bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intraspecific variation of transposable elements reveals differences in the evolutionary history of fungal phytopathogen pathotypes
Authors: Nakamoto Anne A. , Joubert Pierre M. , Krasileva Ksenia V. 
Published: November 2022

AbstractTransposable elements (TEs) contribute to intraspecific variation and play important roles in the evolution of fungal genomes. However, our understanding of the processes that shape TE landscapes is limited, as is our understanding of the relationship between TE content, population structure, and evolutionary history of fungal species. Fungal plant pathogens, which often have host-specific populations, are useful systems in which to study intraspecific TE content diversity. Here, we describe TE dynamics in five lineages ofMagnaporthe oryzae, the fungus that causes blast disease of rice, wheat, and many other grasses. We identified differences in TE content across these lineages, and showed that recent lineage-specific expansions of certain TEs have contributed to overall greater TE content in rice-infecting andSetaria-infecting lineages. We reconstructed the evolutionary histories of LTR-retrotransposon expansions and found that in some cases they were caused by complex proliferation dynamics of one element, and in others by multiple elements from an older population of TEs multiplying in parallel. Additionally, we found evidence suggesting the recent transfer of a DNA transposon between rice and wheat-infectingM. oryzaelineages, and a region showing evidence of homologous recombination between those lineages, which could have facilitated such a transfer. By investigating intraspecific TE content variation, we uncovered key differences in the proliferation dynamics of TEs in various pathotypes of a fungal plant pathogen, giving us a better understanding of the evolutionary history of the pathogen itself.
Meta-analysis of the Effect of Orlistat on The Body Mass Index in Obese Subjects
Authors: Jeong Gyeonghwa , Han Dongwoo , Ahmed Mahmoud , Kim Deok Ryong 
Published: November 2022

AbstractObesity is a widespread health issue worldwide. Therefore, evaluating existing pharmaceuticals and developing new effective strategies to mitigate the problem is essential. Although literature reviews of a broad range of interventions for managing obesity exist, a recent evaluation of the efficacy of orlistat is lacking. This meta-analysis aims to quantify the efficacy of orlistat on body mass index (BMI) and the impact of age, dose, duration, and comorbidities. A literature search of orlistat on PubMed was carried out, and 177 placebo-controlled randomized clinical trials published in the last twenty years were identified. Sixteen studies that met the inclusion criteria were selected for further analysis. Two investigators independently extracted data from the clinical reports using a predefined protocol. We conducted a meta-analysis using random and mixed effects models with different moderators. We found that, on aggregate, the orlistat group reduced their BMI by 0.72 kg/m2(P< 0.05) compared to the placebo group. In addition, a longer duration of intervention led to a greater decrease in BMI. Moreover, patients with comorbidities experienced a smaller change in BMI. In conclusion, the evidence suggests that orlistat moderately reduces BMI in obese subjects. The effect of lifestyle modifications, side effects, and drug interactions should be assessed in future studies.
Characterization of yield and fruit quality parameters of Vietnamese elite tomato lines generated through phenotypic selection and conventional breeding methods
Authors: Nguyen Cam Chau , Shelake Rahul Mahadev , Van Tien Vu , Van Hai Tong , Thi Nhan Nguyen , Nguyen Xuan Canh , Do Vo-Anh-Khoa , Thanh Hai Nguyen , Kim Jae-Yean 
Published: November 2022

AbstractTomato (Solanum lycopersicumL.) is the second most important vegetable crop after potatoes, and global demands have been steadily increasing in recent years. Conventional breeding has been applied to breed and domesticate tomato varieties to meet the need for higher yield or superior agronomical traits that allow to sustain under different climatic conditions. In the current study, we applied bulk population breeding by crossing eight tomato accessions procured from the Asian Vegetable Research and Development Center (AVRDC) with three heat-resistant tomato inbred lines from Vietnam and generated ten elite tomato (ET) lines in the F8 generation. The individual F8 lines exhibited robust vigor and adaptability to Vietnamese climate conditions. Among the ten lines, ET1 and ET3 displayed indeterminate growth. ET2 showed semi-determinate, while all the other lines had determinate growth. The different ET lines showed distinctive superior agronomical traits, including early maturing (ET4, ET7, and ET10), highly efficient fruit set (ET1), higher yield (ET1, ET8, ET10), jointless pedicels (ET2), and partial parthenocarpy (ET9). Molecular analysis revealed that the ET3 line consisted ofTy-1andTy-3loci that positively contribute toTomato yellow leaf curl virus(TYCLV) resistance in tomato plants. The elite tomato lines developed in this study would contribute significantly to the Vietnamese and Asian gene pool for improved tomato production and may be a valuable resource for various breeding goals.
Genomic consequences of range expansion and colonisation in the reed warbler (Acrocephalus scirpaceus)
Authors: Sætre Camilla Lo Cascio , Rönkä Katja , Ravinet Mark , Vitulano Severino , Caldarella Matteo , Procházka Petr , Stokke Bård , Cuevas Angélica , Bergman Nora , Thorogood Rose , Jakobsen Kjetill S. , Tørresen Ole K. , Eroukhmanoff Fabrice 
Published: November 2022

AbstractRange expansion is a common natural phenomenon, which may be intensified by human-induced drivers such as climate change and alterations of habitat. The genetic consequences of range expansion are potentially major, and it is important to study known cases of range expansion to understand how human activities affect contemporary evolution, and to learn more about the genetic adaptive potential of species. The reed warbler (Acrocephalus scirpaceus) is a long-distance migratory bird breeding in Eurasia and wintering south of Sahara. It is currently expanding its range northwards, likely as a consequence of climate change. Interestingly, however, reed warblers have also recently colonised new territory southwards, following habitat restoration at the southern range margin. In this study, we investigate the genetic consequences of these two-directional range expansions with RAD-seq, looking at 10 populations from north to south in Europe. We investigate population structure and genome diversity, and assess the role of selection in divergence between populations across the species range. We do not find evidence of strong genetic structure in the reed warbler populations, and the youngest edge populations do not exhibit any substantial loss in genetic diversity, suggesting ongoing gene flow. On a smaller scale, the edge populations are the most genetically distinct, and we identify environmental disparity, especially in precipitation variability, as the main barrier of gene flow, to a greater extent than geographic distance. We find no evidence that the loci involved in population divergence and adaptation in the core populations are the same that are involved in adaptation at the range edges. Using three genome scan methods to identify selection, we found 49 SNPs putatively under selection, of which 33 were located in introns of 28 unique genes. Most of these are correlated with differences in climatic variables of temperature and precipitation. Some genome scan outliers show signs of being part of nascent selective sweeps, especially one which is distinct for the northern range edge. Our results suggest that in the reed warbler, contemporary range expansion has had little effect on molecular diversity and has been rapidly followed by local adaptation to climatic conditions, which could further corroborate the rapid pace at which colonisation of novel environments has occurred both northwards and southwards.
Phage-antibiotic synergy: cell filamentation is a key driver of successful phage predation
Authors: Bulssico Julián , Papukashvili Irina , Espinosa Leon , Gandon Sylvain , Ansaldi Mireille 
Published: November 2022

AbstractPhages are promising tools to fight antibiotic-resistant bacteria, and as for now, phage therapy is essentially performed in combination with antibiotics. Interestingly, combined treatments including phages and a wide range of antibiotics lead to an increased bacterial killing, a phenomenon called phage-antibiotic synergy (PAS), suggesting that antibiotic-induced changes in bacterial physiology alter the dynamics of phage propagation. Using single-phage and single-cell techniques, each step of the lytic cycle of phage HK620 was studied inE. colicultures treated with either ciprofloxacin or cephalexin, two filamentation-inducing antibiotics. In the presence of sublethal doses of antibiotics, multiple stress tolerance and DNA repair pathways are triggered following activation of the SOS response. One of the most notable effects is the inhibition of bacterial division. As a result, a significant fraction of cells forms filaments that stop dividing but have higher rates of mutagenesis. Antibiotic-induced filaments become easy targets for phages due to their enlarged surface areas, as demonstrated by fluorescence microscopy and flow cytometry techniques. Adsorption, infection and lysis occur more often in filamentous cells compared to regular-sized bacteria. In addition, the reduction in bacterial numbers caused by impaired cell division may account for the faster elimination of bacteria during PAS. We developed a mathematical model to capture the interaction between sublethal doses of antibiotics and exposition to phages. This model shows that the induction of filamentation by sublethal doses of antibiotics can amplify the replication of phages and therefore yield PAS. We also use this model to study the consequences of PAS on the emergence of antibiotic resistance. A significant percentage of hyper-mutagenic filamentous bacteria are effectively killed by phages due to their increased susceptibility to infection. As a result, the addition of even a very low number of bacteriophages produced a strong reduction of the mutagenesis rate of the entire bacterial population. We confirm this prediction experimentally using reporters for bacterial DNA repair. Our work highlights the multiple benefits associated with the combination of sublethal doses of antibiotics with bacteriophages.
The direct interaction with transcriptional factor TEAD4 implied a straightforward regulation mechanism of tumor suppressor NF2
Authors: Hu Liqiao , Wu Mengying , He Lingli , Yuan Liang , Yang Lingling , Zhao Bin , Zhang Lei , He Xiaojing 
Published: November 2022

AbstractAs an output effecter of Hippo signaling pathway, the transcription factor TEAD and co-activator YAP play crucial functions in promoting cell proliferation and organ size. The tumor suppressor NF2 has been shown to activate LATS1/2 kinases and interplay with Hippo pathway to suppress YAP-TEAD complex. But, whether and how NF2 could directly regulate TEAD remains unknown. We identified a direct link and physical interaction between NF2 and TEAD4. NF2 interacted with TEAD4 through its FERM domain and the C-terminal tail, and decreased protein stability of TEAD4 independently of LATS1/2 and YAP. Furthermore, NF2 inhibited TEAD4 palmitoylation and retained the cytoplasmic translocation of TEAD4, resulting in ubiquitination and dysfunction of TEAD4. Moreover, the interaction with TEAD4 is required for NF2 function to suppress cell proliferation. These findings revealed a new role of NF2 as a binding partner and inhibitor of the transcription factor TEAD, and would shed light on an alternative mechanism of how NF2 functions as a tumor suppressor through the Hippo signaling cascade.
A configuration taxonomy based on business process orientation: evidence from organizations in Indonesia
Authors: ER Mahendrawathi , Nurkasanah Ika , Pratama Annisa Rizki 
Published: November 2022

PurposeThis study aims to develop a taxonomy of organizations according to business process orientation (BPO) maturity and investigate the difference between clusters in terms of performance outcome.Design/methodology/approachA survey of various organizations in Indonesia is conducted. The main variables are critical practices (CPs) as the measurement variables of BPO maturity and performance outcome. Cluster analysis is performed to obtain an empirical taxonomy of the organizations. ANOVA test is used to test if there are statistically different performance outcomes across different clusters.FindingsCluster analysis resulted in six archetypes labeled according to their characteristics: Beginners, Non-technical, Domestics, IT laggards, Excellers, and Champions. The ANOVA test results show that the archetypes with high CPs tend to have high perceived performance results.Research limitations/implicationsThis study is limited because the authors use a single dataset from organizations in Indonesia. Further study involving more organizations will be beneficial to validate and enrich the taxonomy of organizational archetypes.Practical implicationsResults of the study can be used as a benchmarking tool by organizations to identify their positions against other organizations and set their areas for improvement. It can also help them identify a roadmap for improvement that will benefit their organization.Originality/valueUsing the CPs as a measure of BPO enables the authors to identify supplier orientation and information and technology (IT) implementation as the primary differentiators within the taxonomy. The use of IT differentiates the bottom, middle and top clusters.
Analysis of COVID-19 Gov PK app user reviews to determine online privacy concerns of Pakistani citizens
Authors: Yaqub Ussama , Saleem Tauqeer , Zaman Salma 
Published: November 2022

Purpose
The purpose of this paper is to explore the reaction of Pakistani citizens toward online privacy in the context of the Pakistan Government's COVID-19 app privacy breach.

Design/methodology/approach
The authors implemented supervised and unsupervised machine learning methods, that is, topic modeling and sentiment analysis on Google app store user review data.

Findings
There was no visible concern shown by the citizens toward the COVID-19 app privacy breach, even though it was well highlighted in the news. Other studies have also indicated that concern for online privacy remains low in developing countries, which aligns with the findings of this paper.

Originality/value
Globally COVID-19 apps have been a cause of concern in terms of public privacy. To the best of the authors’ knowledge, this paper is the first in the Pakistani context to show the impact of a well-document privacy breach of a government COVID-19 app.
Discretionary impacts of the risk management committee attributes on firm performance: do board size matter?
Authors: Karim Sitara , Vigne Samuel A. , Lucey Brian M. , Naeem Muhammad Abubakr 
Published: November 2022

PurposeWhile there is an increased demand from various corporate stakeholders on the need for public companies to have risk management frameworks as well as a stand-alone risk management committee to mitigate risks and simultaneously improve performance, this study investigates the effects of the risk management committee attributes on firm performance, and the role of board size is highlighted on this relationship in Malaysian listed companies.Design/methodology/approachBoth accounting- and market-based performance measures have been used for measuring performance. A dynamic model using the generalized method of moments (GMM) has been employed to control for potential endogeneity, simultaneity and unobserved heterogeneity.FindingsThe findings reveal that risk management committee attributes such as size, independence and meetings negatively affect book-based performance measures and positively affect market-based performance measures. Moreover, board size positively moderates the risk management committee attributes and performance relationship. The study embraces the predictions of agency theory and resource dependence theory.Practical implicationsThe findings are practically significant for Bursa Malaysia, Securities Commission Malaysia to assess the compliance of the Corporate Governance Code (MCCG, 2017) and for academia to further explore significant relationships in other emerging economies.Originality/valueThe paper contributes to multiple aspects: first, it studies the impact of risk management committee attributes on firm performance; second, it investigates the moderating effect of board size on RMC–performance relationship; in the end, the study employs dynamic modeling for estimation process to avoid dynamic endogeneity considered a main econometric problem for CG–performance relationships.
Identification of corrosion formation in CORTEN steel using acousto-ultrasonic approach and deep learning
Authors: Barile Claudia , Casavola Caterina , Pappalettera Giovanni , Paramsamy Kannan Vimalathithan 
Published: November 2022

PurposeThe acousto-ultrasonic approach is used for propagating stress waves through different configurations of CORTEN steel specimens. The propagated waves are recorded and analysed by piezoelectric sensors. The purpose of the study is to study the characteristics of the CORTEN steel by analysing the propagated waves.Design/methodology/approachTo investigate the attenuation in acoustic wave propagation due to the corrosion formation in CORTEN steel specimens and to train a neural network model to classify the attenuated acoustic waves automatically.FindingsDue to the corrosion formation in CORTEN steel specimens, attenuation is observed in amplitude, energy, counts and duration of the propagated waves. When the waves are analysed in their time-frequency characteristics, attenuation is observed in their frequency and spectral energy.Originality/valueThe corrosion formation in CORTEN steel can automatically be analysed by using the acousto-ultrasonic approach and the trained deep learning neural network.
Evaluating the effects of indoor air quality on teacher performance using artificial neural network
Authors: Alzahrani Hamdan , Arif Mohammed , Kaushik Amit Kant , Rana Muhammad Qasim , Aburas Hani M. 
Published: November 2022

Purpose
A building's Indoor Air Quality (IAQ) has a direct impact on the health and productivity on its occupants. Understanding the effects of IAQ in educational buildings is essential in both the design and construction phases for decision-makers. The purpose of this paper is to outline the impact air quality has on occupants' performance, especially teachers and students in educational settings.

Design/methodology/approach
This study aims to evaluate the effects of IAQ on teachers' performances and to deliver air quality requirements to building information modelling-led school projects. The methodology of the research approach used a quasi-experiment through questionnaire surveys and physical measurements of indoor air parameters to associate correlation and deduction. A technical college building in Saudi Arabia was used for the case study. The study developed an artificial neural network (ANN) model to define and predict relationships between teachers' performance and IAQ.

Findings
This paper contains a detailed investigation into the impact of IAQ via direct parameters (relative humidity, ventilation rates and carbon dioxide) on teacher performance. Research findings indicated an optimal relative humidity with 65%, ranging between 650 to 750 ppm of CO2, and 0.4 m/s ventilation rate. This ratio is considered optimum for both comfort and performance

Originality/value
This paper focuses on teacher performance in Saudi Arabia and used ANN to define and predict the relationship between performance and IAQ. There are few studies that focus on teacher performance in Saudi Arabia and very few that use ANN in data analysis.
The coloration of polyester fabric with Prangos ferulacea natural dye: new approaches toward a cleaner production
Authors: Khajeh Mehrizi Mohammad , Jokar Mostafa , Shahi Zahra 
Published: November 2022

Purpose
Natural colorants are believed to be safe because of their nontoxic, noncarcinogenic and biodegradable nature, and also, the demand for natural dyes is steadily increasing. This study aims to investigate the dyeing of polyethylene terephthalate (PET) fabrics under cold plasma and ultraviolet (UV) radiation conditions with Prangos ferulacea.

Design/methodology/approach
In the first, some PET fabrics were modified using UV radiation and some others by cold plasma (oxygen/argon), and then the dyeing of fabrics with the natural dye was done (100°C/130°C) without using metallic mordant. Dyeability (color strengths) of the treated samples, colorfastness to washing, light and rubbing, water absorption time, crease recovery angle, air permeability and mechanical behavior were investigated.

Findings
The maximum color strength (k/s = 4.87) was achieved for the fabric exposed to UV radiation for 2 h and then dyed with Prangos ferulacea at 130 °C. The results indicated that the dyed fabric showed acceptable colorfastness (very good–excellent) properties in washing and rubbing fastness except for colorfastness to light (moderate). The strength and the angle of crease recovery of treated and dyed samples have increased, while the time of water absorption and air permeability have decreased.

Originality/value
The surface modification of PET (UV radiation and plasma treatment) provides a new idea to improve the dyeability of PET with Prangos ferulacea natural dye without using metallic mordant.
Analyzing the champions league teams via decision models
Authors: Gökgöz Fazıl , Yalçın Engin 
Published: November 2022

Purpose
The purpose of this study is to evaluate the performance of the Champions League teams using the entropy-integrated Multi Attribute Ideal-Real Comparative Analysis (MAIRCA) and super-slack-based data envelopment analysis for the 2012–2022 period.

Design/methodology/approach
This study consists of two sections. First, this study uses the entropy-integrated MAIRCA approach, which is a novel multi-criteria decision-making (MCDM) technique developed by Gigović, to measure the performance of Champions League clubs. Second, this study proceeds with the super-slack-based DEA to evaluate the efficiency of the Champions League clubs.

Findings
As per the empirical results, Real Madrid is found to be the best-performing club over the past 10 years in terms of financial and sportive performance. Over the analyzed period, teams from the five Major Leagues of Europe perform better.

Originality/value
To the best of the authors’ knowledge, performance measurement studies in football have focused on either DEA or MCDM. This study aims to present novelty for football literature by evaluating holistically both the sportive and financial dimensions. This paper also analyzes Champions League teams from the perspective of both MCDM and super-slack-based DEA methods.