bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cyclic and Multilevel Causation in Evolutionary Processes
Authors: Warrell Jonathan , Gerstein Mark 
Published: November 2019

AbstractMany models of evolution are implicitly causal processes. Features such as causal feedback between evolutionary variables and evolutionary processes acting at multiple levels, though, mean that conventional causal models miss important phenomena. We develop here a general theoretical framework for analyzing evolutionary processes drawing on recent approaches to causal modeling developed in the machine-learning literature, which have extended Pearl’s ‘do’-calculus to incorporate cyclic causal interactions and multilevel causation. We also develop information-theoretic notions necessary to analyze causal information dynamics in our framework, introducing a causal generalization of the Partial Information Decomposition framework. We show how our causal framework helps to clarify conceptual issues in the contexts of complex trait analysis and cancer genetics, including assigning variation in an observed trait to genetic, epigenetic and environmental sources in the presence of epigenetic and environmental feedback processes, and variation in fitness to mutation processes in cancer using a multilevel causal model respectively, as well as relating causally-induced to observed variation in these variables via information theoretic bounds. In the process, we introduce a general class of multilevel causal evolutionary processes which connect evolutionary processes at multiple levels via coarse-graining relationships. Further, we show how a range of ‘fitness models’ can be formulated in our framework, as well as a causal analog of Price’s equation (generalizing the probabilistic ‘Rice equation’), clarifying the relationships between realized/probabilistic fitness and direct/indirect selection. Finally, we consider the potential relevance of our framework to foundational issues in biology and evolution, including supervenience, multilevel selection and individuality. Particularly, we argue that our class of multilevel causal evolutionary processes, in conjunction with a minimum description length principle, provides a conceptual framework in which identification of multiple levels of selection may be reduced to a model selection problem.
Evaluation of CD8 T cell killing models with computer simulations of 2-photon imaging experiments
Authors: Rastogi Ananya , Robert Philippe , Halle Stephan , Meyer-Hermann Michael 
Published: November 2019

AbstractIn vivo imaging of cytotoxic T lymphocyte (CTL) killing activity revealed that infected cells have a higher observed probability of dying after multiple contacts with CTLs, suggesting memory effect in CTLs or infected cells. We developed a three-dimensional agent-based model of CTL killing activity to discriminate different hypotheses about how infected cells get killed based on quantitative 2-photon in vivo observations. We compared a constant CTL killing probability with mechanisms of signal integration in CTL or infected cells. The most likely scenario implied increased susceptibility of infected cells with increasing number of CTL contacts where the total number of contacts was a critical factor as opposed to signal integration over many contacts. However, when allowing in silico T cells to interact with apoptotic target cells (zombie contacts), a contact history independent killing mechanism was also in agreement with the experimental datasets. We showed that contacts that take place between CTLs and dying infected cells impact the observed killing dynamics because even in absence of modulation of cell properties, we saw an increase of the observed probability of killing infected cells with more interactions. The duration taken by an infected cell to die and the per capita killing rate (PCKR) of CTLs, parameters hard to measure directly, were determined from the model and turned out predictive to distinguish the different CTL killing models in future experiments. The comparison of observed datasets to simulation results, revealed limitations in interpreting 2-photon data, and provided prediction for additional measurements to distinguish CTL killing models.HighlightsKilling of infected cells by cytotoxic T cells typically involves more than a single contact.Cytotoxic T cells or infected cells integrate signals from multiple interactions.T cell contacts with dying infected cells have a major impact on in vivo data interpretation.Significance StatementDespite having a clear understanding of cytotoxic T lymphocyte (CTL) mediated cytotoxicity mechanisms, the quantitative dynamics remain unexplored at a cellular level. We developed an agent-based model to compare different hypotheses for mechanisms of CTL mediated cytotoxicity that could lead to an increase in observed probability of killing infected cells at higher interactions with CTLs as seen in vivo. We showed that this behaviour can be explained by modulation of properties by infected cells or CTLs with increasing number of contacts. For the modulation, we compared two modes of signal integration and showed that time is not a relevant parameter in signal integration. We also studied the impact of contacts between CTLs and apoptotic infected cells on observed killing properties.
Alpha 6 integrins promote cytokinesis by regulating the expression of RSK2 and MKLP1
Authors: Singh Neetu , Xu Hao , Thiemann Renee , DeSantis Kara A. , Larsen Melinda , LaFlamme Susan E. 
Published: November 2019

ABSTRACTThe integrin-mediated interaction of cells with components of the extracellular matrix (ECM) regulates many cellular processes including cell division. Cytokinesis is the last step of cell division and is critical for normal development and tissue homeostasis as it ensures the proper segregation of genetic and cytoplasmic material between daughter cells. Cytokinesis failure leads to defects in development and tissue differentiation, as well as tumorigenesis. Abscission of intercellular bridge that connects presumptive daughter cells is the last step of cell division. The mitotic kinesin-like protein 1 (MKLP1) plays a central role in positioning the abscission machinery. Here, we show that α6 integrins promote successful cytokinesis in salivary gland epithelial cells by regulating the expression of MKLP1. RNAi-mediated depletion of α6 integrins inhibits cytokinesis and the expression of MKLP1 and p90 ribosomal-S6-kinase 2 (RSK2). Depletion of RSK2 results in similar defects in cytokinesis and also inhibits the expression of MKLP1, suggesting that the expression of RSK2 is required downstream of integrins to promote MKLP1 expression and successful cytokinesis. RNAi-mediated depletion of RSK2 in embryonic salivary glands in organ culture also results in the inhibition of cytokinesis and MKLP1 expression, indicating the physiological significance of this pathway.
Pathogen transmission from vaccinated hosts can cause dose-dependent reduction in virulence
Authors: Bailey Richard I. , Cheng Hans H. , Chase-Topping Margo , Mays Jody K. , Anacleto Osvaldo , Dunn John R. , Doeschl-Wilson Andrea 
Published: November 2019

AbstractMany livestock and human vaccines are leaky as they block symptoms but do not prevent infection or onward transmission. This leakiness is concerning as it increases vaccination coverage required to prevent disease spread, and can promote evolution of increased pathogen virulence. Despite leakiness, vaccination may reduce pathogen load, affecting disease transmission dynamics. However, the impacts on post-transmission disease development and infectiousness in contact individuals are unknown. Here, we use transmission experiments involving Marek’s disease virus in chickens to show that vaccination with a leaky vaccine substantially reduces viral load in both vaccinated individuals and unvaccinated contact individuals they infect. Consequently, contact birds are less likely to develop disease symptoms or die, show less severe symptoms, and shed less infectious virus themselves, when infected by vaccinated birds. These results highlight that even partial vaccination with a leaky vaccine can have unforeseen positive consequences in controlling the spread and symptoms of disease.
GmPTF1 Modifies Root Architecture Responses to Phosphate Starvation in Soybean
Authors: Yang Zhaojun , He Ying , Liu Yanxing , Lai Yelin , Zheng Jiakun , Li Xinxin , Liao Hong 
Published: November 2019

ABSTRACTThough root architecture modifications may be critically important for improving phosphorus (P) efficiency in crops, the regulatory mechanisms triggering these changes remain unclear. In this study, we demonstrate that genotypic variation in GmEXPB2 expression is strongly correlated with root elongation and P acquisition efficiency, and enhancing its transcription significantly improves soybean yield in the field. Promoter deletion analysis was performed using six 5’ truncation fragments (P1-P6) of GmEXPB2 fused with the GUS reporter gene in transgenic hairy roots, which revealed that the P1 segment containing 3 E-box elements significantly enhances induction of gene expression in response to phosphate (Pi) starvation. Further experimentation demonstrated that GmPTF1, a bHLH transcription factor, is the regulatory factor responsible for the induction of GmEXPB2 expression in response to Pi starvation. In short, Pi starvation induced expression of GmPTF1, with the GmPTF1 product not only directly binding the E-box motif in the P1 region of the GmEXPB2 promoter, but also activating GUS expression in a dosage dependent manner. Further work with soybean transgenic composite plants showed that, altering GmPTF1 expression significantly impacted GmEXPB2 transcription, and thereby affected root growth, biomass and P uptake. Taken together, this work identifies a novel regulatory factor, GmPTF1, involved in changing soybean root architecture through regulation the expression of GmEXPB2. These findings contribute to understanding the molecular basis of root architecture modifications in response to P deficiency, and, in the process, suggest candidate genes and a promoter region to target for improving soybean yield through molecular breeding of P efficiency.One Sentence SummaryThe bHLH transcription factor GmPTF1 regulates the expression of β-expansin gene GmEXPB2 to modify root architecture, and thus promote phosphate acquisition, and biomass in soybean.
Blood RNA Signatures Predict Recent Tuberculosis Exposure in Mice, Macaques and Humans
Authors: Ault Russell C. , Headley Colwyn A. , Hare Alexander E. , Carruthers Bridget J. , Mejias Asuncion , Turner Joanne 
Published: November 2019

AbstractTuberculosis (TB) is the leading cause of death due to a single infectious disease. Knowing when a person was infected withMycobacterium tuberculosis(M.tb) is critical as recent infection is the strongest clinical risk factor for progression to TB disease in immunocompetent individuals. However, time sinceM.tbinfection is challenging to determine in routine clinical practice. To define a biomarker for recent TB exposure, we determined whether gene expression patterns in blood RNA correlated with time sinceM.tbinfection or exposure. First, we found RNA signatures that accurately discriminated early and late time periods after experimental infection in mice and cynomolgus macaques. Next, we found a 6-gene blood RNA signature that identified recently exposed individuals in two independent human cohorts, including adult household contacts of TB cases and adolescents who recently acquiredM.tbinfection. Our work supports the need for future longitudinal studies of recent TB contacts to determine whether biomarkers of recent infection can provide prognostic information of TB disease risk in individuals and help map recent transmission in communities.
TGS-GapCloser: fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads
Authors: Xu Mengyang , Guo Lidong , Gu Shengqiang , Wang Ou , Zhang Rui , Fan Guangyi , Xu Xun , Deng Li , Liu Xin 
Published: November 2019

AbstractThe completeness and accuracy of genome assemblies determine the quality of subsequent bioinformatics analysis. Despite benefiting from the medium/long-range information of third-generation sequencing techniques, current gap-closing tools to enhance assemblies suffer multi-alignments and high error rates, resulting in huge time and money costs.We developed a software tool, TGS-GapCloser that uses the low depth (>=10X) single molecule sequencing long reads without any error correction to close gaps. The algorithm distinguishes gap regions from the alignments of long reads against original scaffolds, corrects only the candidate regions, and assigns the best sequences to each gap. We demonstrate that TGS-GapCloser improves the contig N50 value of draft assembly by 25-fold on average, updating above 90% gaps with 93.96% positive predictive value. Despite of high error rate of raw long reads, improved assemblies archive Q50 (99.999%) single-base accuracy with only 11.8% decrement to inputs. Besides it could complete more gaps, and is also ∼29-fold faster than mainstream gap-closing tools. BUSCO analysis revealed that 3.4%-13.1% more expected genes were complete. TGS-GapCloser also shows its power to fill gaps for ultra large genome assembly of ginkgo (∼12Gb) with 71.6% of gaps closed. The validation of inserted or merged gap sequences was conducted with NGS reads and reference genomes, respectively. The updated genome assemblies may promote the gene annotation, structure variant calling and thus improving the downstream analysis of ontogeny, phylogeny, and evolution.
Dynamic Palmitoylation Events Following T-Cell Receptor Signaling
Authors: Morrison Eliot , Wegner Tatjana , Zucchetti Andres Ernesto , Álvaro-Benito Miguel , Zheng Ashley , Kliche Stefanie , Krause Eberhard , Brügger Britta , Hivroz Claire , Freund Christian 
Published: November 2019

AbstractPalmitoylation is the reversible addition of palmitate to cysteine via a thioester linkage. Following stimulation of the T-cell receptor we find a number of proteins are newly palmitoylated, including those involved in vesicle-mediated transport and Ras signal transduction. Among these stimulation-dependent palmitoylation targets are the v-SNARE VAMP7, important for docking of vesicular LAT during TCR signaling, and the largely undescribed palmitoyl acyltransferase DHHC18 that is expressed in two isoforms in T cells. Using our newly developed On-Plate Palmitoylation Assay (OPPA), we show DHHC18 is capable of palmitoylating VAMP7 at Cys183. Cellular imaging shows that the palmitoylation-deficient protein fails to be retained at the Golgi.
A brand-new world: brand-endorsers-users fit on social media
Authors: Borges-Tiago Maria Teresa , Tiago Flavio , Veríssimo José Manuel , Silva Tiago 
Published: November 2019

Purpose
The digital relationship between brand and users, and brand and endorsers has been analyzed from different angles. The purpose of this paper is to investigate how these three elements co-create online the brand personality of the firm, through user-generated content.

Design/methodology/approach
This study gathered data from the hotels’ websites, Facebook, Twitter and TripAdvisor accounts, examining the content posted by the hotel, by tourists and by the celebrity endorsing some of the hotels. To pursue the aims, the brand personality dimensions communicated online were assessed through content analysis for the global presence and for each social network by user typology to establish the alignment of brand personality traits communicated.

Findings
Digital communication was found to vary significantly between the hotels and tourists in different social networks. The amount of content created by tourists is significantly higher than the ones produced by the hotel. The sincerity dimension of brand personality was confirmed in both communications. However, tourists’ brand image impacts brand personality differently than the hotels themselves. Furthermore, an analysis of the influence of customers on social networks indicates that celebrity personality traits seem to impact on the image of a hotel brand.

Originality/value
This research can be used to help brand managers to understand better the digital co-branding with clients and celebrity, as well as to identify gaps in their brand personality strategy. It could also assist future researchers focusing on digital celebrity endorsement since few researchers have analyzed digital communication in different social networks.
Searching for high pressure processing parameters for Escherichia coli O157:H7, Salmonella enterica and Listeria monocytogenes reduction in Concord grape juice
Authors: Petrus Rodrigo , Churey John , Worobo Randy 
Published: November 2019

Purpose
High pressure processing (HPP) has been widely used for high-acid (pH<4.6) juices. The purpose of this study was to investigate optimal parameters aimed at achieving 5-log reduction of the pathogens of reference in Concord grape juice (pH 3.39).

Design/methodology/approach
Grape juice was inoculated with five strain cocktails of Escherichia coli O157:H7, Salmonella enterica and Listeria monocytogenes. In total, 11 trials were carried out based on a Central Composite Rotational Design (CCRD). The pressure (P), ranging from 319 to 531 MPa, and dwell time (t), from 35 to 205 s, were tested. The performance of the combinations (P × t) was evaluated by pathogen challenge microbiological assays.

Findings
E. coli O157:H7 was more resistant to HPP than S. enterica. L. monocytogenes did not grow in unprocessed juice (before HPP). Findings demonstrated that moderate pressures (~400 MPa) and short dwell times (~2 min) were effective in achieving a greater than 5-log reduction in the pathogens of reference.

Practical implications
Because the maintenance costs of equipment exponentially increase with pressure beyond 600 MPa, significant reductions in process pressure are highly desirable.

Originality/value
The results of this study can supplement the dearth of information on the applicability of high pressure as a Concord grape juice processing technology in terms of the pathogens inactivation. Furthermore, the use of a cocktail of five strains of pathogens inoculated in Concord grape juice to challenge different HPP parameters has not been reported.
Research on production process optimization of precast concrete component factory based on value stream mapping
Authors: Wang Shuqiang , Tang Jia , Zou Yiquan , Zhou Qihui 
Published: November 2019

Purpose
The purpose of this paper is to investigate the process optimization of a precast concrete component production line by using value stream mapping.

Design/methodology/approach
This paper is an empirical focused on of lean production theory and value stream mapping. The data in the case study were collected in real time on-site for each process during the production process of a prefabricated exterior wall.

Findings
The results of the current value stream map indicate that the main problems of the current production process are related to equipment, technology and organization. The equipment problems include simple demolding and cleaning tools and the lack of professional transfer channels. The technology problems include the lack of a marking mechanism and pipeline exit mechanism. There is a lack of standard operating procedures and incomplete process convergence. A comparison and analysis of the current value stream and the future value flow indicate that optimizations of the process flow, the production line layout, and the standard operating procedures have shortened the delivery cycle, reduced the number of workers, improved the operator’s operating level and balanced the production line.

Practical implications
The results of this study provide practitioners with a clear understanding of the optimization of the precast concrete component production and represent a method and basis for the process optimization of a factory production line; the approach is suitable for process optimization in other areas.

Originality/value
This research represents an innovative application of lean production theory and value stream mapping in a complex production line of precast concrete components and thereby fills the gap between the theory and practice of the optimization of a precast concrete component production line.
Whom to please: the government or the company? A case study of Ayla Hotels and Resorts in Djibouti, East Africa
Authors: Darwish Doa'a , Ahmad Syed Zamberi 
Published: November 2019

Subject area
International Business Management, Global Business Strategy and Human Resource Management

Study level/applicability
This case is suitable for Bachelor of Business Administration (BBA) program, specifically in human resources management, business strategy and international business management courses.

Learning outcomes
The learning outcomes are as follows: to figure out the appropriate staffing approaches for the foreign investment projects; to understand the challenges that companies face when they expand in the foreign market; to understand the different foreign markets entry modes.

Case overview/synopsis
The Nayel and Bin Harmal Investment Co. LCC. is an experienced company that owns a hotel chain with three properties in the UAE. In 2011, it decided to invest in Africa and build a new hotel – Ayla Djibouti Hotel – in Djibouti. The hotel’s construction is nearly complete. This has urged Bashar Al Tamimi to begin devising a staffing strategy for the hotel. Of particular concern is Djibouti’s lack of manpower with hospitality qualifications and expertise. Consequently, Al Tamimi must grapple with some difficult questions: Should he hire staff with the appropriate international hospitality experience? Or should NBHI invest in the human capital in Djibouti and train Djiboutian people to operate the hotel? Which strategy or approach will lead to the most successful and profit-making outcome for Ayla Djibouti

Complexity academic level
This case is suitable for Bachelor of Business Administration (BBA) program, specifically in human resources management, business strategy and international business management courses.

Supplementary materials
Teaching Notes are available for educators only. Please contact your library to gain login details or email support@emeraldinsight.com to request teaching notes.

Subject code
CSS 5: International Business.