bluuebunny/crossref_metadata_2025_split huggingface dataset:
Endomembrane systems are reorganized by ORF3a and Membrane (M) of SARS-CoV-2
Authors: Lee Yun-Bin , Jung Minkyo , Kim Jeesoo , Kang Myeong-Gyun , Kwak Chulhwan , Kim Jong-Seo , Mun Ji-Young , Rhee Hyun-Woo 
Published: June 2021

SummaryThe endomembrane reticulum (ER) is largely reorganized by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). SARS-CoV-2 ORF3a and membrane (M) protein expression affects ER-derived structures including cubic membrane and double membrane vesicles in coronavirus-infected cells; however, the molecular mechanisms underlying ER remodeling remain unclear. We introduced a “plug and playable” proximity labeling tool (TurboID-GBP) for interactome mapping of GFP-tagged SARS-CoV-2 ORF3a and M proteins. Through mass spectrometric identification of the biotinylated lysine residue (K+226 Da) on the viral proteins using Spot-TurboID workflow, 117 and 191 proteins were robustly determined as ORF3a and M interactomes, respectively, and many, including RNF5 (E3 ubiquitin ligase), overlap with the mitochondrial-associated membrane (MAM) proteome. RNF5 expression was correlated to ORF3a ubiquitination. MAM formation and secreted proteome profiles were largely affected by ORF3a expression. Thus, SARS-CoV-2 may utilize MAM as a viral assembly site, suggesting novel anti-viral treatment strategies for blocking viral replication in host cells.HighlightsSARS-CoV-2 proteins ORF3a and M alter endoplasmic reticulum proteome profileORF3a affects mitochondrial-associated membrane formationSARS-CoV-2 may utilize mitochondrial-associated membrane as viral assembly siteORF3a and M interactome proteins may serve as targets for COVID-19 treatmenteTOC BlurbER remodelling by SARS-CoV-2 ORF3a and M protein
Two marine GH29 α-L-fucosidases from an uncultured Paraglaciecola sp. specifically hydrolyze fucosyl-N-acetylglucosamine regioisomers
Authors: Schultz-Johansen Mikkel , Stougaard Peter , Svensson Birte , Teze David 
Published: June 2021

ABSTRACTl-Fucose is the most widely distributed l-hexose in marine and terrestrial environments, and presents a variety of functional roles. l-Fucose is the major monosaccharide in the polysaccharide fucoidan from cell walls of brown algae, and is found in human milk oligosaccharides and the Lewis blood group system, where it is important in cell signaling and immune response stimulation. Removal of fucose from these biomolecules is catalyzed by fucosidases belonging to different carbohydrate-active enzyme (CAZy) families. Fucosidases of glycoside hydrolase family 29 (GH29) release α-l-fucose from non-reducing ends of glycans and display activities targeting different substrate compositions and linkage types. While several GH29 fucosidases from terrestrial environments have been characterized, much less is known about marine members of GH29 and their substrate specificities, as only four marine GH29 enzymes were previously characterized. Here, five GH29 fucosidases originating from an uncultured fucoidan-degrading marine bacterium (Paraglaciecola sp.) were cloned and produced recombinantly in E. coli. All five enzymes (Fp231, Fp239, Fp240, Fp251, Fp284) hydrolyzed the synthetic substrate CNP-α-l-fucose. By screening each of these enzymes against up to 17 fucose-containing oligosaccharides Fp231 and Fp284 showed strict substrate specificities against the fucosyl-N-acetylglucosamine regioisomers Fuc(α1,4)GlcNAc and Fuc(α1,6)GlcNAc, respectively, the former representing a new specificity. Fp231 is a monomeric enzyme with pH and temperature optima at pH 5.6–6.0 and 25°C, hydrolyzing Fuc(α1,4)GlcNAc with kcat = 1.3 s−1 and Km = 660 μM. Altogether, the findings extend our knowledge about GH29 family members from the marine environment, which are so far largely unexplored.
Efficacy of epetraborole against Mycobacterium abscessus is increased with norvaline
Authors: Sullivan Jaryd R. , Lupien Andréanne , Kalthoff Elias , Hamela Claire , Taylor Lorne , Munro Kim A. , Schmeing T. Martin , Kremer Laurent , Behr Marcel A. 
Published: June 2021

AbstractCertain aminoacyl-tRNA synthetases developed a proofreading mechanism to ensure aminoacylation of tRNAs with cognate amino acids. Epetraborole (EPT) was identified as an inhibitor of the leucyl-tRNA synthetase (LeuRS) editing site in Mycobacterium abscessus. EPT displayed enhanced activity against M. abscessus over Mycobacterium tuberculosis. Crystallographic and equilibrium binding data showed that EPT binds LeuRSMabs and LeuRSMtb with similar Kd. Proteomic analysis revealed that when M. abscessus LeuRS mutants were fed the non-proteinogenic amino acid norvaline, leucine residues in proteins were replaced by norvaline, inducing expression of GroEL chaperonins and Clp proteases. In vitro data revealed that supplementation of media with norvaline reduced the emergence of EPT mutants in both M. abscessus and M. tuberculosis. The combination of EPT and norvaline had improved in vivo efficacy compared to EPT in a murine model of M. abscessus infection.
Synergistic block of SARS-CoV-2 infection by combined drug inhibition of the host entry factors PIKfyve kinase and TMPRSS2 protease
Authors: Kreutzberger Alex J.B. , Sanyal Anwesha , Ojha Ravi , Pyle Jesse D. , Vapalahti Olli , Balistreri Giuseppe , Kirchhausen Tom 
Published: June 2021

ABSTRACTRepurposing FDA-approved inhibitors able to prevent infection by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) could provide a rapid path to establish new therapeutic options to mitigate the effects of coronavirus disease 2019 (COVID-19). Proteolytic cleavages of the spike S protein of SARS-CoV-2, mediated by the host cell proteases cathepsin and TMPRSS2, alone or in combination, are key early activation steps required for efficient infection. The PIKfyve kinase inhibitor apilimod interferes with late endosomal viral traffic, and through an ill-defined mechanism preventsin vitroinfection through late endosomes mediated by cathepsin. Similarly, inhibition of TMPRSS2 protease activity by camostat mesylate or nafamostat mesylate prevents infection mediated by the TMPRSS2-dependent and cathepsin-independent pathway. Here, we combined the use of apilimod with camostat mesylate or nafamostat mesylate and found an unexpected ~5-10-fold increase in their effectiveness to prevent SARS-CoV-2 infection in different cell types. Comparable synergism was observed using both, a chimeric vesicular stomatitis virus (VSV) containing S of SARS-CoV-2 (VSV-SARS-CoV-2) and SARS-CoV-2 virus. The substantial ~5-fold or more decrease of half maximal effective concentrations (EC50values) suggests a plausible treatment strategy based on the combined use of these inhibitors.IMPORTANCEInfection by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is causing the coronavirus disease 2019 (COVID-2019) global pandemic. There are ongoing efforts to uncover effective antiviral agents that could mitigate the severity of the disease by controlling the ensuing viral replication. Promising candidates include small molecules that inhibit the enzymatic activities of host proteins, thus preventing SARS-CoV-2 entry and infection. They include Apilimod, an inhibitor of PIKfyve kinase and camostat mesylate and nafamostat mesylate, inhibitors of TMPRSS2 protease. Our research is significant for having uncovered an unexpected synergism in the effective inhibitory activity of apilimod used together with camostat mesylate or with nafamostat mesylate.
The endemic plant species of Mt Kupe, Cameroon with a new Critically Endangered cloud-forest tree species,Vepris zapfackii(Rutaceae)
Authors: Cheek Martin , Onana Jean Michel 
Published: June 2021

SummaryWe revise and update the records of strict and near-endemic species of Mt Kupe, Cameroon respectively from 31 strict endemics in 2004, to 25 today, and with near-endemic species 30, unchanged in number but with turnover. The changes result from new collections, discoveries and taxonomic changes in the last 16 years. While 15 of the provisionally named putative endemic species have now been formally published, a further 18 have not. The majority of the 30 near-endemic species (18) are shared with the adjacent Bakossi Mts, far exceeding the numbers shared with the more distant Mt Etinde-Mt Cameroon, Rumpi Hills and Ebo forest areas (sharing three near-endemic species each with Mt Kupe). We test the hypothesis that a further one of the provisionally named putative Mt Kupe species,Veprissp. 1 from submontane forest near the summit, is indeed new to science. We compare it morphologically with the two other bicarpellate high altitude Cameroon Highland tree speciesVepris montisbambutensisOnana andVepris baliCheek, concluding that it is a new undescribed species here named asVepris zapfackii. The new species is illustrated, mapped and its conservation status assessed as Critically Endangered using the 2012 IUCN standard due to habitat clearance from agricultural pressures at its sole location which is unprotected.Vepris zapfackiiandV. baliappear unique in African trifoliolate species of the genus in having opposite leaves.Vepris zapfackiidiffers in having hairy petiolules and midribs and petiolules with the blade decurrent distally, narrowing towards a winged-canaliculate base (vs glabrous and petiolule long, terete), and sparsely golden hairy pistillodes and a glabrous calyx (vs densely black hairy pistillodes, and sepals hairy).
Blinking fluorescent probes for tubulin nanoscopy in living and fixed cells
Authors: Gerasimaitė Rūta , Bucevičius Jonas , Kiszka Kamila A. , Kostiuk Georgij , Koenen Tanja , Lukinavičius Gražvydas 
Published: June 2021

ABSTRACTHere we report a small molecule probe for single molecule localisation microscopy (SMLM) of tubulin in living and fixed cells. We explored a series of constructs composed of taxanes and spontaneously blinking far-red dye hydroxymethyl silicon-rhodamine (HMSiR). We found that the linker length profoundly affects the probe permeability and off-targeting. The best performing probe, HMSiR-tubulin, is composed of cabazitaxel and 6’-regioisomer of HMSiR bridged by a C6 linker. Microtubule diameters of ≤50 nm can be routinely measured in SMLM experiments on living and fixed cells. HMSiR-tubulin also performs well in 3D stimulated emission depletion (STED) microscopy, allowing a complementary use of both nanoscopy methods for investigating microtubule functions in living cells.
Genome-wide association mapping of transcriptome variation inMimulus guttatusindicates differing patterns of selection on cis- versus trans-acting mutations
Authors: Brown Keely E. , Kelly John K. 
Published: June 2021

ABSTRACTWe measured the floral bud transcriptome of 151 fully sequenced lines ofMimulus guttatusfrom one natural population. Thousands of single nucleotide polymorphisms (SNPs) are implicated as transcription regulators, but there is a striking difference in the Allele Frequency Spectrum (AFS) of cis-acting and trans-acting mutations. Cis-SNPs have intermediate frequencies (consistent with balancing selection) while trans-SNPs exhibit a rare-alleles model (consistent with purifying selection). This pattern only becomes clear when transcript variation is normalized on a gene-to-gene basis. If a global normalization is applied, as is typically in RNAseq experiments, asymmetric transcript distributions combined with “rarity disequilibrium” produce a super-abundance of false positives for trans-acting SNPs. To explore the cause of purifying selection on trans-acting mutations, we identified gene expression modules as sets of co-expressed genes. The extent to which trans-acting mutations influence modules is a strong predictor of allele frequency. Mutations altering expression of genes with high “connectedness” (those that are highly predictive of the representative module expression value) have the lowest allele frequency. The expression modules can also predict whole-plant traits such as flower size. We find that a substantial portion of the genetic (co)variance among traits can be described as an emergent property of genetic effects on expression modules.
Investigation of effect of abrasive water jet (AWJ) machining parameters on aramid fiber-reinforced polymer (AFRP) composite materials
Authors: Akıncıoğlu Sıtkı 
Published: June 2021

Purpose
The purpose of this study was to optimize the surface roughness (Ra), delamination damage at the hole entrance (FdT) and at the hole exit (FdB) and kerf angle (K) in the drilling of aramid fiber-reinforced polymer (AFRP) composite material using abrasive water jet (AWJ) machining.

Design/methodology/approach
The AFRP composite was produced by the vacuum infusion method. The drilling experiments were performed on an AWJ machine using a three-axis computerized numerical control system. Machine processing parameters were determined as water pressure (2,000, 3,000 and 4,000 bar), stand-off distance (2, 4 and 6 mm) and traverse feed rate (150, 250 and 350 mm/min). Optimization of processing parameters in the drilling experiments was carried out according to the Taguchi L27 (33) orthogonal array. In addition, gray relational analysis (GRA) was used to analyze the complex uncertainty affecting the results.

Findings
Results of the drilling operations demonstrated that water pressure (P) was the most effective parameter, with 65.3%, 65.2%, 49.8% and 52.1% contribution rates for Ra, FdT, FdB and K, respectively.

Practical implications
Reliable results have been obtained with Taguchi-based GRA while drilling AFRP composite material using AWJ. Significant results have been achieved to increase the hole quality in the drilling of AFRP composite material.

Originality/value
The new approach is to present more detailed analysis by using Taguchi method and multi-decision Taguchi-based gray relation analysis in AFRP composite material drilling using AWJ. Thus, time and experiment costs are saved.
What are the investment risk differences of solar PV power generation projects between constructional and operational periods? An empirical study in China
Authors: Ding Liping , Li Jiangshan , Wang Yuqing , Shuai Jing , Xu Xinxin 
Published: June 2021

Purpose
Under the pressure of environment degradation and energy consumption rises, solar photovoltaic power generation (SPPG) has been seen as a strategic emerging industry in China. However, the SPPG projects have many uncertain factors in the process of the life cycle. The purpose of this paper is to evaluate the investment risk comprehensively.

Design/methodology/approach
Specifically, this paper firstly identified the risk factors and consequences of SPPG project investment and constructed the investment risk factor evaluation index system. Secondly, the factor analysis method was used to reveal the key investment risk factors and risk consequences. Then, the research hypotheses and conceptual model were proposed, and the empirical analysis was conducted based on the structural equation model (SEM).

Findings
The results showed that the six key risk factors (political, economic, technological, management, market and natural) have a significant impact on the risks during the whole period. The influence degree of risk factors in the operational period is such that market factor > political factor > economic factor > management factor > natural factor > technical factor. In addition, the risk of constructional period has a significant impact during the risk of operational period. Except for natural factors, all risk factors are correlated among the mutual influence relationship of risk factors. Finally, this paper puts forward management implications based on the above conclusions: effectively identify investment risk factors and comprehensively improve risk management ability; (refine the risk factors of SPPG project investment and develop targeted risk prevention and control strategies; define risk management objectives and make relevant strategic plans.

Research limitations/implications
Because of the chosen research approach, the research results may lack generalisability. Therefore, researchers are encouraged to test the proposed propositions further.

Practical implications
It can also help stakeholders propose risk prevention strategies throughout the entire process, to promote the sustainable development of SPPG projects.

Originality/value
This study focuses on the investment risk of SPPG projects, by building an evaluation index system to identify key risk factors, and then establishes a SEM covering constructional period risks and operational period risks to better explore SPPG project risks, in an effort to reveal the mutual influence relationship and influence path of investment risk factors of the projects.
Wealth transfers and labour supply: impact of inheritances and gifts by gender in Europe
Authors: Malo Miguel Á. , Sciulli Dario 
Published: June 2021

PurposeThe authors analyse how the receipt of a wealth transfer (inheritance or gift) affects labour force participation in 14 EU countries. They compare the effect of receiving an inheritance or a gift and investigate different behaviours at the gender level and educational level and for elderly individuals.Design/methodology/approachThe authors use data from the Household Finance and Consumption Survey for 14 European countries and adopt an instrumental variable approach. They use information on the type of donor (family and nonfamily) to infer the degree of anticipation of a wealth transfer.FindingsThe authors find that unexpected wealth transfers have a negative impact on labour force participation, with a stronger impact for gifts than for inheritances. For gender, they find larger negative impacts for females than for males, which is in line with a weaker attachment to the labour market. Receiving an unexpected wealth transfer may also result in early retirement.Originality/valueThe paper offers a novel comparison of the effect of receiving an inheritance or a gift on labour force participation using a unique European dataset. The authors investigate whether males and females react differently to the receipt of a wealth transfer and the existence of different responses at the educational level and for elderly individuals.
From governance to choreography: coordination of innovation ecosystems
Authors: Santos Diego Alex Gazaro dos , Zen Aurora , Bittencourt Bruno Anicet 
Published: June 2021

PurposeInnovation ecosystems can emerge and grow organically, but the process can also be managed through conscious intervention. Therefore, this study observes different motivations and expectations for each group of actors. The lack of alignment between actors could have a negative influence on the development of innovation ecosystems. This study aims to analyze the coordination strategies of the actors throughout the life cycle of innovation ecosystems.Design/methodology/approachThis study develops and proposes a model for coordinating innovation ecosystems based on the theoretical backgrounds of the ecosystem life cycle and ecosystem coordination.FindingsThis study argues that each stage of an innovation ecosystem’s life cycle – inception, launching, growth and maturity – demands different coordination strategies. Initially, networks are simpler and thus the coordination issues are less difficult. However, as the ecosystem evolves and the complexity of the networks increases, a more sophisticated strategy, such as orchestration or choreography, is needed.Research limitations/implicationsThis is a theoretical study that recommends further research to test this model.Practical implicationsThe understanding of coordination and stages of the life cycle of an innovation ecosystem can guide actors in the design of strategies for developing of ecosystems.Social implicationsThe proposed framework could support strategies to engage civil society in actions to develop innovation ecosystems.Originality/valueThis study presents a framework to understand the coordination strategies better, considering the stages of an innovation ecosystem’s life cycle.
Students' perception on learning methods in engineering disciplines
Authors: Vidal Borja , Fenollosa Ribera M. Loreto , Ribal Francisco Javier , Sanchis Pablo , García-Rupérez Jaime , Bes-Piá M. Amparo , Blasco-Tamarit E. , Noguera Patricia , Muñoz-Portero María José , Tortajada Luis A. 
Published: June 2021

PurposeThis study explores the preferences for learning methods among the students of seven engineering disciplines in a Spanish technical university. The purpose of this paper is to investigate the students' views and from them contribute to the knowledge of the effectiveness of learning methodologies.Design/methodology/approachAn online anonymous questionnaire survey was adopted to collect students' perceptions. Seven learning methods were compared in seven engineering degrees. The authors sampled 1660 students, and 426 completed responses were analysed. In addition to a descriptive analysis of the results, a multiple correspondence analysis (MCA) was performed using R data processing software.FindingsIt was found that project-based learning and problem-based learning were perceived as the more effective ones. MCA identified response patterns between the preference and the efficiency of learning methods showing that students can be classified into two groups according to their preferred level of activeness in learning.Research limitations/implicationsThe study focusses on a single technical university and not all engineering degrees could be sampled. However, five different engineering fields were studied and no significant differences among them were found.Practical implicationsThe results add up to the known literature showing that students have different learning needs and consequently they perceive some methods as more effective. Instructors can use this information to strengthen their learning activities. Results also suggest that students can be classified into two groups in relation to their level of activeness in learning. This can also help to enhance general student motivation if two paths with different levels of activeness are planned.Originality/valueNo previous studies have compared several learning methods in different engineering fields. Thus, this study contributes to fill this gap and contributes to the body of evidence around learning methodologies from the perspective of students.
Cross-cultural study of the qualitative aspects of higher education teachers' emotional intelligence: Kazakhstan and Russia
Authors: Algozhina Anar , Sabirova Raikhan , Alimbayeva Roza , Kapbasova Gulzada , Sarmantayev Ayan 
Published: June 2021

PurposeThe emotional intelligence (EI) model is widely used in pedagogy, management and other spheres as a useful concept with great potential for application. At the same time, there are significant differences in the traits of EI in different social groups, in particular, in different countries, which are just beginning to be studied. To date, there is a significant gap in the research literature on cross-cultural research in the field of EI, especially in the area of measuring its performance. This work is devoted to the study of the quantitative aspects of the differences in the traits of EI between teachers of higher educational institutions in Kazakhstan and Russia.Design/methodology/approachFor the study, 700 participants from two countries were involved, 350 people from each with an approximately equal distribution by gender and age. Mann–Whitney U test and Fisher transformation were used for statistical analysis of the results of the N. Hall test for teachers from two countries.FindingsAs a result of assessing the level of EI by the method of N. Hall, significant differences were found in the manifestation of various scales of EI in representatives of these two groups (Fisher's transformation relative to the scales: “emotional awareness” was f*em = 5.466).Originality/valueThe practical value of the study lies in the discovery of a methodology for determining the difference in the traits of EI, which can be used in the correction of teaching methods, personnel management in higher educational institutions and in the formation of educational teams.