bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative genomics provides insight into the function of broad-host range sponge symbionts
Authors: Waterworth Samantha C. , Parker-Nance Shirley , Kwan Jason C. , Dorrington Rosemary A. 
Published: December 2020

ABSTRACTAs the oldest extant metazoans, sponges (PhylumPorifera) have been forming symbiotic relationships with microbes that may date back as far as 700 million years. Most symbionts are conserved within a narrow host range and perform specialized functions. However, there are widely distributed bacterial taxa such asPoribacteria, SAULandTethybacteralesthat are found in a broad range of invertebrate hosts. Here, we added eleven new genomes to theTethybacteralesorder, identified a novel family, and show that functional potential differs between the threeTethybacteralesfamilies. We compare theTethybacteraleswith the well-characterizedEntoporibacteriaand show that these broad-host range, sponge-associated bacteria likely perform distinct functions within their hosts and that their respective phylogenies are incongruent with their host phylogenies. These results suggests that ancestors of these bacteria may have undergone multiple association events, rather than a single association event followed by co-evolution.IMPORTANCEMarine sponges often form symbiotic relationships with bacteria that fulfil a specific need within the sponge holobiont, and these symbionts are often conserved within a narrow range of related taxa. To date, there exist only three know bacterial taxa (Entoporibacteria, SAULandTethybacterales) that are globally distributed and found in a broad range of sponge hosts, and little is known about the latter two. Understanding what distinguishes these broad-host range symbionts from specialized symbionts will provide insight into the mechanisms by which sponges form these symbioses. We show that the functional potential of broad-host range symbionts is conserved at a family level and that these symbionts have been acquired several times over evolutionary history. This contrasts with specialized symbionts, where function is often a strain-specific trait and have co-evolved with their host following a single association event.
Limitations of DNA barcoding in determining the origin of smuggled seahorses and pipefishes
Authors: Serite Conny P. , Ntshudisane Ofentse K. , Swart Eugene , Simbine Luisa , Jaime Graça L. M. , Teske Peter R. 
Published: December 2020

AbstractSeahorses and pipefishes are heavily exploited for use in Traditional Chinese Medicine (TCM), and less frequently for curio markets or as aquarium fish. A number of recent studies have used DNA barcoding to identify species sold at TCM markets in East Asia, but the usefulness of this approach in determining the region of origin remains poorly explored. Here, we generated DNA barcodes of dried seahorses and pipefishes destined for TCM that were confiscated at South Africa’s largest airport because they lacked the export permits required for the CITES-listed seahorses. These were compared with published sequences and new sequences generated for Mozambican seahorses, with the aim of determining whether it is possible to identify their country of origin. All pipefishes were identified asSyngnathoides biaculeatus, a widespread Indo-Pacific species, but the published sequence data did not provide sufficient resolution to identify the region of origin. The same was true of the majority of seahorses, which could not even be identified to species level because they clustered among an unresolved species complex whose sequences were published under the namesHippocampus kuda, H. fuscusandH. capensis. The presence of a few specimens of a second seahorse,H. camelopardalis, suggests that the shipment originated from East Africa because the range of this seahorse is centred around this region, but again, it was not possible to determine their country of origin. Even though seahorses and pipefishes have high levels of genetic population structure because of their low dispersal potential, DNA barcoding was only suitable to tentatively identify species, but not their region of origin. DNA barcoding is increasingly used to identify illegally traded wildlife, but our results show that more sophisticated methods are needed to monitor and police the trade in seahorses and pipefishes.
Short stop is a gatekeeper at the ring canals ofDrosophilaovary
Authors: Lu Wen , Lakonishok Margot , Gelfand Vladimir I. 
Published: December 2020

SUMMARYMicrotubules and actin filaments are two major cytoskeletal components essential for a variety of cellular functions. Spectraplakins are a family of large cytoskeletal proteins cross-linking microtubules and actin filaments among other components. In this study, we aim to understand how Short stop (Shot), the singleDrosophilaspectraplakin, coordinates microtubules and actin filaments for oocyte growth. The oocyte growth completely relies on the acquisition of cytoplasmic materials from the interconnected sister cells (nurse cells), through ring canals, cytoplasmic bridges that remained open after incomplete germ cell division. Given the open nature of the ring canals, it is unclear how the direction of transport through the ring canal is controlled. Here we show that Shot controls the directionality of flow of material from the nurse cells towards the oocyte. Knockdown ofshotchanges the direction of transport of many types of cargo through the ring canals from unidirectional (toward the oocyte) to bidirectional, resulting in small oocytes that fail to grow over time. In agreement with this flow-directing function of Shot, we find that it is localized at the asymmetric actin fibers adjacent to the ring canals at the nurse cell side, and controls the uniform polarity of microtubules located in the ring canals connecting the nurse cells and the oocyte. Together, we propose that Shot functions as a gatekeeper directing the material flow from the nurse cells to the oocyte, via organization of microtubule tracks.
Calculating sample size requirements for temporal dynamics in single cell proteomics
Authors: Boekweg Hannah , Guise Amanda J. , Plowey Edward D. , Kelly Ryan T. , Payne Samuel H. 
Published: December 2020

AbstractSingle cell measurements are uniquely capable of characterizing cell-to-cell heterogeneity, and have been used to explore the large diversity of cell types and physiological functions present in tissues and other complex cell assemblies. An intriguing application of single cell proteomics is the characterization of proteome dynamics during biological transitions, like cellular differentiation or disease progression. Time course experiments, which regularly take measurements during state transitions, rely on the ability to detect dynamic trajectories in a data series. However, in a single cell proteomics experiment, cell-to-cell heterogeneity complicates the confident identification of proteome dynamics as measurement variability may be higher than expected. Therefore, a critical question for these experiments is how many data points need to be acquired during the time course to enable robust statistical analysis. We present here an analysis of the most important variables that affect statistical confidence in the detection of proteome dynamics: fold-change, measurement variability, and the number of cells measured during the time course. Importantly, we show that datasets with less than 16 measurements across the time domain suffer from low accuracy and also have a high false-positive rate. We also demonstrate how to balance competing demands in experimental design to achieve a desired result.
Integrating continuous hypermutation with high-throughput screening for optimization ofcis,cis-muconic acid production in yeast
Authors: Jensen Emil D. , Ambri Francesca , Bendtsen Marie B. , Javanpour Alex A. , Liu Chang C. , Jensen Michael K. , Keasling Jay D. 
Published: December 2020

SummaryDirected evolution is a powerful method to optimize proteins and metabolic reactions towards user-defined goals. It usually involves subjecting genes or pathways to iterative rounds of mutagenesis, selection, and amplification. While powerful, systematic searches through large sequence-spaces is a labor-intensive task, and can be further limited bya prioriknowledge about the optimal initial search space, and/or limits in terms of screening throughput. Here we demonstrate an integrated directed evolution workflow for metabolic pathway enzymes that continuously generates enzyme variants using the recently developed orthogonal replication system, OrthoRep, and screens for optimal performance in high-throughput using a transcription factor-based biosensor. We demonstrate the strengths of this workflow by evolving a ratelimiting enzymatic reaction of the biosynthetic pathway forcis,cis-muconic acid (CCM), a precursor used for bioplastic and coatings, inSaccharomyces cerevisiae. After two weeks of simply iterating between passaging of cells to generate variant enzymes via OrthoRep and high-throughput sorting of best-performing variants using a transcription factor-based biosensor for CCM, we ultimately identified variant enzymes improving CCM titers >13-fold compared to reference enzymes. Taken together, the combination of synthetic biology tools as adopted in this study, is an efficient approach to debottleneck repetitive workflows associated with directed evolution of metabolic enzymes.
Genome-wide sequence data show no evidence of admixture and introgression among pollinator wasps associated with a community of Panamanian strangler figs
Authors: Satler Jordan D. , Herre Edward Allen , Heath Tracy A. , Machado Carlos A. , Gómez Zúñiga Adalberto , Nason John D. 
Published: December 2020

AbstractInteractions between plants and their animal pollinators can shape processes of divergence and gene flow within associated lineages. For example, in the obligate mutualism between figs (Ficus) and fig pollinator wasps (family Agaonidae), each wasp species typically pollinates a single fig species, potentially reinforcing reproductive isolation among different wasp species. Multiple pollinator species, however, can sometimes reproduce in the same host fig species, potentially enabling hybridization and introgression between wasp species. In a community of Panamanian strangler figs (sectionAmericana), we use genome-wide ultraconserved element (UCE) loci to estimate phylogenetic relationships and test for hybridization and gene flow among 19 pollinator species associated with 16 host fig species. Previous studies showing ongoing pollinator sharing and a history of pollinator host switching are consistent with documented genetic admixture in their host figs. Here we investigate if host sharing and a dynamic evolutionary history including host switching has also resulted in hybridization and gene flow between pollinator species. Phylogenetic analyses recover strong support for well-delimited wasp species coupled with high interspecific divergence. There is no evidence for ongoing hybridization or introgression, even among pairs of pollinator species currently reproducing within the same host. In contrast to work suggesting admixture among Panamanian host figs, we conclude hybridization and interspecific gene flow have not been important processes shaping the evolutionary history of their pollinating wasps.
The biophysical basis of protein domain compatibility
Authors: Coyote-Maestas Willow , Nedrud David , Suma Antonio , He Yungui , Matreyek Kenneth A. , Fowler Douglas M. , Carnevale Vincenzo , Myers Chad L. , Schmidt Daniel 
Published: December 2020

AbstractUnderstanding the biophysical mechanisms that govern the combination of protein domains into viable proteins is essential for advancing synthetic biology and biomedical engineering. Here, we use massively parallel genotype/phenotype assays to determine cell surface expression of over 300,000 variants of the inward rectifier K+channel Kir2.1 recombined with hundreds of protein motifs. We use machine learning to derive a quantitative biophysical model and practical rules for domain recombination. Insertional fitness depends on nonlinear interactions between the biophysical properties of inserted motifs and the recipient protein, which adds a new dimension to the rational design of fusion proteins. Insertion maps reveal a generalizable hierarchical organization of Kir2.1 and several other ion channels that balances stability needed for folding and dynamics required for function.SummaryMassively parallel assays reveal interactions between donor domains and recipient proteins govern domain compatibility
A systematic conduct of POE for polyclinic facilities in Saudi Arabia
Authors: Salaheldin Mohammad H. , Hassanain Mohammad A. , Ibrahim Ahmed M. 
Published: December 2020

PurposeThis paper presents a systematic conduct of post-occupancy evaluation (POE) for polyclinic facilities at public hospitals.Design/methodology/approachThis is a mixed design research, where a review of literature was utilized, to qualitatively synthesize POE research on healthcare facilities. Three polyclinic facilities at Saudi Arabia were then assessed. The assessment was systematically conducted by the utilization of surveys and relative importance indices to solicit the experts’ and users' perspectives. The research included the conduct of physical measurements and walkthroughs inspections. Lastly, focus group meetings were conducted to generate recommendations that would improve the built environment conditions of polyclinic facilities.FindingsThe research identified unsatisfactory zoning, indoor air quality and concerns related to installations of different systems. Performance elements and subsequent indicators were identified and evaluated for their significance. The knowledge of these, enables the systematic conduct of POE, by exemplary case studies, for the managers and decision-makers of polyclinic facilities.Originality/valueThis research presents a comprehensive approach for the systematic conduct of POE at polyclinic facilities. The research enriches the literature and fulfils a contextual gap. The recommendations serve to enhance feedforward, the design and management of healthcare facilities.
Architecture students' satisfaction with and perceptions of online design studios during COVID-19 lockdown: the case of Jordan universities
Authors: Alnusairat Saba , Al Maani Duaa , Al-Jokhadar Amer 
Published: December 2020

PurposeThe purpose of this study is to examine the attitudes of students in higher educational institutions in Jordan towards the use of online design studios during coronavirus disease 2019 (COVID-19) lockdown and discusses how their use could enhance the learning process.Design/methodology/approach615 undergraduate students studying architecture in Jordanian universities were recruited to explore the factors that constituted and affected their perceptions of online design studios.FindingsThe findings of this study highlight that many of the participants felt uncertain about aspects of their online learning experience and wanted more guidance and support. Reasons of this disengagement include technical factors, such as poor network quality and lack of familiarity with the new applications. Students and tutors' personal situations when working and studying from home are also relevant due to the tutors' lack of expertise in online teaching, and the limitations of peer interaction. Together, these factors can make the experience of the online design studio more challenging.Research limitations/implicationsThe sample was nationally representative of architecture students from various institutions. However, the study was limited to an exploration of students' opinions, and it did not include the points of view of tutors and decision-makers.Originality/valueThis research was conceived during the period of the COVID-19 lockdown, whilst both tutors and students were experiencing dramatic changes in their modes of teaching and learning due to the sudden move from on-campus design studios to a virtual alternative, with only the bare minimum of resources and relevant experience. Learners' perspectives can enhance understanding of online design studios to assess their quality and effectiveness.
Management control system for corporate social responsibility implementation – a stakeholder perspective
Authors: Adib Mohamed , Zhang Xianzhi , A.A.Zaid Mohammad , Sahyouni Ahmad 
Published: December 2020

Purpose
The purpose of this paper is to build a framework that intends to help organizations define, implement and control their corporate social responsibility (CSR) strategies. Based on the stakeholder perspective, this paper proposes a sustainability management control system (SMCS) specifically made for the definition and implementation of CSR strategy, by linking the firm’s material topics to its key stakeholders, thus, allowing our model to be dynamic to different business environments.

Design/methodology/approach
In this paper, the authors constructed their model based on a review of selective relevant studies about CSR and SMCSs. This paper also went through different practical concepts from leading sustainability guidelines and stakeholder’s engagement manuals, discussing the stakeholder identification and prioritization, to re-center the debate to the strategic importance of the stakeholder perspective in defining and implementing CSR strategy, as well as its importance in how organizations can define proxies to assess the performance of their CSR initiatives.

Findings
Adopting the stakeholder theory as a key lens to re-frame, organize and guide the debate over the performance consequences of CSR has the potential to overcome the simplistic and (eventual) misleading conceptions of CSR strategy implementation, thus fostering the move toward more effective and efficient CSR strategies, by developing management control system (MCS) typical for CSR issues.

Social implications
The full process of the model outlined in this paper aims to provide a comprehensive and forward-looking tool for CSR and sustainability strategy implementation and assessment. Our model could help companies to gain an overview and an understanding of the relative importance of the material topics of their business activities that should be addressed and how they are related to the key stakeholders, thus, eventually leading to more equitable and sustainable social development by giving those who have a right to be heard the opportunity to be considered in the sustainability decision-making and strategy processes, in the aim of making valuable contributions to social, economic and environmental spheres.

Originality/value
The paper answers the call for research for developing novel theoretical foundations to design MCSs for CSR implementation. Therefore, the paper suggests an innovative model of SMCS for CSR strategy definition, development and implementation and helping organizations to define and develop key sustainability indicators specific to their business environment. The model also presents an opportunity to rethink and advance the understanding of how managers can prioritize competing stakeholders’ claims, which are constrained by the company’s business activities impacts.
Optimizing construction and demolition waste transportation for sustainable construction projects
Authors: Elshaboury Nehal , Marzouk Mohamed 
Published: December 2020

PurposeThere have been numerous efforts to tackle the problem of accumulated construction and demolition wastes worldwide. In this regard, this study develops a model for identifying the optimum fleet required for waste transportation. The proposed model is validated through a case study from the construction sector in New Cairo, Egypt.Design/methodology/approachVarious fleet combinations are assessed against the time, cost, energy and emissions generated from waste transportation. Genetic algorithm optimization is performed to select the near-optimum solutions. Complex proportional assessment and operational competitiveness rating analysis decision-making techniques are applied to rank Pareto frontier solutions. These rankings are aggregated using an ensemble approach based on the half-quadratic theory. Finally, a sensitivity analysis is implemented to determine the most sensitive attribute.FindingsThe results reveal that the optimum fleet required for construction and demolition wastes (CDW) transportation consists of one wheel loader of bucket capacity 2.5 cubic meters and nine trucks of capacity 22 cubic meters. Furthermore, consensus index and trust level of 0.999 are obtained for the final ranking. This indicates that there is a high level of agreement between the rankings. Moreover, the most sensitive criterion (i.e. energy) is identified using a sensitivity analysis.Originality/valueThis study proposes an efficient and effective construction and demolition waste transportation strategy that will lead to economic gains and protect the environment. It aims to select the optimum fleet required for waste transportation based on economic, social and environmental aspects. The usefulness of this study is establishing a consensual decision through the aggregation of conflicting decision makers' preferences in waste transportation and management.
Exploring the roles of hotel wellness attributes in customer satisfaction and dissatisfaction: application of Kano model through mixed methods
Authors: Park Hyekyung , Lee Minwoo , Back Ki-Joon 
Published: December 2020

Purpose
This paper aims to explore the underlying structure of wellness in upper-upscale and luxury hotels and the roles wellness attributes play in customer satisfaction and dissatisfaction.

Design/methodology/approach
This study uses a mixed methods approach consisting of content analysis and social media analytics. In Study 1, the authors integrate and review the structure of wellness attributes by conducting a literature review on prior research on wellness and analyzing websites of upper-upscale and luxury hotels. In Study 2, the authors implement text analytics and regression analysis to determine the roles of wellness attributes in customer satisfaction and dissatisfaction by examining the final data gathered from 141,973 reviews of 226 upper-upscale and luxury hotels in NYC.

Findings
This research introduces the underlying structure of wellness in the upper-upscale and luxury hotels. Findings demonstrate a significant relationship between wellness attributes and customer satisfaction/dissatisfaction. This study shows each wellness attribute’s specific roles in customer satisfaction and dissatisfaction through the Kano model.

Research limitations/implications
The current study extends the research on wellness by discovering the underlying structure of wellness in the upper-upscale and luxury hotels. Based on the Kano Model, the study reveals specific roles of wellness attributes regarding their dichotomous impact on customer satisfaction and dissatisfaction. The study makes a novel approach to the topic of wellness through a mixed methods approach consisted of content analysis and social media analytics. Analyzing online customer reviews derived from TripAdvisor.com, the study provides an in-depth insight and understanding of customers’ perceptions of wellness attributes.

Practical implications
The study guides hotel operators to perform wellness attributes by defining the unique roles of wellness attributes in customer satisfaction and dissatisfaction. Using the findings of the current study, hotel operators can prioritize wellness attributes regarding their core strategies and provide satisfying wellness attributes to customers.

Originality/value
Prior research merely focuses on hotels in wellness destinations or wellness-focused hotels with a lack of research on wellness offered in the general lodging industry. This research fills the gap by discovering the underlying wellness structure embedded in the general lodging industry, specifically in the upper-upscale and luxury hotels.