bluuebunny/crossref_metadata_2025_split huggingface dataset:
5’-NADylation of RNA is well-tolerated by bacterial cell
Authors: Wiedermannova Jana , Babu Ravishankar , Yuzenkova Yulia 
Published: April 2023

AbstractRecently discovered ability of various RNA polymerases (RNAPs) of bacteria and eukaryotes to initiate RNA synthesis with cofactors such as NAD+/NADH (nicotinamide adenine dinucleotide). This phenomenon was quickly dubbed “non-canonical capping” as the extra 5’ moieties of RNA resemble eukaryotic m7G cap superficially. NAD must outcompete abundant ATP, to serve as initiating nucleotide. It is still unclear which physiological conditions permit significant RNA NADylation and to what degree NADylation serves typical functions of a canonical cap in bacteria.Here we found that the extent of NADyation depends primarily on fidelity of transcription initiation –NAD concentration, specific contacts of RNAP active site with NAD/ATP alternative substrates, and genomic DNA supercoiling. It is much less affected by posttranscriptional processes such as de-capping, processing by main 5’-dependent ribonucleases RNaseE and oligoribonuclease. 5’-NAD inhibits neither translation of a leaderless 5’-NAD-RNA nor a physiological base-pairing of small regulatory NADylated RNA with its antisense target RNA. Translation exposes 5’-NAD for de-capping by NudC enzyme.
A role for cytoglobin in regulating intracellular hydrogen peroxide and redox signals in the vasculature
Authors: Mathai Clinton , Jourd’heuil Frances , Pham Le Gia Cat , Gilliard Kurrim , Balnis Joseph , Jen Annie , Overmyer Katherine A. , Coon Joshua J , Jaitovich Ariel , Boivin Benoit , Jourd’heuil David 
Published: April 2023

AbstractThe oxidant hydrogen peroxide serves as a signaling molecule that alters many aspects of cardiovascular functions. Recent studies suggest that cytoglobin – a hemoglobin expressed in the vasculature – may promote electron transfer reactions with proposed functions in hydrogen peroxide decomposition. Here, we determined the extent to which cytoglobin regulates intracellular hydrogen peroxide and established mechanisms. We found that cytoglobin decreased the hyperoxidation of peroxiredoxins and maintained the activity of peroxiredoxin 2 following challenge with exogenous hydrogen peroxide. Cytoglobin promoted a reduced intracellular environment and facilitated the reduction of the thiol-based hydrogen peroxide sensor Hyper7 after bolus addition of hydrogen peroxide. Cytoglobin also limited the inhibitory effect of hydrogen peroxide on glycolysis and reversed the oxidative inactivation of the glycolytic enzyme GAPDH. Our results indicate that cytoglobin in cells exists primarily as oxyferrous cytoglobin (CygbFe2+-O2) with its cysteine residues in the reduced form. We found that the specific substitution of one of two cysteine residues on cytoglobin (C83A) inhibited the reductive activity of cytoglobin on Hyper7 and GAPDH. Carotid arteries from cytoglobin knockout mice were more sensitive to glycolytic inhibition by hydrogen peroxide than arteries from wildtype mice. Together, these results support a role for cytoglobin in regulating intracellular redox signals associated with hydrogen peroxide through oxidation of its cysteine residues, independent of hydrogen peroxide reaction at its heme center.
Rescue of blood coagulation Factor VIII exon-16 mis-splicing by antisense oligonucleotides
Authors: Tse Victor , Chacaltana Guillermo , Gutierrez Martin , Forino Nicholas M. , Jimenez Arcelia G. , Tao Hanzhang , Do Phong H. , Oh Catherine , Chary Priyanka , Quesada Isabel , Hamrick Antonia , Lee Sophie , Stone Michael D. , Sanford Jeremy R. 
Published: April 2023

ABSTRACTThe humanFactor VIII(F8) protein is essential for the blood coagulation cascade and specificF8mutations cause the rare bleeding disorder Hemophilia A (HA). Here, we investigated the impact of HA-causing single-nucleotide mutations onF8pre-mRNA splicing. We found that 14/97 (∼14.4%) coding sequence mutations tested in our study induced exon skipping. Splicing patterns of 4/11 (∼36.4%)F8exons tested were especially sensitive to the presence of common disease-causing mutations. RNA-chemical probing analyses revealed a three-way junction structure at the 3′ end of intron 15 (TWJ-3-15). TWJ-3-15 sequesters the polypyrimidine tract, a key determinant of 3′ splice site strength. Using exon-16 of theF8gene as a model, we designed specific antisense oligonucleotides (ASOs) that target TWJ-3-15 and identified three that promote the splicing ofF8exon-16. Interaction of TWJ-3-15 with ASOs increases accessibility of the polypyrimidine tract and inhibits the binding of hnRNPA1-dependent splicing silencing factors. Moreover, ASOs targeting TWJ-3-15 rescue diverse splicing-sensitive HA-causing mutations, most of which are distal to the 3’ splice site being impacted. The TWJ-3-15 structure and its effect on mRNA splicing provide a model for HA etiology in patients harboring specificF8mutations and provide a framework for precision RNA-based HA therapies.
Quorum-sensing gene regulates hormetic effects induced by sulfonamides in Comamonadaceae
Authors: Lin Hui , Ning Xue , Wang Donglin , Wang Qiaojuan , Bai Yaohui , Qu Jiuhui 
Published: April 2023

AbstractHormesis is a toxicological phenomenon whereby exposure to low-dose stress results in stimulation of various biological endpoints. Among these, the induction of cell proliferation by antibiotics is critical, but the underlying molecular mechanisms remain poorly understood. Here, we showed that sulfonyl-containing chemicals (e.g., sulfonamides) can induce cell-proliferation hormesis ofComamonas testosteroni. Investigation of the hormesis mechanism revealed that low-dose sulfonamides bind to theLuxR-type quorum sensing protein LuxR solo, thereby triggering the transcription of 3-ketoacyl-CoA thiolase, a key enzyme of the fatty acid β-oxidation. This provides additional ATP, NADPH, and acetyl-CoA for purine and pyrimidine biosynthesis, allowing cells to synthesize sufficient nucleotides to support rapid cell growth. Our work reports on a previously unknown mechanism for the hormetic effect and highlights its generality in the Comamonadaceae family.
Discovering motifs and genomic patterns with SMT: a high-performance data structure for counting kmers
Authors: Caldonazzo Garbelini Jader M. , Sanches Danilo Sipoli , Pozo Aurora Trinidad Ramirez 
Published: April 2023

AbstractMotivationThe search for conserved motifs in DNA sequences is an important problem in bioinformatics. The growing availability of large-scale genomic data poses significant challenges for computational biology, particularly in terms of efficiency in analysis, kmer identification, and noise presence. The detection of conserved motifs and patterns in DNA sequences is crucial for understanding gene functions and regulations. Therefore, it is essential to develop a data structure that can handle these large volumes of information and provide accurate and fast results.ResultsWe present SMT, an innovative tool designed to efficiently store and count kmers, optimizing memory usage and computation time. The application of SMT has also proven effective in discovering motifs in noisy datasets, allowing the identification of conserved regions in sequences. Furthermore, SMT enables exact searches in constant time and recovers the most abundant k-mers, as well as performs approximate searches in linear time to find fragments with up todmutations. This approach facilitates large-scale data analysis and provides important insights into the conserved properties of biological sequences. The application of SMT in motif discovery demonstrates its potential to drive research in bioinformatics and genomics. Supplementary data and results are available to provide additional information and support the conclusions presented in this work.Availability and implementationThe source code of the presented method is publicly available athttps://github.com/jadermcg/SMT.
3D genome organization drives gene expression in trypanosomes
Authors: Díaz-Viraqué Florencia , Chiribao María Laura , Libisch Gabriela , Robello Carlos 
Published: April 2023

AbstractIn trypanosomes —eukaryotic unicellular pathogens that cause disabling human and animal diseases— very few transcriptional regulatory elements have been described and it is largely accepted that they regulate gene expression mainly post-transcriptionally. In this regard, the role of the spatial organization of the genome on gene expression and vice versa remains practically unexplored. The genome of these parasites is partitioned into core (highly conserved syntenic) and species-specific disruptive regions (synteny disruption), containing multigene families encoding for surface glycoproteins. By mapping genome-wide chromatin interactions we demonstrate that these regions constitute 3D compartments (C and D). These chromatin compartments present significant differences in DNA methylation, nucleosome positioning and chromatin interactions, affecting genome expression dynamics. We show that the genome is organized into chromatin folding domains and transcription is dramatically determined by the local chromatin structure. Our results support a model in which epigenetic mechanisms dramatically impact gene expression in these eukaryotic pathogens.
The moderating role of narcissism in predicting the behavior intention of the Palestinian university students towards adopting the new Facebook currency
Authors: Baidoun Samir Daoud , Salem Mohammed Zedan , Wagner Ralf 
Published: April 2023

PurposeThis paper aims to identify the factors affecting university students’ behavioral intentions towards adopting the new Facebook currency while controlling for the direct and the moderating impacts of narcissism.Design/methodology/approachA self-administered questionnaire of 344 respondents from six major Palestinian universities was analyzed. The structural model is fitted for assessing the hypothesized relations.FindingsFindings indicate that the effect of Facebook advertisement in predicting the behavioral intentions to adopt the new Facebook currency relies on: privacy, security, the expectations in the new Facebook currency and knowledge about the targeting options within the Facebook platform. Moreover, the moderating role of narcissism supported the relationships between perceived privacy, the expectations in the new Facebook currency and knowledge about the targeting options within the Facebook platform but did not support the moderating role of narcissism in the relationships between perceived security and the behavioral intentions.Research limitations/implicationsIn this study, only the Facebook platform and the behavioral intention were investigated with data collected from Palestinian University students through self-reported cross-sectional survey.Practical implicationsThis study adds insight on the moderating role of narcissism in predicting the behavior intentions towards adopting the new Facebook currency (Diem) which has a substantial potential to threaten all other crypto currencies and the other alternatives. Therefore, managers should consider altering or adapting their Facebook advertising tactics accordingly.Originality/valueThis study is the first to contribute through empirical evidence from a developing country to theory building the results of clarifying the propensity to adopt the new Facebook currency, outlining the consumers’ reaction to social media advertising and its influential factors and providing evidence proving relevance of narcissism for non-Western users.Peer reviewThe peer review history for this article is available at:https://publons.com/publon/10.1108/OIR-12-2021-0666
Racial attitudes and belief in redeemability: Most Whites believe justice‐involved Black people can change
Authors: Butler Leah C. , Cullen Francis T. , Burton Velmer S. 
Published: April 2023

AbstractPublic belief in redeemability reduces punitiveness and increases support for policy measures such as rehabilitation, expungement, and housing and employment opportunities. Although racial attitudes are known to influence a wide range of criminal justice policy opinions, their effects on beliefs about redeemability and condemnation have not been fully explored. Using data from a 2019 YouGov survey of a national sample of White U.S. adults (N = 766), the current study estimates the effects of three distinct racial attitudes—racial resentment, racial sympathy, and White nationalism—on three measures of belief in redeemability: 1) a race‐neutral measure, 2) a measure of belief in redeemability of Black offenders, and 3) a measure of condemnation of Black offenders. The results indicate that belief in redeemability is high—for offenders in general and for Black offenders. These findings are supported by a second 2022 YouGov survey of White U.S. adults (N = 1,505). Racial sympathy and White nationalism have significant effects across all three outcomes, with the positive effect of White nationalism on condemnation of Black offenders being the largest across the three models. These findings suggest that although most Whites agree that formerly incarcerated people are redeemable, racial attitudes influence these beliefs, especially for Black offenders.
Monitoring temporal and spatial trends of illegal and legal fishing in marine conservation areas across Canada's three oceans
Authors: Iacarella Josephine C. , Burke Lily , Clyde Georgia , Wicks Adam , Clavelle Tyler , Dunham Anya , Rubidge Emily , Woods Paul 
Published: April 2023

AbstractExpansion of marine conservation areas (CA) necessitates resource‐efficient and achievable strategies for monitoring and evaluation of ongoing fishing activity at national levels. To demonstrate and explore such a strategy, we conducted the first extensive analysis of fishing activity within Canada's static, geographically defined marine CAs with fishing regulations (n = 264 areas). We used 8 years of Automatic Identification System data to estimate fishing effort across three oceans and conducted temporal and spatial comparisons specific to each CA's regulations and enactment date. We addressed questions on CA effectiveness, fishing displacement, fishing the line behavior, and relationships between fishing activity and spatial CA attributes. We estimated 22,000 h of fishing activity within CAs after enactments, 22% of which was identified as illegal. CA effectiveness appeared to be lowest for Atlantic CAs based on illegal fishing effort density within CAs. Fishing displacement and fishing the line was generally not apparent as buffer areas around CAs tended to already have higher fishing effort prior to enactments. CA effectiveness and responses to CAs varied considerably, as was visualized using timeseries plots and maps developed for each CA. Our evaluation of a nation's full suite of CAs provides managers with a foundation and approach for continued monitoring and reporting.
Fetal cardiac interventions: First‐year experience of a tertiary referral center in Turkey
Authors: Deren Ozgur , Aykan Hayrettin Hakan , Ozyuncu Ozgur , Aypar Ebru , Cagan Murat , Ozen Ozge , Karagoz Tevfik 
Published: April 2023

AbstractAimTo present the first‐year experience of fetal cardiac interventions (FCIs) in a tertiary referral hospital and to evaluate the outcomes.MethodsThis retrospective study consisted of four pregnant women who underwent fetal pulmonary or aortic balloon valvuloplasty between November 2020 and June 2021. The procedures were performed with a percutaneous cardiac puncture under the ultrasonography guidance. Gestational age at intervention, procedural success, complications, and perinatal outcomes were evaluated. Procedural complications defined as fetal bradyarrhythmia requiring treatment, pericardial effusion requiring drainage, balloon rupture, and fetal death. The procedure was considered technically successful if the valve was dilated with a balloon catheter. Ultimately successful procedure was defined as the discharge of infants alive with biventricular circulation.ResultsA total of 5 FCIs attempted between 26 + 3 and 28 + 2 gestational weeks. While the procedure was technically successful in 2 cases with pulmonary stenosis, both attempts were unsuccessful in the fetus with pulmonary atresia. Although the procedure was technically successful in the patient with critical aortic stenosis, it ultimately failed. No fetal death occurred in our series and there were no procedure‐related significant maternal complications. However, three interventions were complicated by fetal bradycardia and pericardial effusion necessitating treatment, and balloon rupture cropped up in one case.ConclusionFCIs may lead to improving the likelihood of a biventricular outcome for selected fetuses. Careful selection of patients and centralization of experience are essential for obtaining favorable outcomes. Operators should be aware of procedural complications. Improved procedural techniques with a lower complication rate will be achieved through advanced medical technology and special balloon catheters.
More complex than you think: Taxonomic and temporal patterns of plant–pollinator networks of caraway (Carum carvi L.)
Authors: Kilian Isabel C. , Swenson Stephanie J. , Mengual Ximo , Gemeinholzer Birgit , Hamm Andrée , Wägele J. Wolfgang , Peters Ralph S. 
Published: April 2023

AbstractCaraway (Carum carvi L.) is a crop species that is gaining in importance in Europe, especially as a condiment and medicinal plant. Here, we present the plant–pollinator network of caraway in a central European agricultural landscape, focusing on two diverse potential pollinator taxa, Diptera: Brachycera (= true flies) and Hymenoptera (sawflies, bees, and wasps). We specifically studied qualitative differences in interactions between the two insect taxa as well as the intraday and intraseasonal variability of the network. Insect and pollen plant species determination was done via morphological identification and DNA (meta)barcoding. In total, 121 species representing 33 families of Hymenoptera and Brachycera were found to carry caraway pollen. These taxa included many nonhoneybee and nonhoverfly species, showing a wide taxonomic breadth of potential pollinators and a higher network complexity than previously anticipated. There are distinct qualitative differences between Brachycera and Hymenoptera networks, suggesting complementary roles of both taxa in the pollination of native and crop plants. Strong intraday differences in potential pollinator diversity make it necessary to collect insects and pollen at different times of the day to compile complete plant–pollinator networks. Intraseasonal analyses of the plant–pollinator network of caraway show the potential of caraway as an important food source for insect species with an activity peak in late summer.
Occurrence and field evaluation of sugarcane genotypes for resistance to pokkah boeng disease in China
Authors: Xu Yuzhi , Wei Yibin , Jiang Chunxiu , Pan Kaiyuan , Wang Maoyao , Deng Zuhu , Zhang Muqing 
Published: April 2023

AbstractSugarcane pokkah boeng disease (PBD), caused by aFusariumspecies complex, is one of the most critical diseases causing a significant economic loss of sugarcane production in China. It is important to standardize the evaluation method for screening sugarcane cultivars for resistance to PBD. Field trials were conducted to investigate the occurrence of sugarcane PBD in different months and growth stages from 2018 to 2019 and to evaluate the PBD resistance of 169 sugarcane genotypes from 2019 to 2022. PBD mainly occurred in the early and middle elongation stages at a plant height of approximately 1–2 m. The most severe and common incidence of PBD was from June to August. Variance analysis showed genotype, year and the interaction of genotype and year had a significant effect on disease incidence and disease index. The 169 sugarcane genotypes were divided into five categories by cluster analysis and discriminant analysis, of which 33 were rated as highly resistant, 37 as resistant, 38 as moderately susceptible, 26 as susceptible and 35 as highly susceptible. These findings enhance our understanding of sugarcane resistance to PBD and lay the foundation for breeding new resistant varieties.
DIGITAL THEOLOGY AND A POTENTIAL THEOLOGICAL APPROACH TO A METAPHYSICS OF INFORMATION
Authors: Phillips Peter M. 
Published: April 2023

AbstractIn this article, I offer a background to digital theology and its methodology, exploring especially aspects of transhumanism and metaphysical enquiry. The article moves on to engage with several articles given at the Science and Religion Forum at Birmingham in 2022, especially the Gowland Lecture given by Professor Niels Gregersen and the Peacocke Lecture by Andrew Jackson. Both offer a metaphysical approach to information linked closely to the concept of Logos drawn from the Prologue of John—Jackson focusing on Maximus the Confessor's exploration of phylogeneticlogoi; Gregersen on a further development of “Deep Incarnation” through the title “God with Clay” drawn from Bonaventure. The article extends this engagement with John by querying the model of incarnation in “deep incarnation” but building on the Logos/logoi to set out some initial building blocks for an alternative metaphysics of information.
RESPONSIVE BODIES: ROBOTS, AI, AND THE QUESTION OF HUMAN DISTINCTIVENESS
Authors: Balle Simon , Nissen Ulrik 
Published: April 2023

AbstractIn this article, we argue two points in relation to the challenge to human distinctiveness emerging as artificial intelligence systems and humanlike robots simulate various human capabilities. First, that, in the context of theological anthropology, it is advisable to respond to this challenge by turning toward the human body. Second, following this point, we propose the responsive body hypothesis, suggesting that what makes us distinct from androids are capacities that rise from and depend on our responsive bodies.