bluuebunny/crossref_metadata_2025_split huggingface dataset:
Whole-Colony Modeling of Escherichia coli
Authors: Skalnik Christopher J. , Agmon Eran , Spangler Ryan K. , Talman Lee , Morrison Jerry H. , Peirce Shayn M. , Covert Markus W. 
Published: April 2021

AbstractBacterial behavior is the outcome of both molecular mechanisms within each cell and interactions between cells in the context of their environment. Whereas whole-cell models simulate a single cell’s behavior using molecular mechanisms, agent-based models simulate many agents independently acting and interacting to generate complex collective phenomena. To synthesize agent-based and whole-cell modeling, we used a novel model integration software, called Vivarium, to construct an agent-based model ofE. colicolonies where each agent is represented by a current source code snapshot from theE. coliWhole-Cell Modeling Project and interacts with other cells in a shared spatial environment. The result is the first “whole-colony” computational model that mechanistically links expression of individual proteins to a population-level phenotype. Simulated colonies exhibit heterogeneous effects on their environments, heterogeneous gene expression, and media-dependent growth. Extending the cellular model with mechanisms of antibiotic susceptibility and resistance, our model also suggested that variation in the expression level of the betalactamase AmpC, and not of the multi-drug efflux pump AcrAB-TolC, was the key mechanistic driver of survival in the presence of nitrocefin. We see this as a significant step forward in the creation of more comprehensive multi-scale models, and it broadens the range of phenomena that can be modeled in mechanistic terms.Author summaryThis work combines several models of molecular and physical processes that impact the physiology and behavior of the common microbeEscherichia coliinto a multiscale model. Colonies comprised of multiple individual cells are simulated as they grow and divide—each with complex internal mechanisms, and with physical interactions and molecular diffusion in their environments. The integrative modeling methodology supports the addition of new submodels. The flexibility of this methodology is demonstrated by adding models of antibiotic resistance and simulating the colony’s response to antibiotic treatment.
A northern range extension of a Canadian species of Special Concern,Dielis pilipes(Hymenoptera: Scoliidae), in the Okanagan Valley of British Columbia
Authors: Nelson Tyler D. , Moffat Chandra E. 
Published: April 2021

AbstractThe only known Canadian records of the yellow scarab hunter wasp,Dielis pilipes(Saussure) (Hymenoptera: Scoliidae), are from the southern Okanagan and Similkameen valleys of British Columbia. We report a 25-km northern range extension of the species into the Ponderosa Pine Biogeoclimatic Ecosystem Classification zone, collected in an unmanaged agricultural field in Summerland, British Columbia. This finding is of conservation importance and has implications for natural biological control of ten-lined June beetles,Polyphylla decemlineata(Say) andP. crinitaLeConte (Coleoptera: Scarabaeidae), incidental agricultural pests in the Okanagan.
Recurrent Emergence of an Antiviral Defense through Repeated Retrotransposition and Truncation of CHMP3
Authors: Rheinemann Lara , Downhour Diane Miller , Davenport Kristen A. , McKeown Alesia N. , Sundquist Wesley I. , Elde Nels C. 
Published: April 2021

SummaryMost restriction factors recognize virus features to execute antiviral functions. In contrast, we discovered retroCHMP3, which instead impairs the host endosomal complexes required for transport (ESCRT) pathway to inhibit budding of enveloped viruses, including HIV-1. The ESCRT pathway is essential, so ESCRT inhibition creates the potential for cytotoxicity. We chart independent courses of retroCHMP3 emergence and reduction of cytotoxicity in New World monkeys and mice using ancestral reconstructions. Overexpression of full-length CHMP3 results in modest antiviral activity, which is enhanced by truncating mutations but causes increased cytotoxicity. We show that retroCHMP3 from squirrel monkeys acquired ancient mutations mitigating cytotoxicity before gaining the activating truncation. In contrast, a truncating mutation arose soon after the independent appearance of murine retroCHMP3, but the variant exhibits regulated expression by interferon signaling, illustrating distinct paths in the emergence of antiviral functions. RetroCHMP3 genes can repeatedly emerge in different species to independently create new immune functions.
Biosynthetic heme of malaria parasite induces cerebral pathogenesis by regulating hemozoin formation and griseofulvin can prevent cerebral malaria
Authors: Chandana Manjunatha , Anand Aditya , Ghosh Sourav , Beura Subhashree , Jena Sarita , Suryawanshi Amol Ratnakar , Padmanaban Govindarajan , Nagaraj Viswanathan Arun 
Published: April 2021

ABSTRACTHeme-biosynthetic pathway of malaria parasite is dispensable for asexual stages, but essential for sexual and liver stages. Despite having backup mechanisms to acquire hemoglobin-heme, pathway intermediates and/or enzymes from the host, asexual parasites express heme pathway enzymes and synthesize heme. Here we show heme synthesized in asexual stages promotes cerebral pathogenesis by enhancing hemozoin formation. Hemozoin is a parasite molecule associated with inflammation, aberrant host-immune responses, disease severity and cerebral pathogenesis. The heme pathway knockout parasites synthesize less hemozoin, and mice infected with knockout parasites are completely protected from cerebral malaria and death due to anaemia is delayed. Biosynthetic heme regulates food vacuole integrity and the food vacuoles from knockout parasites are compromised in pH, lipid unsaturation and proteins, essential for hemozoin formation. Targeting parasite heme synthesis by griseofulvin - a FDA-approved drug, prevents cerebral malaria in mice and provides a new adjunct therapeutic option for cerebral and severe malaria.
Evaluating the effectiveness of Farsi-English query production using ontology: a case of scientometric ontology
Authors: Manouchehri Sanaz , Mirzabeigi Mahdieh , Jowkar Tahere 
Published: April 2021

PurposeThis paper aims to discover the effectiveness of Farsi-English query using ontology.Design/methodology/approachThe present study is quasi-experimental. The sample consisted of 60 students and graduate and doctoral staff from Shiraz University and the Regional Center for Science and Technology. A researcher-made questionnaire was used to assess the level of English language proficiency of users, background knowledge and their level of satisfaction with search results before and after using ontology. Each user also evaluated the relevance of the top ten results on the Google search engine results page before and after using ontology.FindingsThe findings showed that the level of complexity of the task, the use of ontology, the interactive effect of the level of complexity of the task with the domain knowledge of the users, and the interactive effect of the level of complexity of the task with ontology, influence the effectiveness of retrieval results from the users' point of view. The results of the present study also showed that the level of complexity of the task, the use of ontology, and the interactive effect of the level of complexity of the task and the use of ontology, affect the level of user satisfaction.Originality/valueThe results of this research are significant in both theoretical and practical aspects. Theoretically, given the lack of research in which the interactive effect of the use of ontology has examined the level of complexity of tasks and domain knowledge of users, the present study can be considered as an attempt to improve information retrieval systems. From a practical point of view, the results of this research will help researchers and designers of information retrieval systems to understand that the use of ontologies can be used to retrieve information and improve the query and assess the needs of users and their satisfaction in this field, and ultimately, making the information retrieval process more effective.
Materials passport's review: challenges and opportunities toward a circular economy building sector
Authors: Munaro Mayara Regina , Tavares Sergio Fernando 
Published: April 2021

PurposeReuse and recycling building materials depend on an efficient set of information and tracking, which can be obtained by the materials passport (MP) tool. Although MP introduces principles of circular economy (CE) and brings environmental, social and economic benefits, it is little-explored in the construction sector. The purpose of this study is to explore the adoption of the MP in the sector to raise awareness about this tool. This analysis leads to the conception of a model and identifies the main challenges and opportunities to increase MP implementation in the sector.Design/methodology/approachThrough a systematic literature review, based on the descriptive and thematic analysis, articles were selected, and analyzed to (1) review the MP state-of-the-art in the construction sector; (2) propose a materials passport model and (3) list the main challenges and opportunities to MP adoption.FindingsThe studies about MP were concentrated on strategies to implement general concepts and business opportunities. The MP model was proposed to overcome the lack of studies and understanding showed in the review. The model aimed to improve the recovery and reuse of materials across a building's life cycle. Challenges and opportunities were raised to direct decision-makers and support the development of this tool. A systematic regulation in the construction value chain and policy systems is crucial for creating digital platforms for data management of buildings' material.Originality/valueThis study developed an MP model to enable the management of building materials at different stages of the building's life cycle and contributes to future developments of the studies on this knowledge domain.
Expanding the PGI certification scheme as a marketing tool in the olive oil industry: a perspective on consumer behavior
Authors: Di Vita Giuseppe , Cavallo Carla , Del Giudice Teresa , Pergamo Raffaella , Cicia Gianni , D'Amico Mario 
Published: April 2021

PurposeRecently, several regional protected geographical indications (PGI) have been introduced in Italy for extra virgin olive oil (EVOO) with the aim of coping with the substantial failure of protected designations of origin (PDO). This study aims to identify which characteristics consumers expect, in order to anticipate the market success.Design/methodology/approachIn this study, a survey has been used on a sample of consumers from Sicily, one of the first regions which recently developed a regional PGI for EVOO. Data have been analyzed with a rank-ordered logit model.FindingsResults yielded that consumers would accept this new product and their expectations correspond to a product with attributes such as: green color, not filtered, not with a sweet taste and with a known brand. A possible target can be represented by young men.Practical implicationsThe results obtained anticipate whether this product would be accepted and provides direct indications for producers who wish to enter the market with a PGI EVOO.Originality/valueThis work focuses on consumer behavior toward products that are specifically certified with a recently introduced PGI label, and they still are not so common on the market.
Performance evaluation of privatized ports by entropy based TOPSIS and ARAS approach
Authors: Gök-Kısa A. Cansu , Çeli̇k Pelin , Peker İskender 
Published: April 2021

PurposePorts are the key elements of maritime transportation, which is crucial for world trade. Approximately 180 port facilities are located in Turkey. After 2007, 5 of the ports, which are formerly owned by Turkish Republic Railways Administration (TRRA), are privatized. The aim of the study is to evaluate the performance of these privatized ports by multi-criteria decision-making (MCDM) approach.Design/methodology/approachThe application process is performed by a MCDM model. This model includes both criteria (dry bulk, liquid bulk, general cargo, container, RO-RO capacity, total port area, total berth, total berths length and depth) and alternatives (Mersin, Samsun, Bandirma, Iskenderun and Derince Ports). It determines the weights of the criteria by entropy and ranks the alternatives by ARAS and Technique for Order Preference by Similarity to Ideal Solution (TOPSIS) methods.FindingsThe results of entropy, ARAS and TOPSIS methods are compared. According to these results, “container” is the most important criteria while Mersin port has the best performance.Originality/valueIn the literature, most of the studies about this subject were analyzed by data envelopment analysis (DEA) and there are no studies had been taken into consideration ports that are owned by TRRA, in Turkey. Moreover, few of these studies used integrated MCDM models, and this is the first study that integrates entropy, ARAS and TOPSIS methods in this field.
Does the risk aversion of crude oil market investors have directional predictability for the precious metal and agricultural markets?
Authors: Zhang Yue-Jun , Pan Xu 
Published: April 2021

PurposeRisk aversion is considered as an important factor in predicting asset prices. Many studies have proved that there exists important price information spillover among crude oil, precious metals and agricultural markets. Then there naturally follows the question: Is the risk aversion of investors in crude oil market predictable for the returns of precious metals and agricultural products? The purpose of this paper is to answer this question. For this reason, the authors explore the directional predictability and the cross-quantile dependence between risk aversion of crude oil market investors and returns of precious metals and agricultural products.Design/methodology/approachTo better describe the risk aversion of investors, this paper uses high-frequency data and model-free calculation method to obtain variance risk premium of crude oil. Then, this paper uses the cross-quantilogram method to investigate the directional predictability and cross-quantile dependence between risk aversion of crude oil market investors and returns of precious metals and agricultural products. Meanwhile, it employs the partial cross-quantilogram (PCQ) method to test the impact of control variables on the empirical results.FindingsFirstly, risk aversion of crude oil market investors has directional predictability for returns of precious metals and agricultural products. Secondly, different degrees of risk aversion of crude oil market investors have different impacts on returns of precious metals and agricultural products. A low (high) degree of crude oil market investors' risk aversion has negative (positive) predictability for returns of precious metals and agricultural products. Finally, during the sample period, the returns of precious metals are more affected by risk aversion of crude oil market investors than returns of agricultural products.Originality/valueFirst of all, this paper studies the impact of risk aversion of crude oil market investors on returns of precious metals and agricultural products. It updates previous relevant studies on the factors influencing the prices of precious metals and agricultural products, and provides a new idea for the forecast of those commodity returns. Secondly, this paper provides the evidence that different degrees of risk aversion of investors have different effects on the returns of commodities, and expands the research on the topic of commodity returns prediction. Finally, high-frequency data are employed in this paper to better capture the risk aversion of investors than commonly used daily data.
Comparative study of academic research on project management in Iran and the World with text mining approach and TF–IDF method
Authors: Toosi Hossein , Ghaaderi Mohammad Amin , Shokrani Zahra 
Published: April 2021

Purpose
The purpose of this study is to compare the trend of academic project management research in Iran and the World in five-year periods with a text mining approach and TF–IDF method.

Design/methodology/approach
The research population consists of 1205 theses presented between 2000 and 2019 in Iranian universities. The central library website of the mentioned universities was used for data collection, and the text mining approach with the TF–IDF method was used for data analysis.

Findings
The remarkable results of this study include: Concrete structures are the most frequent among structural systems, Risk Management is the most frequent among PMBOK Knowledge Areas, Design-build (DB) system is the most frequent among Project Delivery Systems, Engineering, procurement and construction (EPC) is the most frequent among DB Project Delivery Systems, Financial Management is the most frequent among specialized construction knowledge areas, Soft Skills is the most frequent among Global Trends, Contracting Companies is the most frequent among Project Parties, Construction Projects is the most frequent among Project Areas, Power Plant and Refinery is the most frequent among Project Subjects, Optimization is the most frequent among Problem-Solving Approaches, Fuzzy Logic is the most frequent among Novel Algorithms and Motivation is the most frequent among Soft Skills.

Originality/value
The innovative aspect of this research is that for the first time, text mining has been used to analyze academic research on project and construction management, and also for the first time, academic research on construction industry in Iran has been compared with global research.
Actionable strategy framework for digital transformation in AECO industry
Authors: Bhattacharya Sanjay , Momaya K.S. 
Published: April 2021

PurposeThe Fourth Industrial Revolution (4IR) holds the potential to improve capabilities- and technology-based innovation, which will enable breakout for architectural, engineering, construction and operation and maintenance (AECO) companies, for international competitiveness. Though the top management of such companies is convinced on the utility of the applications, they are unsure on the strategy of implementing the same. The objective of this research is to suggest a strategy framework for digital transformation of the AECO value chain.Design/methodology/approachThe nascent level of research on 4IR in construction necessitated the adoption of the integrative review methodology for the study. Extensive literature review of research on strategy and 4IR has been utilized to establish the validity of the first two pillars, namely “a strategy of simple rules in a complex environment; and deployment of dynamic capabilities.” The validation of a construct for the third pillar of “confluence of change and continuity forces” has been achieved via hypothesis testing of data obtained through a questionnaire survey.FindingsThe present study has integrated three diverse ideas of strategy, named as the pillars, to facilitate sustainable digital transformation. Within the third pillar, top three continuity forces which offer resistance to change are organization culture, existing delivery processes and networks, and existing standard operating procedures. On the other hand, the leading drivers of change are needs of competitiveness; global industry trends and the advent of new technologies/innovations.Research limitations/implicationsThis provides a practical approach to operationalize digital transformation of the AECO at an organization level. The validation relied on opinion and perspectives of a sample frame in the Indian context, which was its limitation.Originality/valueThis paper suggests a strategy framework of three pillars to help address specific strategy dilemmas during implementation of digital transformation of particular organizations in AECO. The study contributes to both theory and practice by helping leaders of AECO companies, associations, policymakers and the academia to strategize transformations successfully.
Structural model for the relationships between age-friendly communities and quality of life of older adults in Hefei, China
Authors: Yu Jingyu , Ma Guixia , Ding Wenxuan , Mao Jiangfeng , Wang Jingfeng 
Published: April 2021

Purpose
China is experiencing tremendous changes of rapid urbanization and aging society. The development of age-friendly communities (AFCs) has been encouraged for improving health and well-being of older adults. Hence, this study aimed to deepen the understanding of AFCs in China and to investigate the integrated relationships between AFCs and the quality of life (QoL) of older adults, using a large-scale questionnaire survey.

Design/methodology/approach
A questionnaire survey was conducted in Hefei, China, to investigate the complicated relationships between the components of AFCs and the QoL of older adults. Ultimately, 1,383 valid questionnaires were collected from senior respondents aged more than 60 years. Several statistical methods, including reliability analysis, correlation analysis and structural equation modeling (SEM), were adopted to develop an integrated model for AFC components and the QoL of older adults.

Findings
Six AFC components and four older adults' QoL factors were identified. The SEM results revealed integrated relationships between specific AFC components and the QoL of older adults: (1) physical QoL was affected by outdoor spaces, public transportation, housing and community and health services; (2) psychological QoL was predicted by most of the AFC components except community and health services; and (3) environmental QoL and social QoL were both influenced by outdoor spaces, communication and information and community and health services.

Practical implications
In order to enhance the QoL of older adults, it is suggested that outdoor spaces need to be enlarged by fully using the facilities and playgrounds of middle schools and renovating the older buildings. The locations of public transportation stations are recommended to be revised to be within a 5-minute walking distance of senior residents. Improvements to the social environment of AFCs, by increasing the coverage of medical services and creating multiple approaches to recreational activities, are encouraged.

Originality/value
These findings have empirical significance for urban planners and policy-makers in regard to identifying major components of AFCs and understanding the effect of those components on the QoL of older adults.