bluuebunny/crossref_metadata_2025_split huggingface dataset:
Old foe, new host: epidemiology, genetic diversity and pathogenic characterization of maize streak virus in rice fields from Burkina Faso
Authors: Fouad Noun Magdy Ibrahim , Barro Mariam , Bangratz Martine , Sérémé Drissa , Filloux Denis , Fernandez Emmanuel , Julian Charlotte , Saïbou Nignan , Kassankogno Abalo Itolou , Guigma Abdoul Kader , Roumagnac Philippe , Wonni Issa , Tollenaere Charlotte , Poulicard Nils 
Published: October 2023

ABSTRACTRice is of critical significance regarding food security worldwide including in Africa. Only two viruses impacting rice production in Africa have been deeply investigated for decades: the rice yellow mottle virus (Solemoviridae) and the rice stripe necrosis virus (Benyviridae). Using viral metagenomics, we aimed at exploring the diversity of viruses circulating in Burkina Faso rice fields. We performed an epidemiological survey in this country between 2016 and 2019 involving 57 small farmer’s rice fields under two production systems (rainfed lowlands and irrigated areas). More than 2700 rice samples were collected withouta priori(not based on symptom observation) following a regular scheme. In addition, wild and cultivated (maize and sugarcane)Poaceaegrowing nearby rice fields were also collected. Unexpectedly, metagenomics detected maize streak virus (MSV,Geminiviridae) in analyzed rice samples. Further molecular analyses using RCA-PCR showed that MSV is widely distributed and highly prevalent in both rainfed lowlands and irrigated rice areas. MSV-A and MSV-G strains were identified. MSV-G, exclusively identified so far in wild grasses, was the most prevalent strain while MSV-A, known to cause severe symptoms in maize, was sporadically identified. No genetic differentiation was detected between MSV isolates either infecting wild or cultivated plant species. Using infectious clones in experimental conditions, we confirmed the pathogenicity of both MSV strains on rice. Thus, in addition to contribute to the epidemiological surveillance of rice production in Africa, our results illuminate new epidemiological and pathogenic aspects of one of the most studied plant viruses with significant economic consequences in Africa.FundingFrench National Research Agency «Investissements d’avenir» program (ANR-10-LABX-001-01), Agropolis Fondation (ANR-16-IDEX-006), French National Research Agency “young researchers” program (ANR-20-CE35-0008-01), CGIAR Research Program on Rice Agri-food Systems (RICE), Cooperation and cultural action department of the French Embassy (SCAC) in Burkina Faso.
Allosteric activation of VCP, a AAA unfoldase, by small molecule mimicry
Authors: Jones N.H. , Liu Q. , Urnavicius L. , Dahan N.E. , Vostal L.E. , Kapoor T.M. 
Published: October 2023

AbstractThe loss of function of AAA (ATPases associated with diverse cellular activities) mechanoenzymes has been linked to diseases, and small molecules that activate these proteins can be powerful tools to probe mechanisms and test therapeutic hypotheses. Unlike chemical inhibitors that can bind a single conformational state to block enzyme activity, activator binding must be permissive to different conformational states needed for enzyme function. However, we do not know how AAA proteins can be activated by small molecules. Here, we focus on valosin-containing protein (VCP)/p97, a AAA unfoldase whose loss of function has been linked to protein aggregation-based disorders, to identify druggable sites for chemical activators. We identified VCP Activator 1 (VA1), a compound that dose-dependently stimulates VCP ATPase activity up to ∼3-fold. Our cryo-EM studies resulted in structures (∼2.9-3.5 Å-resolution) of VCP in apo and ADP-bound states, and revealed VA1 binding an allosteric pocket near the C-terminus in both states. Engineered mutations in the VA1 binding site confer resistance to VA1, and furthermore, modulate VCP activity to a similar level as VA1-mediated activation. The VA1 binding site can alternatively be occupied by a phenylalanine residue in the VCP C-terminal tail, a motif that is post-translationally modified and interacts with cofactors. Together, our findings uncover a druggable allosteric site and a mechanism of enzyme regulation that can be tuned through small molecule mimicry.SignificanceThe loss of function of valosin-containing protein (VCP/p97), a mechanoenzyme from the AAA superfamily that hydrolyzes ATP and uses the released energy to extract or unfold substrate proteins, is linked to protein aggregation-based disorders. However, druggable allosteric sites to activate VCP, or any AAA mechanoenzyme, have not been identified. Here, we report cryo-EM structures of VCP in two states in complex with VA1, a compound we identified that dose-dependently stimulates VCP’s ATP hydrolysis activity. The VA1 binding site can also be occupied by a phenylalanine residue in the VCP C-terminal tail, suggesting that VA1 acts through mimicry of this interaction. Our study reveals a druggable allosteric site and a mechanism of enzyme regulation.
Multiple independent acquisitions of ACE2 usage in MERS-related coronaviruses
Authors: Ma Cheng-Bao , Liu Chen , Park Young-Jun , Tang Jingjing , Chen Jing , Xiong Qing , Lee Jimin , Stewart Cameron , Asarnow Daniel , Brown Jack , Tortorici M. Alejandra , Yang Xiao , Sun Ye-Hui , Chen Yuan-Mei , Yu Xiao , Si Jun-Yu , Liu Peng , Tong Fei , Huang Mei-Ling , Li Jing , Shi Zheng-Li , Deng Zengqin , Veesler David , Yan Huan 
Published: October 2023

SUMMARYThe angiotensin-converting enzyme 2 (ACE2) receptor is shared by various coronaviruses with distinct receptor-binding domain (RBD) architectures, yet our understanding of these convergent acquisition events remains elusive. Here, we report that two European bat MERS-related coronaviruses (MERSr-CoVs) infectingPipistrellus nathusii(P.nat), MOW15-22 and PnNL2018B, use ACE2 as their receptor, with narrow ortholog specificity. Cryo-electron microscopy structures of the MOW15-22 RBD-ACE2 complex unveil an unexpected and entirely distinct binding mode, mapping 50Å away from that of any other known ACE2-using coronaviruses. Functional profiling of ACE2 orthologs from 105 mammalian species led to the identification of host tropism determinants, including an ACE2 N432-glycosylation restricting viral recognition, and the design of a soluble P.nat ACE2 mutant with potent viral neutralizing activity. Our findings reveal convergent acquisition of ACE2 usage for merbecoviruses found in European bats, underscoring the extraordinary diversity of ACE2 recognition modes among coronaviruses and the promiscuity of this receptor.Graphic abstract
Quantitative target engagement of RIPK1 in human whole blood via the cellular thermal shift assay for potential pre-clinical and clinical applications
Authors: Patel Shitalben , Karlsson Marie , Klahn Joseph T. , Gambino Frank , Costa Helena , McGuire Kathleen A. , Baumgartner Christina K. , Williams Jon , Sandoz Sarah , Kath James E. 
Published: October 2023

AbstractThe cellular thermal shift assay (CETSA®) is a target engagement method widely used for preclinical characterization of small molecule compounds. CETSA® has been used for semi-quantitative readouts in whole blood with PBMC isolation, and quantitative, plate-based readouts using cell lines. However, there has been no quantitative evaluation of CETSA® in unprocessed human whole blood, which is preferred for clinical applications. Here we report two separate assay formats – Alpha CETSA® and MSD CETSA® – that require less than 100 μL of whole blood per sample without PBMC isolation. We chose RIPK1 as a proof-of-concept target and, by measuring engagement of seven different inhibitors, demonstrate high assay sensitivity and robustness. These quantitative CETSA® platforms enable possible applications in preclinical pharmacokinetic-pharmacodynamic studies, and direct target engagement with small molecules in clinical trials.
Shared mechanisms drive ocular following and motion perception
Authors: Kreyenmeier Philipp , Kumbhani Romesh , Movshon J. Anthony , Spering Miriam 
Published: October 2023

AbstractHow features of complex visual patterns combine to drive perception and eye movements is not well understood. We simultaneously assessed human observers’ perceptual direction estimates and ocular following responses (OFR) evoked by moving plaids made from two summed gratings with varying contrast ratios. When the gratings were of equal contrast, observers’ eye movements and perceptual reports followed the motion of the plaid pattern. However, when the contrasts were unequal, eye movements and reports during early phases of the OFR were biased toward the direction of the high-contrast grating component; during later phases, both responses more closely followed the plaid pattern direction. The shift from component- to pattern-driven behavior resembles the shift in tuning seen under similar conditions in neuronal responses recorded from monkey MT. Moreover, for some conditions, pattern tracking and perceptual reports were correlated on a trial-by-trial basis. The OFR may therefore provide a precise behavioural read-out of the dynamics of neural motion integration for complex visual patterns.
Phosphatidylinositol 4-kinase II β downregulation induces ER stress mediated ROS generation and increases radio-sensitivity in MCF-7
Authors: Chaudhry Sonica , Checker Rahul , Thoh Maikho , Sandur Santosh Kumar , Subrahmanyam Gosukonda 
Published: October 2023

AbstractType II phosphatidylinositol 4-kinase has historically been associated with vesicular trafficking and growth factor receptor signaling. Recently, it was shown to influence apoptosis, cell adhesion, motility, and inflammatory reactions. Previous study from our group showed that down regulation of PtdIns 4-kinase II β inhibits NF-κB translocation to the nucleus and induce apoptosis in cancer cell lines. Since, NF-κB regulates redox homeostasis and stress signaling, the role of PtdIns 4-kinase II β in regulating these signaling cascades was investigated using human breast cancer cell line (MCF-7 cells). Knockdown of PtdIns 4-kinase II β inhibited NF-κB nuclear translocation and down regulated Bcl-2 and AKT-3 mRNA levels. Silencing of PtdIns 4-kinase II β increased ROS levels with a concomitant decrease in GSH: GSSG ratio, increased DNA damage and induced apoptosis. Inhibition of NADPH oxidase (NOX) activity restored redox homeostasis. Since NOX gets activated during ER stress and the resultant increase in ROS can induce apoptosis, we studied the role of PtdIns 4-kinase II β shRNA in ER stress and observed an increase in ER stress markers, pERK, IRE-1α, BiP and PDI and up regulation of GADD153. At cellular level, these cells showed ER deformity. ROS scavengers and ER chemical chaperone could rescue MCF-7 cells from PtdIns 4-kinase II β shRNA induced apoptosis. These results indicate involvement of PtdIns4-kinase II β in regulation of ER function. Interestingly, irradiation of MCF-7 cells increased PtdIns 4-kinase II β mRNA levels and knock-down of PtdIns 4-kinase II β increased radio-sensitivity of the cells indicating potential role of PtdIns 4-kinase II β in cancer radio-resistance.
Workforce agility, organizational identity and solidarity as antecedents of innovative work behaviour – an examination using structural equation modelling
Authors: AlAbood Abdulaziz , Manakkattil MohammedIsmail Sulphey 
Published: October 2023

PurposeThe purpose of the study was to identify the inter-relationship of certain antecedents of innovative work behaviour (IWB). The antecedents identified for the study were workplace agility (WA), organizational identity (OI) and organizational solidarity (OS).Design/methodology/approachData for the study were collected online using four standardized and validated questionnaires from 364 gainfully employed respondents from across Saudi Arabia. The respondents belonged to various forms of organizations like manufacturing, service, hospital and banking. The data collected for the study were analysed using structural equation modelling (SEM).FindingsThe study found a significant positive relationship between the identified concepts of WA, workplace identity, OS and IWB.Originality/valueA detailed review of the literature found that no previous studies had examined the complex relationship between the identified constructs. The results of the study found a significant positive relationship between the constructs. The findings of the study have many theoretical and practical values and implications. It also enriches the literature about the antecedents of IWB. It is expected that the present study will act as a trigger for more empirical examinations in this interesting area.
Identifying emerging trends and hot topics through intelligent data mining: the case of clinical psychology and psychotherapy
Authors: Sokolova Anna , Lobanova Polina , Kuzminov Ilya 
Published: October 2023

Purpose
The purpose of the paper is to present an integrated methodology for identifying trends in a particular subject area based on a combination of advanced text mining and expert methods. The authors aim to test it in an area of clinical psychology and psychotherapy in 2010–2019.

Design/methodology/approach
The authors demonstrate the way of applying text-mining and the Word2Vec model to identify hot topics (HT) and emerging trends (ET) in clinical psychology and psychotherapy. The analysis of 11.3 million scientific publications in the Microsoft Academic Graph database revealed the most rapidly growing clinical psychology and psychotherapy terms – those with the largest increase in the number of publications reflecting real or potential trends.

Findings
The proposed approach allows one to identify HT and ET for the six thematic clusters related to mental disorders, symptoms, pharmacology, psychotherapy, treatment techniques and important psychological skills.

Practical implications
The developed methodology allows one to see the broad picture of the most dynamic research areas in the field of clinical psychology and psychotherapy in 2010–2019. For clinicians, who are often overwhelmed by practical work, this map of the current research can help identify the areas worthy of further attention to improve the effectiveness of their clinical work. This methodology might be applied for the identification of trends in any other subject area by taking into account its specificity.

Originality/value
The paper demonstrates the value of the advanced text-mining approach for understanding trends in a subject area. To the best of the authors’ knowledge, for the first time, text-mining and the Word2Vec model have been applied to identifying trends in the field of clinical psychology and psychotherapy.
Theoretical and numerical analysis of free vibrations of piezoelectric circular plate reinforced with boron nitride
Authors: Moradi Mohammad Hadi , Ranjbar-Roeintan Mehdi 
Published: October 2023

PurposeThe purpose of this research is to extract the natural frequencies of a circular plate containing a central hole reinforced with boron nitride nanotubes (BNNTs) and containing piezoelectric layers.Design/methodology/approachA unit cell shall be taken into account for the simulation of BNNT's volume fraction. A rectangular micromechanical model is used to obtain the mechanical properties of unit cell of piezoelectric fiber-reinforced composite (PFRC). The three-dimensional (3D) elasticity method is presented to provide the relationship between displacements and stresses. The one-dimensional differential quadrature method (1D-DQM) and the state-space methodology are combined to create the semi-analytical technique. The state-space approach is utilized to implement an analytical resolution in the thickness direction, and 1D-DQM is used to implement an approximation solution in the radial direction. The composite consists of a polyvinylidene fluoride (PVDF) matrix and BNNTs as reinforcement.FindingsA study on the PFRC is carried, likewise, the coefficients of its properties are obtained using a micro-electromechanical model known as the rectangular model. To implement the DQM, the plate was radially divided into sample points, each with eight state variables. The boundary situation and DQM are used to discretize the state-space equations, and the top and bottom application surface conditions are used to determine the natural frequencies of the plate. The model's convergence is assessed. Additionally, the dimensionless frequency is compared to earlier works and ABAQUS simulation in order to validate the model. Finally, the effects of the thickness, lateral wavenumber, boundary conditions and BNNT volume fraction on the annular plate's free vibration are investigated. The important achievements are that increasing the volume fraction of BNNTs increases the natural frequency.Originality/valueThe micromechanical “XY rectangle” model in PFRC along with the three-dimensional elasticity model is used in this literature to assess how the piezoelectric capabilities of BNNTs affect the free vibration of polymer-based composite annular plates under various boundary conditions.
Using geographical information systems in literary tourism: an analysis to the “An English family” novel, from Júlio Dinis
Authors: Oliveira Sofia , Albuquerque Helena 
Published: October 2023

Purpose
The paper aims to present a literary itinerary inspired in Julio Dinis’ novel An English Family (Uma Família Inglesa) through a comparative analysis of the places identified in the novel and the touristic attraction proposed by Visit Porto website. This novel is representative of the cultural identity and society of Porto city in the 19th century. Developing an itinerary based on this novel can facilitate the reading and understanding of the historical and cultural development of Porto.

Design/methodology/approach
This case study is based on the reading of the Julio Dinis’ novel An English Family (Uma Família Inglesa), whose storyline takes place in Porto city, Portugal in the 19th century. It used QGIS v. 3.12 software, a geographical information system to identify the places, to produce the maps and to create the itinerary.

Findings
The comparison between the places identified in the novel and the tourist attraction in Visit Porto website revealed that only 6 points in the novel are referenced on Visit Porto website. These points correspond to the ones in the historical city centre of Porto. However, the creation of an itinerary that brings together all the points mentioned by Julio Dinis in his novel, will allow the development of a new touristic itinerary, alternative to existing itineraries in the city and that can be seen as a distinguish offer that allows a different view of the urban space of Porto.

Research limitations/implications
There are some limitations to this study that can be highlighted. First, it was difficult to find the correct location of some points identified in the novel, due to difficulty of finding historical maps with quality of the data. At the same time, as tourist information is dispersed by several sources, and most of those data is not georeferenced, it was time consuming the integration of all the information in the same geodatabase. The choice of the shortest path can also be considered as a limitation, rather than the route followed by the author in the novel, but geographic information systems operates on spatial and temporal scale, which can present a limitation in tourism analysis. In the case of this project, we have chosen the shortest path, assuming that tourist would prefer that.

Originality/value
This research allowed to address two areas of knowledge that are emerging in the study of urban centres as tourist areas: the use of GIS and literary tourism. Despite the fact that there are already articles on this subject, the originality focuses on the approach made around one of the greatest writers of Portugal in the 19th century, allowing to present a tourist itinerary about one of his literary works, and the comparison made between the places identified in the novel and the tourist points identified on the Visit Porto website.
COVID-19 pandemic and trade flows: empirical evidence from selected Asian Pacific countries
Authors: Bhat Mudaser Ahad , Wani Farhana , Amin Aadil , Bhat G.M. , Beg Farhat Bano 
Published: October 2023

Purpose
This paper aims to investigate the effects of the COVID-19 crisis on trade flows in Asia Pacific countries and explores the causality between COVID-19-related shocks and trade.

Design/methodology/approach
The authors used two novel techniques, namely, two-stage instrumental-variables (2SIV) approach and Juodis, Karavias and Sarafids (JKS) causality test, to examine trade dynamics in the Asia Pacific region during the pandemic.

Findings
Using the monthly trade data of 17 Asia Pacific countries between January 2020 and December 2021, the results were threefold. Firstly, the empirical analysis showed that during the COVID-19 crisis, the flow of exports tended to persist idiosyncratically in comparison to the flow of imports. In particular, a specific finding was that the persistence level in exports was about 20%–25% higher than that in imports. Secondly, the authors found that the past values of COVID-19 cases and COVID-19 deaths contain information that helps to predict exports/imports over and above the information contained in the past values of exports/imports alone. Finally, the study established that the government response and stringency indexes have a Granger-causal relationship with exports and imports.

Research limitations/implications
For the foreseeable future, these findings have significant policy ramifications. Firstly, if a COVID-19 crisis-like situation emerges in the future, it will be critical for countries to maintain their competitiveness throughout the crisis, like the COVID-19 pandemic, while also rebuilding trade relationships wherever possible. Secondly, because information about government responses and measures can also be used to predict future trade flows, prudent management of government responses and stringent measures will be necessary in a crisis like COVID-19 to achieve the optimum level of exports and imports. At the same time, the trading partners should give up the idea of trade protection and focus on finding a way to balance the conflicting needs of imports and exports.

Originality/value
To the best of the authors’ knowledge, the authors, for the first time, used a 2SIV approach and JKS causality test to examine trade dynamics in the Asia Pacific region during the pandemic. In addition, the authors present the first comprehensive analysis of the evolving relationships between export and import flows and governmental policy responses under COVID-19. As a result, it contributes uniquely to both public and international economics.