bluuebunny/crossref_metadata_2025_split huggingface dataset:
Switching on the light: using metagenomic shotgun sequencing to characterize the intestinal microbiome of Atlantic cod
Authors: Riiser Even Sannes , Haverkamp Thomas H.A. , Varadharajan Srinidhi , Borgan Ørnulf , Jakobsen Kjetill S. , Jentoft Sissel , Star Bastiaan 
Published: February 2019

AbstractThe biological roles of the intestinal microbiome and how it is impacted by environmental factors are yet to be determined in wild marine fish species. Atlantic cod (Gadus morhua) is an ecologically important species with a wide-spread distribution in the North Atlantic Ocean. 16S rRNA-based amplicon analyses found no geographical differentiation between the intestinal microbiome of Atlantic cod from different locations. Nevertheless, it is unclear if this lack of differentiation results from an insufficient resolution of this method to resolve fine-scaled biological complexity. Here, we take advantage of the increased resolution provided by metagenomic shotgun sequencing to investigate the intestinal microbiome of 19 adult Atlantic cod individuals from two coastal populations in Norway – located 470 km apart. Our results show that the intestinal microbiome is dominated by theVibrionalesorder, consisting of varying abundances ofPhotobacterium, AliivibrioandVibriospecies. Moreover, resolving the species community to unprecedented resolution, we identify two abundant species,P. iliopiscariumandP. kishitanii,which comprise over 50% of the classified reads. Interestingly, genomic data shows that the intestinalP. kishitaniistrains have functionally intactluxgenes, and its high abundance suggests that fish intestines form an important part of its ecological niche. These observations support a hypothesis that bioluminescence plays an ecological role in the marine food web. Despite our improved taxonomical resolution, we identify no geographical differences in bacterial community structure, indicating that the intestinal microbiome of these coastal cod is colonized by a limited number of closely related bacterial species with a broad geographical distribution that are well suited to thrive in this host-associated environment.
Generation of inducible SMARCAL1 knock-down iPSC to model severe Schimke immune-osseous dysplasia reveals a link between replication stress and altered expression of master differentiation genes
Authors: Pugliese Giusj Monia , Salaris Federico , Palermo Valentina , Marabitti Veronica , Morina Nicolò , Rosa Alessandro , Franchitto Annapaola , Pichierri Pietro 
Published: February 2019

ABSTRACTThe Schimke immuno-osseous dysplasia is an autosomal recessive genetic osteochondrodysplasia characterized by dysmorphism, spondyloepiphyseal dysplasia, nephrotic syndrome and frequently T cell immunodeficiency. Several hypotheses have been proposed to explain pathophysiology of the disease, however, the mechanism by which SMARCAL1 mutations cause the syndrome is elusive. Indeed, animal models of the disease are absent or useless to provide insight into the disease mechanism, since they do not recapitulate the phenotype. We generated a conditional knockdown model of SMARCAL1 in iPSCs to mimic conditions of cells with severe form the disease. Here, we characterize this model for the presence of phenotype linked to the replication caretaker role of SMARCAL1 using multiple cellular endpoints. Our data show that conditional knockdown of SMARCAL1 in human iPSCs induces replication-dependent and chronic accumulation of DNA damage triggering the DNA damage response. Furthermore, they indicate that accumulation of DNA damage and activation of the DNA damage response correlates with increased levels of R-loops and replication-transcription interference. Finally, we provide data showing that, in SMARCAL1-deficient iPSCs, DNA damage response can be maintained active also after differentiation, possibly contributing to the observed altered expression of a subset of germ layer-specific master genes. In conclusion, our conditional SMARCAL1 iPSCs may represent a powerful model where studying pathogenetic mechanisms of severe Schimke immuno-osseous dysplasia, thus overcoming the reported inability of different model systems to recapitulate the disease.
Environmental DNA (eDNA) metabarcoding of pond water as a tool to survey conservation and management priority mammals
Authors: Harper Lynsey R. , Handley Lori Lawson , Carpenter Angus I. , Murray-Dickson Gill , Muri Cristina Di , Macgregor Callum J. , Logan Thomas W. , Law Alan , Breithaupt Thomas , Read Daniel S. , McDevitt Allan D. , Hänfling Bernd 
Published: February 2019

AbstractEnvironmental DNA (eDNA) metabarcoding is largely used to survey aquatic communities, but can also provide data on terrestrial taxa utilising aquatic habitats. However, the entry, dispersal, and detection of terrestrial species’ DNA within waterbodies is understudied.We evaluated eDNA metabarcoding of pond water for monitoring semi-aquatic, ground-dwelling, and arboreal mammals, and examined spatiotemporal variation in mammal eDNA signals using experiments in captive and wild conditions.We selected nine focal species of conservation and management concern: European water vole, European otter, Eurasian beaver, European hedgehog, European badger, red deer, Eurasian lynx, red squirrel, and European pine marten. We hypothesised that eDNA signals (i.e. proportional read counts) would be stronger for semi-aquatic than terrestrial species, and at sites where mammals exhibited behaviours (e.g. swimming, urination). We tested this by sampling waterbodies in enclosures of captive focal species at specific sites where behaviours had been observed (‘directed’ sampling) and at equidistant intervals along the shoreline (‘stratified’ sampling). We then surveyed natural ponds (N = 6) where focal species were present using stratified water sampling, camera traps, and field signs. eDNA samples were metabarcoded using vertebrate-specific primers.All focal species were detected in captivity. eDNA signal strength did not differ between directed and stratified samples across or within species, between species lifestyles (i.e. semi-aquatic, ground-dwelling, arboreal), or according to behaviours. Therefore, eDNA was evenly distributed within artificial waterbodies. Conversely, eDNA was unevenly distributed in natural ponds. eDNA metabarcoding, camera trapping, and field signs detected beaver, red deer, and roe deer. Badger and red fox were recorded with cameras and field signs, but not eDNA metabarcoding. However, eDNA metabarcoding detected small mammals missed by cameras and field signs, e.g. water vole. Terrestrial mammal eDNA signals were weaker and detected in fewer samples than semi-aquatic mammal eDNA signals.eDNA metabarcoding has potential for inclusion in mammal monitoring schemes by enabling large-scale, multi-species distribution assessment for priority and difficult to survey species, and could provide early indication of range expansions or contractions. However, eDNA surveys need high spatiotemporal resolution and metabarcoding biases require further investigation before this tool is routinely implemented.
Defining mucosal immunity using mass cytometry following experimental human pneumococcal challenge
Authors: Jochems Simon P. , Ruiter Karin de , Solórzano Carla , Voskamp Astrid , Mitsi Elena , Nikolaou Elissavet , Carniel Beatriz F , Pojar Sherin , German Esther L. , Reiné Jesús , Soares-Schanoski Alessandra , Hill Helen , Robinson Rachel , Hyder-Wright Angela D. , Weight Caroline M. , Durrenberger Pascal F. , Heyderman Robert S. , Gordon Stephen B. , Smits Hermelijn H. , Urban Britta C. , Rylance Jamie , Collins Andrea M. , Wilkie Mark D. , Lazarova Lepa , Leong Samuel C. , Yazdanbakhsh Maria , Ferreira Daniela M. 
Published: February 2019

SummaryStreptococcus pneumoniae (Spn) is a common cause of respiratory infection, but also frequently colonises the nasopharynx in the absence of disease. We used mass cytometry to study immune cells from nasal biopsy samples, collected following experimental human pneumococcal challenge, in order to identify immunological changes that follow and control spn colonisation. Using 37 markers, we characterized 293 nasal immune cell clusters, of which 7 were associated with Spn colonisation. B cell and CD8+CD161+ T cell clusters were significantly higher in non-colonised than in colonised subjects. Spn colonization led to recirculation of not only Spn-specific but also aspecific nasal B cells. This associated with increased numbers of circulating plasmablasts and increased antibody levels against the unrelated bacterium Haemophilus influenzae. In addition, we demonstrated that baseline functionality of blood mucosal associated invariant T (MAIT) cells associated with protection against Spn. These results identify new host-pathogen interactions at the mucosa upon Spn colonisation.
Does competitiveness moderate inclusive growth: a panel study of low-income countries
Authors: Kalim Rukhsana , Arshed Noman , Shaheen Sadaf 
Published: February 2019

Purpose
In the past few years, the concept of competitiveness developed by the World Economic Forum has become the focal point. Global competitiveness index (GCI) presents the constructs which are possible means of productivity of the country. The purpose of this study is to explore whether boosting the productivity of agriculture, services and industry sector is the possible channel of competitiveness leading to growth.

Design/methodology/approach
For this, panel GMM moderator model has been used for 16 low-income countries.

Findings
The results indicate that competitiveness helps agriculture and industry sector to become more growth productive, while it reduces the productivity of services sector.

Originality/value
This study urges that the gains from following the competition promotion policies overweigh the costs. Hence, low-income countries can break the low productivity trap.
Developing a benchmarking system for architecture design firms
Authors: Salvatierra José Luis , Gálvez Miguel Ángel , Bastías Freddy , Castillo Tito , Herrera Rodrigo Fernando , Alarcón Luis Fernando 
Published: February 2019

Purpose
The construction industry’s business model is mainly based on the interaction among the architecture office, the engineering office and the construction company. The performance and practices of architects’ offices, unlike those of the other actors, are difficult to characterize and there have been few studies on these issues. To better understand architects’ performance, the purpose of this paper is to develop a benchmarking tool based on real practices identified by managers of Chilean architecture offices.

Design/methodology/approach
The research method includes a complete literature review, followed by a study of a sample of nine Chilean architecture offices, with whom a series of four workshops was developed, to establish both performance indicators and relevant management practices. Finally, these metrics were applied in an architectural office as a pilot case.

Findings
Four management dimensions were defined: client management, external coordination, internal organization and human resources. Key performance indicators were divided into process, financial and quality indicators. The workshops carried out with the architectural offices demonstrated the relevance of benchmarking tools such as the one developed, which enables the systematic measurement of both management practices and performance indicators.

Originality/value
Although there have been several efforts to create benchmarking tools for the construction industry, few efforts have focused on architecture offices. Therefore, this research aims to explicitly identify management practices that can be used for this type of organization and to coordinate among multiple actors to find the best way to measure their performance, other than the fulfilment of schedules and budgets.
Client and contractor roles in schedule incentive/disincentive projects
Authors: Hasan Abid , Jha Kumar Neeraj 
Published: February 2019

Purpose
Delays in construction projects can be very expensive due to their adverse effects on project cost and profit margin. To overcome this problem, clients in the construction industry sometimes use schedule incentive/disincentive (I/D) contracting strategy. However, previous studies have shown that inadequate understanding and wrong implementation of schedule I/D provisions could result in unintended results. Moreover, the use of the I/D contracting method is in its initial stages in many countries such as India. The purpose of this paper is to identify various factors that are essential for schedule I/D success in construction projects.

Design/methodology/approach
A questionnaire survey was conducted among experienced professionals (clients, contractors and consultants) from across the Indian construction industry.

Findings
Top success factors related to clients in the descending order of their importance are: realistic targets; detailed guidelines for I/D implementation; close coordination with other stakeholders; correct estimation of I/D duration and amount; and imposing disincentives after due consideration. Meanwhile, factors related to contractor organisations are: continuous monitoring and control; thorough understanding of schedule I/D targets; specific considerations in appointing senior project personnel; effective communication; and proper labour management.

Research limitations/implications
This empirical research was conducted in the Indian construction industry. Similar studies from developed construction markets may provide more insights into the successful use of schedule I/D provisions in construction projects.

Practical implications
The uptake of these recommendations is likely to increase the success of schedule I/D provisions in construction projects, especially in developing countries where the use of I/D contracting strategy is not very popular.

Originality/value
This research highlights the specific roles of both clients and contractors in the success of schedule I/D projects in developing countries such as India.
Facilities management in the NHS: overlapping authority and demarcation disputes
Authors: May Daryl 
Published: February 2019

Purpose
This research aims to investigate the implementation of the new ward housekeeper role in a hospital setting. The purpose is to propose a model to demonstrate how facilities management (FM) departments and clinical ward teams work together effectively to deliver catering and cleaning services.

Design/methodology/approach
The context of the implementation of the role was deemed a necessary feature, particularly to understand the organisational structures. In this case, the context was a hospital, and the underlying mechanisms that were in place included local recruitment and retention issues. Therefore, an interpretive approach was taken, and a series of semi-structured interviews was the primary method to collect data, supplemented by some non-participant observation and document analysis.

Findings
The findings from the two themes enable the development of a model to illustrate the working relationships between FM departments and clinical ward teams.

Practical implications
The findings from the study are of significance for hospital facilities and estates departments and clinical stakeholders who have the responsibility of ward catering, cleaning and the environment.

Originality/value
The significance of this study emerges through the advancement of methodology within the context of facilities in health care and through the contribution to knowledge and practice as a result of the proposed mode. This was the first type of study to look in detail at ward housekeeping models, using an interpretive approach over a relatively long period of time.
Long-term trajectories of human civilization
Authors: Baum Seth D. , Armstrong Stuart , Ekenstedt Timoteus , Häggström Olle , Hanson Robin , Kuhlemann Karin , Maas Matthijs M. , Miller James D. , Salmela Markus , Sandberg Anders , Sotala Kaj , Torres Phil , Turchin Alexey , Yampolskiy Roman V. 
Published: February 2019

PurposeThis paper aims to formalize long-term trajectories of human civilization as a scientific and ethical field of study. The long-term trajectory of human civilization can be defined as the path that human civilization takes during the entire future time period in which human civilization could continue to exist.Design/methodology/approachThis paper focuses on four types of trajectories: status quo trajectories, in which human civilization persists in a state broadly similar to its current state into the distant future; catastrophe trajectories, in which one or more events cause significant harm to human civilization; technological transformation trajectories, in which radical technological breakthroughs put human civilization on a fundamentally different course; and astronomical trajectories, in which human civilization expands beyond its home planet and into the accessible portions of the cosmos.FindingsStatus quo trajectories appear unlikely to persist into the distant future, especially in light of long-term astronomical processes. Several catastrophe, technological transformation and astronomical trajectories appear possible.Originality/valueSome current actions may be able to affect the long-term trajectory. Whether these actions should be pursued depends on a mix of empirical and ethical factors. For some ethical frameworks, these actions may be especially important to pursue.
Customer data security and theft: a Malaysian organization’s experience
Authors: Abidin Mohd Aizuddin Zainal , Nawawi Anuar , Salin Ahmad Saiful Azlin Puteh 
Published: February 2019

PurposeThis study aims to identify weaknesses in current internal control systems in protecting customer data and the drivers that motivate employees to steal customer data and the impact of customer data theft on the organization.Design/methodology/approachA case study approach was taken to investigate and analyze internal control system weaknesses. One organization that involved investor and treasury services was selected as a case study in this research. A mixed method of data collection, specifically survey questionnaires and observations, was used.FindingsThis study revealed that employees are aware of the policy to protect customer data in their organization. Ironically, customer data theft still occurred despite the company having an internal control system. The main concern was the attitude of the employees to adhere to the policies in place, which becomes the major cause of internal control violation. Employees tend to ignore policies and standard operating procedures, providing opportunities for data theft and fraud to occur, although they realize this will result in a severe impact on the reputation of a company.Research limitations/implicationsThe results provide further confirmation of the fraud triangle theory, i.e. opportunity on the possible causes of the data theft and fraud, supporting prior empirical research and surveys conducted by researchers and global professional firms on fraud. This study, however, was conducted on only one organization with limited participation from employees because of the sensitivity of the nature of the topic.Practical implicationsThis study provided recommendations that can be a reference for companies and regulatory bodies in preventing customer data theft cases, such as regular training and awareness campaigns to the staff, stringent recruitment policies, close monitoring on the accessibility of customer data and continuous use of advanced technology to prevent a data breach.Originality/valueThis study is original, as it focuses on an organization that operates in the financial services industry, which is one of the most attacked sectors for data theft and cybercrime activity globally. Furthermore, this kind of research is rare in fraud literature, particularly in developing markets such as Malaysia. The findings of this study are inferred from the direct observation of the organizational and employee work environments, activities and behaviors, which are private and confidential and difficult to access by researchers for publication in academic journals.
Actionable threat intelligence for digital forensics readiness
Authors: Serketzis Nikolaos , Katos Vasilios , Ilioudis Christos , Baltatzis Dimitrios , Pangalos George J. 
Published: February 2019

PurposeThe purpose of this paper is to formulate a novel model for enhancing the effectiveness of existing digital forensic readiness (DFR) schemes by leveraging the capabilities of cyber threat information sharing.Design/methodology/approachThis paper uses a quantitative methodology to identify the most popular cyber threat intelligence (CTI) elements and introduces a lightweight approach to correlate those with potential forensic value, resulting in the quick and accurate triaging and identification of patterns of malicious activities.FindingsWhile threat intelligence exchange steadily becomes a common practice for the prevention or detection of security incidents, the proposed approach highlights its usefulness for the digital forensics (DF) domain.Originality/valueThe proposed model can help organizations to improve their DFR posture, and thus minimize the time and cost of cybercrime incidents.
Gamble more than you want?
Authors: Ho Ying , Lam Long W. , Lam Desmond 
Published: February 2019

Purpose
This study aims to explore the influence of casino servicescape on unplanned gaming behaviors by examining the mediating role of casino customers’ perceived behavioral control (i.e. perceived internal and external control).

Design/methodology/approach
Data were collected from 475 casino customers using street intercept survey. Multiple regression analysis was used to evaluate the mediating role of perceived behavioral control.

Findings
Results show a negative indirect effect of casino servicescape evaluation on customers’ unplanned gaming behaviors through perceived internal control. Moreover, casino customers’ perceived external control does not mediate the relationship between casino servicescape evaluation and unplanned gaming behaviors.

Research limitations/implications
Findings suggest that a favorable casino servicescape may enhance customers’ perception of control over their personal resources (e.g. skills and knowledge), which in turn facilitate self-regulation of their unplanned gaming behaviors. The findings are limited to Chinese casino customers, and researchers should further validate the results for non-Chinese casino patrons.

Practical implications
To casino operators, results suggest that the Friedman-style casino design (i.e. compact gambling areas and low ceilings) potentially encourages unplanned gaming behaviors of casino customers. From social-policy perspective, governments can create effective responsible gaming programs by enhancing casino customers’ perceived internal control.

Originality/value
This study illuminates the process that connects casino servicescape with unplanned gaming behavior by explicitly testing the mediating role of customers’ perceived behavioral control. Moreover, it examines unplanned gaming behaviors of leisure gamblers who represent the mass gaming population.