bluuebunny/crossref_metadata_2025_split huggingface dataset:
Zebrafish DANA retroposon can form large zebrafish sequence in human Hepg2 and 293T cell lines
Authors: Cao Zheming , Ding Weidong , Qiang Jun , Bing Xuwen , Xu Pao 
Published: December 2018

AbstractIn this study, we cloned small zebrafish retroposon DANA from zebrafish genome and constructed the lentiviral expression vector pEB-GFP (T2A)PURO. Three human cell lines including 293T, Hepg2 and LO2 were selected as infection targets. After detecting the expression of DANA, we found that the expression of DANA retroposon in three cells had different effects on cell lines through chromosome walking. Among these cells, LO2 showed no DANA retrotrans-position, while 293T and Hepg2 cell lines displayed retrotrans-position with the formation of some zebrafish genome fragments. Thereafter, we constructed a mutant of DANA retroposon and infected it in 293T cells, but no retrotrans-position was found after chromosome walking. Re-sequencing of the two cell lines (293T and Hepg2) showed that a large number of zebrafish genome fragments were found in the genomes of both cell lines, which could be divided into four types. The first type was zebrafish microsatellite sequence, accounting for 79.23% and 74.45% in 293T cell line and Hepg2 cell line, respectively. The second type was the sequence with a small amount of poly A or T, and the third type was the sequence with poly G or C, and the second and third types accounted very low proportion. The fourth type was composed of coding sequence and non-coding sequence, with large difference and very low proportion of common sequences between the two cell lines. Taken together, this study indicated that zebrafish DANA retroposon can result in retrotrans-position using the retrotrans system of human cell lines.
Genome-wide association meta-analysis identifies novel GP2 gene risk variants for pancreatic cancer in the Japanese population
Authors: Lin Yingsong , Nakatochi Masahiro , Ito Hidemi , Kamatani Yoichiro , Inoko Akihito , Sakamoto Hiromi , Kinoshita Fumie , Kobayashi Yumiko , Ishii Hiroshi , Ozaka Masato , Sasaki Takashi , Matsuyama Masato , Sasahira Naoki , Morimoto Manabu , Kobayashi Satoshi , Fukushima Taito , Ueno Makoto , Ohkawa Shinichi , Egawa Naoto , Kuruma Sawako , Mori Mitsuru , Nakao Haruhisa , Adachi Yasushi , Okuda Masumi , Osaki Takako , Kamiya Shigeru , Wang Chaochen , Hara Kazuo , Shimizu Yasuhiro , Miyamoto Tatsuo , Hayashi Yuko , Hosono Yasuyuki , Ebi Hiromichi , Kohmoto Tomohiro , Imoto Issei , Murakami Yoshinori , Akiyama Masato , Ishigaki Kazuyoshi , Matsuda Koichi , Hirata Makoto , Shimada Katsuaki , Okusaka Takuji , Kawaguchi Takahisa , Takahashi Meiko , Watanabe Yoshiyuki , Kuriki Kiyonori , Kadota Aya , Wakai Kenji , Yamaji Taiki , Iwasaki Motoki , Sawada Norie , Tsugane Shoichiro , Kinoshita Kengo , Fuse Nobuo , Katsuoka Fumiki , Shimizu Atsushi , Nishizuka Satoshi S. , Tanno Kozo , Suzuki Ken , Okada Yukinori , Horikoshi Momoko , Yamauchi Toshimasa , Kadowaki Takashi , Yoshida Teruhiko , Matsuda Fumihiko , Kubo Michiaki , Kikuchi Shogo , Matsuo Keitaro 
Published: December 2018

AbstractThe etiology of pancreatic cancer remains largely unknown. Here, we report the results of a meta-analysis of three genome-wide association studies (GWASs) comprising 2,039 pancreatic cancer cases and 32,592 controls, the largest sample size in the Japanese population. We identified 3 (13q12.2, 13q22.1, and 16p12.3) genome-wide significant loci (P<5.0×10-8) and 4 suggestive loci (P<1.0×10-6) for pancreatic cancer. Of these risk loci, 16p12.3 is novel; the lead SNP maps to rs78193826 (odds ratio (OR)=1.46, 95% CI=1.29-1.66, P=4.28×10-9), an Asian-specific, nonsynonymous glycoprotein 2 (GP2) gene variant predicted to be highly deleterious. Additionally, the gene-based GWAS identified a novel gene, KRT8, which is linked to exocrine pancreatic and liver diseases. The identified GP2 gene variants were pleiotropic for multiple traits, including type 2 diabetes, hemoglobin A1c (HbA1c) levels, and pancreatic cancer. Mendelian randomization analyses corroborated causality between HbA1c and pancreatic cancer. These findings suggest that GP2 gene variants are associated with pancreatic cancer susceptibility in the Japanese population, prompting further functional characterization of this locus.
A Nanopore-based method for generating complete coding region sequences of dengue virus in resource-limited settings
Authors: Stubbs Samuel , Blacklaws Barbara , Yohan Benediktus , Yudhaputri Frisalita A , Schwem Brian , Salvaña Edsel M , Destura Raul V , Myint Khin S , Sasmono R. Tedjo , Frost Simon D W 
Published: December 2018

AbstractDengue virus (DENV) sequencing is a vital tool for surveillance and epidemiology studies. However, the current methods employed for sequencing DENV are expensive, laborious and technically demanding, often due to intra- and inter-serotype variability. Therefore, on-site DENV sequencing is not feasible in many of the areas where DENV is endemic. Surveillance in these areas can only be performed by shipping samples to well-equipped central laboratories for sequencing. However, long periods of inadequate storage and unreliable shipping conditions mean that such samples can arrive degraded, rendering sequence recovery difficult. We therefore aimed to develop an approach that is simple, portable and effective, to be used for on-site DENV sequencing in limited resource settings.To achieve this, we first used the ‘Primal Scheme’ primer design tool to develop a simple and robust protocol for generating multiple short amplicons, covering the complete coding-region of DENV isolates. We then paired this method with the Nanopore MinION, a portable and affordable sequencing device, well-suited to minimal resource settings.The multiplex PCR method produced full-coding-region coverage of all DENV samples tested with no optimisation required, and Nanopore sequencing of the short amplicons generated consensus sequences with high accuracy (99.52 - 99.92 %). Phylogenetic analysis of the consensus sequences generated using the new method showed that they formed monophyletic clusters with those produced by the current, long-amplicon, Illumina method, thus demonstrating that the two approaches are comparable. The multiplex method’s simplicity and portability compared to the current DENV sequencing approach make it well-suited for use in resource-limited, DENV-endemic regions. Deployment of the method in these regions would increase the capacity for DENV surveillance and has the potential to provide vital resolution for future DENV epidemiology studies.
Massively Parallel FPGA Hardware for Spike-By-Spike Networks
Authors: Rotermund David , Pawelzik Klaus R. 
Published: December 2018

ABSTRACTWhile inspired by the brain, currently successful artificial neural networks lack key features of the biological original. In particular, the deep convolutional networks (DCNs) neither use pulses as signals exchanged among neurons, nor do they include recurrent connections which are both core properties of real neuronal networks. This not only puts to question the relevance of DCNs for explaining information processing in nervous systems but also limits their potential for modeling natural intelligence.Spike-By-Spike (SbS) networks are a promising new approach that combines the computational power of artificial networks with biological realism. Instead of separate neurons they consist of neuronal populations performing inference. Even though the underlying equations are rather simple implementations of such networks on currently available hardware are several orders of magnitude slower than for comparable non-spiking deep networks.Here, we develop and investigate a framework for SbS networks on chip. Thanks to the communication via spikes, already moderately sized deep networks based on the SbS approach allows a parallelization into thousands of simple and fully independent computational cores. We demonstrate the feasibility of our design on a Xilinx Virtex 6 FPGA while avoiding proprietary cores (except block memory) that cannot be realized on a custom-designed ASIC. We present memory access optimized circuits for updating the internal variables of the neurons based on incoming spikes as well as for learning the connection’s strength. The optimized computational circuits as well as the representation of variables fully exploit the non-negative properties of all data in the SbS approach. We compare the sizes of the arising circuits for floating and fixed point numbers. In addition we show how to minimize the number of components that are required for the computational cores by reusing their components for different functions.
Invasive DNA elements modify nuclear architecture by KNOT-Linked Silencing in plants
Authors: Grob Stefan , Grossniklaus Ueli 
Published: December 2018

AbstractBackgroundThe three-dimensional (3D) organization of chromosomes is linked to epigenetic regulation and transcriptional activity. However, only few functional features of 3D chromatin architecture have been described to date. The KNOT is a 3D chromatin structure in Arabidopsis, comprising 10 interacting genomic regions termed KNOT ENGAGED ELEMENTs (KEEs). KEEs are enriched in transposable elements and small RNAs, suggesting a function in transposon biology.ResultsHere, we report the KNOT’s involvement in regulating invasive DNA elements. Transgenes can specifically interact with the KNOT, leading to perturbations of 3D nuclear organization, which correlates with the transgene’s expression: high KNOT-contact frequencies are associated with transgene silencing. KNOT-Linked Silencing (KLS) cannot readily be connected to canonical silencing mechanisms, such as RNA-directed DNA methylation and post-transcriptional gene silencing, as both cytosine methylation and small RNA abundance do not correlate with KLS. Furthermore, KLS exhibits paramutation-like behavior, as silenced transgenes can lead to the silencing of active transgenes in trans.ConclusionTransgene silencing can be readily connected to a specific feature of Arabidopsis 3D nuclear organization, namely the KNOT. KLS likely acts either independent or prior canonical silencing mechanisms and, hence, its characterization promises to not only contribute to our understanding of chromosome folding but moreover provides valuable insight into how genomes are defended against invasive DNA elements.
Signals from the brood modulate the sleep of brood tending bumblebee workers
Authors: Nagari Moshe , Gera Ariel , Jonsson Sara , Bloch Guy 
Published: December 2018

AbstractSleep is ubiquitous in vertebrates and invertebrates, and its chronic lost is typically associated with reduced performance, health, or survival. Nevertheless, some animals can give up sleep in order to increase survival or mating opportunities. We studied the interplay between sleep and brood care in the social bumblebeeBombus terrestris. We first used video recording and detailed behavioral analyses to confirm that the bumblebee shows the essential behavioral characteristics of sleep. Based on these analyses we next used immobility bouts of >5′ as proxy for sleep in automatic activity monitoring records, and found that sleep is severely reduced in the presence of larvae that require feeding or pupae that are not fed. Reduced sleep was correlated with wax pot building, which is a behavior typical to nest founding mother queens. Sleep was also reduced in the presence of empty cocoons, but this effect was transient and reduced with time. This observation that is consistent with the presence of a sleep modulating pheromonal signal. These results provide the first evidence for brood modulation of sleep in an insect, and are consistent with the hypothesis that plasticity in sleep can evolve as a mechanism to improve care for dependent juveniles.
De novo Design of Translational RNA Repressors
Authors: Carlson Paul D. , Glasscock Cameron J. , Lucks Julius B. 
Published: December 2018

ABSTRACTA central goal of synthetic biology is the development of methods for the predictable control of gene expression. RNA is an attractive substrate by which to achieve this goal because the relationship between its sequence, structure, and function is being uncovered with increasing depth. In addition, design approaches that use this relationship are becoming increasingly effective, as evidenced by significant progress in the de novo design of RNA-based gene regulatory mechanisms that activate transcription and translation in bacterial cells. However, the design of synthetic RNA mechanisms that are efficient and versatile repressors of gene expression has lagged, despite their importance for gene regulation and genetic circuit construction. We address this gap by developing two new classes of RNA regulators, toehold repressors and looped antisense oligonucleotides (LASOs), that repress translation of a downstream gene in response to an arbitrary input RNA sequence. Characterization studies show that these designed RNAs robustly repress translation, are highly orthogonal, and can be multiplexed with translational activators. We show that our LASO design can repress endogenous mRNA targets and distinguish between closely-related genes with a high degree of specificity and predictability. These results demonstrate significant yet easy-to-implement improvements in the design of synthetic RNA repressors for synthetic biology, and point more broadly to design principles for repressive RNA interactions relevant to modern drug design.
Numerical study on flow over a confined oscillating cylinder with a splitter plate
Authors: Ghiasi Arya , Razavi Seyed Esmaeil , Rouboa Abel , Mahian Omid 
Published: December 2018

Purpose
This study aims to investigate the effect of the simultaneous usage of active and passive methods (which in this case are rotational oscillation and attached splitter plate, respectively) on the flow and temperature fields to find an optimum situation which this combination results in heat transfer increment and drag reduction.

Design/methodology/approach
The method of the solution was based on finite volume discretization of Navier–Stokes equations. A dynamic grid is coupled with the solver by the arbitrary Lagrangian–Eulerian (ALE) formulation for modeling cylinder oscillation. Parametric studies were performed by altering oscillation frequency, splitter plate length and Reynolds number.

Findings
Oscillation in different frequencies was found to be complicated. Higher frequencies provide more heat transfer, but in the lock-on region, they bring remarkable increment to the drag coefficient. It was observed that simultaneous usage of oscillation and splitter plate may have both positive and negative effects on drag reduction and heat transfer increment. Finally F = 2 and L = 0.5 were chosen as an optimum combination.

Originality/value
In this study, the laminar incompressible flow and heat transfer from a confined rotationally oscillating circular cylinder with an attached splitter plate are investigated. Parametric studies are performed by changing oscillation frequency, splitter plate length and Reynolds number.
Stability analysis, solition solutions and Gaussian solitons of the generalized nonlinear Schrödinger equation with higher order terms
Authors: Wang Hui , Zhang Tian-Tian 
Published: December 2018

Purpose
The purpose of this paper is to study stability analysis, solition solutions and Gaussian solitons of the generalized nonlinear Schrödinger equation with higher order terms, which can be used to describe the propagation properties of optical soliton solutions.

Design/methodology/approach
The authors apply the ansatz method and the Hamiltonian system technique to find its bright, dark and Gaussian wave solitons and analyze its modulation instability analysis and stability analysis solution.

Findings
The results imply that the generalized nonlinear Schrödinger equation has bright, dark and Gaussian wave solitons. Meanwhile, the authors provide the graphical analysis of such solutions to better understand their dynamical behavior. Some constraint conditions are provided which can guarantee the existence of solitons. The authors analyze its modulation instability analysis and stability analysis solution.

Originality/value
These results may help us to further study the local structure and the interaction of solutions in generalized nonlinear Schrödinger -type equations. The authors hope that the results provided in this work can help enrich the dynamic behavior of the generalized nonlinear Schrödinger--type equations.
Asymmetric sensitivities of house prices to housing fundamentals: evidence from UK regions
Authors: Alqaralleh Huthaifa 
Published: December 2018

Purpose
This paper aims to examine asymmetries in the house price cycle and to understand the dynamic of housing prices, incorporating macroeconomic variables at regional and country level, namely, housing affordability, the unemployment rate, mortgage rate and inflation rate.

Design/methodology/approach
To highlight significant differences in the asymmetric patterns of house prices between regions, the STAR model is adopted.

Findings
The authors highlight significant differences in the asymmetric patterns of house prices between regions, in which some areas showed asymmetric response over the housing cycle; here the LSTAR model outperforms other models. In contrast, some regions (the South West and the North West) showed symmetric properties in the tails of the cycle; therefore, the ESTAR model was adopted in their case.

Practical implications
Being limited to a few fundamentals, this study opens an avenue for further research to investigate this dynamic using in addition such demand-supply factors as land supply, construction cost and loans made for housing. These findings can also be used to examine whether other models such as ARIMA, exponential smoothing or artificial neural networks can more accurately forecast housing prices.

Originality/value
The present paper aims to highlight housing affordability as a cause of asymmetric behaviour in house prices. Put differently, the authors seek to understand the dynamics of housing prices with other fundamentals incorporating macroeconomic variables in regions and country level data as a means of achieving a more concise result.
“You get what you appreciate”
Authors: Hassi Abderrahman 
Published: December 2018

PurposeThe purpose of this study is to examine the influences of transactional and transformational leadership styles on employee job satisfaction, employee affective commitment and organisational citizenship behaviour (OCB) within Moroccan organisations.Design/methodology/approachData were gathered from a sample of 219 employees working in seven different industries in Morocco and analysed using Structural Equations Modelling (SEM).FindingsSEM analyses reveal that employee job satisfaction, affective commitment and OCB are only impacted by thepersonal recognitiondimension of the transformational leadership style. The study indicates thatcharismaandintellectual stimulation(transformational leadership) as well ascontingent rewardandmanagement-by-exception(transactional leadership) did not yield significant results.Research limitations/implicationsThe use of a cross-sectional research design limits establishing cause-and-effect relationships.Practical implicationsThe results of the current study may be of use and interest for organisations in designing effective leadership training programs, as it takes into account how managers and/or practitioners tap into their subordinates’ effective behaviour.Originality/valueWith insights derived from a non-Western perspective, the major theoretical contribution of the present study lies in exploring the effects of transactional and transformational leadership styles on employee job satisfaction, employee affective commitment and OCB in Morocco.
Implementation of a volunteer fire corps activity support system during fires
Authors: Ishida Tomoyuki , Hoshino Shogo 
Published: December 2018

Purpose
The purpose of this paper is to implement an activity support system for volunteer fire corps using Web-GIS technology.

Design/methodology/approach
In this study, the authors implemented a volunteer fire corps activity support system comprising a dispatch request system, a water sources geographic information system, a fire-vehicle location confirmation system, a route history system and an integrated management system. They implemented this system as a Web application in consideration of responsive design assuming that it is used on mobile terminals.

Findings
To evaluate the effectiveness of the proposed system, the authors conducted a survey of 18 fire corps volunteers who were asked to evaluate the system for operability, relevance, functionality, usability and effectiveness.

Originality/value
In this research work, the authors implemented the volunteer fire corps activity support system using Web-GIS technology. The authors conducted a questionnaire survey of the volunteer fire corps activity support system, asking 18 fire corps volunteers to evaluate the system for operability, relevance, functionality, usability and effectiveness. The results of the survey indicate an overwhelming positive response to the volunteer fire corps activity support system for all five measures.
Tribological performance of commercial Mobil grade lubricants operating with titanium dioxide nanoparticle additives
Authors: Suryawanshi Shubham Rajendra , Pattiwar Jayant T. 
Published: December 2018

Purpose
The purpose of this study is to investigate the tribological performance (anti-friction and anti-wear properties) of commercial Mobil grade lubricants used in a journal bearing system in a power plant.

Design/methodology/approach
Three grades of Mobil lubricants (DTE 24, DTE 25 and DTE 26) are considered during the study. Titanium dioxide nanoparticles (TiO2, 0.5 Wt.%) of size 40 nm are used as a lubricant additive to examine the performance of the lubricants. The viscosity of the lubricant is computed using modified Krieger–Dougherty viscosity model. The morphology of TiO2 nanoparticles is studied with the help of scanning electron microscopy, ultra violet spectrophotometer and X-ray diffraction. The study of antifriction and antiwear properties for lubricants is carried out on four-ball tribo-tester for operating conditions specified by ASTM standards.

Findings
The tribochemical reaction film is formed between ball surfaces during the experiments on four-ball tester that minimizes the asperity contact due to addition of TiO2 nanoparticles in the lubricant. The viscosity of the lubricant is enhanced due to the addition of TiO2 nanoparticles. The frictional coefficient and wear scar diameters of balls in the lubricants are reduced in the range of 6-26 and 2-7 per cent, respectively.

Originality/value
The tribological properties of TiO2 as a lubricant additive in three commercial Mobil grade lubricants are investigated in this paper. The results obtained in this paper are expected to be helpful to bearing designers, researchers and academicians concerned with the relevant study.