=1)). While themcr-8 positiveK. pneumoniaedisplayed resistance to colistin, all sevenmcr-9 harbouring Enterobacterales remained susceptible. All isolates demonstrated multi-drug resistance and through whole genome sequencing analysis, were found to harbour a wide variety of antimicrobial resistance genes i.e., 30 ± 4.1 (10-61), including the carbapenemases,blaOXA-48(n=2) andblaNDM-1(n=1), which were harboured by three of the isolates. Themcrgenes were located on IncHI2, IncFIIK and IncI1-like plasmids. The findings of this study highlight potential sources and reservoirs ofmcrgenes in the environment and illustrate the need for further research to gain a better understanding of the role the environment plays in the persistence and dissemination of antimicrobial resistance.
OsPSTOL1is prevalent in upland rice and its expression in wheat enhances root growth and hastens low phosphate signaling
Authors: Kettenburg Alek Thomas , Lopez Miguel Angel , Yogendra Kalenahalli , Prior Matthew J. , Rose Teresa , Bimson Sabrina , Heuer Sigrid , Roy Stuart John , Bailey-Serres Julia 
Published: November 2022

ABSTRACTPHOSPHORUS-STARVATION TOLERANCE 1(OsPSTOL1) benefits crown root growth and phosphorus (P) sufficiency in rice (Oryza sativaL.). To better understand the importance of this variably present gene, we carried out a biogeographic survey of landraces and cultivars, confirming that functionalOsPSTOL1alleles prevail in low nutrient and drought-prone rainfed ecosystems, whereas loss-of-function alleles and absence haplotypes predominate in control-irrigated paddy varieties of east Asia. To address the evolutionary history ofOsPSTOL1and related genes in cereal crops, phylogenetic and transcript meta-analyses were performed. Finally, to evaluate its potential value in another Gramineae, wheat (Triticum aestivumL.) lines overexpressingOsPSTOL1were evaluated under field and controlled low P conditions.OsPSTOL1enhances growth, crown root number, and overall root plasticity under low P in wheat. Survey of root and shoot crown transcriptomes at two developmental stages identifies transcription factors that are differentially regulated inOsPSTOL1wheat that are similarly controlled by the gene in rice. In wheat,OsPSTOL1alters the timing and amplitude of regulators of root development in dry soils and hastens induction of the core P-starvation response. Based on these findings,OsPSTOL1and related genes may aid more sustainable cultivation of cereal crops.Summary statementMight a rice gene that controls root plasticity confer a similar benefit in another grain crop. Here, we evaluate the genetic variation and evolutionary history ofOsPSTOL1and demonstrate its impact in wheat.
EvoAug: improving generalization and interpretability of genomic deep neural networks with evolution-inspired data augmentations
Authors: Lee Nicholas Keone , Tang Ziqi , Toneyan Shushan , Koo Peter K 
Published: November 2022

ABSTRACTDeep neural networks (DNNs) hold promise for functional genomics prediction, but their generalization capability may be limited by the amount of available data. To address this, we propose EvoAug, a suite of evolution-inspired augmentations that enhance the training of genomic DNNs by increasing genetic variation. However, random transformation of DNA sequences can potentially alter their function in unknown ways. Thus, we employ a fine-tuning procedure using the original non-transformed data to preserve functional integrity. Our results demonstrate that EvoAug substantially improves the generalization and interpretability of established DNNs across prominent regulatory genomics prediction tasks, offering a robust solution for genomic DNNs.
Understanding the role and adoption of artificial intelligence techniques in rheumatology research: an in-depth review of the literature
Authors: Madrid-García Alfredo , Merino-Barbancho Beatriz , Rodríguez-González Alejandro , Fernández-Gutiérrez Benjamín , Rodríguez-Rodríguez Luis , Menasalvas-Ruiz Ernestina 
Published: November 2022

ABSTRACTThe major and upward trend in the number of published research related to rheumatic and musculoskeletal diseases, in which artificial intelligence plays a key role, has exhibited the interest of rheumatology researchers in using these techniques to answer their research questions. In this review, we analyse the original research articles that combine both worlds in a five-year period (2017-2021). In contrast to other published papers on the same topic, we first studied the review and recommendation articles that were published during that period, including up to October 2022, as well as the publication trends. Secondly, we review the published research articles and classify them into one of the following categories: disease classification, disease prediction, predictors identification, patient stratification and disease subtype identification, disease progression and activity, and treatment response. Thirdly, we provide a table with illustrative studies in which artificial intelligence techniques have played a central role in more than twenty rheumatic and musculoskeletal diseases. Finally, the findings of the research articles, in terms of disease and/or data science techniques employed, are highlighted in a discussion. Therefore, the present review aims to characterise how researchers are applying data science techniques in the rheumatology medical field. The most immediate conclusions that can be drawn from this work are: multiple and novel data science techniques have been used in a wide range of rheumatic and musculoskeletal diseases including rare diseases; the sample size and the data type used are heterogeneous, and new technical approaches are expected to arrive in the short-middle term.HighlightsThe rheumatology research community is increasingly adopting novel AI techniquesThere is an upward trend in the number of articles that combine AI and rheumatologyRheumatic and musculoskeletal rare diseases are gaining from AI techniquesIndependent validation of the models should be promoted
How to start a LINE: 5’ switching rejuvenates LINE retrotransposons in tobacco and relatedNicotianaspecies
Authors: Hartig Nora , Seibt Kathrin M. , Heitkam Tony 
Published: November 2022

AbstractIn contrast to their conserved mammalian counterparts, plant long interspersed nuclear elements (LINEs) are highly variable, splitting into many low-copy families. Curiously, LINE families from the RTE clade retain a stronger sequence conservation and hence reach higher copy numbers. The cause of this RTE-typical property is not yet understood, but would help clarifying why some transposable elements are removed quickly whereas others persist in plant genomes. Here, we bring forward the first detailed study of RTE LINE structure, diversity and evolution in plants. For this, we argue that the Nightshade family is the ideal taxon to follow the evolutionary trajectories of RTE LINEs, given their high abundance, recent activity and partnership to non-autonomous elements.Using bioinformatic, cytogenetic and molecular approaches, we detect 4029 full-length RTE LINEs across theSolanaceae. We finely characterize and manually curate a core group of 458 full-length LINEs in allotetraploid tobacco, show amplification after polyploidization, and trace hybridization events by RTE LINE composition of parental genomes. Finally, we reveal the role of the untranslated regions (UTRs) as causes for the unique RTE LINE amplification and evolution pattern in plants: On one hand, we detect a highly conserved motif at the 3’ UTR, suggesting strong selective constraints acting on the RTE terminus. On the other hand, we observed successive rounds of 5’ UTR cycling, constantly rejuvenating the promoter sequences. This interplay between exchangeable promoters and conserved LINE bodies and 3’ UTR likely allows RTE LINEs to persist and thrive in plant genomes.