bluuebunny/crossref_metadata_2025_split huggingface dataset:
CryoEM structure of the EBV ribonucleotide reductase BORF2 and mechanism of APOBEC3B inhibition
Authors: Shaban Nadine M. , Yan Rui , Shi Ke , Moraes Sofia N. , Cheng Adam Z. , Carpenter Michael A. , McLellan Jason S. , Yu Zhiheng , Harris Reuben S. 
Published: August 2021

AbstractViruses use a plethora of mechanisms to evade immune responses. A new example is neutralization of the nuclear DNA cytosine deaminase APOBEC3B by the Epstein-Barr virus (EBV) ribonucleotide reductase subunit BORF2. Cryo-EM studies of APOBEC3B-BORF2 complexes reveal a large >1000 Å2binding surface comprised of multiple structural elements from each protein, which effectively blocks the APOBEC3B active site from accessing single-stranded DNA substrates. Evolutionary optimization is suggested by unique insertions in BORF2 absent from other ribonucleotide reductases and preferential binding to APOBEC3B relative to the highly related APOBEC3A and APOBEC3G enzymes. An atomic understanding of this novel pathogen-host interaction may contribute to the development of drugs that block the interaction and liberate the natural antiviral activity of APOBEC3B.One-Sentence SummaryThese studies show how a conserved viral nucleotide metabolism protein is repurposed to inhibit a potent antiviral factor.
Unraveling Phylogenetic Relationships, Reticulate Evolution, and Genome Composition of Polyploid Plant Complexes by Rad-Seq and Hyb-Seq
Authors: Karbstein Kevin , Tomasello Salvatore , Hodač Ladislav , Wagner Natascha , Marinček Pia , Barke Birthe Hilkka , Pätzold Claudia , Hörandl Elvira 
Published: August 2021

AbstractComplex genome evolution of young polyploid complexes is poorly understood. Besides challenges caused by hybridization, polyploidization, and incomplete lineage sorting, bioinformatic analyses are often exacerbated by missing information on progenitors, ploidy, and reproduction modes. By using a comprehensive, self-developed bioinformatic pipeline integrating phylogenetic, structure, network, and SNP-origin analyses, we for the first time unraveled polyploid phylogenetic relationships and genome evolution within the large Eurasian Ranunculus auricomus species complex comprising more than 840 taxa. Our results rely on 97,312 genomic RAD-Seq loci, target enrichment of 576 nuclear genes (48 phased), and 71 plastid regions (Hyb-Seq; OMICS-data) derived from the 75 most widespread polyploid apomictic taxa and four di- and one tetraploid potential sexual progenitor species. Phylogenetic tree and structure analyses consistently showed 3–5 supported polyploid groups, each containing sexual progenitor species. In total, analyses revealed four diploid sexual progenitors and a one unknown, probably extinct progenitor, contributing to the genome composition of R. auricomus polyploids. Phylogenetic network, structure, and SNP-origin analyses based on RAD-Seq loci and phased nuclear genes completed by plastid data demonstrated predominantly allopolyploid origins, each involving 2–3 different diploid sexual subgenomes. Allotetraploid genomes were characterized by subgenome dominance and large proportions of interspecific, non-hybrid SNPs, indicating an enormous degree of post-origin evolution (i.e., Mendelian segregation of the diploid hybrid generations, back-crossings, and gene flow due to facultative sexuality of apomicts), but only low proportions of lineage-specific SNPs. The R. auricomus model system is the first large European polyploid species complex studied with reduced representation OMICS data. Our bioinformatic pipeline underlines the importance of combining different approaches and datasets to successfully unveil how reticulate evolution and post-origin processes shape the diversity of polyploid plant complexes.
Trick or Treat? Pollinator attraction inVanilla pompona(Orchidaceae)
Authors: Watteyn Charlotte , Scaccabarozzi Daniela , Muys Bart , Van Der Schueren Nele , Van Meerbeek Koenraad , Guizar Amador Maria F. , Ackerman James D. , Cedeño Fonseca Marco V. , Chinchilla Alvarado Isler F. , Reubens Bert , Pillco Huarcaya Ruthmery , Cozzolino Salvatore , Karremans Adam P. 
Published: August 2021

ABSTRACTNatural pollination of species belonging to the pantropical orchid genusVanillaremains poorly understood. Based on sporadic records, euglossine bees have been observed visiting flowers of NeotropicalVanillaspecies. Our research aimed at better understanding the pollinator attraction mechanism of the Neotropical speciesVanilla pompona, a crop wild relative with valuable traits for vanilla crop improvement programs. Using video footage, we identified floral visitors and examined their behavior. The flowers ofV. pomponaattractedEulaema cingulatamales, which distinctively displayed two behaviors: floral scent collection and nectar search; with the latter leading to pollen removal. Morphological measurements of floral and visitor traits showed that otherEulaemaspecies may also act as potential pollinators. Additionally, we recorded natural fruit set in three populations and over a period of two years, tested for nectar presence and analyzed floral fragrances through gas chromatography - mass spectrometry. We observed a low natural fruit set (2.42%) and did not detect nectar. Twenty floral volatile compounds were identified, with the dominant compound trans-carvone oxide previously found to attractEulaema cingulatamales. We hypothesize a dual attraction ofEulaema cingulatamales toV. pomponaflowers, based on floral fragrance reward as the primary long-distance attraction, and food deception for successful pollen removal. Further research confirming this hypothesis is recommended to develop appropriate conservation policies forVanillacrop wild relatives, which are the primary reserves of this crop’s genetic variation.
Global distribution of anaerobic dichloromethane degradation potential
Authors: Murdoch Robert W. , Chen Gao , Murdoch Fadime Kara , Mack E. Erin , Villalobos Solis Manuel I. , Hettich Robert L. , Löffler Frank E. 
Published: August 2021

AbstractAnthropogenic activities and natural processes release dichloromethane (DCM), a toxic chemical with substantial ozone-depleting capacity. Specialized anaerobic bacteria metabolize DCM; however, the genetic basis for this process has remained elusive. Comparative genomics of the three known anaerobic DCM-degrading bacterial species revealed a homologous gene cluster, designated the methylene chloride catabolism (mec) gene cassette, comprising eight to ten genes with predicted 79.6 – 99.7% amino acid identity. Functional annotation identified genes encoding a corrinoid-dependent methyltransferase system, and shotgun proteomics applied to two DCM-catabolizing cultures revealed high expression of proteins encoded on the mec gene cluster during anaerobic growth with DCM. In a DCM-contaminated groundwater plume, the abundance of mec genes strongly correlated with DCM concentrations (R2 = 0.71 – 0.85) indicating their value as process-specific bioremediation biomarkers. mec gene clusters were identified in metagenomes representing peat bogs, the deep subsurface, and marine ecosystems including oxygen minimum zones (OMZs), suggesting DCM turnover in diverse habitats. The broad distribution of anaerobic DCM catabolic potential suggests a relevant control function for emissions to the atmosphere, and a role for DCM as a microbial energy source in critical zone environments. The findings imply that the global DCM flux might be far greater than emission measurements suggest.ImportanceDichloromethane (DCM) is an increasing threat to stratospheric ozone with both anthropogenic and natural emission sources. Anaerobic bacterial metabolism of DCM has not yet been taken into consideration as a factor in the global DCM cycle. The discovery of the mec gene cassette associated with anaerobic bacterial DCM metabolism and its widespread distribution in environmental systems highlight a strong attenuation potential for DCM. Knowledge of the mec cassette offers new opportunities to delineate DCM sources, enables more robust estimates of DCM fluxes, supports refined DCM emission modeling and simulation of the stratospheric ozone layer, reveals a novel, ubiquitous C1 carbon metabolic system, and provides prognostic and diagnostic tools supporting bioremediation of groundwater aquifers impacted by DCM.
Molecular evidence of intertidal habitats selecting for repeated ice-binding protein evolution in invertebrates
Authors: Box Isaiah C. H. , Matthews Benjamin J. , Marshall Katie E. 
Published: August 2021

ABSTRACTIce-binding proteins (IBPs) have evolved independently in multiple taxonomic groups to improve their survival of sub-zero temperatures. Intertidal invertebrates in temperate and polar regions frequently encounter sub-zero temperatures, yet there is little information on IBPs in these organisms. We hypothesized that there are far more ice-binding proteins than are currently known and that the occurrence of freezing in the intertidal zone selects for these proteins. We compiled a list of genome-sequenced invertebrates across multiple habitats and a list of known IBP sequences and used BLAST to identify a wide array of putative IBPs in those invertebrates. We found that the probability of an invertebrate species having an ice-binding protein was significantly greater in intertidal species as compared to those primarily found in open ocean or freshwater habitats. These intertidal IBPs had high sequence similarity to fish and tick antifreeze glycoproteins and fish type II antifreeze proteins. Previously established classifiers based on machine learning techniques further predicted ice-binding activity in the majority of our newly identified putative IBPs. We investigated the potential evolutionary origin of one putative IBP from the hard-shelled mussel Mytilus coruscus and suggest that it arose through gene duplication and neofunctionalization. We show that IBPs likely readily evolve in response to freezing risk, that there is an array of uncharacterized ice binding proteins and highlight the need for broader laboratory-based surveys of the diversity of ice binding activity across diverse taxonomic and ecological groups.Summary statementIntertidal invertebrates have a disproportionate number of putative ice-binding proteins relative to other habitats. These putative proteins are highly similar to antifreeze glycoproteins and type II antifreeze proteins from fish.
Monosomies, trisomies and segmental aneuploidies differentially affect chromosomal stability
Authors: Hintzen Dorine C. , Soto Mar , Schubert Michael , Bakker Bjorn , Spierings Diana C.J. , Szuhai Karoly , Lansdorp Peter M. , Foijer Floris , Medema René H. , Raaijmakers Jonne A. 
Published: August 2021

AbstractAneuploidy and chromosomal instability are both commonly found in cancer. Chromosomal instability leads to karyotype heterogeneity in tumors and is associated with therapy resistance, metastasis and poor prognosis. It has been hypothesized that aneuploidy per se is sufficient to drive CIN, however due to limited models and heterogenous results, it has remained controversial which aspects of aneuploidy can drive CIN. In this study we systematically tested the impact of different types of aneuploidies on the induction of CIN. We generated a plethora of isogenic aneuploid clones harboring whole chromosome or segmental aneuploidies in human p53-deficient RPE-1 cells. We observed increased segregation errors in cells harboring trisomies that strongly correlated to the number of gained genes. Strikingly, we found that clones harboring only monosomies do not induce a CIN phenotype. Finally, we found that an initial chromosome breakage event and subsequent fusion can instigate breakage-fusion-bridge cycles in segmental aneuploidies. This suggests that monosomies, trisomies and segmental aneuploidies have fundamentally different effects on chromosomal instability and these results help us to decipher the complex relationship between aneuploidy and CIN.
Ownership vs access: consumers' digital ownership perceptions and preferences
Authors: Zhu Xiaohua , Cho Moonhee 
Published: August 2021

PurposeThis study investigated the interrelations of US consumers' perceptions of their ownership of digital media content, their perceived importance of various digital rights and ownership rights and their preferences for owning vs accessing media content.Design/methodology/approachThis study used an online questionnaire survey and analyzed data from 437 participants recruited via Amazon's Mechanical Turk mechanism.FindingsParticipants' perceived importance of digital rights correlates with consumers' ownership perceptions, and people who value certain digital rights tend to have narrower ownership perceptions. Users' ownership and access preferences vary with their perceived importance of ownership rights, especially concerning music and movies. Notably, people who prefer the access model were less concerned about ownership rights to possess, use and resell content.Social implicationsThe study provides empirical evidence of consumers' ownership perceptions in the digital age and warns consumers of the dangers of the erosion of their digital ownership rights.Originality/valueLegal ownership and psychological ownership are usually considered separate constructs and seldom examined together. By showing the correlation between consumers' ownership perceptions and their perceived importance of digital rights, this study demonstrates the connection between legal ownership and psychological ownership.
Numerical solution of large deflection beams by using the Laplace Adomian decomposition method
Authors: Lin Ming-Xian , Tseng Chia-Hsiang , Chen Chao Kuang 
Published: August 2021

PurposeThis paper presents the problems using Laplace Adomian decomposition method (LADM) for investigating the deformation and nonlinear behavior of the large deflection problems on Euler-Bernoulli beam.Design/methodology/approachThe governing equations will be converted to characteristic equations based on the LADM. The validity of the LADM has been confirmed by comparing the numerical results to different methods.FindingsThe results of the LADM are found to be better than the results of Adomian decomposition method (ADM), due to this method's rapid convergence and accuracy to obtain the solutions by using fewer iterative terms. LADM are presented for two examples for large deflection problems. The results obtained from example 1 shows the effects of the loading, horizontal parameters and moment parameters. Example 2 demonstrates the point loading and point angle influence on the Euler-Bernoulli beam.Originality/valueThe results of the LADM are found to be better than the results of ADM, due to this method's rapid convergence and accuracy to obtain the solutions by using fewer iterative terms.
Simulation-based learning in tertiary-level disaster risk management education: a class-room experiment
Authors: Tasantab Jerry Chati , Gajendran Thayaparan , Owi Toinpre , Raju Emmanuel 
Published: August 2021

PurposeConventional lecture-based educational approaches alone might not be able to portray the complexity of disaster risk management practice and its real-life dynamics. One work-integrated learning practice that can give students practical work-related experiences is simulation-based learning. However, there is a limited discourse on simulation-based learning in disaster risk management education at the tertiary level. As tertiary education plays a crucial role in developing capabilities within the workforce, simulation-based learning can evoke or replicate substantial aspects of the real world in a fully interactive fashion. This paper aims to present outcomes of simulation-based learning sessions the authors designed and delivered in a disaster risk management course.Design/methodology/approachThe authors developed a framework to illustrate simulation-based learning in a disaster risk management programme. It was then used as a guide to design and execute simulation-based learning sessions. An autoethnographic methodology was then applied to reflectively narrate the experiences and feelings during the design and execution of the simulations.FindingsThe evaluation of the simulation sessions showed that participants were able to apply their knowledge and demonstrate the skills required to make critical decisions in disaster risk reduction. The conclusion from the simulation-based learning sessions is that making simulation-based learning a part of the pedagogy of disaster risk management education enables students to gain practical experience, deliberate ethical tensions and practical dilemmas and develop the ability to work with multiple perspectives.Originality/valueThe simulated workplace experience allowed students to experience decision-making as disaster risk management professionals, allowing them to integrate theory with practice.
The effect of unemployment benefits on health and living standards in Turkey: evidence from structural equation modelling and regression discontinuity design
Authors: Giovanis Eleftherios , Ozdamar Oznur , Özdaş Burcu 
Published: August 2021

PurposeUnemployment can negatively affect individuals, their families and communities in various ways. When individuals are out of work may experience mental and physical health problems, material deprivation and poverty. This study aims to examine the impact of unemployment benefits on health and living standards in Turkey.Design/methodology/approachThe authors employ a structural equation modelling (SEM) to consider the simultaneous relationships among the unemployment benefits and the latent variables of health and Standard of Living (SoL). We propose a fuzzy Regression Discontinuity Design (FRDD) and a Regression Kink Design (RKD) within the SEM framework to infer causality. For the empirical analysis, the authors employ the panel Income and Living Conditions Survey (ILCS) in 2007–2015.FindingsThe authors’ findings suggest that those who receive these benefits are more likely to report higher levels of health and improve their living standards compared to the non-recipients. Furthermore, unemployment benefits replacement rates are associated with improved levels in health and living standards. The authors’ results indicate a substantial heterogeneity on the impact of unemployment benefits since males, low educated individuals and those belonging to the lower levels of income are affected more in terms of their health status and living standards.Originality/valueThe majority of earlier studies have focused on the impact of unemployment benefits on labor outcomes. The originality of this study is that we implement the FRDD and RKD within the SEM framework to explore, simultaneously, the impact of unemployment insurance on health and living standards. Moreover, future research studies can implement this framework to infer causality and explore the impact of related policies and reforms.
Green sourcing in the era of industry 4.0: towards green and digitalized competitive advantages
Authors: Fallahpour Alireza , Yazdani Morteza , Mohammed Ahmed , Wong Kuan Yew 
Published: August 2021

PurposeIn the last decade, sustainable sourcing decision has gained tremendous attention due to the increasing governmental restrictions and public attentiveness. This decision involves diverse sets of classical and environmental parameters, which are originated from a complex, ambiguous and inconsistent decision-making environment. Arguably, supply chain management is fronting the next industrial revolution, which is named industry 4.0, due to the fast advance of digitalization. Considering the latter's rapid growth, current supplier selection models are, or it will, inefficient to assign the level of priority of each supplier among a set of suppliers, and therefore, more advanced models merging “recipes” of sustainability and industry 4.0 ingenuities are required. Yet, no research work found towards a digitalized, along with sustainability's target, sourcing.Design/methodology/approachA new framework for green and digitalized sourcing is developed. Thereafter, a hybrid decision-making approach is developed that utilizes (1) fuzzy preference programming (FPP) to decide the importance of one supplier attribute over another and (2) multi-objective optimization on the basis of ratio analysis (MOORA) to prioritize suppliers based on fuzzy performance rating. The proposed approach is implemented in consultation with the procurement department of a food processing company willing to develop a greener supply chain in the era of industry 4.0.FindingsThe proposed approach is capable to recognize the most important evaluation criteria, explain the ambiguity of experts' expressions and having better discrimination power to assess suppliers on operational efficiency and environmental and digitalization criteria, and henceforth enhances the quality of the sourcing process. Sensitivity analysis is performed to help managers for model approval. Moreover, this work presents the first attempt towards green and digitalized supplier selection. It paves the way towards further development in the modelling and optimization of sourcing in the era of industry 4.0.Originality/valueCompetitive supply chain management needs efficient purchasing and production activities since they represent its core, and this arises the necessity for a strategic adaptation and alignment with the requirement of industry 4.0. The latter implies alterations in the avenue firms operate and shape their activities and processes. In the context of supplier selection, this would involve the way supplier assessed and selected. This work is originally initiated based on a joint collaboration with a food company. A hybrid decision-making approach is proposed to evaluate and select suppliers considering operational efficiency, environmental criteria and digitalization initiatives towards digitalized and green supplier selection (DG-SS). To this end, supply chain management in the era of sustainability and digitalization are discussed.
The implication of multicultural education on students' learning approaches in biosciences and pharmacy courses
Authors: Ng Zhi Xiang , Yong Phaik Har 
Published: August 2021

PurposeThe globalisation of higher education has created new challenges for educators to remain dynamic in teaching science undergraduates with diverse cultural backgrounds. The current study explores this challenge by evaluating the different personal factors among biosciences and pharmacy undergraduates that affect their learning approaches as well as to identify course-specific teaching approaches in order to determine their impacts on students' learning.Design/methodology/approachA cross-sectional survey design based on study process questionnaire (SPQ), and approaches and study skills inventory for students (ASSIST) was utilised to collect quantitative data from 129 biosciences and pharmacy undergraduates.FindingsBiosciences undergraduates adopted deep and achieving learning approaches as they progressed through the curriculum, whilst surface learners dominated the pharmacy course. Ethnicity was shown to affect the learning approaches among the undergraduates. Although male undergraduates from both courses were more competitive than the female, elder female undergraduates tend to adopt deep learning approach. Pre-university qualifications did not significantly influence the undergraduate's learning approach. The contrasting finding on the preferred teaching approaches between biosciences and pharmacy undergraduates has highlighted the importance of providing tailored teaching and learning strategies to cater different students' learning needs.Originality/valueThis study has demonstrated the combinational use of SPQ and ASSIST instruments to compare undergraduate's learning approaches with preferred teaching approaches. The current finding could support the development of teaching and learning practice among the biosciences and pharmacy undergraduates with multicultural background.