bluuebunny/crossref_metadata_2025_split huggingface dataset:
Changes in global repression underlie the evolution of Drosophila abdominal pigmentation
Authors: Méndez-González Iván D. , Williams Thomas M. , Rebeiz Mark 
Published: September 2022

AbstractChanges in gene regulation represent an important path to generate developmental differences affecting anatomical traits. Interspecific divergence in gene expression often results from changes in transcription-stimulating enhancer elements. While gene repression is crucial for precise spatiotemporal expression patterns, the relative contribution of repressive transcriptional silencer to regulatory evolution remains to be addressed. Here, we show that the Drosophila pigmentation gene ebony has mainly evolved through changes in the spatial domains of silencers patterning its abdominal expression. By precisely editing the endogenous ebony locus of D. melanogaster, we demonstrate the requirement of two redundant abdominal enhancers and three silencers that repress the redundant enhancers in a patterned manner. We observe a role for changes in these silencers in every case of ebony evolution observed to date. Our findings suggest that negative regulation by silencers likely has an under-appreciated role in gene regulatory evolution.
CP204L Is a Multifunctional Protein of African Swine Fever Virus That Interacts with The VPS39 Subunit of HOPS Complex and Promotes Lysosome Clustering
Authors: Dolata Katarzyna Magdalena , Fuchs Walter , Caignard Grégory , Dupré Juliette , Pannhorst Katrin , Blome Sandra , Mettenleiter Thomas C. , Karger Axel 
Published: September 2022

AbstractVirus replication depends on a complex interplay between viral and host proteins. In the case of African swine fever virus (ASFV), a large DNA virus, only few virus-host protein-protein interactions have been identified to date. In this study, we demonstrate that the ASFV protein CP204L directly interacts with the cellular homotypic fusion and protein sorting (HOPS) protein VPS39, blocking its association with the lysosomal HOPS complex, that modulates endolysosomal trafficking and promotes lysosome clustering. Instead, VPS39 is targeted to the sites of virus replication termed virus factories. Furthermore, we show that loss of VPS39 reduces the levels of virus proteins synthesized in the early phase of infection and delays ASFV replication but does not completely inhibit it. Collectively, these results identify a novel virus-host protein interaction that modulates host membrane rearrangement during infection and provide evidence that CP204L is a multifunctional protein engaged in distinct steps of the ASFV life cycle.ImportanceAfrican swine fever virus (ASFV) was first identified over a hundred years ago. Since then, much effort has been made to understand the pathogenesis of ASFV. Yet, the specific roles of many individual ASFV proteins during the infection remain enigmatic. This study provides evidence that CP204L, one of the most abundant ASFV proteins, modulates endosomal trafficking during virus infection. Through direct protein-protein interaction, CP204L prevents the recruitment of VPS39 to the endosomal and lysosomal membranes, resulting in their accumulation. Consequently, CP204L and VPS39 become sequestered to the ASFV replication site. These results uncover a novel function of viral protein CP204L and extend our understanding of complex interaction between virus and host.
Gibson Assembly-based direct cloning of plasmid DNA in Lactiplantibacillus plantarum WCSF1
Authors: Blanch Asensio Marc , Dey Sourik , Sankaran Shrikrishnan 
Published: September 2022

ABSTRACTLactobacilli are gram-positive bacteria that are growing in importance for the healthcare industry and genetically engineering them as living therapeutics is highly sought after. However, progress in this field is hindered since most strains are difficult to genetically manipulate, partly due since their complex and thick cell walls limit our capability to transform them with exogenous DNA. To overcome this, large amounts of DNA (>1 μg) are normally required to successfully transform these bacteria. An intermediate host, like E. coli, is often used to amplify recombinant DNA to such amounts although this approach poses unwanted drawbacks such as increase in plasmid size, different methylation patterns and limitation of introducing only genes compatible with the intermediate host. In this work, we have developed a direct cloning method based on Gibson assembly and PCR to amplify the DNA to sufficient quantities for successful transformation in L. plantarum WCFS1. This advantage of this method is demonstrated in terms of shorter experimental duration and the possibility to introduce a gene incompatible with E. coli into L. plantarum WCFS1.
Comparative analysis of CRISPR off-target activity discovery tools followingex vivoediting of CD34+hematopoietic stem and progenitor cells
Authors: Cromer M. Kyle , Majeti Kiran R. , Rettig Garrett R. , Murugan Karthik , Kurgan Gavin L. , Hampton Jessica P. , Vakulskas Christopher A. , Behlke Mark A. , Porteus Matthew H. 
Published: September 2022

AbstractWhile CRISPR-based editing most often occurs at DNA sequences with perfect homology to the guide RNA (gRNA), unintended editing can occur at highly homologous regions (i.e., off-target (OT) sites). Due to the pace at which genome editing therapies are approaching clinical applications, there is an emerging need to define effective workflows for investigating OT editing effects. A number of homology-dependent,in silico-basedprediction methods and wet lab-based empirical methods exist to investigate OT editing, but few have been subjected to analytical assessment or head-to-head comparison in human primary cells using anex vivoediting process optimized for high-fidelity gene editing. Therefore, we sought to compare publicly availablein silicotools (COSMID, CCTop, and Cas-OFFinder) as well as empirical methods (CHANGE-Seq, CIRCLE-Seq, DISCOVER-Seq, GUIDE-Seq, and SITE-Seq) in the context ofex vivohematopoietic stem and progenitor cell (HSPC) editing. To do so, we edited CD34+HSPCs using 11 different guide RNAs (gRNAs) complexed with HiFi Cas9, then performed targeted next-generation sequencing of ~200-site panels containing a range of nominated OT sites identified byin silicoand empirical methods. We identified an average of 0.45 OT sites per gRNA at an indel detection limit of 0.5%. This study confirmed the marked improvement in specificity with HiFi Cas9 compared to wild-type Cas9 without compromising on-target activity when delivered as an RNP. Additionally, all HiFi Cas9 OT sites using a standard 20nt gRNA were identified by all OT detection methods with one exception (SITE-seq did not identify an OT generated by an AAVS1 gRNA). This resulted in high sensitivity for the majority of OT nomination tools, however due to the large number of false positives called by most methods,in silico-based COSMID and empirical methods DISCOVER-Seq and GUIDE-Seq attained the highest positive predictive value. We did not find the empirical methods identified off-target sites that were not also identified by bioinformatic methods when delivered as an RNP complex. Finally, this study supports that refined bioinformatic algorithms could be developed that maintain both high sensitivity as well as positive predictive value which would enable more efficient identification of potential off-target sites without compromising a thorough examination for any given gRNA.
Fitness of a clonal population can be inferred from lineage trees without knowledge of the biological details
Authors: Escabi Javier , Hormoz Sahand 
Published: September 2022

AbstractInferring the rate at which a clonal population grows, or its fitness, is important for many biomedical applications. For example, measuring the fitness of mutated cells in a patient with cancer may provide important information about prognosis and treatment. Similarly, measuring the fitness of new viral strains that emerge during a pandemic can inform how to plan an effective response. In previous work, the lineage trees constructed from individuals randomly sampled from the population at the final time-point have been used to infer the fitness and the times at which the mutation providing the fitness advantage arose in a diverse set of systems, such as blood cancers [1], [2] and the influenza virus [3]. However, it is not clear to what extent the inferred values depend on the exact biological details assumed in the models used for the inference. In this paper we show that coalescent statistics of lineage trees are invariant to changes in key parameters underlying the expansion, such as the distribution of the number of progenies produced by each individual and heterogeneity in the expansion rate. In addition, we show that competition between drift and selection imply that the fitness of the mutated population and when the mutation occurred can be inferred without knowledge of the mutation rate per generation even though the population size itself cannot be inferred. Lastly, we show that our results also generalize to cases where multiple competing mutations result in multiple distinct subclones with different values of fitness. Taken together, our results show that inferring fitness from lineage trees is robust to most model assumptions.
Parallel genomic basis of age at maturity across spatial scales in Atlantic Salmon
Authors: Kess Tony , Lehnert Sarah J. , Bentzen Paul , Duffy Steven , Messmer Amber , Dempson J. Brian , Newport Jason , Whidden Christopher , Robertson Martha J. , Chaput Gerald , Breau Cindy , April Julien , Gillis Carole-Anne , Kent Matthew , Nugent Cameron M. , Bradbury Ian R. 
Published: September 2022

AbstractComplex traits often exhibit complex underlying genetic architectures resulting from a combination of evolution from standing variation, hard and soft sweeps, and alleles of varying effect size. Increasingly, studies implicate both large-effect loci and polygenic patterns underpinning adaptation, but the extent that common genetic architectures are utilized during repeated adaptation is not well understood. Sea age or age at maturation represents a significant life history trait in Atlantic Salmon (Salmo salar), the genetic basis of which has been studied extensively in European Atlantic populations, with repeated identification of large-effect loci. However, the genetic basis of sea age within North American Atlantic Salmon populations remains unclear, as does the potential for a parallel trans-Atlantic genomic basis to sea age. Here, we used a large SNP array and low coverage whole genome re-sequencing to explore the genomic basis of sea age variation in North American Atlantic Salmon. We found significant associations at the gene and SNP level with large-effect loci (vgll3, six6) previously identified in European populations, indicating genetic parallelism, but found that this pattern varied based on both sex and geographic region. We also identified largely non-repeated sweep signatures and sets of highly predictive loci associated with sea age among populations and sexes within North America, indicating polygenicity and low rates of repeated genomic parallelism. Despite low genome-wide parallelism, we uncovered a set of conserved molecular pathways associated with sea age that were consistently enriched among comparisons. Together, our results indicate parallelism of the molecular basis of sea age in North American Atlantic Salmon across large-effect genes and molecular pathways despite population-specific patterns of polygenicity. These findings reveal roles for both contingency and repeated adaptation at the molecular level in the evolution of life history variation.
Detecting the research structure and topic trends of social media using static and dynamic probabilistic topic models
Authors: Inaam ul haq Muhammad , Li Qianmu , Hou Jun , Iftekhar Adnan 
Published: September 2022

PurposeA huge volume of published research articles is available on social media which evolves because of the rapid scientific advances and this paper aims to investigate the research structure of social media.Design/methodology/approachThis study employs an integrated topic modeling and text mining-based approach on 30381 Scopus index titles, abstracts, and keywords published between 2006 and 2021. It combines analytical analysis of top-cited reviews with topic modeling as means of semantic validation. The output sequences of the dynamic model are further analyzed using the statistical techniques that facilitate the extraction of topic clusters, communities, and potential inter-topic research directions.FindingsThis paper brings into vision the research structure of social media in terms of topics, temporal topic evolutions, topic trends, emerging, fading, and consistent topics of this domain. It also traces various shifts in topic themes. The hot research topics are the application of the machine or deep learning towards social media in general, alcohol consumption in different regions and its impact, Social engagement and media platforms. Moreover, the consistent topics in both models include food management in disaster, health study of diverse age groups, and emerging topics include drug violence, analysis of social media news for misinformation, and problems of Internet addiction.Originality/valueThis study extends the existing topic modeling-based studies that analyze the social media literature from a specific disciplinary viewpoint. It focuses on semantic validations of topic-modeling output and correlations among the topics and also provides a two-stage cluster analysis of the topics.
Demystifying the link between knowledge management capability and innovation ambidexterity: organizational structure as a moderator
Authors: Shafique Imran , Kalyar Masood Nawaz , Shafique Muhammad , Kianto Aino , Beh Loo-See 
Published: September 2022

PurposeThis study examines the relationship between knowledge management (KM) capability and innovation ambidexterity, and their subsequent influence on firm performance. It also investigates whether organizational structure – in terms of connectedness and centralization – helps to develop a suitable context that either hinders or catalyzes the effectiveness of KM capability in predicting innovation ambidexterity.Design/methodology/approachData were collected from 336 manufacturing organizations in Pakistan using a random sampling technique. Partial least square-based structural equation modelling (PLS–SEM) was employed to analyze the data.FindingsResults reveal that KM capability is positively linked with innovation ambidexterity and firm performance. Innovation ambidexterity positively mediates the link between KM capability and firm performance. Connectedness positively moderates the association between KM capability and innovation ambidexterity. However, centralization negatively moderates the link between KM capability and innovation ambidexterity.Research limitations/implicationsThis research offers theoretical insights into when and how KM capability is effective in prompting performance through innovation ambidexterity by creating a suitable context.Practical implicationsThe study indicates that innovation may develop in an ambidextrous manner in an organization as long as the organization is proficient in creating a suitable context, i.e. structure to support it. Organizations should strive to develop sustained KM capabilities because these are seminal for enabling the challenging task of exploiting existing resources for innovation while also tapping on new opportunities for explorative breakthroughs.Originality/valueThis research contributes to a novel understanding regarding the importance of KM capability in fostering manufacturing organizations to engage in ambidexterity by creating a suitable context where optimal amount of each form of innovation activities is calibrated using KM capability.HighlightsKnowledge management capability is crucial for simultaneous exploitation and exploration of innovationInnovation ambidexterity (i.e. simultaneous exploitation and exploration of innovation) fosters firm performanceInnovation ambidexterity mediates the positive effect of knowledge management capability on firm performanceConnectedness strengthens the relationship between knowledge management capability and innovation ambidexterityCentralization weakens the effect of knowledge management capability on innovation ambidexterityInnovation can be developed in an ambidextrous way in organizations as long as organizations have knowledge-based competencies and proficient in creating suitable context
Exploring the nexus between microlevel and contextual influencers on women leaders’ paradox mindset
Authors: Amaro Lydia , Scheepers Caren Brenda 
Published: September 2022

Purpose
Women leaders struggle with the persistent paradoxical expectations. Literature suggests that a paradox mindset helps to leverage these tensions. This study aims to understand the nexus between the microfoundations of individual women leaders’ experiences, their responses and the organisational context, which enables or hinders their paradox mindset.

Design/methodology/approach
This study adopted a qualitative approach by conducting semistructured interviews with 14 women, all senior leaders in corporate South Africa.

Findings
The results reveal the interaction in the nexus between, firstly, women leaders’ authenticity and awareness as key anchors that enable them to adopt a paradox mindset and, secondly, the organisation’s role in creating hindrances or opportunities to leverage tensions. Women leaders in our sample applied one of two strategies: they either adapted to the environment or curated a subenvironment. This study shows that, if done authentically, through her own agency, a woman can influence interactions that make it easier to manage tensions within her environment, especially those created by negative performance evaluation because of unconscious institutional gender bias.

Research limitations/implications
The extent to which the findings of this research can be generalised is constrained by the selected research context.

Originality/value
This research contributes to the literature on paradox theory by revealing organisational contextual influencers, such as institutional bias in negative performance evaluation, which hinders a woman leader’s opportunity to be hired or promoted. These organisational influences also interact with women leaders’ ability to embrace paradox and internally leverage agentic and communal tensions.
Transient and passage to steady state in fluid flow and heat transfer within fractional models
Authors: Turkyilmazoglu Mustafa 
Published: September 2022

Purpose
The classical integer derivative diffusionmodels for fluid flow within a channel of parallel walls, for heat transfer within a rectangular fin and for impulsive acceleration of a quiescent Newtonian fluid within a circular pipe are initially generalized by introducing fractional derivatives. The purpose of this paper is to represent solutions as steady and transient parts. Afterward, making use of separation of variables, a fractional Sturm–Liouville eigenvalue task is posed whose eigenvalues and eigenfunctions enable us to write down the transient solution in the Fourier series involving also Mittag–Leffler function. An alternative solution based on the Laplace transform method is also provided.

Design/methodology/approach
In this work, an analytical formulation is presented concerning the transient and passage to steady state in fluid flow and heat transfer within the diffusion fractional models.

Findings
From the closed-form solutions, it is clear to visualize the start-up process of physical diffusion phenomena in fractional order models. In particular, impacts of fractional derivative in different time regimes are clarified, namely, the early time zone of acceleration, the transition zone and the late time regime of deceleration.

Originality/value
With the newly developing field of fractional calculus, the classical heat and mass transfer analysis has been modified to account for the fractional order derivative concept.
Effects of supply chain quality event announcements on stock market reaction: an empirical study from China
Authors: Liu Weihua , Liu Xinyun , Choi Tsan-Ming 
Published: September 2022

PurposeThis study aims to explore the impact of supply chain quality event (SCQE) announcements on enterprises’ stock market value.Design/methodology/approachThis study adopts the event study approach and analyzes the changes in shareholder value of companies listed in China based on data from 118 SCQE announcements. In the event study, the market, market-adjusted and Carhart four-factor models are used to estimate abnormal stock market returns, and a cross-sectional regression model is performed to examine the effects of SCQE announcements on enterprises’ stock market value.FindingsSCQE announcements have a negative impact on shareholder value. From the perspective of the supply chain network structure, the market reacts more negatively to SCQE announcements issued by the enterprises with higher supply chain concentration. From the perspective of companies’ characteristics, announcements that do not reflect the establishment of supply chain quality cooperation have a more negative effect on stock market value, which indicates that the supply chain network structure and firm-level characteristic can moderate the market reaction.Practical implicationsThe findings demonstrate a quantitative evaluation of how SCQE announcements affect the stock market value of listed companies and provide guidance for managers to enhance the value of SCQE announcements.Originality/valueThis study fills the research gap on the impact of SCQE announcements on stock market value by using secondary data and first explores the relationship between SCQE announcements and stock market value from the perspective of supply chain network. Furthermore, this study contributes to the literature on SCQE using an empirical study in China.
Life cycle assessment teaching innovation: experiences from a Brazilian higher education institution
Authors: Silva Diogo Aparecido Lopes , Giusti Gabriela , Rampasso Izabela Simon , Farrapo Junior Antonio Carlos , Anholon Rosley 
Published: September 2022

Purpose
The inclusion of sustainability in higher education courses has been debated in recent decades and has gained particular emphasis throughout the COVID-19. This paper aims to show how the context of the pandemic, which demanded the transition from in-person classes to virtual classes, was used to illustrate better the concepts of life cycle assessment (LCA) for Production Engineering students in a Brazilian University.

Design/methodology/approach
The research strategy used was action research. Throughout the discipline offering, the environmental impacts resulting from in-person and remote classes were comparatively assessed through a practical activity using LCA. Students’ behaviour and perception of the activities were recorded by the professor and discussed with the other researchers on the team. At the end of the course, students answered a questionnaire to assess their satisfaction with different aspects of the discipline, and these data were analysed via Fuzzy Delphi.

Findings
The results focus on discussing the pedagogical aspects of this experience and not the environmental impacts resulting from each class modality. It was possible to notice a greater engagement of students when using a project that directly involved their daily activities (food, transportation, use of electronics, etc.) compared to the traditional approach of teaching LCA concepts. In this traditional approach, the examples focussed on the industrial sector, a more distant context from the reality of most students. Student feedback demonstrated great acceptance by them regarding the approach adopted.

Originality/value
This study contributes to expanding debates about sustainability insertion in higher education and the training of professionals more aligned with the sustainable development agenda.