bluuebunny/crossref_metadata_2025_split huggingface dataset:
The evolution of a counter-defense mechanism in a virus constrains its host range
Authors: Srikant Sriram , Guegler Chantal K. , Laub Michael T. 
Published: April 2022

SummaryBacteria use diverse immunity mechanisms to defend themselves against their viral predators, bacteriophages. In turn, phages can acquire counter-defense systems, but it remains unclear how such mechanisms arise and what factors constrain viral evolution. Here, we experimentally evolved T4 phage to overcome a phage-defensive toxin-antitoxin system, toxIN, in E. coli. Through recombination, T4 rapidly acquires segmental amplifications of a previously uncharacterized gene, now named tifA, encoding an inhibitor of the toxin, ToxN. These amplifications subsequently drive large deletions elsewhere in T4’s genome to maintain a genome size compatible with capsid packaging. The deleted regions include accessory genes that help T4 overcome defense systems in alternative hosts. Thus, our results reveal a trade-off in viral evolution; the emergence of one counter-defense mechanism can lead to loss of other such mechanisms, thereby constraining host range. We propose that the accessory genomes of viruses reflect the integrated evolutionary history of the hosts they infected.HighlightsExperimentally evolved T4 to overcome E. coli toxIN, a phage-defensive TA systemDiscovered TifA, a phage-encoded protein inhibitor of ToxNAmplification of the tifA locus drives large deletions elsewhere in the T4 genomeDeleted genes in evolved T4 clones include those necessary to infect alternative hosts
IL-33 priming and antigenic stimulation synergistically promote the transcription of proinflammatory cytokine and chemokine genes in human skin mast cells
Authors: Gao Junfeng , Li Yapeng , Guan Xiaoyu , Mohammed Zahraa , Gomez Gregorio , Hui Yvonne , Zhao Dianzheng , Oskeritzian Carole A. , Huang Hua 
Published: April 2022

AbstractBackgroundAntigenic stimulation through cross-linking the IgE receptor and epithelial cell-derived cytokine IL-33 are potent stimuli of mast cell (MC) activation. Moreover, IL-33 primes a variety of cell types, including MCs to respond more vigorously to external stimuli. However, target genes induced by the combined IL-33 priming and antigenic stimulation have not been investigated in human skin mast cells (HSMCs) in a genome-wide manner. Furthermore, epigenetic changes induced by the combined IL-33 priming and antigenic stimulation have not been evaluated.ResultsWe found that IL-33 priming of HSMCs enhanced their capacity to promote transcriptional synergy of theIL1BandCXCL8genes by 16- and 3-fold, respectively, in response to combined IL-33 and antigen stimulation compared to without IL-33 priming. We identified the target genes in IL-33-primed HSMCs in response to the combined IL-33 and antigenic stimulation using RNA sequencing (RNA-seq). We found that the majority of genes synergistically upregulated in the IL-33-primed HSMCs in response to the combined IL-33 and antigenic stimulation were predominantly proinflammatory cytokine and chemokine genes. Moreover, the combined IL-33 priming and antigenic stimulation increase chromatin accessibility in the synergy target genes but not synergistically. Transcription factor binding motif analysis revealed more binding sites for NF-κB, AP-1, GABPA, and RAP1 in the induced or increased chromatin accessible regions of the synergy target genes.ConclusionsOur study demonstrates that IL-33 priming greatly potentiates MCs’ ability to transcribe proinflammatory cytokine and chemokine genes in response to antigenic stimulation, shining light on how epithelial cell-derived cytokine IL-33 can cause exacerbation of skin MC-mediated allergic inflammation.
Infection with Listeria monocytogenes alters the placental transcriptome and eicosanome
Authors: Conner Kayla N. , Holman Derek , Lydic Todd , Hardy Jonathan W. 
Published: April 2022

AbstractIntroductionPlacental infection and inflammation are risk factors for adverse pregnancy outcomes, including preterm labor. However, the mechanisms underlying these outcomes are poorly understood.MethodsTo study this response, we have employed a pregnant mouse model of placental infection caused by the bacterial pathogen Listeria monocyogenes, which infects the human placenta. Through in vivo bioluminescence imaging, we confirm the presence of placental infection and quantify relative infection levels. Infected and control placentas were collected on embryonic day 18 for RNA sequencing to evaluate gene expression signatures associated with infection by Listeria.ResultsWe identified an enrichment of genes associated with eicosanoid biosynthesis, suggesting an increase in eicosanoid production in infected tissues. Because of the known importance of eicosanoids in inflammation and timing of labor, we quantified eicosanoid levels in infected and uninfected placentas using semi-targeted mass spectrometry. We found a significant increase in the concentrations of several key eicosanoids: leukotriene B4, lipoxin A4, prostaglandin A2, prostaglandin D2, and eicosatrienoic acid.DiscussionOur study provides a likely explanation for dysregulation of the timing of labor following placental infection. Further, our results suggest potential biomarkers of placental pathology and targets for clinical intervention.
Vaeda computationally annotates doublets in single-cell RNA sequencing data
Authors: Schriever Hannah , Kostka Dennis 
Published: April 2022

AbstractMotivationSingle-cell RNA sequencing (scRNA-seq) continues to expand our knowledge by facilitating the study of transcriptional heterogeneity at the level of single cells. Despite this technology’s utility and success in biomedical research, technical artifacts are present in scRNA-seq data. Doublets/multiplets are a type of artifact that occurs when two or more cells are tagged by the same barcode, and therefore they appear as a single cell. Because this introduces non-existent transcriptional profiles, doublets can bias and mislead downstream analysis. To address this limitation computational methods to annotate and remove doublets form scRNA-seq datasets are needed.ResultsWe introduce vaeda, a new approach for computational annotation of doublets in scRNA-seq data. Vaeda integrates a variational auto-encoder and Positive-Unlabeled learning to produce doublet scores and binary doublet calls. We apply vaeda, along with seven existing doublet annotation methods, to sixteen benchmark datasets and find that vaeda performs competitively in terms of doublet scores and doublet calls. Notably, vaeda outperforms other python-based methods for doublet annotation. All together, vaeda is a robust and competitive method for scRNA-seq doublet annotation and may be of particular interest in the context of python-based workflows.AvailabilityVaeda is available at https://github.com/kostkalab/vaedaContactkostka@pitt.edukostka@pitt.edu
The one-step preparation and corrosion resistance of a Ca–Mn–Zn ternary phosphate conversion coating on magnesium alloy AZ91D
Authors: Yang Jun , Zhang Pei , Su Lihuizi , Yan Fuan , Yong Zhou 
Published: April 2022

PurposeThe aim of this work was to propose a method to prepare composite phosphate conversion coating (CPCC), including ternary phosphate conversion coating (TPCC) and binary phosphate conversion coatings (BPCC), with one-step chemical conversion and to reveal and compare the corrosion resistance between TPCC and BPCC.Design/methodology/approachIn this work, a calcium–manganese–zinc (Ca–Mn–Zn) TPCC was prepared on the surface of magnesium alloy (MA) AZ91D with one-step chemical conversion method; for Ca-Mn-Zn@TPCC, its microstructure was characterized with scanning electron microscope observation and scanning tunneling microscope detection, and its composition was characterized with energy dispersion spectroscopy and X-ray photoelectron spectroscopy analyses. Particularly, the corrosion resistance of Ca-Mn-Zn@TPCC and its comparison with Ca–Mn, Ca–Zn and Mn–Zn BPCCs were clarified with electrochemical and immersion measurements.FindingsCa-Mn-Zn@TPCC, which was composed of Ca, Mn, Zn, P and O, exhibited a mud-shaped with cracks microstructure, and the average crack width, terrain fluctuation and coating thickness were 0.61 µm, 23.78 nm and 2.47 µm, respectively. Ca-Mn-Zn@TPCC provided good corrosion resistance to MA AZ91D; in NaCl solution, the total degradation of Ca-Mn-Zn@TPCC consumed eight days; corrosion products with poor adhesion peeled out from Ca-Mn-Zn@TPCC-coated MA AZ91D spontaneously. Besides, the corrosion resistance of Ca-Mn-Zn@TPCC was better than that of Ca-Mn@BPCC, Ca-Zn@BPCC or Mn-Zn@BPCC.Originality/valueThe successful preparation of Ca-Mn-Zn@TPCC on MA AZ91D surface confirmed the proposed method to prepare CPCC with one-step chemical conversion was feasible; at the same time, it was further confirmed that for phosphate conversion coating, ternary coating had better corrosion resistance than binary coating did.
A comprehensive performance optimization method for the honeycomb buffer of a legged-type lander
Authors: Wang Hui , He Tianyu , Wang Chunjie 
Published: April 2022

Purpose
In the field of planetary exploration, the legged-type lander is a common landing buffer device. There are two important performance metrics for legged-type landers: the energy absorption capacity and landing stability. In this paper, a novel method is proposed to optimize the honeycomb buffer of a legged-type lander. Optimization design variables are the dimension parameters of honeycomb and the objective functions are the evaluation parameters of the above two performance metrics.

Design/methodology/approach
A multi-body dynamic model of a lander and a finite-element model of the metal honeycomb are established. Based on the simulation results of the finite-element model and the quartic polynomial, the surrogate models are established to evaluate the energy absorption capacity of honeycomb. Considering both the multi-body dynamic model and the surrogate models, the study designed the optimization flow of dimension parameters of honeycomb. Besides, the non-dominated sorting genetic algorithm II is used for iterative calculation.

Findings
Images of surrogate models show the monotonous functional relationship between the honeycomb’s energy absorption characteristics and its dimension parameters. Optimization results show an apparent contradiction among the objective functions. Besides, according to the simulation results, this method can significantly improve the comprehensive performance of the lander.

Originality/value
The novel method can effectively reduce the cost of honeycomb compression tests and improve the lander’s design. Therefore, it can be used for optimizing buffers of other types of legged-type landers.
Explaining the alienation of megaproject environmental responsibility behavior: a fuzzy set qualitative comparative analysis study in China
Authors: Xie Linlin , Xu Ting , Ju Tianhao , Xia Bo 
Published: April 2022

PurposeThe alienation of megaproject environmental responsibility (MER) behavior is destructive, but its mechanism has not been clearly depicted. Based on fraud triangle theory and the fuzzy set qualitative comparative analysis (fsQCA) method, this study explored the combined effect of antecedent factors on alienation of MER behavior.Design/methodology/approachBased on the fraud triangle theory and literature review, eight influencing factors associated with the alienation of MER behavior were first identified. Subsequently, the fuzzy-set qualitative comparative analysis was used in this study to reveal configurations influencing alienation of MER behavior.FindingsThe study found nine configurations of MER behavioral alienation antecedent factors, integrated into three types of driving modes, i.e. “economic pressure + learning effect,” “institutional defect + moral rejection,” and “information asymmetry + economic pressure + expectation pressure.”Originality/valueBy analyzing the configuration effects of various induced conditions, this study puts forward a comprehensive analysis framework to solve the alienation of MER behavior in the megaprojects and a practical strategy to control alienation of MER behavior.
Coping strategies and social support are associated with post-traumatic stress disorder symptoms in Saudi paramedics
Authors: Alshahrani Khalid , Johnson Judith , O’Connor Daryl B. 
Published: April 2022

PurposeThree main objectives of this study were as follows: (1) To estimate the prevalence rate of post-traumatic stress disordered (PTSD) symptoms among Saudi paramedics, (2) To investigate which types of coping strategies were associated with PTSD symptoms among Saudi paramedics, (3) To explore which sources of social support were associated with PTSD symptoms among Saudi paramedics.Design/methodology/approachData were collected from 217 paramedics working in the Saudi Red Crescent Authority from September to December 2019. Participants completed questionnaires measuring PTSD symptoms (the Screen of Post-Traumatic Stress Disorders; SPTSD), passive and active coping strategies (Brief COPE Scale; BC), and three forms of social support: support from friends, family and organizational support. Associations between coping strategies, social support and PTSD symptoms were investigated using correlational analyses, hierarchical linear regression and binary logistic regression.Findings46% of participants experienced one or more PTSD symptom, 28.6% scored above the cut-off for partial PTSD and 17.5% scored above the cut-off for full PTSD. PTSD symptoms were significantly positively correlated with passive coping and negatively associated with both family and friends support. Passive coping was positively associated with a greater risk of meeting criteria for PTSD.Originality/valueThe current findings suggest that interventions to help reduce PTSD in Saudi paramedics should include strategies to reduce passive coping. Future research is urgently required to help understand the psychological, social and work-related factors that contribute to these high levels of PTSD.
Historic public paths in rural areas: engine of development and origin of new conflicts
Authors: Moscoso-Sánchez David , Nasarre-Sarmiento José María , Trujillo-Carmona Manuel , González-Fernández Manuel T. , Luque-Gil Ana , Sánchez-Sanz Víctor , Vidal-González Pablo 
Published: April 2022

PurposeIn this article, the authors analyse a complex social process affecting historic public paths in rural areas in southern Spain. Despite the fact that urban populations are demanding the enhancement of this type of natural heritage for tourism, sports and recreational use, some parts of the network have been abandoned or usurped.Design/methodology/approachThe study is multidisciplinary, comprising three interlinked studies. The cartographic study comprises an inventory of public paths in rural areas based on administrative sources. The legal study analyses local, regional and national regulations governing agricultural, environmental, heritage, sports and tourism uses of the infrastructure. The sociological study analyses social discourses on the uses of public paths, and identifies conflicts between farmers, landowners, environmentalists, sportspeople and tourists.FindingsThe preliminary results identified an important public paths network in Andalusia, approximately 160,000 km. The legal study found that there are laws regulating use, although local authorities do not monitor compliance or provide solutions to enhance management. The sociological study determined the attribution of environmental, cultural and economic value to public paths, but also the existence of conflicts between rural and urban populations.Research limitations/implicationsGiven that this is ongoing research, only state of the art and some preliminary albeit sufficiently consistent results are presented.Practical implicationsThe results could help to guide public policy and governance of public paths.Social implicationsPublic paths promote rural development and a green/sustainable economy.Originality/valueThe research results and conclusions are original.
A bibliometric and visual analysis of hospitality and tourism marketing research from 2000–2020
Authors: Liu Juan , Wei Wei , Zhong Meiying , Cui Yaqi , Yang Shuang , Li Haiyan 
Published: April 2022

PurposeThis study aimed to bibliometrically and visually analyze and review hospitality and tourism marketing studies published from 2000–2020.Design/methodology/approachA total of 3,942 articles collected from the databases of Social Science Citation Index (SSCI) and Science Citation Index Expanded (SCI-E) in the Web of Science (WoS) along with their references were used for analyses. The bibliometric software HistCiteTM and literature measurement visualization tools, VOSviewer and CiteSpace, were employed to analyze the selected articles.FindingsThe results of the study demonstrated top influential scholars and institutions, intellectual structure and emerging trends of the study topics, and future research opportunities in the field of hospitality and tourism marketing.Research limitations/implicationsFirst, academic influence of a scholar was evaluated by citations of his/her publications, which did not take the order of authorship into consideration. Second, this study was restricted to the English language journals. Third, other types of published documents related to the studied field such as review papers were not considered by this research.Originality/valueIn comparison to traditional qualitative analysis such as content analysis, bibliometric analysis is a more objective approach to vividly demonstrate trends and performance of a research field, offers unique insights for its advancement with wider inclusiveness of a larger amount of data.
Peer workers disseminating lived experience research: a perfect match?
Authors: Honey Anne , Boydell Katherine , Clissold Nathan , Coniglio Francesca , Do Trang Thuy , Dunn Leonie , Fuller Candice Jade , Gill Katherine , Glover Helen , Hines Monique , Scanlan Justin Newton , Tooth Barbara , Wagner Darren 
Published: April 2022

Purpose
This paper aims to explore the use of lived experience research in peer work.

Design/methodology/approach
A suite of user-friendly and engaging lived experience research resources was introduced to consumers by peer workers. In-depth interviews were conducted with 33 consumer participants and five peer workers about their experiences. The data were analysed using qualitative content analysis.

Findings
The role of the peer workers appeared critical in ensuring that participants, despite their varied needs, preferences and backgrounds, derived optimum benefit from each resource. Features in resource delivery that promoted a positive experience included presenting the resources in the context of an existing relationship, providing clear explanations, going through resources together, encouraging reflection, taking enough time; and flexible delivery. Peer workers viewed the resources as potentially useful in their everyday peer work and as a valuable addition to their peer work toolkit.

Practical implications
The benefit of lived experience research to consumers is likely to be optimised by supportive and thoughtful delivery of the resources. Peer workers have the skills and are in an ideal position to do this. Bringing lived experience research to consumers provides peer workers with a potentially unique and helpful approach for supporting and promoting recovery and is congruent with their overall practice.

Originality/value
Lived experience research has the potential to benefit consumers directly but is rarely brought to their attention. This paper is the first to examine the potential role of peer workers in introducing learnings from lived experience research to consumers.
System-based barriers for seaports in contributing to Sustainable Development Goals
Authors: Katuwawala Hansini Charupraba , Bandara Yapa Mahinda 
Published: April 2022

PurposeThe main purpose of this paper is to identify the reasons for the stagnant behaviour of seaports contributing towards Sustainable Development Goals (SDGs).Design/methodology/approachGlobal seaport sustainability practices that correspond with SDGs were identified through an extensive literature review. In total, five focus interviews were carried out with port managers in Sri Lanka to identify the existing knowledge about seaport sustainability, and the reasons for disparities between the global standards and country-level port sustainability practices. Data collected from a questionnaire survey of 55 seaport terminal managers in Sri Lanka were analysed using exploratory factor analysis (EFA) and thematic analysis.FindingsDeficient collaborative policies, structural and managerial constraints, market constraints and the absence of a well-established SDG-driven global port framework were identified as significant barriers for seaports to contribute towards SDGs.Social implicationsIdentifying barriers in implementing sustainable practices in ports help the responsible authorities tackle them. Hence, seaports in return and the wider society benefit from the spillover effects of port operations aligning to SDGs.Originality/valueThis paper provides port organizations insights on the barriers needing to be addressed in their operational and management systems to best incorporate practices aligning to SDGs in seaports.
Working with the chaos in an adult inpatient mental health setting: the role of an integrated therapies team
Authors: Cotter Pádraig , Papasileka Eirini , Eugster Mario , Chauhan Varsha , Garcha Eshia , Kunkler Marie , Brooks Michelle , Otvos Iulia , Srithar Abberaame , Pujol Irene , Sarafi Christina , Hughes Tom 
Published: April 2022

Purpose
The purpose of this study is to outline a process-oriented psychology informed view of the impact of ever-increasing acuity within an adult inpatient system and conceptualise how an integrated therapies team (ITT) can work with the chaos that this brings.

Design/methodology/approach
A reflective scientist-practitioner based approach was used over a two-year period.

Findings
Several factors lead to “chaos” in an inpatient unit, including societal inequality, the trauma and adversity it creates and the impact of this at a systemic, interpersonal and intrapersonal level. Chaos is one means of coping and can dominate inpatient working, whereas understanding the underlying distress is often marginalised. Developing an ITT can support working with chaos. The ITT holds the therapeutic perspective for the wider multi-disciplinary team (MDT) and therapeutic and facilitation skills are central to how it operates. Processing the chaos and working with the underlying distress is its overarching function.

Practical implications
Developing an ITT offers a robust structure for evolving inpatient MDT working to cope with increasing acuity in a psychologically informed way.

Social implications
The chaos in question is often viewed as patients’ issue but from a collectivist perspective it is something that all members of society are responsible for.

Originality/value
To the best of the authors’ knowledge, this is the first paper to conceptualise the chaos on an inpatient ward as a process needed by the system as a way of coping and propose the addition of an ITT to inpatient working.