bluuebunny/crossref_metadata_2025_split huggingface dataset:
The role ofCaulobactercell surface structures in colonization of the air-liquid interface
Authors: Fiebig Aretha 
Published: January 2019

AbstractIn aquatic environments,Caulobacterspp. are often present at the boundary between liquid and air known as the neuston. I report an approach to study temporal features ofCaulobacter crescentuscolonization and pellicle biofilm development at the air-liquid interface, and have defined the role of cell surface structures in this process. At this interface,C. crescentusinitially forms a monolayer of cells bearing a surface adhesin known as the holdfast. When excised from the liquid surface, this monolayer strongly adheres to glass. The monolayer subsequently develops into a three-dimensional structure that is highly enriched in clusters of stalked cells known as rosettes. As this pellicle film matures, it becomes more cohesive and less adherent to a glass surface. A mutant strain lacking a flagellum does not efficiently reach the surface, and strains lacking type IV pili exhibit defects in organization of the three-dimensional pellicle. Strains unable to synthesize holdfast fail to accumulate at the boundary between air and liquid and do not form a pellicle. Phase contrast images support a model whereby the holdfast functions to trapC. crescentuscells at the air-liquid boundary. Unlike the holdfast, neither the flagellum nor type IV pili are required forC. crescentusto partition to the air-liquid interface. While it is well established that the holdfast enables adherence to solid surfaces, this study provides evidence that the holdfast has physicochemical properties required for partitioning of non-motile mother cells to the air-liquid interface, which facilitates colonization of this microenvironment.ImportanceIn aquatic environments the boundary at the air interface is often highly enriched with nutrients and oxygen. Colonization of this niche likely confers a significant fitness advantage in many cases. This study provides evidence that the cell surface adhesin known as a holdfast enablesCaulobacter crescentusto partition to and colonize the air-liquid interface. Additional surface structures including the flagellum and type IV pili are important determinants of colonization and biofilm formation at this boundary. Considering that holdfast-like adhesins are broadly conserved inCaulobacterspp. and other members of the diverse classAlphaproteobacteria, these surface structures may function broadly to facilitate colonization of air-liquid boundaries in a range of ecological contexts including freshwater, marine, and soil ecosystems.
Comprehensive genome-wide identification of angiosperm upstream ORFs with peptide sequences conserved in various taxonomic ranges using a novel pipeline, ESUCA
Authors: Takahashi Hiro , Hayashi Noriya , Yamashita Yui , Naito Satoshi , Takahashi Anna , Fuse Kazuyuki , Satou Kenji , Endo Toshinori , Kojima Shoko , Onouchi Hitoshi 
Published: January 2019

AbstractBackgroundUpstream open reading frames (uORFs) in the 5′-untranslated regions (5′-UTRs) of certain eukaryotic mRNAs encode evolutionarily conserved functional peptides, such as cis-acting regulatory peptides that control translation of downstream main ORFs (mORFs). For genome-wide searches for uORFs with conserved peptide sequences (CPuORFs), comparative genomic studies have been conducted, in which uORF sequences were compared between selected species. To increase chances of identifying CPuORFs, we previously developed an approach in which uORF sequences were compared using BLAST betweenArabidopsisand any other plant species with available transcript sequence databases. If this approach is applied to multiple plant species belonging to phylogenetically distant clades, it is expected to further comprehensively identify CPuORFs conserved in various plant lineages, including those conserved among relatively small taxonomic groups.ResultsTo efficiently compare uORF sequences among many species and efficiently identify CPuORFs conserved in various taxonomic lineages, we developed a novel pipeline, ESUCA. We applied ESUCA to the genomes of five angiosperm species, which belong to phylogenetically distant clades, and selected CPuORFs conserved among at least three different orders. Through these analyses, we identified 88 novel CPuORF families. As expected, ESUCA analysis of each of the five angiosperm genomes identified many CPuORFs that were not identified from ESUCA analyses of the other four species. However, unexpectedly, these CPuORFs include those conserved in wide taxonomic ranges, indicating that the approach used here is useful not only for comprehensive identification of narrowly conserved CPuORFs but also for that of widely conserved CPuORFs. Examination of the effects of 11 selected CPuORFs on mORF translation revealed that CPuORFs conserved only in relatively narrow taxonomic ranges can have sequence-dependent regulatory effects, suggesting that most of the identified CPuORFs are conserved because of functional constraints of their encoded peptides.ConclusionsThis study demonstrates that ESUCA is capable of efficiently identifying CPuORFs likely to be conserved because of the functional importance of their encoded peptides. Furthermore, our data show that the approach in which uORF sequences from multiple species are compared with those of many other species, using ESUCA, is highly effective in comprehensively identifying CPuORFs conserved in various taxonomic ranges.
Integrin cytoplasmic domain and pITAM compete for spleen tyrosine kinase binding
Authors: Antenucci Lina , Hellman Maarit , Hytönen Vesa P. , Permi Perttu , Ylänne Jari 
Published: January 2019

ABSTRACTIn hematopoietic tissues cell-cell communication involves immunoreceptors and specialized cell adhesion receptors that both mediate intracellular signals. Spleen tyrosine kinase (Syk) is a non-receptor tyrosine kinase involved in the downstream signaling of both immunoreceptors tyrosine activation motif (ITAM) receptors and integrin family cell adhesion receptors. Both phosphorylated ITAM (pITAM) and integrins bind to the regulatory domain of Syk composed of two Src homology 2 (SH2) domains. The interaction with pITAM is mediated by binding of a specific phosphotyrosine to each of the SH2 domains, leading to conformational changes and Syk kinase activation. Integrins bind to the interdomain A segment between the two SH2 domains and to the N-terminal SH2 domain, but the detailed binding site is not known. In order to map the binding site, we performed NMR titration experiments. We found that integrin cytoplasmic domain peptide induced chemical shift changes near the IA segment and at the phosphotyrosine binding site of the N-terminal SH2 domain of Syk. These changes were distinct, but partially overlapping with those induced by pITAM peptide. We were also able to show that pITAM peptide inhibited integrin binding to Syk regulatory domain. These results suggest that ITAM receptors and integrins cannot bind simultaneously to Syk, but provide two distinct routes for Syk activation.
Managing genomic variant calling workflows with Swift/T
Authors: Ahmed Azza E. , Heldenbrand Jacob , Asmann Yan , Fadlelmola Faisal M. , Katz Daniel S. , Kendig Katherine , Kendzior Matthew C. , Li Tiffany , Ren Yingxue , Rodriguez Elliott , Weber Matthew R. , Wozniak Justin M. , Zermeno Jennie , Mainzer Liudmila S. 
Published: January 2019

AbstractGenomic variant discovery is frequently performed using the GATK Best Practices variant calling pipeline, a complex workflow with multiple steps, fans/merges, and conditionals. This complexity makes management of the workflow difficult on a computer cluster, especially when running in parallel on large batches of data: hundreds or thousands of samples at a time. Here we describe a wrapper for the GATK-based variant calling workflow using the Swift/T parallel scripting language. Standard built-in features include the flexibility to split by chromosome before variant calling, optionally permitting the analysis to continue when faulty samples are detected, and allowing users to analyze multiple samples in parallel within each cluster node. The use of Swift/T conveys two key advantages: (1) Thanks to the embedded ability of Swift/T to transparently operate in multiple cluster scheduling environments (PBS Torque, SLURM, Cray aprun environment, etc.,) a single workflow is trivially portable across numerous clusters; (2) The leaf functions of Swift/T permit developers to easily swap executables in and out of the workflow, conditional on the analyst’s choice, which makes the workflow easy to maintain. This modular design permits separation of the workflow into multiple stages and the request of resources optimal for each stage of the pipeline. While Swift/T’s implicit data-level parallelism eliminates the need for the developer to code parallel analysis of multiple samples, it does make debugging of the workflow a bit more difficult, as is the case with any implicitly parallel code. With the above features, users have a powerful and portable way to scale up their variant calling analysis to run in many traditional computer cluster architectures.https://github.com/ncsa/Swift-T-Variant-Callinghttp://swift-t-variant-calling.readthedocs.io/en/latest/
A fresh view on particle swarm optimization to develop a precise model for predicting rock fragmentation
Authors: Sayevand Khosro , Arab Hossein 
Published: January 2019

Purpose
The purpose of this paper is to propose a gauge for the convergence of the deterministic particle swarm optimization (PSO) algorithm to obtain an optimum upper bound for PSO algorithm and also developing a precise equation for predicting the rock fragmentation, as important aims in surface mines.

Design/methodology/approach
In this study, a database including 80 sets of data was collected from 80 blasting events in Shur river dam region, in Iran. The values of maximum charge per delay (W), burden (B), spacing (S), stemming (ST), powder factor (PF), rock mass rating (RMR) and D80, as a standard for evaluating the fragmentation, were measured. To check the performance of the proposed PSO models, artificial neural network was also developed. Accuracy of the developed models was evaluated using several statistical evaluation criteria, such as variance account for, R-square (R2) and root mean square error.

Findings
Finding the upper bounds for the difference between the position and the best position of particles in PSO algorithm and also developing a precise equation for predicting the rock fragmentation, as important aims in surface mines.

Originality/value
For the first time, the convergence of the deterministic PSO is studied in this study without using the stagnation or the weak chaotic assumption. The authors also studied application of PSO inpredicting rock fragmentation.
Modelling of ice rubble in the punch shear tests with cohesive 3D discrete element method
Authors: Sorsimo Arto , Heinonen Jaakko 
Published: January 2019

PurposeThis paper aims to simulate a punch shear test of partly consolidated ice ridge keel by using a three-dimensional discrete element method. The authors model the contact forces between discrete ice blocks with Hertz–Mindlin contact model. For freeze bonds between the ice blocks, the authors apply classical linear cohesion model with few modifications. Based on punch shear test simulations, the authors are able to determine the main characteristics of an ice ridge from the material parameters of the ice and freeze bonds.Design/methodology/approachThe authors introduced a discrete model for ice that can be used for modelling of ice ridges. The authors started with short introduction to current status with ice ridge modelling. Then they introduced the model, which comprises Hertz–Mindlin contact model and freeze bond model with linear cohesion and softening. Finally, the authors presented the numerical results obtained using EDEM is commercial Discrete Element Modeling software (EDEM) and analysed the results.FindingsThe Hertz–Mindlin model with cohesive freeze bonds and linear softening is a reasonable model for ice rubble. It is trivial that the ice blocks within the ice ridge are not spherical particles, but according to results, the representation of ice blocks as spheres gave promising results. The simulation results provide information on how the properties of freeze bond affect the results of punch shear test. Thus, the simulation results can be used to approximate the freeze bonds properties within an ice ridge when experimental data are available.Research limitations/implicationsAs the exact properties of ice rubble are unknown, more research is required both in experimental and theoretical fields of ice rubble mechanics.Originality/valueBased on this numerical study, the authors are able to determine the main characteristics of an ice ridge from material parameters of ice and freeze bonds. Furthermore, the authors conclude that the model creates a promising basis for further development in other applications within ice mechanics.
Evaluating local vulnerability and organisational resilience to frequent flooding in Africa: the case of Northern Cameroon
Authors: Bang Henry , Miles Lee , Gordon Richard 
Published: January 2019

Purpose
The purpose of this paper is to evaluate local vulnerability and organisational resilience including coping/adaptive capacity to climate risks, specifically frequent flooding in Northern Cameroon.

Design/methodology/approach
The research is exploratory/deductive and draws upon qualitative methods, secondary and empirical techniques supplemented by semi-structured qualitative interviews with senior disaster managers. Secondary information sources, which include peer review articles, government reports/plans, newspaper articles and other grey literature, enhanced the analysis.

Findings
The research findings have unveiled the physical and social vulnerability of Northern Cameroon to frequent flooding. Results also show that institutional performance for flood management in Cameroon is ineffective, and adaptive capacity is highly deficient. Cameroon’s legislative framework for flood management is weak, and this exacerbates the poor implementation of structural and non-structural flood management measures. Results also indicate issues with relief, evacuation and foreign assistance in flood management. Recommendations that focus on enhancing capacity of response to frequent flooding via reducing vulnerabilities, managing resilience and enhancing adaptive capacity are provided.

Originality/value
Using Gallopin’s (2006) model of vulnerability, this paper makes a distinct contribution by offering insights into the role of adaptive capacity in disaster management systems in developing (African) countries via an evaluation of vulnerabilities and organisational resilience to repeated flooding in Northern Cameroon.
The crossover effect of work–family conflict among hotel employees
Authors: Pan Su-Ying , Yeh Ying-Jung 
Published: January 2019

PurposeWork–family research has established the existence of a crossover effect, wherein a given perception is transferable between two intimate persons. However, little research has been done to delineate this crossover process. Therefore, grounded in the conservation of resources theory, the present study aims to examine why and how a supervisor’s work–family conflict (WFC) is related to his or her subordinates’ WFC. The authors focus on three resource-related mechanisms and explore the consequences of subordinates’ WFC.Design/methodology/approachQuestionnaire surveys were collected from 180 supervisor–subordinate dyads from five hotels. Mplus was used to test the framework.FindingsThe results support the notion that supervisor’s negative affect and subordinate’s workload account for the crossover effect of WFC. Moreover, subordinates’ WFC is found to be related to lower job satisfaction and higher turnover intention.Research limitations/implicationsThe current study highlights the downward effect of supervisors’ WFC, a phenomenon that has been understudied in the extant research. Alternative mediators or moderators in the relationship between supervisors’ WFC and subordinates’ WFC can be explored by future research.Practical implicationsHotels should help supervisors to effectively manage the work and family dynamic through training and changing the “face time” culture.Originality/valueGrounded in the conservation of resources theory, the authors propose a framework that incorporates WFC into the crossover model.
Analysis of the determinants of foreign direct investment in Ghana
Authors: Asiamah Michael , Ofori Daniel , Afful Jacob 
Published: January 2019

Purpose
The factors that determine foreign direct investment (FDI) are important to policy-makers, investors, the banking industry and the public at large. FDI in Ghana has received increased attention in recent times because its relevance in the Ghanaian economy is too critical to gloss over. The purpose of this paper is to examine the determinants of FDI in Ghana between the period of 1990 and 2015.

Design/methodology/approach
The study employed a causal research design. The study used the Johansen’s approach to cointegration within the framework of vector autoregressive for the data analysis.

Findings
The study found a cointegrating relationship between FDI and its determinants. The study found that both the long-run and short-run results found statistically significant negative effects of inflation rate, exchange rate and interest rate on FDI in Ghana while gross domestic product, electricity production and telephone usage (TU) had a positive effect on FDI.

Research limitations/implications
The study found a cointegrating relationship between FDI and its determinants. The study found that both the long-run and short-run results found statistically significant negative effects of inflation rate, exchange rate and interest rate on FDI in Ghana whiles gross domestic product, electricity production and TU had a positive effect on FDI.

Practical implications
This study has potential implication for boosting the economies of developing countries through its policy recommendations which if implemented can guarantee more capital inflows for the economies.

Social implications
This study has given more effective ways of attracting more FDI into countries which in effect achieve higher GDP and also higher standard of living through mechanisms and in the end creating more social protection programs for the people.

Originality/value
Although studies have been conducted to explore the determinants of FDI, some of the core macroeconomic variables such as inflation, interest rate, telephone subscriptions, electricity production, etc., which are unstable and have longstanding effects on FDI have not been much explored to a give a clear picture of the relationships. Therefore, a study that will explore these and other macroeconomic variables to give clear picture of their relationships and suggest some of the possible ways of dealing with these variables in order to attract more FDI for the country to achieve its goal is what this paper seeks to do.
Using social media to create engagement: a social marketing review
Authors: Shawky Sara , Kubacki Krzysztof , Dietrich Timo , Weaven Scott 
Published: January 2019

PurposeRecognising the potential of social media as an integral driver of communication that can create engaged communities through dialogic or two-way conversations, this study aims to identify and describe the use of social media in creating participants’ engagement in various social marketing programmes conducted worldwide between 2005 and 2017.Design/methodology/approachA total of 29 social marketing programmes were identified using systematic literature review procedures.FindingsThe majority of the identified programmes used Facebook, and social media were mostly used to share content-based information in an attempt to connect with target audiences, raise awareness and reach less accessible populations with programme messages. Social media served as an extended channel to traditional media efforts, and very few programmes used social media to create mechanisms for supporting their target audiences’ ability to revisit their social media communications and encourage them to act as advocates for the programmes’ activities.Research limitations/implicationsThe analysis presented in this paper is limited by the information provided in the identified studies.Originality/valueDespite the growing popularity and significance of social media as a channel for consumer engagement, little has been done to synthesise how social marketers are incorporating the use of social media in their social marketing programmes. This research fills this gap by providing systematic understanding of the use of social media in social marketing programmes to date.
Sustainability in finance teaching: evaluating levels of reflection and transformative learning
Authors: Brunstein Janette , Sambiase Marta Fabiano , Kerr Roberto Borges , Brunnquell Claudine , Perera Luiz Carlos Jacob 
Published: January 2019

Purpose
The purpose of this study is to argue for the need for more critical-reflective teaching-learning experiences in finance teaching, capable of promoting changes in students’ frames of reference toward sustainability. The aim was to evaluate the levels of reflection and the transformative learning experiences perceived by undergraduate students enrolled in three finance disciplines at a Business Administration course of a Brazilian business school. This course has been the object of pedagogical experience toward sustainability teaching-learning for some years.

Design/methodology/approach
The authors used mixed data. For quantitative data, the authors collected 188 questionnaires, as well as 160 student-written reports for qualitative data.

Findings
Incorporating sustainability topics into finance disciplines, longitudinally, stimulates critical reflection and transformations in students’ mindsets toward sustainable rationality in finance. Despite the high number of agreements with reflection and critical reflection levels, emphasis only on the theoretical discussion of sustainability presuppositions does little to contribute to the practical application of concepts.

Research limitations/implications
Although the study was conducted in a particular Business School, the authors expect that the results can be replicated and improved in comparative studies, encouraging transformative learning in the teaching-learning of finance.

Practical implications
The results show the potential and limitations of the experiences studied and its implications for theoretical and didactics in finance teaching. The discussions and the examples of practical activities presented can bring contributions to educators, professors and researchers.

Originality/value
Few studies in finance seeks to evaluate pedagogical experiences from the point of view of students’ learning, especially in relation to the development of a new rationality.