bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antimicrobial activity of the quinoline derivative HT61, effective against non-dividing cells, inStaphylococcus aureusbiofilms
Authors: Frapwell C.J. , Skipp P.J. , Howlin R.P. , Angus E.M. , Hu Y. , Coates A.R.M. , Allan R.N. , Webb J.S. 
Published: January 2020

AbstractStaphylococcus aureusis an opportunistic pathogen responsible for a wide range of chronic infections. Disease chronicity is often associated with biofilm formation, a phenotype that confers enhanced tolerance towards antimicrobials, a trait which can be attributed to a dormant, non-dividing subpopulation within the biofilm. Development of antibiofilm agents that target these populations could therefore improve treatment success. HT61 is a quinoline derivative that has demonstrated efficacy towards non-dividing planktonicStaphylococcus spp. and therefore, in principal, could be effective against staphylococcal biofilms. In this study HT61 was tested on matureS. aureusbiofilms, assessing both antimicrobial efficacy and characterising the cellular response to treatment. HT61 was found to be more effective than vancomycin in killingS. aureusbiofilms (minimum bactericidal concentrations: HT61; 32 mg/L, vancomycin; 64 mg/L), and in reducing biofilm biomass. Scanning electron microscopy of HT61-treated biofilms also revealed disrupted cellular structure and biofilm architecture. HT61 treatment resulted in increased expression of proteins associated with the cell wall stress stimulon anddcwcluster, implying global changes in peptidoglycan and cell wall biosynthesis. Altered expression of metabolic and translational proteins following treatment also confirm a general adaptive response. These findings suggest that HT61 represents a new treatment forS. aureusbiofilm-associated infections that are otherwise tolerant to conventional antibiotics targeting actively dividing cells.
Supervised Adversarial Alignment of Single-Cell RNA-seq Data
Authors: Ge Songwei , Wang Haohan , Alavi Amir , Xing Eric , Bar-Joseph Ziv 
Published: January 2020

AbstractDimensionality reduction is an important first step in the analysis of single cell RNA-seq (scRNA-seq) data. In addition to enabling the visualization of the profiled cells, such representations are used by many downstream analyses methods ranging from pseudo-time reconstruction to clustering to alignment of scRNA-seq data from different experiments, platforms, and labs. Both supervised and unsupervised methods have been proposed to reduce the dimension of scRNA-seq. However, all methods to date are sensitive to batch effects. When batches correlate with cell types, as is often the case, their impact can lead to representations that are batch rather than cell type specific. To overcome this we developed a domain adversarial neural network model for learning a reduced dimension representation of scRNA-seq data. The adversarial model tries to simultaneously optimize two objectives. The first is the accuracy of cell type assignment and the second is the inability to distinguish the batch (domain). We tested the method by using the resulting representation to align several different datasets. As we show, by overcoming batch effects our method was able to correctly separate cell types, improving on several prior methods suggested for this task. Analysis of the top features used by the network indicates that by taking the batch impact into account, the reduced representation is much better able to focus on key genes for each cell type.
Scanning electron microscopy preparation of the cellular actin cortex: a quantitative comparison between critical point drying and hexamethyldisilazane drying
Authors: Schu M. , Terriac E. , Koch M. , Paschke S. , Lautenschläger F. , Flormann D.A.D. 
Published: January 2020

AbstractThe cellular cortex is an approximately 200-nm-thick actin network that lies just beneath the cell membrane. It is responsible for the mechanical properties of cells, and as such, it is involved in many cellular processes, including cell migration and cellular interactions with the environment. To develop a clear view of this dense structure, high-resolution imaging is essential. As one such technique, electron microscopy, involves complex sample preparation procedures. The final drying of these samples has significant influence on potential artifacts, like cell shrinkage and the formation of artifactual holes in the actin cortex. In this study, we compared the three most used final sample drying procedures: critical-point drying (CPD), CPD with lens tissue (CPD-LT), and hexamethyldisilazane drying. We show that both hexamethyldisilazane and CPD-LT lead to fewer artifactual mesh holes within the actin cortex than CPD. Moreover, CPD-LT leads to significant reduction in cell height compared to hexamethyldisilazane and CPD. We conclude that the final drying procedure should be chosen according to the reduction in cell height, and so CPD-LT, or according to the spatial separation of the single layers of the actin cortex, and so hexamethyldisilazane.
A simple, cost-effective, and robust method for rRNA depletion in RNA-sequencing studies
Authors: Culviner Peter H. , Guegler Chantal K. , Laub Michael T. 
Published: January 2020

AbstractThe profiling of gene expression by RNA-sequencing (RNA-seq) has enabled powerful studies of global transcriptional patterns in all organisms, including bacteria. Because the vast majority of RNA in bacteria is ribosomal RNA (rRNA), it is standard practice to deplete the rRNA from a total RNA sample such that the reads in an RNA-seq experiment derive predominantly from mRNA. One of the most commonly used commercial kits for rRNA depletion, the Ribo-Zero kit from Illumina, was recently discontinued. Here, we report the development a simple, cost-effective, and robust method for depleting rRNA that can be easily implemented by any lab or facility. We first developed an algorithm for designing biotinylated oligonucleotides that will hybridize tightly and specifically to the 23S, 16S, and 5S rRNAs from any species of interest. Precipitation of these oligonucleotides bound to rRNA by magnetic streptavidin beads then depletes rRNA from a complex, total RNA sample such that ~75-80% of reads in a typical RNA-seq experiment derive from mRNA. Importantly, we demonstrate a high correlation of RNA abundance or fold-change measurements in RNA-seq experiments between our method and the previously available Ribo-Zero kit. Complete details on the methodology are provided, including open-source software for designing oligonucleotides optimized for any bacterial species or metagenomic sample of interest.ImportanceThe ability to examine global patterns of gene expression in microbes through RNA-sequencing has fundamentally transformed microbiology. However, RNA-seq depends critically on the removal of ribosomal RNA from total RNA samples. Otherwise, rRNA would comprise upwards of 90% of the reads in a typical RNA-seq experiment, limiting the reads coming from messenger RNA or requiring high total read depth. A commonly used, kit for rRNA subtraction from Illumina was recently discontinued. Here, we report the development of a ‘do-it-yourself’ kit for rapid, cost-effective, and robust depletion of rRNA from total RNA. We present an algorithm for designing biotinylated oligonucleotides that will hybridize to the rRNAs from a target set of species. We then demonstrate that the designed oligos enable sufficient rRNA depletion to produce RNA-seq data with 75-80% of reads comming from mRNA. The methodology presented should enable RNA-seq studies on any species or metagenomic sample of interest.
Acto-myosin network geometry defines centrosome position
Authors: Jimenez Ana Joaquina , de Pascalis Chiara , Letort Gaelle , Vianay Benoit , Goldman Robert D. , Bornens Michel , Piel Matthieu , Blanchoin Laurent , Théry Manuel 
Published: January 2020

AbstractThe centrosome is the main organizer of microtubules and as such, its position is a key determinant of polarized cell functions. As the name says, the default position of the centrosome is considered to be the cell geometrical center. However, the mechanism regulating centrosome positioning is still unclear and often confused with the mechanism regulating the position of the nucleus to which it is linked. Here we used enucleated cells plated on adhesive micropatterns to impose regular and precise geometrical conditions to centrosome-microtubule networks. Although frequently observed there, the equilibrium position of the centrosome is not systematically at the cell geometrical center and can be close to cell edge. Centrosome positioning appears to respond accurately to the architecture and anisotropy of the actin network, which constitutes, rather than cell shape, the actual spatial boundary conditions the microtubule network is sensitive to. We found that the contraction of the actin network defines a peripheral margin, in which microtubules appeared bent by compressive forces. The disassembly of the actin network away from the cell edges defines an inner zone where actin bundles were absent and microtubules were more radially organized. The production of dynein-based forces on microtubules places the centrosome at the center of this inner zone. Cell adhesion pattern and contractile forces define the shape and position of the inner zone in which the centrosome-microtubule network is centered.
Understanding co-editing mechanism of wiki-based digital humanities projects
Authors: Deng Weihua , Lv Pei , Yi Ming , Liu Ming 
Published: January 2020

PurposeThe purpose of this paper is to reveal the co-editing mechanism aiming at content creation, and an entry of online encyclopedia is taken as a case, for the purpose of promoting and enhancing the development of wiki-based digital humanities projects (WDHPs), specifically, the projects that focus on gathering contextual information in the culture heritage domain.Design/methodology/approachAn exploratory study was conducted by three steps. A representative entry’s editorial records were reorganized to obtain a data set of discussion statements (n=608), based on which linked-structures were built, and PageRank algorithm was used to analyze the co-editing process. Skewness statistic was applied to measure the consensus of co-editing, and consensus evolution over time was explored. Linear or curve fitting was performed to analyze the correlation between consensus evolution and its influential factors.FindingsIn WDHPs, co-editing activity of content creation can be considered as a large-scale group discussion, consensus can evaluate the efficiency of co-editing, which evolves with time and is influenced by the number of statements, breadth and depth of argumentation structure. Taking “Mogao Grottoes” as an example, group discussions around 15 key issues dominate the content creating process, consensus is on a rise with time, finally reaches a relatively high level, and consensus evolution is more influenced by breadth than by depth of argumentation structure, which indicates that co-editing efficiency of “Mogao Grottoes” is fine and more argumentation in a depth manner should be guided.Practical implicationsFor researchers of WDHPs, it is beneficial to apply online encyclopedia platform combining with consensus analysis to develop WDHPs. For designers of WDHPs, the elements related to argumentation structure can be absorbed into the design to promote co-editing in an effective manner. For DH researchers, the analytic procedure can be beneficial of revealing the interest of contributors in a specific DH field.Originality/valueThis research is novel in comprehensively understanding co-editing mechanism of content creation in WDHPs, resulting in a three-step analytic procedure of presenting co-editing process, evaluating and improving co-editing efficiency.
Search optimal control of induction heating modes for a moving workpiece
Authors: Smolyanov Ivan Alexandrovich , Tarasov Fedor 
Published: January 2020

Purpose
This paper aims to create mathematical models and control algorithms allowing the authors to study and form effective modes of operation of multi-inductor system of electrical heating of moving hollow cylindrical blanks.

Design/methodology/approach
The developed mathematical models were based on the finite-difference method, the control volume method and their combination. The reliability of the results obtained was verified by comparing the calculated results with the experimental ones. The temperature control system was synthesized using methods of the object management theory with distributed parameters.

Findings
A set of mathematical instruments has been created that allow modelling the operation modes of installation for induction heating of moving hollow cylindrical blanks. Recommendations were given on the formation of an automatic control system that provides heating of a moving hollow cylindrical billet to the required temperature with simultaneous equalization of temperature along the length of the billet in case of highly uneven initial temperature along the length of the billet.

Practical implications
Part of the paper will be used by the industrial plant for the purpose of heat treatment of iron alloys workpiece. Particularly, a control system will be basically formed based on the models.

Originality/value
The scientific novelty of the paper is to create control algorithms and mathematical models for the induction heating system of tubular workpieces allowing to explore interrelated electromagnetic and thermal processes taking into account nonlinearities and design features of the system, as well as to form effective modes of its operation based on transfer functions and methods of the object management theory with distributed parameters.
Effective methods for optimal design of induction coils on example of surface hardening
Authors: Pleshivtseva Yuliya , Baldan Marco , Popov Anton , Nikanorov Alexander , Rapoport Edgar , Nacke Bernard 
Published: January 2020

Purpose
This paper aims to describe main ideas and demonstrates results of the research activities carried out by the authors in the field of optimal design concepts for induction heater for surface hardening. The main goal of the research studies is the application of different optimization methods and numerical finite element method (FEM) codes for field analysis to solve the optimal design problem that is mathematically formulated in terms of the one of the most important optimization criteria for surface hardening technology, e.g. maximum temperature uniformity within the hardening surface layer.

Design/methodology/approach
Evolutionary algorithm based on Adaptive Gaussian Process-Assisted Differential Evolution for MEMS Design Optimization (AGDEMO) and alternance method of parametric optimization based on optimal control theory are applied as effective tools for the practice-oriented problem for optimization of induction heater design based on non-linear coupled electromagnetic and temperature field analysis. Different approaches are used for combining FEM codes for interconnected field analysis and optimization algorithms into automated optimization procedure.

Findings
Optimization procedures are tested and investigated for optimal design problem solution on the examples of induction hardening of steel cylindrical billet.

Practical implications
Solved problems are based on the design of practical industrial applications. The developed optimization procedures are planned to be applied to the wide range of real-life problems of the optimal design of different electromagnetic devices and systems.

Originality/value
This paper describes main ideas and results of the research activities carried out by the authors in the field of optimal design of induction heaters for hardening based on numerical coupled electromagnetic and temperature field analysis. The implementation of the automated procedure that combines a numerical FEM code for coupled field analysis with an optimization algorithm and its subsequent application for designing induction heaters makes the proposed approach specific and original. This paper also demonstrates that different optimization strategies used (evolutionary algorithm based on AGDEMO and alternance method of optimal control theory) are effective for real-life industrial applications for optimization of induction heaters design.
Influence of vessel dimensions on particles homogenization and heat removing in TMF stirrer
Authors: Evgeny Shvidkiy , Sokolov Igor , Bolotin Kirill , Zakharov Valery 
Published: January 2020

Purpose
The purpose of this paper is to determine how the shape of the container affects the efficiency of a traveling magnetic field (TMF) stirring.

Design/methodology/approach
The modeling approach is based on finite element software Comsol which includes harmonic electromagnetic (EM), transient CFD and particle tracing modules. For evaluating efficiency of stirring the particle, homogenization parameter is used.

Findings
It has been determined that the use of an elliptical cylinder-shaped vessel allows better heat removal from the side surface and, at the same time, the stirring efficiency does not drop significantly.

Practical implications
The results of the work can be used in the design of EM stirring installations in which exothermic reactions occur.

Originality/value
The transient simulation of particle transport in a TMF-driven melt flow gives the opportunity to estimate the efficiency of stirring process in different vessel shapes.
Occupational health and safety performance evaluation of countries based on MAIRCA
Authors: Can Gülin Feryal , Kıran Muzaffer Bertan 
Published: January 2020

Purpose
The purpose of this paper is to develop an approach to compare occupational health and safety (OHS) performances of countries. Additionally, another aim is to debate the impacts of using recorded data and ratios for OHS performance evaluations.

Design/methodology/approach
The number of fatal accidents (NFAs), fatal accident rates (FARs), numbers of lost days (NLDs) and accident severity rates (ASRs) are determined as main criteria and six economic activity areas (EAAs) are considered as sub-criteria. Two different initial decision matrices are used as the initial decision matrix, the first of which consists of recorded data of countries related to NFAs and NLDs, and the second consists of FAR and ASR values as ratios. Importance weights of main and sub-criteria regarding the recorded data and ratios are determined using four different weighting ways. Countries are ranked via utilizing Multi-Attributive Ideal-Real Comparative Analysis considering two different initial decision matrices.

Findings
It can be stated that an evaluation based on ratios for comparison of OHS performance provides more realistic results. Additionally, increasing the effect of the FAR values using the 6,000 equivalent lost days factor is also important in terms of differentiating the data of the countries in question.

Originality/value
To the best of the authors’ knowledge, there is no study in literature that discusses the ranking of countries by means of recorded data and ratios considering different criteria. Additionally, this study is a first in terms of the number of countries evaluated and the comparison of these countries according to their respective EAAs.
Research on spatial positioning of online inspection robots for vertical storage tanks
Authors: Huang Zhiqiang , He Lei , Gao ZhaoXin , Jia Yingqi , Kang Yewei , Xie Dou , Fu Chunli 
Published: January 2020

Purpose
This paper aims to introduce a new acoustic positioning method to solve the problem of space positioning for online inspection robots within the storage tank.

Design/methodology/approach
The proposed positioning system comprises two acoustic signal emitters and two receivers. Emitters are brought by the robot into the storage tank. Receivers are mounted on the external edge of the storage tank floor. The spatial coordinate values and motion directions of the robot in the storage tank are calculated by using the proposed acoustic positioning algorithm.

Findings
The experiment results and positioning error analysis indicate that the method can obtain the data of robotic space coordinates and motion orientation, while the positioning error of the method can be less than 20 cm. The accuracy reaches the positioning technology level of other tank online inspection robots.

Originality/value
This method not only expands the positioning of the inspection robots from 2D plane to 3D space but also significantly reduces the number of positioning sensors carried by a robot and improves the safety of a robot in the tank.
The role of public markets in urban habitability and competitiveness
Authors: Balsas Carlos J.L. 
Published: January 2020

Purpose
The purpose of this paper is to examine public market functions in three different continents (Europe, North America and Asia) and to identify a set of planning implications for their use in contexts of urban regeneration.

Design/methodology/approach
The paper presents a comparative analysis of four downtown market functions based on the LABiMAAM framework: [L]ocation; [A]ccessibility; [B]uilding; [i]nternal structure; [M]ain trading area; [A]menities and services; [A]nimation program; and [M]anagement structure.

Findings
The lessons learned suggest that centrally located public markets possess: social functions aimed at guaranteeing food security, urban development goals that prevent the leap-frog suburbanization of the territory, walkability goals that reduce automobile dependence and welfare goals that support disenfranchised, usually minority, populations.

Research limitations/implications
Positive and dire implications are identified. The former are structured in terms of these five categories, namely, social, financial, macro-spatial, environmental and public space; while the latter tend to result mostly from the abandonment of the public good orientation associated with having a public market function in a central location.

Originality/value
This study results from the realization of increasing developmental pressures and widespread tendencies to multiply specialized retail offers in both traditional, and especially, innovative commercial formats. The findings comprise the identification of public policies aimed at augmenting the relevance of commercial urbanism and urban regeneration strategies.
Cognitive psychology and tourism – surfing the “cognitive wave”: a perspective article
Authors: Scott Noel 
Published: January 2020

Purpose
This paper aims to provide a personal perspective on the application of psychological theory in tourism studies and the importance of cognitive science for future research.

Design/methodology/approach
Empirical findings and theoretical ideas from cognitive science provide insights useful for tourism researchers. The slow uptake of these ideas provides a means to probe systematic weaknesses in the tourism academy’s research practice.

Findings
Theories derived from psychology are applied in tourism research, but these same theories are not reassessed after they are discredited, and new approaches emerge. Instead, “old” ideas continue to be used resulting in a moribund theoretical environment. Further, concepts from different paradigms are often adopted in the same study resulting in a confused and confusing literature.

Originality/value
This paper challenges theoretically conservative “social science”-based tourism researchers to adopt current best practice ideas from cognitive psychology. It highlights the value of cognitive psychology and neuroscience research for understanding social science phenomena.