bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evidence for the digital programming of cellular differentiation: characterization of binary switches in lineage-determining transcription factors
Authors: Li Hongchuan , Rahman Md Ahasanur , Wright Paul W , Cao Jennie , Ratnayake Shashikala , Chen Qingrong , Yan Chunhua , Meerzaman Daoud , Freud Aharon G , Anderson Stephen K 
Published: June 2022

AbstractPrevious studies of the murine Ly49 and human KIR gene clusters have revealed a role for bidirectional promoters in the control of variegated gene expression. Whether or not competing promoters control other instances of cell fate determination remains an outstanding question. Although divergent transcripts within 300 bp are found in ~6% of human genes, an analysis of human transcription factor (TF) genes (1640) revealed that 33% possess stable divergent transcripts with a transcription start site (TSS) less than 300 bp upstream, with many separated by less than 30 bp, indicating an enrichment for potential binary switches in TFs. We have performed a detailed examination of putative bidirectional promoter switches in three lineage-determining TF genes: AHR, GATA3, and RORγT. These genes also contain additional pairs of opposing promoters that would prevent simultaneous transcription of sense and antisense, and thus may represent simple on/off switches rather than probabilistic switches. In situ RNA hybridization of human tissues revealed mutually exclusive expression of sense versus antisense transcription, indicating switching between stable sense or antisense transcriptional states. Single-cell RNAseq confirmed the separate sense/antisense states, and revealed the identity of cells with active switch elements. Differential gene expression analysis of cells with antisense switch transcripts revealed an enrichment for genes found in immature/stem cells and a lack of genes associated with terminally differentiated cells. Taken together, these data indicate that there is a digital component to the differentiation program mediated by binary promoter switches in lineage-determining transcription factors.
Targeted cortical stimulation reveals principles of cortical contextual interactions
Authors: Wang Shen , Palmigiano Agostina , Miller Kenneth D. , Van Hooser Stephen D. 
Published: June 2022

AbstractCross-orientation suppression is a classic form of contextual normalization in visual cortex, yet the degree to which cortical circuits participate in the normalization computation is unclear. We visualized orientation maps of individual ferrets, and provided patterned optogenetic stimulation to both excitatory and inhibitory cells in orientation columns that either matched or were orthogonal to the preferred visual orientation of neurons recorded with electrodes. When visual or optogenetic stimulation of columns preferring one orientation was combined with optogenetic stimulation of columns preferring the orthogonal orientation, we observed less suppression than when orthogonal stimulation was provided visually, suggesting that cortical circuits do not provide a large fraction of visual cross-orientation suppression. Integration of visual and optogenetic signals was linear when neurons exhibited low firing rates and became sublinear when neurons exhibited higher firing rates. We probed the nature of sublinearities in cortex by examining the influence of optogenetic stimulation of cortical interneurons. We observed a range of responses, including evidence for paradoxical responses in which interneuron stimulation caused a decrease in inhibitory firing rate, presumably due to the withdrawal of recurrent excitation. These results are compatible with cortical circuits that exhibit strong recurrent excitation with stabilizing inhibition that provides normalization, albeit normalization that is too weak across columns to account for cross-orientation suppression.
Ancient origin of Jingchuvirales derived glycoproteins integrated in arthropod genomes
Authors: Dezordi Filipe Zimmer , Coutinho Gutembergmann Batista , Dias Yago José Mariz , Wallau Gabriel Luz 
Published: June 2022

AbstractEndogenous virus elements (EVEs) are viral-derived sequences integrated into their host genomes. EVEs of the Jingchuvirales order were detected in a wide range of insect genomes covering several distantly related families and Jingchuvirales-derived glycoproteins were recently associated by our group with the origin of a putative new retrovirus based on a glycoprotein captured by a mosquito retrotransposon. But, except for mosquitoes, there is a lack of a more detailed understanding of the endogenization mechanism, timing and frequency per viral lineages. Here we screened Jingchuvirales glycoprotein-derived EVEs (Jg-EVEs) in eukaryotic genomes. We found six distinct endogenization events of Jg-EVEs, that belong to two out of five known Jingchuvirales families (Chuviridae and Natareviridae). For seven arthropod families bearing Jg-EVEs there is no register of bona fide circulating chuvirus infection. Hence, our results show that Jingchuvirales viruses infected or still infect these host families, expanding their known host range. We estimated that two endogenization events occurred in the ancestors of the Myrmicinae-Ponerinae subfamilies (Pteromalidae - Hymenoptera order) around 155∼54.8 MyA and Bombus genus (Hemiptera order) around (36∼2 MyA). Although we found abundant evidence of LTR-Gypsy retrotransposons fragments associated with the glycoprotein in Hymenoptera and other insect orders, there is no evidence of potential functional glycoprotein capture. Our results show that the widespread distribution of Jingchuvirales glycoproteins in extant Arhtropods is a result of multiple ancient endogenization events and that these viruses’ fossils are being vertically inherited for millions of years through the Arthropods evolutionary tree.Graphical Abstract
Carbon isotope fractionation by an ancestral rubisco suggests biological proxies for CO2through geologic time should be re-evaluated
Authors: Wang Renée Z. , Nichols Robert J. , Liu Albert K. , Flamholz Avi I. , Artier Juliana , Banda Doug M. , Savage David F. , Eiler John M. , Shih Patrick M. , Fischer Woodward W. 
Published: June 2022

AbstractThe history of Earth’s carbon cycle reflects trends in atmospheric composition convolved with the evolution of photosynthesis. Fortunately, key parts of the carbon cycle have been recorded in the carbon isotope ratios of sedimentary rocks. The dominant model used to interpret this record as a proxy for ancient atmospheric CO2is based on carbon isotope fractionations of modern photoautotrophs, and longstanding questions remain about how their evolution might have impacted the record. We tested the intersection of environment and evolution by measuring both biomass (εp) and enzymatic (εRubisco) carbon isotope fractionations of a cyanobacterial strain (Synechococcus elongatusPCC 7942) solely expressing a putative ancestral Form 1B rubisco dating to ≫1 Ga. This strain, nicknamed ANC, grows in ambient pCO2and displays larger εpvalues than WT, despite having a much smaller εRubisco(17.23 ± 0.61‰ vs. 25.18 ± 0.31‰ respectively). Measuring both enzymatic and biomass fractionation revealed a surprising result—ANC εpexceeded ANC εRubiscoin all conditions tested, contradicting prevailing models of cyanobacterial carbon isotope fractionation. However, these models were corrected by accounting for cyanobacterial physiology, notably the CO2concentrating mechanism (CCM). Our model suggested that additional fractionating processes like powered inorganic carbon uptake systems contribute to εp, and this effect is exacerbated in ANC. Understanding the evolution of rubisco and the CCM is therefore critical for interpreting the carbon isotope record. Large fluctuations in that record may reflect the evolving efficiency of carbon fixing metabolisms in addition to changes in atmospheric CO2.Significance StatementEarth scientists rely on chemical fossils like the carbon isotope record to derive ancient atmospheric CO2concentrations, but interpretation of this record is calibrated using modern organisms. We tested this assumption by measuring the carbon isotope fractionation of a reconstructed ancestral rubisco enzyme (>1 billion years old)in vivoandin vitro. Our results contradicted prevailing models of carbon flow in Cyanobacteria, but our data could be rationalized if light-driven uptake of CO2is taken into account. Our study showed that the carbon isotope record tracks both the evolution of photosynthesis physiology as well as changes in atmospheric CO2, highlighting the value of considering both evolution and physiology for comparative biological approaches to understanding Earth’s history.
Molecular Mechanism of Active Cas7-11 in Processing CRISPR RNA and Interfering Target RNA
Authors: Gowswami Hemant , Rai Jay , Das Anuska , Li Hong 
Published: June 2022

AbstractCas7-11 is a Type III-E CRISPR Cas effector that confers programmable RNA cleavage and has potential applications in RNA interference. Cas7-11 encodes a single polypeptide containing four Cas7- and one Cas11-like segments that obscures the distinction between the multi-subunit Class 1 and the single-subunit Class-2 CRISPR-Cas systems. We report a cryo-EM structure of the active Cas7-11 from Desulfonema ishimotonii (DiCas7-11) that reveals the molecular basis for RNA processing and interference activities. DiCas7-11 arranges its Cas7- and Cas11-like domains in an extended form that resembles the backbone made up by four Cas7 and one Cas11 subunits in the multi-subunit enzymes. Unlike the multi-subunit enzymes, however, the backbone of DiCas7-11 contains evolutionarily different Cas7 and Cas11 domains, giving rise to their unique functionality. The first Cas7-like domain nearly engulfs the last 15 direct repeat nucleotides and is responsible for processing and recognition of the CRISPR RNA. Whereas both the second and the third Cas7-like domains mediate target RNA cleavage, they differ in metal requirement for catalysis. The long variable insertion to the fourth Cas7-like domain has little impact to RNA processing or targeting, suggesting the possibility for engineering a compact and programmable RNA interference tool.One Sentence SummaryStructures of Cas7-11 reveal the molecular basis for processing CRISPR RNA and for cleaving target RNA.
Prevalence of Hepatitis B viral infection and associated factors among adults in Moyo district, North-Western Uganda
Authors: Lulu Patrick Madrama , Alege John Bosco 
Published: June 2022

AbstractBackgroundHepatitis B viral infection is a public health problem and estimates show that about 30% of the world’s population is infected with the virus, with about 350 to 400 million of them remaining chronically infected. Northern Uganda has the highest prevalence of HBV in Uganda. In this study, we sought to establish factors influencing the prevalence of Hepatitis B viral infection among adults in Moyo district, North-Western Uganda.MethodsWe used a descriptive cross-sectional study where quantitative data collection methods and analysis was employed. Self-reported HBV infection by respondents who had test result forms diagnosed with HBV within the last one year was reviewed by the researchers to confirm whether the respondent was negative or positive with Hepatitis B. 384 samples were determined using Cochran (1963:75) and a multi-stage sampling technique was used. Bivariate and multivariate analyses were done using SPSS (20.0).ResultsOut of the 384 respondents interviewed, 29 (7.6%, 95%CI: 5.1-10.7) had HBV. Factors influencing the prevalence of HBV were; level of education (p=0.047*), ever having had STIs (aOR=18.090, 95%CI=5.699-57.426, p=0.000*), Health facilities have equipment for screening HEP B viral infection ANC (aOR=10.762, 95%CI=1.316-88.027, p=0.027*) were statically significant in influencing the prevalence of HBV, while the number of sexual partners ever had (p=0.984) was not statistically significant in influencing the prevalence of Hepatitis B viral infection.ConclusionWe found a high prevalence of HBV among adults in Moyo district in North-Western Uganda compared to the national prevalence. Key influences of HBV prevalence included education level, ever being infected with any other STIs (HIV, Syphilis, gonorrhoea), multiple sexual partners and presence of HBV screening equipment at the health facilities. Need for more emphasis on HBV childhood immunization, screening, vaccination of adults, other preventive measures and treatment of those already infected.
Single- and duplex TaqMan-quantitative PCR for determining the copy numbers of integrated selection markers during site-specific mutagenesis in Toxoplasma gondii by CRISPR-Cas9
Authors: Haenggeli Kai Pascal Alexander , Hemphill Andrew , Müller Norbert , Schimanski Bernd , Olias Philipp , Müller Joachim , Boubaker Ghalia 
Published: June 2022

AbstractHerein, we developed a single and a duplex TaqMan quantitative qPCR for absolute quantification of copy numbers of integrated dihydrofolate reductase-thymidylate synthase (mdhfr-ts) drug selectable marker for pyrimethamine resistance in Toxoplasma gondii knockouts (KOs). The single TaqMan qPCR amplifies a 174 bp DNA fragment of the inserted mdhfr-ts and of the wild-type (WT) dhfr-ts (wt-dhfr-ts) which is present as single copy gene in Toxoplasma and encodes a sensitive enzyme to pyrimethamine. Thus, the copy number of the dhfr-ts fragment in a given DNA quantity from KO parasites with a single site-specific integration should be twice the number of dhfr-ts copies recorded in the same DNA quantity from WT parasites. The duplex TaqMan qPCR allows simultaneous amplification of the 174 bp dhfr-ts fragment and the T. gondii 529-bp repeat element. Accordingly, for a WT DNA sample, the determined number of tachyzoites given by dhfr-ts amplification is equal to the number of tachyzoites determined by amplification of the Toxoplasma 529-bp, resulting thus in a ratio of 1. However, for a KO clone having a single site-specific integration of mdhfr-ts, the calculated ratio is 2. We then applied both approaches to test T. gondii RH mutants in which the major surface antigen (SAG1) was disrupted through insertion of mdhfr-ts using CRISPR-Cas9. Results from both assays were in correlation showing a high accuracy in detecting KOs with multiple integrated mdhfr-ts. Southern blot analyses using BsaBI and DraIII confirmed qPCRs results. Both TaqMan qPCRs are needed for reliable diagnostic of T. gondii KOs following CRISPR-Cas9-mediated mutagenesis, particularly with respect to off-target effects resulting from multiple insertions of mdhfr-ts. The principle of the duplex TaqMan qPCR is applicable for other selectable markers in Toxoplasma. TaqMan qPCR tools may contribute to more frequent use of WT Toxoplasma strains during functional genomics.
Predicting the antigenic evolution of SARS-COV-2 with deep learning
Authors: Han Wenkai , Chen Ningning , Xu Xinzhou , Sahil Adil , Zhou Juexiao , Li Zhongxiao , Zhong Huawen , Zhang Ruochi , Wang Yu , Sun Shiwei , Cheung Peter Pak-Hang , Gao Xin 
Published: June 2022

AbstractThe severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) antigenic profile evolves in response to the vaccine and natural infection-derived immune pressure, resulting in immune escape and threatening public health. Exploring the possible antigenic evolutionary potentials improves public health preparedness, but it is limited by the lack of experimental assays as the sequence space is exponentially large. Here we introduce the Machine Learning-guided Antigenic Evolution Prediction (MLAEP), which combines structure modeling, multi-task learning, and genetic algorithm to model the viral fitness landscape and explore the antigenic evolution viain silicodirected evolution. As demonstrated by existing SARS-COV-2 variants, MLAEP can infer the order of variants along antigenic evolutionary trajectories, which is also strongly correlated with their sampling time. The novel mutations predicted by MLAEP are also found in immunocompromised covid patients and newly emerging variants, like XBB1.5. The predictions of MLAEP were validated by conducting in vitro neutralizing antibody binding assay, which demonstrated that the model-generated variants displayed significantly increased immune evasion ability compared with the controls. In sum, our approach enables profiling existing variants and forecasting prospective antigenic variants, thus may help guide the development of vaccines and increase preparedness against future variants. Our model is available athttps://mlaep.cbrc.kaust.edu.sa.
Ce-loaded silica nanoparticles in the epoxy nanocomposite coating for anticorrosion protection of carbon steel
Authors: Nguyen Thien Vuong , Tran Dai Lam , Nguyen Tuan Anh , Nguyen Thi Thanh Huong , Dao Phi Hung , Mac Van Phuc , Do Minh Thanh , Nguyen Thi Mai , Dang Thi My Linh 
Published: June 2022

PurposeThis study aims to explore how the inhibitor-loaded nanocontainers can be used in the epoxy coating for protection of steel against corrosion. A self-healing anticorrosive coating can be easily fabricated by embedding the inhibitor-loaded nanocontainers into the epoxy coating matrices. For this purpose, first, cerium (a catholic corrosion inhibitor) is encapsulated into silica nanoparticles (SiO2@Ce). Thereafter, an epoxy nanocomposite coating has been prepared on steel substrate using these SiO2@Ce nanoparticles as nanofillers.Design/methodology/approachTo examine the effect of SiO2@Ce nanocontainers on mechanical properties of epoxy coating, the abrasion resistance, impact resistance and adhesion strength of coating have been evaluated. To reveal the effect of SiO2@Ce nanocontainer on corrosion behavior of epoxy-coated steel, the electrochemical impedance spectroscopy (EIS) has been conducted in NaCl solution.FindingsTransmission electron microscopy and scanning electron microscopy/Energy-dispersive X-ray spectroscopy analyses indicate that Ce3+cations have been successfully loaded into the surface of silica nanoparticles (at the content of approximately 2 Wt.%). Mechanical tests of epoxy nanocomposite coatings indicate that the nanocomposite coatings with nanoparticles content of 2.5 Wt.% provide the highest values of abrasion resistance, impact resistance and adhesion strength. EIS results show that the presence of SiO2@Ce3+nanocontainers increases both coating resistance and polarization resistance. Along with the improvement the coating barrier performance, Ce inhibitor plays an important role in improving the anticorrosive performance at the steel–electrolyte interface.Originality/valueThe application of self-healing epoxy/SiO2@Ce nanocomposite coatings for the protection of carbon steel is very promising.
Did you get the message? Examining prompted and unprompted recall of messages in a safe food-handling media campaign
Authors: Charlesworth Jessica , Liddelow Caitlin , Mullan Barbara , Tan Henry , Abbott Bree , Potter Abbey 
Published: June 2022

PurposeThe prevalence of foodborne illness remains high in Australia. In response, government initiatives have been implemented to inform consumers of ways to safely handle food. The aim of this study was to examine the accuracy of prompted and unprompted recall of messages from a safe food-handling media campaign in Western Australia, and whether this accuracy of prompted and unprompted recall differed by demographic factors and the mode of delivery of the campaign materials.Design/methodology/approachSurvey responses from 121 participants (Mage = 47.15 years, SD = 15.52) who reported seeing or hearing the campaign were analysed. A series of chi-square tests were used to determine the accuracy of recall when prompted and unprompted, and the accuracy of unprompted and prompted recall across demographic factors and mode of delivery.FindingsResults indicated that more participants accurately recalled the campaign messages when prompted (66.1%) compared to unprompted (35.5%), when they had seen outdoor advertisements (e.g. at bus stops or in shopping malls), and if they were between 30 and 45 years of age.Originality/valueThis study is the first to explore the uptake and comprehension of messages from a safe food-handling media campaign. Evaluation of safe food-handling media campaigns has shown some efficacy in relation to behaviour change; however, little is known about the uptake or comprehension of the campaign messages, and factors that may influence this.
The effect of organizational justice on employee performance in the Indian Public Sector Units: the role of organizational identification
Authors: Pattnaik Subhra , Tripathy Santosh Kumar 
Published: June 2022

PurposePast studies have proved the effect of justice on performance. However, the findings across studies have been inconsistent and there remains a substantial unexplained variance between the constructs. Therefore, justice researchers urge for further exploration of the underlying mechanism of the relationship by introducing influencers. This study responds to such call of the researchers by testing the influence of organizational identification (OID) on the justice-performance relationship in the context of Indian Public Sector Units (PSUs).Design/methodology/approachThe study is grounded in the positivism philosophy. The research hypotheses were tested using cross-sectional data gathered using a pre-tested questionnaire. In this study, the authors have used covariance-based structural equation modeling commercial software (AMOS 24.0).FindingsOID did not mediate the relationship between justice facets and performance. Rather, informational justice, followed by procedural and distributive justice had direct positive influences on performance. OID, however, moderated the procedural justice-performance such that the relationship strengthened at higher levels of OID and the interpersonal justice-performance relationship such that the relationship dampened at higher levels of OID. Interestingly, the relationship between interpersonal justice and performance was insignificant in the absence of the moderator, showcasing the strongest case of moderation.Originality/valueThe paper explores OID as an influencer to justice-performance relationship in Indian PSU context for the very first time, thereby highlighting unique finings. It contributes to the further understanding of the unexplained variance in the justice-performance relationship.