bluuebunny/crossref_metadata_2025_split huggingface dataset:
Struo2: efficient metagenome profiling database construction for ever-expanding microbial genome datasets
Authors: Youngblut Nicholas D. , Ley Ruth E. 
Published: February 2021

AbstractMapping metagenome reads to reference databases is the standard approach for assessing microbial taxonomic and functional diversity from metagenomic data. However, public reference databases often lack recently generated genomic data such as metagenome-assembled genomes (MAGs), which can limit the sensitivity of read-mapping approaches. We previously developed the Struo pipeline in order to provide a straight-forward method for constructing custom databases; however, the pipeline does not scale well with the ever-increasing number of publicly available microbial genomes. Moreover, the pipeline does not allow for efficient database updating as new data are generated. To address these issues, we developed Struo2, which is >3.5-fold faster than Struo at database generation and can also efficiently update existing databases. We also provide custom Kraken2, Bracken, and HUMAnN3 databases that can be easily updated with new genomes and/or individual gene sequences. Struo2 enables feasible database generation for continually increasing large-scale genomic datasets.AvailabilityStruo2:https://github.com/leylabmpi/Struo2Pre-built databases:http://ftp.tue.mpg.de/ebio/projects/struo2/Utility tools:https://github.com/nick-youngblut/gtdb_to_taxdump
Patient derived models of bladder cancer amplify tumor specific gene expression compared to surgical specimen while maintaining gene expression of molecular subtype and epithelial mesenchymal transition markers
Authors: Mastri Michalis , Ramakrishnan Swathi , Shah Shruti , Karasik Ellen , Gillard Bryan M , Moser Michael M , Farmer Bailey K , Azabdaftari Gissou , Chatta Gurkamal S , Woloszynska Anna , Eng Kevin H , Foster Barbara A , Huss Wendy J 
Published: February 2021

AbstractPatient derived models (PDMs) are a powerful tool to study preclinical responses. However, the benefits of each model have not been compared head-to-head when models are derived from the same surgical specimen. PDMs derived from surgical specimens were established as xenografts (PDX), organoids (PDO), and spheroids (PDS). PDMs were molecularly characterized by RNA sequencing. Differential gene expression was determined between the PDMs and surgical specimens. Surgical specimens had the most differentially expressed genes reflecting loss of immune and stromal compartments in PDMs. PDMs and surgical specimens were clustered using the Euclidian distance analysis to test model fidelity. PDMs upregulated a clear, patient-specific bladder cancer signal. Overall, the molecular profiles of PDXs were the most similar to the matching patient surgical specimen than the PDO and PDS from that patient. The epithelial mesenchymal transition (EMT) gene expression profile is maintained in the PDMs showing the persistence of EMT in bothin vivoandin vitromodel setting. The consensus molecular subtype was determined in order to compare PDMs to each other and their matching surgical specimen, and only surgical specimens with Basal/Squamous or Luminal Papillary molecular subtype established PDMs. Patient derived models reduce tumor heterogeneity and allow analysis of specific tumor compartments while maintaining the gene expression profile representative of the original tumor.
Human factors affecting information security in libraries
Authors: Amini Masoumeh , Vakilimofrad Hossein , Saberi Mohammad Karim 
Published: February 2021

PurposeInformation security is a critical issue in all organizations. The success of information security in libraries depends, to a large extent, on the effective behavior of administrators, librarians, users and all human staff. Accordingly, this study aims to design a model for identifying human factors affecting information security in libraries.Design/methodology/approachThis study is applied in terms of research objectives and is a survey in terms of data collection. Moreover, it goes under the rubric of structural equation modeling in terms of the relationship between variables. The statistical population consisted of 100 managers and librarians of academic and public libraries of Hamadan in Iran. A questionnaire was used for data collection. The face and content validity of the questionnaire were examined using the expert’s opinions in the field of Iranian libraries. Also, the reliability of the questionnaire was calculated through Cronbach’s alpha coefficient. Data were analyzed using SPSS 16 and Smart PLS 2.FindingsThe results showed that among the components of information security, the highest score was designated to self-esteem (4.11 ± 0.57) and level of skill (4.07 ± 0.59), whereas the lowest score belonged to the level of education (3.51 ± 0.74). Ranking human factors affecting information security showed that experience with Rank 1 had the most impact, whereas the level of skill with Rank 6 had the least impact on information security.Originality/valueIn this study, for the first time, a model was designed and tested for human factors affecting information security in libraries. Information security professionals, librarians and library and information science researchers can exploit this model in the future.
Sensitivities of Southeast Asian industries to the local and global business cycles
Authors: Iqbal Javed 
Published: February 2021

PurposeThis paper estimates the sensitivities of the output of the manufacturing industries of the four Southeast countries (Indonesia, Malaysia, Philippines, Singapore) to both the country-specific and global business cycle fluctuations. The study investigates whether the business cycle exposures of these industries differ to their nature classified as producing durable or nondurable goods and also to booms and recessions.Design/methodology/approachUsing annual time series data on sectoral manufacturing production indices for major manufacturing industries over the period from 1999 to 2018, this paper uses the seemingly unrelated regression (SUR)–based generalized least square estimator to estimate the exposures of each industry for each of the four countries to local and world business cycle.FindingsThe individual country analysis indicates that generally the sensitivities of the ASEAN manufacturing industries to booms and recessions are different from the pattern observed in the developed countries and Russia. We do not find evidence consistent with the commonly held view among economists and business managers that demand for durable goods flourishes in booms and falls in recessions. Also, very few industries exhibit an asymmetric reaction to booms and busts. However, the analysis of panel data reveals the expected pattern of industrial sensitivities to the local business cycle only.Originality/valueThe paper makes several contributions. Firstly, the model proposed in the paper estimates sensitivities of industries to both the local and global business cycle variations. Secondly, the model enables us to explicitly test the asymmetric reaction of industries to booms and busts. Thirdly, the paper is the first attempt to estimating business cycle exposures for manufacturing industries in emerging markets.
The role of market power in driving innovation and productivity: a firm-level study of emerging ASEAN
Authors: Zhang Jianhua , Islam Mohammad Shahidul 
Published: February 2021

PurposeThe primary purpose of the study is to examine the role of market power in driving innovation and productivity of intangible intensive firms of eight emerging economies of the Association of Southeast Asian Nations (ASEAN-8).Design/methodology/approachThere is hardly any study on emerging economies that explored the causal chain of R&D–innovation–productivity, considering the role of market power in a structural model. Taking advantage of the availability of firm-level data and following the extended version of the Crépon, Duguet and Mairesse (CDM) model, we intend to fill the gap. The CDM model first explores the link between R&D and innovation, then the latter's impact on productivity. Besides, it captures sectoral heterogeneity and the differing roles of technological and institutional innovation on productivity.FindingsThe manufacturing firms that held a higher markup had a more significant contribution to driving innovation than services one. While institutional innovation affected productivity positively, technological innovation had the opposite impact. Nevertheless, firms' higher degree of monopoly, in general, worsened productivity outcomes. The estimated results are robust to a range of alterations.Practical implicationsThe study offers implications for the competition policy of ASEAN.Originality/valueThe sample of this study accounts for almost half of the world's best-performing emerging economies. Thus, the findings are likely to contribute to the thin literature on market power's role in driving innovation and productivity in the intangible economy of emerging markets.
Money matters – primary care providers' perceptions of payment incentives
Authors: Vengberg Sofie , Fredriksson Mio , Burström Bo , Burström Kristina , Winblad Ulrika 
Published: February 2021

PurposePayments to healthcare providers create incentives that can influence provider behaviour. Research on unit-level incentives in primary care is, however, scarce. This paper examines how managers and salaried physicians at Swedish primary healthcare centres perceive that payment incentives directed towards the healthcare centre affect their work.Design/methodology/approachAn interview study was conducted with 24 respondents at 13 primary healthcare centres in two cities, located in regions with different payment systems. One had a mixed system comprised of fee-for-service and risk-adjusted capitation payments, and the other a mainly risk-adjusted capitation system.FindingsFindings suggested that both managers and salaried physicians were aware of and adapted to unit-level payment incentives, albeit the latter sometimes to a lesser extent. Respondents perceived fee-for-service payments to stimulate production of shorter visits, up-coding of visits and skimming of healthier patients. Results also suggested that differentiated rates for patient visits affected horizontal prioritisations between physician and nurse visits. Respondents perceived that risk-adjustments for diagnoses led to a focus on registering diagnosis codes, and to some extent, also up-coding of secondary diagnoses.Practical implicationsPolicymakers and responsible authorities need to design payment systems carefully, balancing different incentives and considering how and from where data used to calculate payments are retrieved, not relying too heavily on data supplied by providers.Originality/valueThis study contributes evidence on unit-level payment incentives in primary care, a scarcely researched topic, especially using qualitative methods.
Entrepreneurship in Turkey and other Balkan countries: are there opportunities for mutual co-operation through internationalisation?
Authors: Tekin Erol , Ramadani Veland , Dana Leo-Paul 
Published: February 2021

Purpose
The aim of this study is to evaluate the entrepreneurship activity in Turkey and the Balkan countries and to show in which fields they can cooperate in the future.

Design/methodology/approach
Document analysis was used in the research. In this context, taking into consideration the Global Entrepreneurship Index data published in 2019, the entrepreneurial potentials of Balkan countries, its current status was examined. Therefore, Turkey’s contribution to the development of entrepreneurial activities in the Balkan countries is shown in the study.

Findings
The results of the research show that entrepreneurship activities in the Balkan countries are not at the expected levels. In addition, it is determined that Turkey is in a central position in the Balkan’s entrepreneurship ecosystem in subjects such as especially, product innovation, risk capital, the ability of entrepreneurial start-up and its enterprises show high growth. Other Balkan countries may cooperate with Turkey about the production of technological products and technology transfer issues. Partner incubation programs can be formed. Training activities related to the entrepreneurship ecosystem can be organised together.

Originality/value
To the best of the authors’ knowledge, this paper is one of the first study that addresses the current situation of Balkan countries by analysing the entrepreneurship index scores of Turkey and Balkan countries (Albania, Bulgaria, Bosnia and Herzegovina, Montenegro, Romania, Croatia, Serbia, northern Macedonia, Greece and Slovenia). It also formulated suggestions on establishing cooperation with Turkey.
Perceived firm ethicality and brand loyalty: the mediating role of corporate social responsibility and perceived green marketing
Authors: Amoako George Kofi , Doe Joshua Kofi , Dzogbenuku Robert Kwame 
Published: February 2021

Purpose
This study aims to establish the link between business ethics and brand loyalty and to investigate the mediating role of corporate social responsibility (CSR) and United Nations Sustainable Development Goals (SDGs) such as green marketing.

Design/methodology/approach
Using the purposive sampling technique, data were obtained from 622 middle-income city dwellers who shop at leading retail malls. Data were analyzed with partial least square–structural equation model.

Findings
The study found a positive and significant relationship between business ethics, CSR, green marketing and business loyalty. Both CSR and green marketing mediate between perceived firm ethicality and brand loyalty.

Research limitations/implications
This research was done based on general knowledge of business ethics, CSR and green marketing from the consumers’ perspective. Future studies can avoid this limitation.

Practical implications
By ensuring ethical codes, CSR and green marketing, firms can contribute to promoting the SDGs, and at the same time, achieving customer loyalty. Brand loyalty is further enhanced if customers see a firm to be practicing CSR.

Social implications
The SDGs of sustainable production patterns, climate change and its impacts, and sustainably using water resources must become the focus of companies as they ultimately yield loyalty. Policymakers and society can design a policy to facilitate adoption of better ethical behavior and green marketing by firms as a way of promoting SDGs.

Originality/value
To the best of the authors’ knowledge, this study is the first to test the mediation effect of green marketing and CSR on how ethical behavior leads to brand loyalty. It is also one of the few papers to examine how SDGs can be promoted by businesses as stakeholders.
Unburnt habitat patches are critical for survival and in situ population recovery in a small mammal after fire
Authors: Shaw Robyn E. , James Alex I. , Tuft Katherine , Legge Sarah , Cary Geoffrey J. , Peakall Rod , Banks Sam C. 
Published: February 2021

Abstract

Fire drives animal population dynamics across many ecosystems. Yet, we still lack an understanding of how most species recover from fire and the effects of fire severity and patchiness on recovery processes. This information is crucial for fire‐mediated biodiversity conservation, particularly as fire regimes change globally.

We conducted an experiment to test whether post‐fire recovery is driven by in situ survival or recolonisation, and to determine whether this varies with fires of increasing percentage area burnt (burn cover) and severity. We used the pale field rat Rattus tunneyi as a model, because it represents the extinction process for a suite of mammal species suffering population collapse across Australia's northern savannas. Our treatments spanned a gradient from patchy, low severity fires (simulating early dry season management burns) to thorough, high severity fires (simulating wildfires). We performed capture–mark–recapture, vegetation and aerial surveys before, 6 weeks after and 1 year after fire.

Six weeks after fire, pale field rats were only captured in unburnt patches of vegetation, and capture rates were proportional to the amount of unburnt habitat. One year later, both vegetation and pale field rat populations recovered across all sites. However, population recovery after low severity fires was likely achieved through in situ survival and reproduction in unburnt micro‐refuges, compared to recolonisation driving recovery after high severity fires.

Synthesis and applications. Pale field rat persistence is strongly dependent on the retention of unburnt habitat patches within fire‐affected areas. Management strategies that increase micro‐refugia within burnt areas may facilitate pale field rat population recovery. Globally, building recovery mechanisms into fire management will be vital for supporting the long‐term persistence of fire‐affected species.
Being Conscious of Unconscionability in Modern Times: Heller v Uber Technologies
Authors: Gardner Jodi 
Published: February 2021

AbstractRequiring low‐paid drivers to sign an Arbitration Clause removing their right to local court processes can be unconscionable and, if so, the clause is not enforceable. This was the conclusion reached by the majority of the Supreme Court of Canada when considering a contractual provision that mandated all external dispute resolution processes go through mediation and arbitration in the Netherlands and required upfront fees of $14,500USD to do so. In this case note, it is argued that the Canadian decision opens the door for the United Kingdom to rethink the role of unconscionability and how the doctrine could apply to modern contractual arrangements. Heller v Uber Technologies provides the opportunity to develop the elements of unconscionability in a way that tackles inequality of bargaining power in standard form contracts, particularly when they fall outside the protection of the Consumer Rights Act 2015.
The micro–macro interactive approach to political trust: Quality of representation and substantive representation across Europe
Authors: NOORDZIJ KJELL , DE KOSTER WILLEM , VAN DER WAAL JEROEN 
Published: February 2021

AbstractThe relevance of the macro‐context for understanding political trust has been widely studied in recent decades, with increasing attention paid to micro–macro level interactive relationships. Most of these studies rely on theorising about evaluation based on the quality of representation, stressing that more‐educated citizens are most trusting of politics in countries with the least corrupt public domains. In our internationally comparative study, we add to the micro–macro interactive approach by theorising and testing an additional way in which the national context is associated with individual‐level political trust, namely evaluation based on substantive representation. The relevance of both types of evaluation is tested by modelling not only macro‐level corruption but also context indicators of the ideological stances of the governing cabinet (i.e., the level of its economic egalitarianism and cultural liberalism), and interacting these with individual‐level education, economic egalitarianism and cultural liberalism, respectively. As we measure context characteristics separately from people's ideological preferences, we are able to dissect how the macro‐context relates to the levels of political trust of different subgroups differently. Data from three waves (2006, 2010, 2014) of the European Social Survey (68,294 respondents in 24 European countries and 62 country‐year combinations), enriched with country‐level data derived from various sources, including the Chapel Hill Expert Survey, are used in the multi‐level regression analyses employed to test our hypotheses. We found support for the micro–macro level interactions theorised by the evaluation based on the quality of representation approach (with higher levels of trust among more‐educated citizens in less corrupt countries), as well as for evaluation based on substantive representation in relation to cultural issues (with higher levels of trust among more culturally liberal citizens in countries with more culturally liberal governing cabinets). Our findings indicate that the latter approach is at least equally relevant as the approach conventionally used to explain context differences in political trust. Finally, we conclude our study with a discussion of our findings and avenues for future research.
Wavelet methods reveal big cat activity patterns and synchrony of activity with preys
Authors: QI Jinzhe , HOLYOAK Marcel , DOBBINS Michael T. , HUANG Chong , LI Qi , SHE Wen , NING Yao , SUN Quan , JIANG Guangshun , WANG Xiaochun 
Published: February 2021

AbstractAppropriate temporal and spatial scales are important prerequisites for obtaining reliable results in studies of wildlife activity patterns and interspecific interactions. The spread of camera‐trap technology has increased interest in and feasibility of studying the activity patterns and interspecific interactions of wildlife. However, such studies are often conducted at arbitrary spatial and temporal scales, and the methods used impose scale on the study rather than determining how activity and species interactions change with spatial scale. In this study, we used a wavelet‐based approach to determine the temporal and spatial scales for activity patterns and interspecific interactions on Amur leopard and their ungulate prey species that were recorded using camera traps in the main Amur leopard occurrence region in northeast China. Wavelets identified that Amur leopards were more active in spring and fall than summer, and fluctuated with periodicities of 9 and 17 days, respectively. Synchronous relationships between leopards and their prey commonly occurred in spring and fall, with a periodicity of about 20 days, indicating the appropriate seasons and temporal scales for interspecific interaction research. The influence of human activities on the activity patterns of Amur leopard or prey species often occurred over longer time periods (60–64 days). Two‐dimensional wavelet analyses showed that interactions between leopard and prey were more significant at spatial scales of 1 km2. Overall, our study provides a feasible approach to studying the temporal and spatial scales for wildlife activity patterns and interspecific interaction research using camera trap data.
Characterization of a new type of mead fermented with Cannabis sativa L. (hemp)
Authors: Romano Raffaele , Aiello Alessandra , De Luca Lucia , Sica Rosario , Caprio Emilio , Pizzolongo Fabiana , Blaiotta Giuseppe 
Published: February 2021

AbstractMead, one of the oldest existing drinks, is a fermented product based on honey, water, and the possible addition of spices and selected yeasts. In this work, various parts (inflorescences, leaves, and steams) of Cannabis sativa L. at different concentrations and Saccharomyces cerevisiae biotype M3/5 were added during mead fermentation. The physicochemical parameters (pH, alcoholic content, sugar content, titratable acidity, and organic acids) of the mead were assessed at the beginning and end of fermentation. Moreover, polyphenols, cannabidiol and volatile organic compounds were identified at the end of fermentation and compared with the control sample prepared without hemp and with only indigenous yeasts. The mead fermented with hemp showed the highest quantity of polyphenols (227 to 256 mg GAE/L) and a level of cannabidiol ranging from 0.26 to 0.49 mg/kg. The volatile organic compounds found were mainly alcohols, esters and terpenes, which were present at higher concentrations in the mead prepared with C. sativa L. than in the control mead and conferred freshness and “hemp aroma” characteristics.Practical ApplicationInflorescences, leaves, and steams of Cannabis sativa L. were added at different concentrations during mead fermentation. This type of mead showed high quantity of polyphenols (227 to 256 mg GAE/L) and a level of cannabidiol ranging from 0.26 to 0.49 mg/kg which have anxiolytic and neuro‐protective properties. Moreover the volatile organic compounds found (mainly alcohols, esters, and terpenes) conferred freshness and “hemp aroma” characteristics.