bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inference of Phylogenetic Networks from Sequence Data using Composite Likelihood
Authors: Kong Sungsik , Swofford David L. , Kubatko Laura S. 
Published: November 2022

AbstractWhile phylogenies have been essential in understanding how species evolve, they do not adequately describe some evolutionary processes. For instance, hybridization, a common phenomenon where interbreeding between two species leads to formation of a new species, must be depicted by a phylogenetic network, a structure that modifies a phylogeny by allowing two branches to merge into one, resulting in reticulation. However, existing methods for estimating networks are computationally expensive as the dataset size and/or topological complexity increase. The lack of methods for scalable inference hampers phylogenetic networks from being widely used in practice, despite accumulating evidence that hybridization occurs frequently in nature. Here, we propose a novel method, PhyNEST (Phylogenetic Network Estimation using SiTe patterns), that estimates phylogenetic networks directly from sequence data. PhyNEST achieves computational efficiency by using composite likelihood as well as accuracy by using the full genomic data to incorporate all sources of variability, rather than first summarizing the data by estimating a set of gene trees, as is required by most of the existing methods. To efficiently search network space, we implement both hill-climbing and simulated annealing algorithms. Simulation studies show that PhyNEST can accurately estimate parameters given the true network topology and that it has comparable accuracy to two popular methods that use composite likelihood and a set of gene trees as input, implemented in SNaQ and PhyloNet. For datasets with a large number of loci, PhyNEST is more efficient than SNaQ and PhyloNet when considering the time required for gene tree estimation. We applied PhyNEST to reconstruct the evolutionary relationships amongHeliconiusbutterflies and Papionini primates, characterized by hybrid speciation and widespread introgression, respectively. PhyNEST is implemented in an open-source Julia package and publicly available athttps://github.com/sungsik-kong/PhyNEST.jl.
H2is a Major Intermediate inDesulfovibrio vulgarisCorrosion of Iron
Authors: Woodard Trevor L. , Ueki Toshiyuki , Lovley Derek R. 
Published: November 2022

AbstractDesulfovibrio vulgarishas been the primary pure culture sulfate reducer for developing microbial corrosion concepts. Multiple mechanisms for how it accepts electrons from Fe0have been proposed. We investigated Fe0oxidation with a mutant ofD. vulgarisin which hydrogenase genes were deleted. The hydrogenase mutant grew as well as the parental strain with lactate as the electron donor, but unlike the parental strain was not able to grow on H2. The parental strain reduced sulfate with Fe0as the sole electron donor, but the hydrogenase mutant did not. H2accumulated over time in Fe0cultures of the hydrogenase mutant and sterile controls, but not in parental strain cultures. Sulfide stimulated H2production in uninoculated controls apparently by both reacting with Fe0to generate H2and facilitating electron transfer from Fe0to H+. Parental strain supernatants did not accelerate H2production from Fe0, ruling out a role for extracellular hydrogenases. Previously proposed electron transfer between Fe0andD. vulgarisvia soluble electron shuttles was not evident. The hydrogenase mutant did not reduce sulfate in the presence of Fe0and either riboflavin or anthraquinone-2,6-disulfonate and these potential electron shuttles did not stimulate parental strain sulfate reduction with Fe0as the electron donor. The results demonstrate thatD. vulgarisprimarily accepts electrons from Fe0via H2as an intermediary electron carrier. These findings clarify the interpretation of previousD. vulgariscorrosion studies and suggest that H2-mediated electron transfer is an important mechanism for iron corrosion under sulfate-reducing conditions.ImportanceMicrobial corrosion of iron in the presence of sulfate-reducing microorganisms is economically significant. There is substantial debate over how microbes accelerate iron corrosion. Tools for genetic manipulation have only been developed for a few Fe(III)-reducing and methanogenic microorganisms known to corrode iron and in each case those microbes were found to accept electrons from Fe0via direct electron transfer. However, iron corrosion is often most intense in the presence of sulfate-reducing microbes. The finding thatDesulfovibrio vulgarisrelies on H2to shuttle electrons between Fe0and cells revives the concept, developed in some of the earliest studies on microbial corrosion, that sulfate reducers consumption of H2is a major microbial corrosion mechanism. The results further emphasize that direct Fe0-to-microbe electron transfer has yet to be rigorously demonstrated in sulfate-reducing microbes.
Parameter optimization of FSW aviation-grade AA8090 using Taguchi grey relational analysis
Authors: Panwar Raghuraj , Chandna Pankaj 
Published: November 2022

PurposeThis paper aims to accomplish friction stir welding (FSW) of Al–Li alloy AA8090 to determine optimal settings of the process parameters for higher tensile strength and higher micro-hardness (MH) to achieve the objective of adequate butt-joint strength.Design/methodology/approachAn empirical relation is implemented to govern the utmost influence parameters, i.e. tool rotation speed (TRS), tool transverse speed (TTS) and dwell time (DT). Taguchi grey relational analysis (GRA) was applied for multi-response optimization of response parameters. The grey relational grades (GRs) have been calculated for both the responses MH and ultimate tensile strength to get optimal parametric settings. The variance test has been performed to check the adequacy of the model.FindingsThe Taguchi L9 orthogonal array design was used in establishing the relation between input parameter and output parameter (tensile and MH). TTS and DT have been predicted to be the two most important parameters that influence the extreme quality features of joints by using friction stir welding. Scanning electron microscopy fractography shows the ductile failure of the welded joints.Originality/valueThe experimental trials provided the followings results, maximum ultimate tensile strength (UTS) of 219 MPa and MH 107.1 HV under 1,400 rpm of TRS, 40 mm/min of TTS and 8 s of DT founded the optimum value through GRA.
Inclusive leadership and workers' safety behaviour during Covid-19 pandemic
Authors: Kusumawardani Kunthi Afrilinda , Arquisola Maria Jacinta , Amin Grace , Restiawati Meta 
Published: November 2022

PurposeCOVID-19 pandemic underlines the need for effective leadership to resolve the crisis. This study aims to examine the impact of inclusive leadership on safety behaviours via the mediating role of the safety climate.Design/methodology/approachThis research studied and compared two of the industries most affected by the pandemic, specifically banking and education. The questionnaire was undertaken among 111 from the education sector and 159 from the banking sector. Structural equation modelling – partial least square (SEM – PLS) was used to analyse the results.FindingsThe study suggested that inclusive behaviour shaped the safety behaviours among employees through the safety climate. However, the influence of inclusive leadership on the safety environment and safety behaviours of education staff in the company was not as powerful as in the banking sector.Practical implicationsThere's a connection between inclusive leadership and worker protection. Besides, inclusive leadership and its effect on safety behaviour are culturally based. High levels of collectivism encourage leaders to care deeply for their employees' well-being, as demonstrated in this study by the promotion of a healthy working atmosphere, especially in times of crisis.Originality/valueThis research potentially adds to the current literature on leadership and safety behaviour and offers valuable management recommendations.
Cycles of labour protests: public and private sector unions' contentious actions
Authors: Jansson Jenny , Uba Katrin 
Published: November 2022

PurposeThis paper aims to examine the cycle of labour protests in Sweden, comparing the contentious actions of trade unions in public and private sectors over 40 years. Prior studies have focused on industrial conflicts or labour protests, but a long-term perspective on the broad protest repertoire across sectors is lacking. The goal is to test the argument of diversification of action repertoire and differences between the public and private sectors.Design/methodology/approachThe authors apply the grievance and political opportunity theories of social movement research for explaining the cycles of labour protests and differences between sectors in Sweden over 40 years (1980–2020). The unique protest event data are combined with the official strike statistics. The research period includes the globalisation of the economy and two economic crises.FindingsAlthough unions in both sectors have decreased protest mobilisation over time, private sector unions have resigned the most, whereas public sector unions continue to mobilise a diverse set of protest actions. Swedish unions have not replaced strikes with other protest repertoires. The open opportunities have allowed them to use various protests as part of “routine” operations.Research limitations/implicationsProtest event data are derived from newspapers, leading to an over-representation of large events in the urban areas. Future studies should combine data from newspapers with data about online protests.Originality/valueBy thoroughly examining all protest events mobilised by all trade unions in different sectors over 40 years (1980–2020), the paper presents a comprehensive analysis of the cycles of labour protest. The findings should interest industrial relations and social movement scholars.
The value proposition of construction apprenticeships in Ireland: a construction management university student perspective
Authors: Ryan Cathal , Faherty Darragh , Spillane John P. , Bradley Jim G. , Issa Mohamed , McMahon Elma 
Published: November 2022

PurposeTo examine the perspective of third-level university students in the context of the value proposition of construction apprenticeships in Ireland.Design/methodology/approachThe research uses a qualitative method, conducting semi-structured interviews with 20 third-level university students enrolled on a Bachelor of Science (Honours) degree program in Construction Management in Ireland.FindingsThe results highlight six themes. These include that society appears to be directly and/or indirectly steering students towards university. This is driven by what appears to be a prevailing stigma in that apprenticeships are not seen as an achievement by society. Also, apprenticeships are seen as a limited career choice, while also being one which appears to repel female entrants.Practical implicationsIf the shortage of new skilled workers entering the construction industry continues, construction organisations will not have the necessary resources to tender for, and subsequently, complete new work.Social implicationsThe perception of what could have been seen as potential new apprenticeship entrants, but ultimately chose university, is worth examining further with a view to industry addressing the shortcomings identified. This therefore can provide an opportunity to stem the tide of reducing apprenticeship numbers, while also providing a viable alternative to university for those who wish to pursue alternative routes of entering the sector.Originality/valueThe paper uniquely focuses on the third-level university student's perspectives and what influenced their decision to pursue third-level university education over that of an apprenticeship within the built environment; an area which has yet to be investigated.
Exploring the development of change agents for sustainability: outcomes of the Listen, Live and Learn initiative at Stellenbosch University
Authors: Langa Zamokuhle Vanessa , Kushitor Sandra Boatemaa , Koen Nelene , Harper Julia 
Published: November 2022

Purpose
Among the various pro-sustainability strategies that universities adopt, Stellenbosch University’s 2030 Agenda further challenges universities to provide sustainability education that enables students to become change agents for sustainability. The Listen, Live and Learn (LLL) initiative is a co-curricular programme developed at Stellenbosch University, South Africa, that seeks to foster social cohesion and develop change agency among students. This study aims to understand how LLL students had developed agency for change through their experiential learning in the programme.

Design/methodology/approach
Using a transformative sustainability learning approach, this study examined secondary data containing qualitative and quantitative data from the 2018 LLL end-of-year survey. The qualitative data was analysed thematically, and the quantitative data was analysed using counts and frequencies.

Findings
Through their participation in the programme, the students learned about their character and opened up to engage with the ‘others’ whom they lived with in the same residence. They also reported becoming more open-minded, intentional, reflective and confident. Another personal change reported by the students was their ability to collaborate with their housemates. The learners recommended that the programme could be improved by providing resources for house projects, guidance with inviting house theme experts and help with conflict resolution.

Originality/value
Through this research, the authors have demonstrated the ability of a transformative sustainability learning programme to effect a change in the attitudes, norms and behaviours of students at a higher educational institution towards a sustainable and just society.
Harmony in intelligent hybrid teams: the influence of the intellectual ability of artificial intelligence on human members’ reactions
Authors: Chen Aihui , Xiang Mengqi , Wang Mingyu , Lu Yaobin 
Published: November 2022

PurposeThe purpose of this paper was to investigate the relationships among the intellectual ability of artificial intelligence (AI), cognitive emotional processes and the positive and negative reactions of human members. The authors also examined the moderating role of AI status in teams.Design/methodology/approachThe authors designed an experiment and recruited 120 subjects who were randomly distributed into one of three groups classified by the upper, middle and lower organization levels of AI in the team. The findings in this study were derived from subjects’ self-reports and their performance in the experiment.FindingsRegardless of the position held by AI, human members believed that its intelligence level is positively correlated with dependence behavior. However, when the AI and human members are at the same level, the higher the intelligence of AI, the more likely it is that its direct interaction with team members will lead to conflicts.Research limitations/implicationsThis paper only focuses on human–AI harmony in transactional work in hybrid teams in enterprises. As AI applications permeate, it should be considered whether the findings can be extended to a broader range of AI usage scenarios.Practical implicationsThese results are helpful for understanding how to improve team performance in light of the fact that team members have introduced AI into their enterprises in large quantities.Originality/valueThis study contributes to the literature on how the intelligence level of AI affects the positive and negative behaviors of human members in hybrid teams. The study also innovatively introduces “status” into hybrid organizations.
Museums and communicating climate change-related issues on Facebook platforms
Authors: Bikovska Dragana , Liew Chern Li 
Published: November 2022

PurposeThis research examines the ways in which museums have utilised their Facebook platforms to communicate about climate and environmental-related challenges. The aim is to offer a snapshot of the phenomenon of museums as contributors to communicating climate-related topics and climate change education.Design/methodology/approachA content analysis of a purposeful sample of 10 museums’ Facebook postings was conducted. The study examines the themes and topics concerning climate issues that museums have posted and communicated about, the nature of the communication and an examination of responses from the audience.FindingsThis research reveals that not all museums in the study sample have communicated the different research-informed causes or contributors to climate challenges confronting societies today. There is also very little evidence of dialogic engagement with audience and the public-at-large. Most communication is still one-way focussing on the relaying of information.Originality/valueThis research highlights the roles of cultural heritage institutions such as museums in communicating climate change-related topics and the need to move towards a more dialogic mode of engagement with their audience. Museums have a role in serving as a trusted and inspirational space for public debates and community empowerment for dealing with climate challenges.
Dental hygiene students' matching accuracy when comparing antemortem dental radiographs and oral photographs to simulated postmortem WinID3® odontograms
Authors: Bradshaw Brenda T. , Hunt Amber W. , Ludwig Emily , Newcomb Tara L. 
Published: November 2022

AbstractMatching dental antemortem (AM) and postmortem (PM) data for human identification is especially challenging when the workforce is limited. Dental hygienists have served mass fatality incidents (MFIs) due to dental‐related expertise. However, forensics within dental hygiene education and research on transferable skills is limited. This qualitative balance design study assessed senior dental hygiene students' match accuracy of simulated cases varying in dental identifiers based on AM full mouth series (FMS) radiographs and oral photographs to PM WinID3® odontograms to demonstrate possible disaster victim identification (DVI) transferable skills gained during formal education. A convenience sample of senior dental hygiene students (n = 31) was presented information on WinID3® interpretation, then presented with 5 mismatched cases and asked to visually interpret each to make 10 total matches; five based on AM FMS with simulated PM WinID3® odontograms and five based on AM photographs with PM WinID3® odontograms. Match accuracy scores ranged from 41.9% to 58.1% for cases with 1–10 identifiers, and 77.4% to 93.5% for cases with 11–40 identifiers. Accuracy when matching AM radiographs to PM odontograms versus AM photographs to PM odontograms was compared and revealed no statistical differences in match accuracy depending on image type (p = 0.388 to 1.000). Results of this pilot study suggests transferable match accuracy skills resulted from the participants' dental hygiene formal education. These baseline skills with additional specialized training support the rationale for dental hygienists serving on DVI teams. More research is needed in education and practice when preparing dental hygienists for forensic‐based service.
The dynamic changes of genes revealed that persistently overexpressed genes drive the evolution of cyflumetofen resistance in Tetranychus cinnabarinus
Authors: Feng Kaiyang , Liu Jialu , Zhao Mingyu , Jiang Zhixin , Liu Peilin , Wei Peng , Dou Wei , He Lin 
Published: November 2022

AbstractChanges in gene expression are associated with the evolution of pesticide resistance in arthropods. In this study, transcriptome sequencing was performed in 3 different resistance levels (low, L; medium, M; and high, H) of cyflumetofen‐resistant strain (YN‐CyR). A total of 1 685 genes, including 97 detoxification enzyme genes, were upregulated in all 3 stages, of which 192 genes, including 11 detoxification enzyme genes, showed a continuous increase in expression level with resistance development (L to H). RNA interference experiments showed that overexpression of 7 genes (CYP392A1, TcGSTd05, CCE06, CYP389A1, TcGSTz01, CCE59, and CYP389C2) is involved in the development of cyflumetofen resistance in Tetranychus cinnabarinus. The recombinant CYP392A1 can effectively metabolize cyflumetofen, while CCE06 can bind and sequester cyflumetofen in vitro. We compared 2 methods for rapid screening of resistance molecular markers, including short‐term induction and 1‐time high‐dose selection. Two detoxification enzyme genes were upregulated in the field susceptible strain (YN‐S) by induction with 20% lethal concentration (LC20) of cyflumetofen. However, 16 detoxification enzyme genes were upregulated by 1‐time selection with LC80 of cyflumetofen. Interestingly, the 16 genes were overexpressed in all 3 resistance stages. These results indicated that 1 685 genes that were upregulated at the L stage constituted the basis of cyflumetofen resistance, of which 192 genes in which upregulation continued to increase were the main driving force for the development of resistance. Moreover, the 1‐time high‐dose selection is an efficient way to rapidly obtain the resistance‐related genes that can aid in the development of resistance markers and resistance management in mites.
Native forest regeneration and eucalyptus plantations in the Malagasy Highland
Authors: Randriamalala Josoa R. , Rabeniala Radobarimanjaka , Randriambanona Herizo 
Published: November 2022

AbstractEucalyptus plantations (EP) offer a number of goods and services that can reduce pressure on native forests. Eucalyptus trees can also be invasive and have a negative impact on native species diversity and regeneration. This article deals with the complex interaction between EP and native forests by studying the case of the humid forests of Malagasy Central High Land that are surrounded by EP. Floristic inventories were carried out on 400 m2 plots in adjacent secondary forests (n = 5) and EP (n = 6). Eucalyptus has not spread to secondary forests understory. Native species from secondary forests have colonised EP understory.
Congenital mesoblastic nephroma: review of current management and outcomes in a single centre
Authors: Rayner Jessica , Vinycomb Toby , Wanaguru Dylan , Jiwane Ashish 
Published: November 2022

AbstractBackgroundCongenital mesoblastic nephroma (CMN) is a rare tumour of the kidney with an overall excellent prognosis. Once considered a benign tumour, it is now recognized to carry a risk of recurrence and metastases with subsequent poor outcomes. The potential for genetic aberrations such as ETV6‐NTRK3 fusion raises the potential for targeted treatments in certain patients. The optimum mode and frequency of surveillance is unclear. This study aims to assess this institution's experience with CMN and long‐term outcomes.MethodsA single centre retrospective review was performed of all confirmed cases of CMN between October 2001 and January 2021.ResultsNine cases of CMN in patients under 12 months of age were identified. The histopathology, management and outcomes of these patients are discussed.ConclusionCMN overall has a very good prognosis, but a subgroup does exist that will have poor outcomes. It is difficult to accurately identify this group to target adjuvant therapy.