bluuebunny/crossref_metadata_2025_split huggingface dataset:
Targeted inactivation of the AGO1 homeologues of Nicotiana benthamiana reveals their distinct roles in development and antiviral defence
Authors: Ludman Márta , Fátyol Károly 
Published: October 2020

Summary

The Solanaceae family includes numerous highly valuable crops. Understanding the viral diseases that affect them is of great importance. Nicotiana benthamiana has contributed greatly to unravelling antiviral RNA interference, and can also be regarded as an adequate model for studying viral diseases of solanaceous crops. This species, however, as with many of its relatives, possesses an allopolyploid genome, in which homeologous gene pairs frequently occur.

AGO1 is a pivotal component of most plant RNA silencing pathways. The Nicotiana benthamiana genome encodes two highly similar AGO1 homeologues: AGO1A and AGO1B. To understand their roles in planta, their genes were selectively inactivated. Given the inherent limitations of RNA interference‐based techniques, we used genome editing to achieve this goal.

We found that AGO1A was not required for normal development, while AGO1B was indispensable for that. By contrast, the two homeologues both contributed to antiviral defence. Additionally, we observed that AGO1B utilised miR168 poorly, which may help to retain a significant level of antiviral RNA interference during viral infection.

Our results have important implications for the better understanding of viral diseases of economically important solanaceous crops.
The Arabidopsis zinc finger proteins SRG2 and SRG3 are positive regulators of plant immunity and are differentially regulated by nitric oxide
Authors: Cui Beimi , Xu Shiwen , Li Yuan , Umbreen Saima , Frederickson Debra , Yuan Bo , Jiang Jihong , Liu Fengquan , Pan Qiaona , Loake Gary J. 
Published: October 2020

Summary

Nitric oxide (NO) regulates the deployment of a phalanx of immune responses, chief among which is the activation of a constellation of defence‐related genes. However, the underlying molecular mechanisms remain largely unknown. The Arabidopsis thaliana zinc finger transcription factor (ZF‐TF), S‐nitrosothiol (SNO) Regulated 1 (SRG1), is a central target of NO bioactivity during plant immunity. Here we characterize the remaining members of the SRG gene family.

Both SRG2 and, especially, SRG3 were positive regulators of salicylic acid‐dependent plant immunity. Analysis of SRG single, double and triple mutants implied that SRG family members have additive functions in plant immunity and, surprisingly, are under reciprocal regulation.

SRG2 and SRG3 localized to the nucleus and functioned as ethylene‐responsive element binding factor‐associated amphiphilic repression (EAR) domain‐dependent transcriptional repressors: NO abolished this activity for SRG3 but not for SRG2. Consistently, loss of GSNOR function, resulting in increased (S)NO concentrations, fully suppressed the disease resistance phenotype established from SRG3 but not SRG2 overexpression. Remarkably, SRG3 but not SRG2 was S‐nitrosylated in vitro and in vivo.

Our findings suggest that the SRG family has separable functions in plant immunity, and, surprisingly, these ZF‐TFs exhibit reciprocal regulation. It is remarkable that, through neofunctionalization, the SRG family has evolved to become differentially regulated by the key immune‐related redox cue, NO.
Multiple stressors drive convergent evolution of performance properties in marine macrophytes
Authors: Demes Kyle W. , Starko Samuel , Harley Christopher D. G. 
Published: October 2020

Summary

Extreme environments have driven the evolution of some of the most inspiring adaptations in nature. In the intertidal zone of wave‐swept shores, organisms face physical forces comparable to hurricanes and must further endure thermal and desiccation stress during low tides, compromising their physiological and biomechanical performance.

We examine how these multiple stressors have influenced the evolution of tissue properties during desiccation using eight phylogenetically independent pairs of intertidal and subtidal macrophytes.

Intertidal species generally lost water more slowly than their subtidal counterparts, presumably as an adaption to regular emersion. Under partial desiccation, breaking force, strength, and extensibility of intertidal species generally exceeded those of subtidal species, although important differences existed among phylogenetic pairs. This was often true even when subtidal relatives resisted greater forces or were more extensible under full hydration. The interacting effects of mechanical forces and desiccation during low tide are likely a major selective agent in determining macrophyte performance and fitness.

Overall, we found that lineages that have independently evolved to occupy the wave‐swept intertidal have converged on performance metrics that are likely to be adaptive to the interacting stressors associated with their extreme niches.
The role of herpesvirus 6A and 6B in multiple sclerosis and epilepsy
Authors: Dunn Nicky , Kharlamova Nastya , Fogdell‐Hahn Anna 
Published: October 2020

AbstractHuman herpesvirus 6A (HHV‐6A) and 6B (HHV‐6B) are two closely related viruses that can infect cells of the central nervous system (CNS). The similarities between these viruses have made it difficult to separate them on serological level. The broad term HHV‐6 remains when referring to studies where the two species were not distinguished, and as such, the seroprevalence is over 90% in the adult population. HHV‐6B has been detected in up to 100% of infants with the primary infection roseola infantum, but less is known about the primary infection of HHV‐6A. Both viruses are neurotropic and have capacity to establish lifelong latency in cells of the central nervous system, with potential to reactivate and cause complications later in life. HHV‐6A infection has been associated with an increased risk of multiple sclerosis (MS), whereas HHV‐6B is indicated to be involved in pathogenesis of epilepsy. These two associations show how neurological diseases might be caused by viral infections, but as suggested here, through completely different molecular mechanisms, in an autoimmune disease, such as MS, by triggering an overreaction of the immune system and in epilepsy by hampering internal cellular functions when the immune system fails to eliminate the virus. Understanding the viral mechanisms of primary infection and reactivation and their spectrum of associated symptoms will aid our ability to diagnose, treat and prevent these severe and chronic diseases. This review explores the role of HHV‐6A and HHV‐6B specifically in MS and epilepsy, the evidence to date and the future directions of this field.
Novel vaccine design based on genomics data analysis: A review
Authors: Lu Guangli , Shan Sharui , Zainab Bibi , Ayaz Zainab , He Jialiang , Xie Zhenxing , Rashid Umer , Zhang Dalin , Mehmood Abbasi Arshad 
Published: October 2020

AbstractModification of pathogenic strains with the passage of time is responsible for evolution in the timeline of vaccine development for last 30 years. Recent advancements in computational vaccinology on the one hand and genome sequencing approaches on the other have generated new hopes in vaccine development. The aim of this review was to discuss the evolution of vaccines, their characteristics and limitations. In this review, we highlighted the evolution of vaccines, from first generation to the current status, pointing out how different vaccines have emerged and different approaches that are being followed up in the development of more rational vaccines against a wide range of diseases. Data were collected using Google Scholar, Web of Science, Science Direct, Web of Knowledge, Scopus and Science Hub, whereas computational tools such as NCBI, GeneMANIA and STRING were used to analyse the pathways of vaccine action. Innovative tools, such as computational tools, recombinant technologies and intra‐dermal devices, are currently being investigated in order to improve the immunological response. New technologies enlightened the interactions of host proteins with pathogenic proteins for vaccine candidate development, but still there is a need of integrating transcriptomic and proteomic approaches. Although immunization with genomics data is a successful approach, its advantages must be assessed case by case and its applicability depends on the nature of the agent to be immunized, the nature of the antigen and the type of immune response required to achieve effective protection.
Influence of isometric training at short and long muscle‐tendon unit lengths on the history dependence of force
Authors: Hinks Avery , Davidson Brooke , Akagi Ryota , Power Geoffrey A. 
Published: October 2020

The history dependence of force is an intrinsic property of muscle whereby a muscle actively shortened or lengthened to an isometric steady‐state produces less (residual force depression; rFD) or more force (residual force enhancement; rFE), respectively, than a purely isometric contraction at the same muscle length and level of activation. Previous studies on the modifiability of the history dependence of force have been inconclusive, and none have attempted to modify rFD and rFE through isometric resistance training biased to short vs long muscle‐tendon unit (MTU) lengths. We tested maximal voluntary rFD and rFE in seven males and six females before and after 8 weeks of maximal isometric dorsiflexion training 3 days/wk. Participants trained one leg at 0° of plantar flexion (short‐MTU training) and one at 40° of plantar flexion (long‐MTU training). Ultrasonography of the tibialis anterior assessed resting muscle architecture. Tibialis anterior fascicle length decreased by ~3% following short‐MTU training (P = .03) and increased by ~4% following long‐MTU training (P = .01). rFD did not change following training at either MTU length (absolute rFD: P = .53; percent rFD: P = .51), nor did rFE (absolute rFE: P = .78; percent rFE: P = .80), with no relationships between the change in fascicle length and the change in percent rFD (R2 = .01, P = .62) nor rFE (R2 = .001, P = .88). Our data indicate that voluntary rFD and rFE were not modified by isometric training and not related to the fascicle length adaptations we observed.
Telesimulation‐based education during COVID‐19
Authors: Diaz Maria Carmen G. , Walsh Barbara M. 
Published: October 2020

AbstractSimulation is a valuable, immersive educational tool for both health professional trainees and experienced clinicians. By promoting a realistic, collaborative, safe, hands‐on, learning environment, simulation allows interprofessional teams to come together and practise both routine and high stakes, low‐frequency events. The COVID‐19 pandemic and the need for social distancing have shifted traditional simulation‐based medical education towards a virtual platform: telesimulation. Telesimulation is an evolving field and the speed at which clinical educators need to adapt to use this platform is unprecedented. Educators must quickly navigate and leverage the differences between traditional simulation and telesimulation to create robust remote educational experiences. Telesimulation has unique goals and objectives, technology needs, and participant roles that need to be understood and properly operationalized to maximize opportunities for learning. This article reviews the authors’ recommendations for developing and delivering successful telesimulations.
Change agent teaching for interreligious collaboration in Black Lives Matter times
Authors: Miles‐Tribble Valerie 
Published: October 2020

AbstractInterreligious discourse opens ways to discover how shared justice values and ethical actions can inform our responses amid the unjust disparities that privilege some and marginalize many. At present, we live in a public landscape of societal dissonance that heightens the urgency for people with theological grounding to bridge collaborative public witness among varied religious traditions. I describe “Black Lives Matter times” as a present expansive era in which the stew of public tension, stirred by decades of structural disparities, link religion and politics to an agenda to dismantle equitable public policies after the Civil Rights era. My goal for writingChange Agent Church in Black Lives Matter Times: Urgency for Action(2020) is to encourage practitioners and educators to prepare for public justice ministry that I callpublic witness. The book offers analytical discussion points for critical reflection and a toolkit of process methods to mobilize for public justice roles and strategic actions as collaborative change agents. In this article, as in the book,public witnessis described as “faith‐informed commitment to take action in solidarity with the marginalized, and to help mobilize change” (2). As the title conveys, the termchange agentsignifies “the ways in which clergy and interfaith leaders could exemplify a public justice ethic as motivational catalyst” (6). To prepare for “change agent teaching” shifts from teacher‐centered lectures to a learner‐centered focus to build core competencies for interactive relational engagement. Change agent teaching of religion and theology can connect faith and praxis, as theopraxis, to frame justice components of public witness. As well, interactive learning helps to develop competencies under two rubrics: contextualization and conscientization. (a)Contextualizationconnects experiential narratives to respect lived experiences at the intersections of our individual and collective identity. (b)Conscientizationraises awareness with inclusive scrutiny of issues to articulate how theological and ethical values ortheoethicsinfluence our actions. This article focuses on pedagogical approaches and process methods to teach and learn about the change agent role of public witness to support an ethos of restorative justice as understood across faith traditions.
Inhibitory effect and mechanism of three macrophytes extract on Microcystis aeruginosa growth and physiology
Authors: Tazart Zakaria , Caldeira Ana Teresa , Douma Mountasser , Salvador Cátia , Loudiki Mohammed 
Published: October 2020

AbstractMacrophytes are a promising source of bioactive compounds with potential applications in the biocontrol of harmful cyanobacteria blooms. In this study, we investigated the inhibitory effects of extracts from three macrophytes (Nasturtium officinale, Potamogeton natans and Ranunculus aquatilis) on Microcystis aeruginosa. We assessed physiological indicators of inhibition on M. aeruginosa, including lipid peroxidation, protein content, superoxide dismutase activity, catalase activity and growth. The chemical composition of the macrophyte extracts and their specific allelochemicals were analysed using high‐performance liquid chromatography (HPLC). Results showed that M. aeruginosa growth was significantly inhibited after 8 days of exposure, with inhibitory rate varying from 96.98% to 99.01%. The macrophyte extracts caused cyanobacterial cell membrane and antioxidant defence system damage. Thirteen different compounds were identified as allelochemical compounds that could be responsible for M. aeruginosa growth inhibition and oxidative stress. Our findings suggest that allelopathic compounds from macrophytes may be used to effectively control cyanobacteria blooms and promote the restoration of aquatic ecosystems.
Expression profile of Tripartite motif family (TRIM) in human fibroblasts (NHDF) infected with porcine endogenous retrovirus (PERV)
Authors: Emilia Morawiec , Roman Nowak , Barbara Strzałka‐Mrozik , Urszula Mazurek , Krzysztof Łopata , Paweł Olczyk 
Published: October 2020

AbstractBackgroundUnderstanding the interactions between the microRNA (miRNA) and mRNA of genes encoding restriction factors (RFs) can lead to the development of new antiretroviral strategies aimed at providing the resistance and reducing susceptibility of human cells to potential PERV infection. Among RFs TRIM family play an important role in shaping the immune response during various stages of infection. The aim of the study was to evaluate in vitro the transcriptional profile of TRIM family genes and identify complementary miRNAs in NHDF cells infected with PERVs and induced by gram negative lipopolysacharide (LPS).MethodsHuman dermal fibroblasts cells were cultured in four separate conditions‐ 2 monocultures: control (N), treated with LPS (NL) and 2 co‐cultures with porcine PK15 cells: without LPS (NP) and treated with LPS (NLP). Bacterial LPS was used in this study as an inducer of inflammation in NHDF cells. After extraction of DNA and RNA from cells PERV infection was confirmed in co‐cultures by qPCR and RTqPCR. RNA extracts served as a matrix for HGU 133A 2.0 and miRNA 2.0 microarrays to evaluate the expression profile of the selected TRIM family genes and miRNAs adequately. TRIM 2, 14, 22, and 28 were selected for the validation of HGU 133A 2.0 results. Statistical analyses were performed with the use of REST© 2009 and Genespring GX 13.0. Transcriptome Analysis Console 4.0 program (Affymetrix) was used to identify miRNAs that differentiate the studied genes in all conditions.ResultsPorcine endogenous retrovirus infection at DNA and RNA level was confirmed in NHDF cells in each of the tested groups (NP and NLP). Contamination was excluded in N and NL groups. Based on the analysis of HGU 133A 2.0 results 93 mRNA IDs of TRIM family genes differentiating analyzed conditions were selected P < .05. HGU 133A 2.0 mRNA fluorescence profile was confirmed with RTqPCR of TRIM2, TRIM14, TRIM22 and TRIM28 P < .05. TRIM14 down regulation was specific only in PERV monoinfection (group NP). In miRNA 2.0 microarray 346 miRNAs were identified as differentiating NHDF cells in all analyzed conditions, P < .05. According to the analysis with mirTAR platform and Microrna.org datatbase none of the selected miRNAs had the potential to regulate the selected genes of the TRIM family.ConclusionPorcine endogenous retrovirus infection of NHDF cells is accompanied by TRIM14 down regulation suggesting TRIM14 as a possible marker of retroviral infection. None of the selected miRNAs had statistically significant potential to regulate the expression of the selected TRIMs in any of the analyzed conditions.
Pore-Scale Simulation on Pool Boiling Heat Transfer and Bubble Dynamics in Open-Cell Metal Foam by Lattice Boltzmann Method
Authors: Qin Jie , Xu Zhiguo , Ma Xiaofei 
Published: October 2020

AbstractBased on the newly developed geometrical model of open-cell metal foam, pool boiling heat transfer in open-cell metal foam, considering thermal responses of foam skeletons, is investigated by the phase-change lattice Boltzmann method (LBM). Pool boiling patterns are obtained at different heat fluxes. The effects of pore density and foam thickness on bubble dynamics and pool boiling heat transfer are revealed. The results show that “bubble entrainment” promotes fluid mixing and bubble sliding inside metal foam. Based on force analysis, the sliding bubble is pinned on the heating surface and cannot lift off completely at high heat flux due to the increasing surface tension force. Pool boiling heat transfer coefficient decreases with increasing pore density and foam thickness due to high bubble escaping resistance.
Neutronic Analysis of the European Sodium Fast Reactor: Part II—Burnup Results
Authors: Fridman Emil , Álvarez Velarde Francisco , Romojaro Otero Pablo , Tsige-Tamirat Haile , Jiménez Carrascosa Antonio , García Herranz Nuria , Bernard Franck , Gregg Robert , Davies Una , Krepel Jiri , Lindley Ben , Massara Simone , Poumerouly Sandra , Girardi Enrico , Mikityuk Konstantin 
Published: October 2020

Abstract
In the framework of the Horizon 2020 project ESFR-SMART (2017–2021), the European sodium fast reactor (ESFR) core was updated through a safety-related modification and optimization of the core design from the earlier FP7 CP-ESFR project (2009–2013). This study is dedicated to neutronic analyses of the improved ESFR core design. The conducted work is reported in two parts. Part I deals with the evaluation of the safety-related neutronic parameters of the fresh beginning-of-life (BOL) core carried out by eight organizations using both continuous energy Monte Carlo and deterministic computer codes. In addition to the neutronics characterization of the core, a special emphasis was put on the calibration and verification of the computational tools involved in the analyses. Part II is devoted to once-through and realistic batchwise burnup calculations aiming at the establishing of the equilibrium core state, which will later serve as a basis for detailed safety analyses.
Fluid Flow Characteristics of a Co-Flow Fluidic Slot Jet Thrust Augmentation Propulsion System
Authors: Garrett Brian , Ahmed Kareem 
Published: October 2020

Abstract
The UAV industry is booming with investments in research and development on improving UAV systems. Current UAV machines are developed according to the quadcopter design which consists of a rotary propulsion system providing lift needed for flight. This design has some flaws; namely safety concerns and noise/vibration production both of which come stem from the rotary propulsion system. As such, a novel propulsion system using slip stream air passed through high performance slot jets is proposed and an analysis of the fluid characteristics is presented in this report.
The test section for the experiment is developed using 3D printed ABS plastic airfoils modified with internal cavities where pressurized air is introduced and then expelled through slot jets on the pressure side of the airfoils. Entrainment processes develop in the system through high momentum fluid introduction into a sedentary secondary fluid. Entrainment is governed by pressure gradients and turbulent mixing and so turbulent quantities that measure these processes are extracted and analyzed according to the independent variable’s effects on these quantities. Pitot probe testing extracted one dimensional fluid information and PIV analysis is used to characterize the two-dimensional flow aspects.
High slot jet velocities are seen to develop flows dominated by convection pushing momentum mixing downstream reducing the mixing in the system while low slot jet speeds exhibit higher mass fluxes and thrust development. Confinement spacing is seen to cause a decrease in flow velocity and thrust as the spacing is decreased for high speed runs. The most constricted cross sectional runs showed high momentum mixing and developed combined self-similar flow through higher boundary layer interactions and pressures, but this also hurts thrust development by minimizing secondary flows. The Angle of Attack of the assembly proved to be the most important variable. Outward angling showed the influence of coanda effects but also demonstrated the highest bulk fluid flow with turbulence driven momentum mixing. Inward angling created combined fluid flow downstream with high momentum mixing upstream driven by pressure. Minimal mixing is seen when the airfoils are not angled, and high recirculation zones occur along the boundaries. The optimal setup is seen when the airfoils are angled outwards where the highest thrust and bulk fluid movement is developed driven by the turbulent mixing induced by the increasing cross sectional area of the system.