bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chitosan stimulates root hair callose deposition and inhibits root hair growth
Authors: Drs Matěj , Haluška Samuel , Škrabálková Eliška , Krupař Pavel , Potocká Andrea , Brejšková Lucie , Muller Karel , Serrano Natalia , Voxeur Aline , Vernhettes Samantha , Ortmannová Jitka , Caldarescu George , Fendrych Matyáš , Potocký Martin , Žárský Viktor , Pečenková Tamara 
Published: July 2023

AbstractAlthough angiosperm plants have a general capacity to react after the immunity elicitor chitin or chitosan treatment by the cell wall callose deposition, this response in particular cell types and its evolutionary conservation is not understood. Here we show that also the growing root hairs (RHs) of Arabidopsis can respond to a mild (0.001%) chitosan treatment by the callose deposition and by a deceleration of the RH growth. We demonstrate that the glucan synthase-like 5 (GSL5)/PMR4 is vital for chitosan-induced callose deposition but not for RH growth inhibition. Upon the higher chitosan concentration (0.01%) treatment, RHs do not deposit callose, while growth inhibition is prominent. To understand the specificities of the low and high concentration chitosan treatments, we analysed the corresponding PTI signalling components, gene expression, and RH cellular endomembrane and cytoskeleton modifications. Importantly, chitosan-induced callose deposition is also present in the functionally analogous and evolutionarily only distantly related RH-like structures rhizophores (lycophytes) and rhizoids (bryophytes). Our results point to the RH callose deposition as a conserved strategy of soil-anchoring plant cells (rhizoids/rhizophores/RHs) to deal with mild biotic stress. At the same time, high chitosan concentration prominently disturbs intracellular dynamics, tip-localised endomembrane compartments and RH growth, precluding callose deposition.
Mobile retroelements induced by hypomethylating agents are restricted to transpose in myeloid malignancies
Authors: Pavlová Šárka , Krzyžánková Marcela , Volakhava Anastasiya , Smirnova Anastasia , Grigoreva Tatiana , Jašková Zuzana , Synáčková Hana , Wahl Dennis , Bohúnová Michaela , Červinek Libor , Pospíšilová Šárka , Mamedov Ilgar , Plevová Karla 
Published: July 2023

AbstractRetroelements (RE) present in the human genome are silenced via multiple mechanisms, including DNA methylation, to prevent their potentially mutagenic effect. RE activity, demonstrated by their expression and somatic retrotransposition events, is deregulated in multiple tumor types but not in leukemia. We hypothesized that treatment with hypomethylating agents (HMA), commonly used in myelodysplastic syndromes and acute myeloid leukemia, could lead to increased RE activity and somatic retrotranspositions, and contribute to disease progression. We induced expression of ORF1p protein encoded by long interspersed nuclear element-1 (L1) after 72h treatment with HMA in DAMI and HL-60 cell lines. ORF1p was predominantly localized in the cytoplasm, as evidenced by fluorescent microscopy of the DAMI cell line. To study whether long-term HMA therapy may induce somatic retrotranspositions, we (i) treated both cell lines for four weeks, (ii) analyzed a cohort of 17 MDS patients before and on treatment with HMA. Using a previously established sensitive NGS-based method, no RE events were identified. To conclude, we show that although HMA induces the expression of L1-encoded proteins in tumor myeloid cell lines,de novosomatic retrotransposition events do not arise during the long-term treatment of MDS patients and myeloid cell lines with these agents.
Metagenomic ecosystem monitoring of soft scale and mealybug infestations in Australian vineyards
Authors: Ward Chris M. , Onetto Cristobal A. , Van Den Heuvel Steven , Dixon Robyn , Borneman Anthony R. 
Published: July 2023

AbstractSoft scale insects and mealybugs are phloem feeding Hemipterans that are considered majors pests in agricultural and horticultural settings throughout the world. Viticulturally, scale are a major issue due to their ability to secrete honeydew, which facilitates the development of sooty mould and for their propensity as transmission vectors for several viral diseases of grapevine. To facilitate the rapid identification and quantification of vineyard-associated insects a metagenomic-based bioinformatic pipeline was developed for generalised ecosystem monitoring that automated the assembly and classification of insect mitochondrial genomes from shotgun sequencing data using the Barcode of Life Database API.Parthenolecanium corni(European fruit scale), which was thought to be absent from Australian grapevines, was identified as the dominant coccid species infesting all vines sampled, along with secondary infestation byPseudococcus viburni(obscure mealybug) andPseudo. longispinus(long-tailed mealybug). In addition, parisitoidism byCoccophagus scutellaris(Aphelinidae) wasps was also detected. The discovery ofParth. cornias a significant member of scale infestations in Australia has significant implications for the development of effective control strategies for this important group of pests.
ASB3 expression aggravates inflammatory bowel disease by targeting TRAF6 protein stability and affecting the intestinal microbiota
Authors: Cheng Mingyang , Xu Bin , Sun Yu , Wang Junhong , Lu Yiyuan , Shi Chunwei , Pan Tianxu , Zhao Wenhui , Li Xiaoxu , Song Xiaomei , Wang Jianzhong , Wang Nan , Yang Wentao , Jiang Yanlong , Huang Haibin , Yang Guilian , Zeng Yan , Yang Dongqin , Wang Chunfeng , Cao Xin 
Published: July 2023

AbstractE3 ubiquitin ligase (E3) plays a vital role in regulating inflammatory responses by mediating ubiquitination. Previous studies have shown that ankyrin repeat and SOCS box-containing protein 3 (ASB3) is involved in immunomodulatory functions associated with cancer. However, the impact of ASB3 on the dynamic interplay of microbiota and inflammatory responses in inflammatory bowel disease (IBD) is unclear. Here we systematically identify the E3 ligase ASB3 as a facilitative regulator in the development and progression of IBD. ASB3-/-mice are resistant to DSS-induced colitis. IκBα phosphorylation levels and production of proinflammatory factors IL-1β, IL-6, and TNF-α were reduced in colonic tissues of ASB3-/-mice compared to WT mice. This colitis-resistant phenotype was suppressed after coprophagic microbial transfer and reversed after combined antibiotic clearance of the microbiota. Mechanistically, ASB3 specifically catalyzes K48-linked polyubiquitination of TRAF6 in IECs. In contrast, in ASB3-deficient organoids, the integrity of the TRAF6 protein is shielded, consequently decelerating the onset of intestinal inflammation. Taken together, Our findings demonstrates that ASB3 is associated with dysregulation of the colitis microbiota and promotes proinflammatory factors production by disrupting the TRAF6 stability. Strategies to limit the protein level of ASB3 in intestinal epithelial cells may help in the treatment of colitis.
Identification of Sequence Determinants for the ABHD14 Enzymes
Authors: Vaidya Kaveri , Rodrigues Golding , Gupta Sonali , Devarajan Archit , Yeolekar Mihika , Madhusudhan M. S. , Kamat Siddhesh S. 
Published: July 2023

ABSTRACTOver the course of evolution, enzymes have developed remarkable functional diversity in catalyzing important chemical reactions across various organisms, and understanding how new enzyme functions might have evolved remains an important question in modern enzymology. To systematically annotate functions, based on protein sequences and available biochemical studies, enzymes with similar catalytic mechanisms and/or aspects of catalysis have been clustered together into an enzyme superfamily. Typically, enzymes within a superfamily have similar overall three-dimensional structures, conserved key catalytic residues, but large variations in substrate recognition sites and residues to accommodate the diverse biochemical reactions that are catalyzed within the superfamily. The serine hydrolases are an excellent example of such an enzyme superfamily, that based on known enzymatic activities and protein sequences, is split almost equally into the serine proteases and metabolic serine hydrolases. Within the metabolic serine hydrolases, are two outlying members, ABHD14A and ABHD14B, that have high sequence similarity, but their functions remained cryptic till recently. While ABHD14A still lacks any functional annotation to date, we recently showed that ABHD14B functions as a lysine deacetylase in mammals. Given their high sequence similarity, automated databases wrongly assign ABHD14A and ABHD14B as the same enzyme, and therefore, annotating functions to them in various organisms maybe problematic. In this paper, we present a bioinformatics study coupled to biochemical experiments, that identifies key sequence determinants for both ABHD14A and ABHD14B, and enables better classification for them. Additionally, we map these enzymes on an evolutionary timescale, and provide a resource in studying these interesting enzymes in different organisms.
NetVA: An R Package for Network Vulnerability and Influence Analysis
Authors: Kumar Swapnil , Pauline Grace , Vindal Vaibhav 
Published: July 2023

AbstractIn biological network analysis, identifying key molecules plays a decisive role in the development of potential diagnostic and therapeutic candidates. Among various approaches of network analysis, network vulnerability analysis is quite important, as it assesses significant associations between topological properties and the functional essentiality of a network. Further, some node centralities are also used to screen out key molecules. Among these node centralities, escape velocity centrality (EVC), and its extended version (EVC+) outperform others,viz., Degree, Betweenness, and Clustering coefficient. Keeping this in mind, we aimed to develop a first-of-its-kind R package named NetVA, which analyzes networks to identify key molecular players through network vulnerability and EVC+-based approaches. To demonstrate the application and relevance of our package in network analysis, previously published and publicly available protein-protein interactions (PPIs) data of human breast cancer were analyzed. This resulted in identifying some most important proteins. These included essential proteins, non-essential proteins, hubs, and bottlenecks, which play vital roles in breast cancer development. Thus, the NetVA package, available athttps://github.com/kr-swapnil/NetVAwith a detailed tutorial to download and use, assists in predicting potential candidates for therapeutic and diagnostic purposes by exploring various topological features of a disease-specific PPIs network.
Nanoscale analysis of human G1 and metaphase chromatinin situ
Authors: Chen Jon Ken , Liu Tingsheng , Cai Shujun , Ruan Weimei , Ng Cai Tong , Shi Jian , Surana Uttam , Gan Lu 
Published: July 2023

ABSTRACTThe structure of chromatin at the nucleosome level inside cells is mysterious. Here we presentin situelectron cryotomography analyses of chromatin in both G1 and metaphase RPE-1 cells. G1 nucleosomes are concentrated in globular chromatin domains and metaphase nucleosomes are concentrated in the chromatids. Classification analysis reveals that canonical mononucleosomes, ordered stacked dinucleosomes, and mononucleosomes with a disordered gyre-proximal density are abundant in both cell-cycle states. Class averages that have more than two stacked nucleosomes or that have side-by-side dinucleosomes are not detected, suggesting that groups of more than two nucleosomes are heterogeneous. Large multi-megadalton structures are abundant in G1 nucleoplasm, but not found in G1 chromatin domains and metaphase chromatin. The macromolecular phenotypes studied here represent a starting point for the comparative analysis of compaction in normal and unhealthy human cells, other cell-cycle states, other organisms, andin vitrochromatin assemblies.
Aeroengine gas trajectory prediction using time-series analysis auto regressive integrated moving average
Authors: Mary Victoria Florence M. , Priyadarshini E. 
Published: July 2023

Purpose
This study aims to propose the use of time series autoregressive integrated moving average (ARIMA) models to predict gas path performance in aero engines. The gas path is a critical component of an aero engine and its performance is essential for safe and efficient operation of the engine.

Design/methodology/approach
The study analyzes a data set of gas path performance parameters obtained from a fleet of aero engines. The data is preprocessed and then fitted to ARIMA models to predict the future values of the gas path performance parameters. The performance of the ARIMA models is evaluated using various statistical metrics such as mean absolute error, mean squared error and root mean squared error. The results show that the ARIMA models can accurately predict the gas path performance parameters in aero engines.

Findings
The proposed methodology can be used for real-time monitoring and controlling the gas path performance parameters in aero engines, which can improve the safety and efficiency of the engines. Both the Box-Ljung test and the residual analysis were used to demonstrate that the models for both time series were adequate.

Research limitations/implications
To determine whether or not the two series were stationary, the Augmented Dickey–Fuller unit root test was used in this study. The first-order ARIMA models were selected based on the observed autocorrelation function and partial autocorrelation function.

Originality/value
Further, the authors find that the trend of predicted values and original values are similar and the error between them is small.
Clients as drivers of innovation in the infrastructure sector: implications of hard and soft project management approaches
Authors: Guerrero Jacob , Engström Susanne 
Published: July 2023

Purpose
By adopting the “hard” and “soft” project management (PM) approaches from the PM-literature, this paper aims to problematize the expected role of client organizations in driving innovation in the transport infrastructure sector.

Design/methodology/approach
Addressing a large public client in Sweden, a case study design was initially applied to provide in-depth insights and perspectives of client project managers’ views and experiences of managing projects expected to drive innovation. In this paper, the concepts of “hard” and “soft” are used to discuss empirical findings on challenges associated with adopting a PM-approach for driving innovation in projects. The empirical material consists of interview data, complemented with observations and archival data.

Findings
Findings reveal challenges associated with combining hard and soft approaches, frequently demonstrating difficulties in balancing short-term project expectations with the promotion of innovation. In line with the literature, project managers note that there is a need for soft approaches to promote development and drive innovation. Yet, findings reflect a situation in which operational success criteria predominate, whereas soft approaches are not sufficiently used to create the grounds required for fostering innovation.

Originality/value
Insights are provided into how PM-approaches may impact construction innovation in the infrastructure sector, demonstrating a need for further research on the challenges and implications of applying and combining hard and soft PM-approaches.
Innovation as a firm-level factor of the gender wage gap
Authors: Masso Jaan , Vahter Priit 
Published: July 2023

PurposeThis paper investigates the relationship of both technological (product and process) and non-technological (organizational and marketing) innovation with the gender wage gap at firms.Design/methodology/approachUsing employer–employee level data from Estonia, the authors estimate Mincerian wage equations, in order to show how innovation at the firm level is associated with the gender wage gap. Next, the authors use propensity score matching (PSM) to study the effects of the movement of men and women into innovative firms, how this shapes the gender wage gap at firms.FindingsThe authors find that both technological and non-technological innovation are associated with a larger gender wage gap at firms. The relationship between innovation and the contemporaneous gender wage gap at firms reflects to a significant extent the different selection of men and women with different time-invariant characteristics to innovative firms. Further, the authors find that movement of men and women to work at innovative firms is in longer term associated with larger gains in wages for men. The authors also observe that the relationship of innovation with gender wage gap is stronger in the case of women with children.Originality/valueMuch of the prior analysis focuses on the effects of technological innovation on gender-related labour market outcomes. The authors show here that the relationship of innovation at firms with higher gender wage gap is not only specific to technological innovation, but is more general, and is observed across different types of innovation indicators, including non-technological innovation. This study's results suggest that the effects of innovation on gender wage gap may reflect to an extent the higher demand for flexibility of employees for work purposes at innovative firms, which may increase the gender wage gap, especially between men and women with children.
A new perspective on behavior-based sales control system and salespersons’ job outcomes: an outbound pharmaceutical sales perspective
Authors: Khan Faheem Ahmad , Ahmad Maria , Saeed Tahir 
Published: July 2023

Purpose
This study aims to investigate the direct effect of the behavior-based sales control system on job outcomes: salesperson’s performance and turnover intentions. The current study also intends to integrate these two streams by conceptualizing work engagement as a mediating variable between behavior-based sales control systems and salespersons’ job outcomes in the pharmaceutical sales context.

Design/methodology/approach
Data was collected through multi-stage stratified random sampling from a sample of 619 salespersons working in 20 pharmaceutical firms (multinational and national) through self-administered questionnaires.

Findings
The structural equation model yielded results indicating that the behavior-based sales control system was positively related to salespersons’ work engagement and negatively to turnover intentions while the relationship between the behavior-based sales control system and salespersons’ job outcomes was mediated by work engagement.

Originality/value
Two relatively separate lines of investigation have appeared in academic literature. The first line centered on sales force control systems and salespersons’ related consequences, whereas the second line of investigation emphasizes work engagement and its consequences. Although both lines are important, a diminutive research effort has been made to join these two different lines of investigation in sales management, specifically, in the pharmaceutical context. Focusing on this, the current research explores the role of an unexplored construct of work engagement in a pharmaceutical sales context. Second, it addresses the need to identify additional mediating variables to clarify the inconsistent relationship between sales control systems and job outcomes, such as job performance and turnover intentions.
Dismissing uncertainties about open innovation constraints to organizational agility in emerging markets: is knowledge hiding a perfect storm?
Authors: Urresta-Vargas Daniela , Carvajal-Vargas Valeria , Arias-Pérez José 
Published: July 2023

PurposeAs a key driver of organizational agility, open innovation allows for improving time-to-market and complexity, which are the mechanisms that most significantly lower the risk of knowledge expropriation in emerging markets. For this reason, there is concern about the negative impacts of hiding knowledge in the context of inter-organizational collaborative work. Therefore, the research goal is to analyze the moderating effect of the three types of knowledge hiding (playing dumb, evasive hiding and rationalized hiding) on the relationship between open innovation (both inbound and outbound) and agility.Design/methodology/approachThe research model was tested with survey data from a sample of 248 companies located in an emerging country, mostly from sectors of high turbulence in demand and technology.FindingsNone of the three types of knowledge hiding has a negative effect on the relationship between open innovation and agility. Surprisingly, evasive hiding has a positive and significant effect, specifically on the relationship between inbound open innovation and agility.Originality/valueThe study contributes to the discussion on the contradictory influence of knowledge hiding. Although the presence of knowledge hiding in business relationships with their external partners is undeniable, this research makes clear that, when faced with the particular need to be agile, businesses recognize that the benefits of open innovation in terms of time-to-market improvement and complexity outweigh the protectionism underlying hiding. Moreover, the study results suggest evasive hiding is essential for the inbound process to use time effectively and avoid wasting it in discussions that do not promote agility.
Is there an optimum way for the commercial property market to adjust to the changing circumstances?
Authors: Banytė Jurgita , Mulhearn Christopher 
Published: July 2023

PurposeThis article seeks to offer an answer. It explores the criteria on which commercial property market participants can develop strategies in hugely challenging circumstances. For this purpose, a survey-based approach was developed with work conducted with property-market professional in the United Kingdom (UK), France, Germany and Sweden to produce a criteria-based tool supporting adaption to changing market circumstances.Design/methodology/approachThe data have been analyzed using statistical analysis. The data's statistical analysis included Cronbach's alpha's application to evaluate the respondents' replies' reliability. A entral tendency test was used to identify the means of relevance of the criteria. The Mann–Whitney U test was used to determine potential material differences between the UK and other countries with Bonferroni corrections applied to minimize type-I errors.FindingsThirty characteristics have been identified that impact the dynamics of the commercial property market. Their relevance to the commercial property market was determined using a survey. The literature analysis showed that the researchers paid more attention to quantitative criteria and their comparison. The survey showed that the relevance of criteria to the commercial property market dynamics is unequal. However, the survey results showed that it is most important to pay attention to emotional criteria to adapt to uncertainty changing conditions. The problem of the environment has been on the agenda for the last four decades. Therefore, the fact that the results of the study showed that the environmental criteria are the least significant is unexpected.Research limitations/implicationsThe study involved economically developed countries of Europe. Extending the study's geographical scope would be valuable in revealing whether the same differences exist in other geographical areas (such as Australia or the USA).Practical implicationsThe practical implication of the analysis may be to facilitate the decision-making process of either selecting a country for commercial property investment or selecting the most sensitive and relevant criteria for the decision-making.Originality/valueCriteria for commercial property market performance which promote successful property investment have been developed. Moreover, the criteria affecting the commercial property market have been weighted by their relevance to the market and their sequence of relevance has been established. And finally, the developed criteria have been placed into five groups that could serve as a foundation for a macro-level assessment of commercial property market dynamics.