bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Peek into the Plasmidome of Global Sewage
Authors: Kirstahler Philipp , Teudt Frederik , Otani Saria , Aarestrup Frank M. , Pamp Sünje Johanna 
Published: March 2021

AbstractPlasmids can provide a selective advantage for microorganisms to survive and adapt to new environmental conditions. Plasmid-encoded traits, such as antimicrobial resistance (AMR) or virulence, impact on the ecology and evolution of bacteria and can significantly influence the burden of infectious diseases. Insight about the identity and functions encoded on plasmids on the global scale are largely lacking. Here we investigate the plasmidome of 24 samples (22 countries, 5 continents) from the global sewage surveillance project. We obtained 105 Gbp Oxford Nanopore and 167 Gbp Illumina DNA sequences from plasmid DNA preparations and assembled 165,302 contigs (159,322 circular). Of these, 58,429 encoded for genes with plasmid-related and 11,222 with virus/phage-related proteins. About 90% of the circular DNA elements did not have any similarity to known plasmids. Those that exhibited similarity, had similarity to plasmids whose hosts were previously detected in these sewage samples (e.g.Acinetobacter, Escherichia, Moraxella, Enterobacter, Bacteroides, andKlebsiella). Some AMR classes were detected at a higher abundance in plasmidomes (e.g. macrolide-lincosamide-streptogramin B, macrolide, and quinolone), as compared to the respective complex sewage samples. In addition to AMR genes, a range of functions were encoded on the candidate plasmids, including plasmid replication and maintenance, mobilization, and conjugation. In summary, we describe a laboratory and bioinformatics workflow for the recovery of plasmids and other potential extrachromosomal DNA elements from complex microbiomes. Moreover, the obtained data could provide further valuable insight into the ecology and evolution of microbiomes, knowledge about AMR transmission, and the discovery of novel functions.ImportanceThis is, to the best of our knowledge, the first study to investigate plasmidomes at a global scale using long read sequencing from complex untreated domestic sewage. Previous metagenomic surveys have detected AMR genes in a variety of environments, including sewage. However, it is unknown whether the AMR genes were encoded on the microbial chromosome or are located on extrachromosomal elements, such as plasmids. Using our approach, we recovered a large number of plasmids, of which most appear novel. We identified distinct AMR genes that were preferentially located on plasmids, potentially contributing to their transmissibility. Overall, plasmids are of great importance for the biology of microorganisms in their natural environments (free-living and host-associated), as well as molecular biology, and biotechnology. Plasmidome collections may therefore be valuable resources for the discovery of fundamental biological mechanisms and novel functions useful in a variety of contexts.
Characterization of RNA content in individual phase-separated coacervate microdroplets
Authors: Wollny Damian , Vernot Benjamin , Wang Jie , Hondele Maria , Hyman Anthony , Weis Karsten , Camp J. Gray , Dora Tang T.-Y. , Treutlein Barbara 
Published: March 2021

AbstractLiquid-liquid phase separation or condensation is a form of macromolecular compartmentalization. Condensates formed by complex coacervation were hypothesized to have played a crucial part during the origin-of-life. In living cells, condensation organizes biomolecules into a wide range of membraneless compartments. Although RNA is a key component of condensation in cells and the central component of the RNA world hypothesis, little is known about what determines RNA accumulation in condensates and how single condensates differ in their RNA composition. Therefore, we developed an approach to read the RNA content from single condensates using high-throughput sequencing. We find that RNAs which are enriched for specific sequence motifs efficiently accumulate in condensates. These motifs show high sequence similarity to short interspersed elements (SINEs). We observed similar results for protein-derived condensates, demonstrating applicability across different in vitro reconstituted membraneless organelles. Thus, our results provide a new inroad to explore the RNA content of phase-separated droplets at single condensate resolution.
Comprehensive design analysis of a 3D printed sensor for readiness assessment applications
Authors: Agarwal Tanushree , Rahmani Fatemeh , Zaman Ishtique , Gasbarri Federico , Davami Keivan , Barzegaran Mohammadreza 
Published: March 2021

Purpose
This paper aims to develop a comprehensive model of a magnetic sensor array that will be operational for a multitude of electric components in continuous and nonintrusive condition monitoring (CM) or in readiness assessment (RA) applications.

Design/methodology/approach
A universal nonintrusive model of a flexible antenna array is introduced to monitor and identify failures in electric machine drives. An adjustable sensor is designed to serve as a RA for a vast range of electrical elements in a typical power system by capturing the low-frequency radiated magnetic fields.

Findings
The optimal placement of the most sensitive radiated fields from several components has been discovered in this case study, enabling the detection of healthy current flow throughout. Thereafter, the short-circuit investigation, representing faulty situations, is implemented and compared with healthy cases.

Practical implications
This sensing technique can be used for nonintrusive CM of components that are out of reach and cannot have the sensor to be held around it such as components in offshore winds, wind energy generation and power and chemical plants.

Originality/value
The results are provided for three commonly used machines with a single sensor array with numerous settings. The three dimensional (3 D) finite element analysis is applied in the structuring of the sensor, detection of the optimum location and recognition of faults in the machines. Finally, based on the setup design, 3 D printing is used for the construction of the sensor array. Thus, the sensor array with fault detection avoids major component failures and increases system reliability/resiliency.
Research data services from the perspective of academic librarians
Authors: Joo Soohyung , Schmidt Gisela M. 
Published: March 2021

Purpose
This study aims to investigate the perceptions of academic librarians regarding research data services (RDS) in academic library environments. This study also examines a range of challenges in RDS from the perspectives of academic librarians.

Design/methodology/approach
A nationwide online survey was administered to academic librarians engaged in data services at research universities around the USA. The collected survey responses were analyzed quantitatively using descriptive statistics, hierarchical clustering and multidimensional scaling.

Findings
Academic librarians perceived that consultation services would be more valuable to users than technical services in offering RDS. Accordingly, skills associated with consultation services such as instructional skills and data management planning were perceived by participants to be more important. The results revealed that academic libraries would need to seek collaboration opportunities with other units on campus to develop and offer RDS, especially technical services.

Originality/value
This study contributes to the existing body of research on the topic of data services in research universities. The study investigated various types of specific professional competencies and used clustering analysis to identify closely associated groups of service types. In addition, this study comprehensively examined both relevant resources for and barriers to RDS.
Perspectives of Australian hospital leaders on the provision of safe care: implications for safety I and safety II
Authors: Leggat Sandra G. , Balding Cathy , Bish Melanie 
Published: March 2021

PurposeThere is evidence that patient safety has not improved commensurate with the global attention and resources dedicated to achieving it. The authors explored the perspectives of hospital leaders on the challenges of leading safe care.Design/methodology/approachThis paper reports the findings of a three-year longitudinal study of eight Australian hospitals. A representative sample of hospital leaders, comprising board members, senior and middle managers and clinical leaders, participated in focus groups twice a year from 2015 to 2017.FindingsAlthough the participating hospitals had safety I systems, the leaders consistently reported that they relied predominantly on their competent well-meaning staff to ensure patient safety, more of a safety II perspective. This trust was based on perceptions of the patient safety actions of staff, rather than actual knowledge about staff abilities or behaviours. The findings of this study suggest this hegemonic relational trust was a defence mechanism for leaders in complex adaptive systems (CASs) unable to influence care delivery at the front line and explores potential contributing factors to these perceptions.Practical implicationsIn CASs, leaders have limited control over the bedside care processes and so have little alternative but to trust in “good staff providing good care” as a strategy for safe care. However, trust, coupled with a predominantly safety 1 approach is not achieving harm reduction. The findings of the study suggest that the beliefs the leaders held about the role their staff play in assuring safe care contribute to the lack of progress in patient safety. The authors recommend three evidence-based leadership activities to transition to the proactive safety II approach to pursuing safe care.Originality/valueThis is the first longitudinal study to provide the perspectives of leaders on the provision of quality and safety in their hospitals. A large sample of board members, managers and clinical leaders provides extensive data on their perspectives on quality and safety.
No woman, no aggressive tax planning? A study on CEO gender and effective tax rates in the Lithuanian retail sector
Authors: Zirgulis Aras , Huettinger Maik , Misiunas Dalius 
Published: March 2021

PurposeThe purpose of this paper is to investigate whether switching to a CEO of the opposite sex affects the tax aggressiveness of firms.Design/methodology/approachRegression analysis using a difference in difference approach and propensity score matching on a dataset of 8,798 firms from 2007 to 2017.FindingsThe authors find evidence that switching to a female CEO reduces the effective tax rate paid, implying a higher level of tax aggressiveness.Social implicationsThe findings contradict the narrative that female CEOs are less tax aggressive.Originality/valueThe authors are the first (to the best of the authors' knowledge) to specifically investigate if changing the CEO gender has an impact on the effective tax rate paid by the firm.
Plant provenance affects pollinator network: Implications for ecological restoration
Authors: Bucharova Anna , Lampei Christian , Conrady Malte , May Emilia , Matheja Janis , Meyer Michael , Ott David 
Published: March 2021

Abstract

The selection of plant provenance for ecological restoration is an intensively debated topic. Throughout this debate, arguments mostly focus on plant performance, but little attention is paid to the effects of provenance on other members of the restored ecosystem. On the other hand, in restoration projects that focus specifically on supporting interacting biota, for example, wildflower strips among fields to support pollinators, the provenance choice is often not considered, partly because the effect of provenance on pollinators is unknown. In this pioneering case study, we tested whether pollinators differentiate between experimental plant communities of different provenances.

We established experimental plant communities with the same species composition but with plants originating from three different provenances. We then recorded plant phenology and observed pollinators and flower visitors interacting with these experimental communities and related the pollinator visitation to the provenance identity.

The provenances of the experimental plant communities had a strong and significant effect on the diversity and abundance of flower–pollinator interactions, with one provenance interacting two times as often as the other two provenances. The effect was driven by the differences in flowering phenology among provenances.

Synthesis and applications. Plant provenances substantially differ in their interactions with local pollinators. Therefore, the selection of plant provenance should be considered when planning restoration projects for the support of pollinators.
Ethno‐essentialisms of the self: A critique of the cultural scripting of obesity in Japan
Authors: Castro‐Vázquez Genaro 
Published: March 2021

AbstractIn challenging the ‘validity’ of the body mass index (BMI), the construct of metabolic syndrome has been used to comprehend how obesity affects Japanese people. This article is grounded in an adaptation of the ‘sexual scripting theory’ (Gagnon and Simon, 2005) and proposes the concept of ‘ethno‐essentialisms of the self’ to explore the cultural scripts underpinning the development of metabolic syndrome. Ethno‐essentialisms of the self indicate a dialectical relationship between a Japanese healthy self and a non‐Japanese unhealthy Other, where ethno‐racial susceptibilities might make a Japanese self prone to develop metabolic‐related diseases. Despite these susceptibilities, Japanese ‘biopedagogy’ (Wright, 2009) to control bodyweight is oriented by a proper daily calculation of food consumption in relation to calorie‐burning. Biopedagogy in the form of food and nutrition education has largely translated into unyielding efforts to (re)traditionalise eating habits to prevent the supposed Westernisation of Japanese food. Overall, medical knowledge serves to propagate ethno‐essentialisms of the self, whose unintended consequence could be ‘clinical iatrogenic disease’ (Illich, 1976).
Risk of cardiovascular outcomes among women with endometriosis in the United Kingdom: a retrospective matched cohort study
Authors: Okoth K , Wang J , Zemedikun D , Thomas GN , Nirantharakumar K , Adderley NJ 
Published: March 2021

ObjectiveTo describe the prevalence and incidence of endometriosis and to estimate the risk of cardiovascular outcomes in women with endometriosis.DesignPopulation‐based cohort study using The Health Improvement Network database.SettingUK primary care.PopulationWomen aged 16–50 years were followed from 1995 to 2018.MethodsAdjusted hazard ratios (aHR) for cardiovascular outcomes comparing women with endometriosis with those without endometriosis were estimated using multivariable Cox regression models. Prevalence and incidence of endometriosis were estimated using annual (1998–2017) sequential cross‐sectional and cohort studies, respectively.Main outcome measureThe primary outcome was composite cardiovascular disease (CVD) including, ischaemic heart disease (IHD), heart failure (HF) and cerebrovascular disease. Secondary outcomes were arrhythmia, hypertension and all‐cause mortality.ResultsIn all, 56 090 women with endometriosis and 223 669 matched controls without endometriosis were included in the analysis of cardiovascular risk. Compared with women without endometriosis, the aHR for cardiovascular outcomes among women with endometriosis were: composite CVD 1.24 (95% CI 1.13–1.37); IHD 1.40 (95% CI 1.22–1.61); cerebrovascular disease 1.19 (95% CI 1.04–1.36); HF 0.76 (95% CI 0.54–1.07); arrhythmia 1.26 (95% CI 1.11–1.43); hypertension 1.12 (95% CI 1.07–1.17) and all‐cause mortality 0.66 (95% CI 0.59–0.74). The incidence of endometriosis was 12.3 per 10 000 person‐years in 1998 and 11.5 per 10 000 person‐years in 2017. The prevalence of endometriosis increased from 119.7 per 10 000 population in 1998 to 201.3 per 10 000 population in 2017.ConclusionEndometriosis is associated with an increased risk of cardiovascular outcomes. Young women with endometriosis are a potential target for CVD risk assessment and prevention.Tweetable abstractEndometriosis is associated with increased risk of cardiovascular outcomes: a UK retrospective matched cohort study.
Pectinmethylesterase affects the flow behavior of orange pulp
Authors: Li Xuan , Reyes‐De‐Corcuera José I. 
Published: March 2021

AbstractIn the orange juice industry, pulp (ruptured juice sacs) is separated from the juice after extraction and pasteurized separately before blending back with juice or sold for other food applications. However, pulp is not always pasteurized immediately after extraction and the flow behavior is affected by endogenous pectinmethylesterase (PME). This is particularly important because of the high power required to pump orange pulp in industrial pasteurizers. This study characterized the effect of PME on the flow behavior of citrus pulp during storage at 4 °C using rotational rheometry and during pulp storage at 22 °C using capillary rheometry. PME activity was 0.011 ± 0.001 PEU for the pulp used in rotational rheometry and 0.030 ± 0.002 PEU for the pulp used in capillary rheometry. Rotational rheometry was used to assess the effect of PME on the Power Law parameters at shear rates () below those that cause slip. There were no significant differences among storage time on the flow behavior index (n). However, the consistency coefficient (K) increased with storage time. Significant differences were found after 12‐hr storage increasing from 120 ± 30 Pa·sn to 160 ± 15 Pa·sn (16.7%) after 24 hr. Capillary rheomtery was used to assess the effect of PME on the pressure drop in a flow system. Significant differences were found at or after 12‐hr storage. The mean pressure drop increased by 34% after 24 hr, for a flow rate of 50 × 10−6 m3/s (0.8 GPM) in an 8.9‐m long (29.2 ft), 0.022‐m (1‐in) diameter pipe.Practical ApplicationDesign and optimization of processing equipment and industrial handling systems of orange pulp require detailed knowledge of its rheological (flow) properties. Citrus pulp is rich in pectinmethylesterase, an enzyme that causes thickening of the product when not inactivated during pasteurization. Understanding how fast PME affects the flow properties of orange pulp is important for citrus processors to decide how long pulp can be stored before pasteurizing it.
Different co‐occurring bacteria enhance or decrease the growth of the microalga Nannochloropsis sp. CCAP211/78
Authors: Lian Jie , Schimmel Patrick , Sanchez‐Garcia Selene , Wijffels Rene H. , Smidt Hauke , Sipkema Detmer 
Published: March 2021

SummaryMarine photosynthetic microalgae are ubiquitously associated with bacteria in nature. However, the influence of these bacteria on algal cultures in bioreactors is still largely unknown. In this study, eighteen different bacterial strains were isolated from cultures of Nannochloropsis sp. CCAP211/78 in two outdoor pilot‐scale tubular photobioreactors. The majority of isolates was affiliated with the classes Alphaproteobacteria and Flavobacteriia. To assess the impact of the eighteen strains on the growth of Nannochloropsis sp. CCAP211/78, 24‐well plates coupled with custom‐made LED boxes were used to simultaneously compare replicate axenic microalgal cultures with addition of individual bacterial isolates. Co‐culturing of Nannochloropsis sp. CCAP211/78 with these strains demonstrated distinct responses, which shows that the technique we developed is an efficient method for screening the influence of harmful/beneficial bacteria. Two of the tested strains, namely a strain of Maritalea porphyrae (DMSP31) and a Labrenzia aggregata strain (YP26), significantly enhanced microalgal growth with a 14% and 12% increase of the chlorophyll concentration, respectively, whereas flavobacterial strain YP206 greatly inhibited the growth of the microalga with 28% reduction of the chlorophyll concentration. Our study suggests that algal production systems represent a ‘natural’ source to isolate and study microorganisms that can either benefit or harm algal cultures.
The Benefits of Deliberative Involvement in the Design of Incomplete Feedback Systems*
Authors: Grasser Robert A. , Majerczyk Michael , Staehle Martin , Yang Di 
Published: March 2021

ABSTRACTThis study examines the benefits of employee involvement in feedback system design for cooperation. Understanding how to enhance cooperation is important given the increasing use of team settings in practice. Control systems often provide feedback on cooperative actions of coworkers, which can help enable cooperation in teams and between organizational units. We predict that involvement in the design of feedback systems can be a source of trust between employees and enhances cooperation. This is particularly important for dynamic environments, in which an incomplete feedback system which initially provides perfect signals of cooperation no longer does so after the environment changes. Adding to prior evidence, we find that an incomplete feedback system can benefit cooperation in a static environment, but the benefit is greater when employees were initially involved in its design. In a dynamic environment, an incomplete feedback system fails to facilitate cooperation unless employees were involved in its design. Our results identify a behavioral benefit for firms that grant decision rights to employees as part of their organizational architecture.
Fuzzy quantification of common and rare species in ecological communities (FuzzyQ)
Authors: Balbuena Juan A. , Monlleó‐Borrull Clara , Llopis‐Belenguer Cristina , Blasco‐Costa Isabel , Sarabeev Volodimir L. , Morand Serge 
Published: March 2021

Abstract

Most species in ecological communities are rare, whereas only a few are common. This distributional paradox has intrigued ecologists for decades but the interpretation of species abundance distributions remains elusive.

We present Fuzzy Quantification of Common and Rare Species in Ecological Communities (FuzzyQ) as an R package. FuzzyQ shifts the focus from the prevailing species‐categorization approach to develop a quantitative framework that seeks to place each species along a rarity‐commonness gradient. Given a community surveyed over a number of sites, quadrats, or any other convenient sampling unit, FuzzyQ uses a fuzzy clustering algorithm that estimates a probability for each species to be common or rare based on abundance–occupancy information. Such a probability can be interpreted as a commonness index ranging from 0 to 1. FuzzyQ also provides community‐level metrics about the coherence of the allocation of species into the common and rare clusters that are informative of the nature of the community under study.

The functionality of FuzzyQ is shown with two real datasets. We demonstrate how FuzzyQ can effectively be used to monitor and model spatiotemporal changes in species commonness, and assess the impact of species introductions on ecological communities. We also show that the approach works satisfactorily with a wide range of communities varying in species richness, dispersion and abundance currencies.

FuzzyQ produces ecological indicators easy to measure and interpret that can give both clear, actionable insights into the nature of ecological communities and provides a powerful way to monitor environmental change on ecosystems. Comparison among communities is greatly facilitated by the fact that the method is relatively independent of the number of sites or sampling units considered. Thus, we consider FuzzyQ as a potentially valuable analytical tool in community ecology and conservation biology.