bluuebunny/crossref_metadata_2025_split huggingface dataset:
Meiosis-specific prophase-like pathway controls cleavage-independent release of cohesin by Wapl phosphorylation
Authors: Challa Kiran , Ghanim Fajish V , Shinohara Miki , Klein Franz , Gasser Susan M. , Shinohara Akira 
Published: January 2018

AbstractSister chromatid cohesion on chromosome arms is essential for the segregation of homologous chromosomes during meiosis I while it is dispensable for sister chromatid separation during mitosis. It was assumed that, unlike the situation in mitosis, chromosome arms retain cohesion prior to onset of anaphase-I. Paradoxically, reduced immunostaining signals of meiosis-specific cohesin, including the kleisin Rec8, from the chromosomes were observed during late prophase-I of budding yeast. This decrease is seen in the absence of Rec8 cleavage and depends on condensin-mediated recruitment of Polo-like kinase (PLK/Cdc5). In this study, we confirmed that this release indeed accompanies the dissociation of acetylated Smc3 as well as Rec8 from meiotic chromosomes during late prophase-I. This release requires, in addition to PLK, the cohesin regulator, Wapl (Rad61/Wpl1 in yeast), and Dbf4-dependent Cdc7 kinase (DDK). Meiosis-specific phosphorylation of Rad61/Wpl1 and Rec8 by PLK and DDK collaboratively promote this release. This process is similar to the vertebrate “prophase” pathway for cohesin release during G2 phase and pro-metaphase. In yeast, meiotic cohesin release coincides with PLK-dependent compaction of chromosomes in late meiotic prophase-I. We suggest that yeast uses this highly regulated cleavage-independent pathway to remove cohesin during late prophase-I to facilitate morphogenesis of condensed metaphase-I chromosomes.Author SummaryIn meiosis the life and health of future generations is decided upon. Any failure in chromosome segregation has a detrimental impact. Therefore, it is currently believed that the physical connections between homologous chromosomes are maintained by meiotic cohesin with exceptional stability. Indeed, it was shown that cohesive cohesin does not show an appreciable turnover during long periods in oocyte development. In this context, it was long assumed but not properly investigated, that the prophase pathway for cohesin release would be specific to mitotic cells and will be safely suppressed during meiosis so as not to endanger the valuable chromosome connections. However, a previous study on budding yeast meiosis suggests the presence of cleavage-independent pathway of cohesin release during late prophase-I. In the work presented here we confirmed that the prophase pathway is not suppressed during meiosis, at least in budding yeast and showed that this cleavage-independent release is regulated by meiosis-specific phosphorylation of two cohesin subunits, Rec8 and Rad61(Wapl) by two cell-cycle regulators, PLK and DDK. Our results suggest that late meiotic prophase-I actively controls cohesin dynamics on meiotic chromosomes for chromosome segregation.
Seiðr: Efficient Calculation of Robust Ensemble Gene Networks
Authors: Schiffthaler Bastian , van Zalen Elena , Serrano Alonso R. , Street Nathaniel R. , Delhomme Nicolas 
Published: January 2018

AbstractGene regulatory and gene co-expression networks are powerful research tools for identifying biological signal within high-dimensional gene expression data. In recent years, research has focused on addressing shortcomings of these techniques with regard to the low signal-to-noise ratio, non-linear interactions and dataset dependent biases of published methods. Furthermore, it has been shown that aggregating networks from multiple methods provides improved results. Despite this, few usable and scalable software tools have been implemented to perform such best-practice analyses. Here, we present Seidr (stylized Seiðr), a software toolkit designed to assist scientists in gene regulatory and gene co-expression network inference. Seidr creates community networks to reduce algorithmic bias and utilizes noise corrected network backboning to prune noisy edges in the networks.Using benchmarks in real-world conditions across three eukaryotic model organisms, Saccharomyces cerevisiae, Drosophila melanogaster, and Arabidopsis thaliana, we show that individual algorithms are biased toward functional evidence for certain gene-gene interactions. We further demonstrate that the community network is less biased, providing robust performance across different standards and comparisons for the model organisms.Finally, we apply Seidr to a network of drought stress in Norway spruce (Picea abies (L.) H. Krast) as an example application in a non-model species. We demonstrate the use of a network inferred using Seidr for identifying key components, communities and suggesting gene function for non-annotated genes.
MicroRNA-122 supports robust innate immunity in hepatocytes by suppressing STAT3 phosphorylation
Authors: Xu Hui , Xu Shi-Jun , Xie Shu-Juan , Zhang Yin , Yang Jian-Hua , Zhang Wei-Qi , Zheng Man-Ni , Zhou Hui , Qu Liang-Hu 
Published: January 2018

ABSTRACTThe intrinsic innate immunity of hepatocytes is essential for the control of hepatitis viruses and influences the outcome of antiviral therapy. MicroRNA-122 (miR-122) is the most abundant microRNA in hepatocytes and is a central player in liver biology and disease. However, little is known about the role of miR-122 in hepatocyte innate immunity. Herein, we show that restoring miR-122 levels in hepatoma cells markedly increased the activation of both type III and type I interferons (IFNs) in response to hepatitis C virus (HCV) RNA or poly(I:C). We determined that miR-122 promotes IFN production through down-regulating the tyrosine (Tyr705) phosphorylation of STAT3. We show that STAT3 represses IFN activation by inhibiting interferon regulatory factor 1 (IRF1), which is rate-limiting for maximal IFN expression, especially type III IFNs. Through large-scale screening, we identified that miR-122 targets MERTK, FGFR1 and IGF1R, three oncogenic receptor tyrosine kinases that directly promote STAT3 phosphorylation. These findings reveal a previously unknown role for miR-122 in hepatic immunity and indicate a new potential strategy for treating hepatic infections through targeting STAT3.
miRge 2.0: An updated tool to comprehensively analyze microRNA sequencing data
Authors: Lu Yin , Baras Alexander S. , Halushka Marc K. 
Published: January 2018

AbstractmiRNAs play important roles in the regulation of gene expression. The rapidly developing field of microRNA sequencing (miRNA-seq; small RNA-seq) needs comprehensive bioinformatics tools to analyze these large datasets. We present the second iteration of miRge, miRge 2.0, with multiple enhancements. miRge 2.0 adds new functionality including novel miRNA detection, A-to-I editing analysis, better output files, and improved alignment to miRNAs. Our novel miRNA detection method is the first to use both miRNA hairpin sequence structure and composition of isomiRs resulting in a more specific capture of potential miRNAs. Using known miRNA data, our support vector machine (SVM) model predicted miRNAs with an average Matthews correlation coefficient (MCC) of 0.939 over 32 human cell datasets and outperformed miRDeep2 and miRAnalyzer regarding phylogenetic conservation. The A-to-I editing analysis implementation strongly correlated with a reference dataset’s prior analysis with adjusted R2 = 0.96. miRge 2.0 comes with alignment libraries to both miRBase v21 and MirGeneDB for 6 species: human, mouse, rat, fruit fly, nematode and zebrafish; and has a tool to create custom libraries. With the redevelopment of the tool in Python, it is now incorporated into bcbio-nextgen and implementable through Bioconda. miRge 2.0 is freely available at: https://github.com/mhalushka/miRge.
Sharq, A versatile preprocessing and QC pipeline for Single Cell RNA-seq
Authors: Candelli Tito , Lijnzaad Philip , Muraro Mauro J , Kerstens Hindrik , Kemmeren Patrick , van Oudenaarden Alexander , Margaritis Thanasis , Holstege Frank 
Published: January 2018

AbstractDespite the meteoric rise of single cell RNA-seq, only a few preprocessing pipelines exist that are able to perform all steps from the originalfastqfiles to a gene expression table ready for further analysis. Here we presentSharq, a versatile preprocessing pipeline designed to work with plate-based 3’-end protocols that include Unique Molecular Identifiers (UMIs).Sharqperforms stringent step-wise trimming of reads, assigns them to features according to a flexible hierarchical model, and uses the barcode and UMI information to avoid amplification biases and produce gene expression tables. Additionally,Sharqprovides an extensive plate diagnostics report for quality control and troubleshooting, including that of spatial artefacts. The diagnostics report includes measures of the quality of the individual plate wells as well as a robust assessment which of them contain material from live cells. Collectively, the innovative approaches presented here provide a valuable tool for processing and quality control of single cell RNA-seq data.
Adaptive robust sliding mode trajectory tracking control for 6 degree-of-freedom industrial assembly robot with disturbances
Authors: Pan Li , Bao Guanjun , Xu Fang , Zhang Libin 
Published: January 2018

PurposeThis paper aims to present an adaptive robust sliding mode tracking controller for a 6 degree-of-freedom industrial assembly robot with parametric uncertainties and external disturbances. The controller is used to achieve both stringent trajectory tracking, accurate parameter estimations and robustness against external disturbances.Design/methodology/approachThe controller is designed based on the combination of sliding mode control, adaptive and robust controls and hence has good adaptation and robustness abilities to parametric variations and uncertainties. The unknown parameter estimates are updated online based on a discontinuous projection adaptation law. The robotic dynamics is first formulated in both joint spaces and workspace of the robot’s end-effector. Then, the design procedure of the adaptive robust sliding mode tracking controller and the parameter update law is detailed.FindingsComparative tests are also conducted to verify the effectiveness of the proposed controller, which show that the proposed controller achieves significantly better dynamic trajectory tracking performances as compared with conventional proportional derivative controller and sliding mode controller under the same conditions.Originality/valueThis is a new innovation for industrial assembly robot to improve assembly automation.
Design parameters improvement of helicopter ducted tail rotor
Authors: Zhong Guo , Huang Jun , Yi Mingxu 
Published: January 2018

Purpose
The purpose of this paper is to reduce the acoustic noise of helicopter ducted tail rotor.

Design/methodology/approach
To predict the noise accurately, a thin-body boundary element method (BEM)/Ffowcs Williams–Hawkings method is developed in this paper. It is a hybrid method combining the BEM with computational aeroacoustics and can be used efficiently to predict the propagation of sound wave in the duct.

Findings
Compared with the experimental results, the proposed method of acoustic noise is rather desirable.

Practical implications
Then several geometry parameters are modified to investigate the noise reduction of ducted tail rotor by using the numerical prediction method.

Originality/value
The aerodynamic and acoustic performance of different modification tasks is discussed. These results demonstrate the validity of design parameters modification of ducted tail rotor in acoustic noise reduction.
Design and prototyping of the novel axial flux-switching permanent-magnet motor
Authors: Rahmani Fard Javad , Ardebili Mohammad 
Published: January 2018

PurposeThe purpose of this paper is to propose a novel axial field flux-switching machine with sandwiched permanent magnets. It is one of the most efficient machines which is appropriate for high-torque and low-speed direct-drive applications. The proposed model is equipped with an advanced phase-group concentrated-coil winding to obtain a unity displacement winding factor. Two configurations of the proposed motors with 6-stator-slot (S)/10-rotor-pole (P) and 12S/19P are investigated. These two structures are compared with optimized a conventional axial-field flux-switching permanent-magnet (CAFFSPM) machine. Unity displacement winding factor increases the back-EMF and electromagnetic torque. Moreover, the prototype 12S/19P motor is built to verify the design.

Design/methodology/approachThe torque equation is obtained and the dimensions of the two proposed motors are determined. Some specific design issues, including the stator/rotor pole sandwiching pole angle, the stator tooth angle and the rotor pole angle have been optimized to minimize the cogging torque while maintaining the high torque density by means of response surface methodology (RSM) and 3-D finite element model of the machine.

FindingsTo improve the performance, especially at high torque density, low cogging torque and high level of fault-tolerant capability, the 12S/19P axial field flux-switching sandwiched permanent-magnet (AFFSSPM) motor is proposed. Based on the optimized design, a prototype of the 12S/19P AFFSSPM motor is fabricated and tested. It is found that the experimental results validate the 3-D finite element method (FEM) simulation results.

Originality/valueThe AFFSSPM motor is one of the most efficient motors, but the 12S/19P AFFSSPM motor with sandwiched permanent magnet and unity displacement winding factor has not been specially reported to date. Thus, in this paper, the authors report on optimal design of a novel axial flux-switching sandwiched permanent-magnet machine for electric vehicles and fabricate a prototype of the 12S/19P AFFSSPM motor.
Comparative study of methods for optimization of electromagnetic devices with uncertainty
Authors: Deng Siyang , Brisset Stéphane , Clénet Stephane 
Published: January 2018

PurposeThis paper compares six reliability-based design optimization (RBDO) approaches dealing with uncertainties for a simple mathematical model and a multidisciplinary optimization problem of a safety transformer to highlight the most effective.Design/methodology/approachThe RBDO and various approaches to calculate the probability of failure are is presented. They are compared in terms of precision and number of evaluations on mathematical and electromagnetic design problems.FindingsThe mathematical example shows that the six RBDO approaches have almost the same results except the approximate moment approach that is less accurate. The optimization of the safety transformer highlights that not all the methods can converge to the global solution. Performance measure approach, single-loop approach and sequential optimization and reliability assessment (SORA) method appear to be more stable. Considering both numerical examples, SORA is the most effective method among all RBDO approaches.Originality/valueThe comparison of six RBDO methods on the optimization problem of a safety transformer is achieved for the first time. The comparison in terms of precision and number of evaluations highlights the most effective ones.
A neural network for electromagnetic based ore sorting
Authors: Li Min , Caushaj Arber , Silva Rodrigo , Lowther David 
Published: January 2018

PurposeThis paper aims to presents a novel application of neural network (NN) pattern recognition to ore rock sorting using inductive electromagnetic (EM) sensors.

Design/methodology/approachThe impedance of a metallic rock can be measured with an inductive method based on Faraday’s law and eddy current theory. A virtual rock model is then created for the simulation of the EM measurements. An NN is trained to differentiate between waste and useful ore samples (containing high amount of minerals) based on the EM sensor signals produced by the rocks.

FindingsThe NN solution showed high accuracy of rock classification and produced relatively robust results from signals with noise.

Originality/valueA pattern recognition NN was applied to classify low- and high-grade ore samples. It has the potential to determine the approximate amount of conductive materials inside ore rocks through multiple classes. This method can be used to improve the performance of EM-based ore sorting for mineral pre-concentration.
The new me or the me I’m proud of?
Authors: Yazdanparast Atefeh , Spears Nancy 
Published: January 2018

PurposeThis study aims to investigate how comparing physical aspects of the self to fashion models in mass-mediated images result in body dissatisfaction and what mechanisms could be used to interrupt the potentially harmful emotional and motivational outcomes of such evaluations.Design/methodology/approachTwo experimental design studies are conducted in which objective self-awareness (OSA; self-focus) is manipulated. In the first study, participants are assigned to control vs relevant vs irrelevant standards of appearance, and in the second study, all participants receive relevant standards of appearance and are randomly primed to experience pride or shame.FindingsFocusing on the physical aspect of the self (i.e. state of OSA) and having access to relevant standards of appearance such as viewing images of beautiful fashion models (vs irrelevant standards of appearance such as images of plants) initiate the process of self-standard evaluation that may lead to body image state dissatisfaction (BISDS). Negative emotions mediate the relationship between BISDS and motivations to pursue cosmetic procedures. Pride and shame are two important self-conscious emotions that differently influence these relationships.Originality/valueThe present research identifies how pride could act as a self-affirming factor to intervene the undesirable outcomes of body image dissatisfaction and discourage unnecessary cosmetic procedures. Pride diminishes the motivation to undergo cosmetic procedures by shifting the focus from pursuing unachievable standards of appearance to pride-inducing achievements and self-affirming positive qualities. Shame, however, keeps individuals focused on discrepancies and lowers their ability to think of substitute goals, resulting in enhanced motivations for cosmetic procedures.
To pay or not to pay: what matters the most for dividend payments?
Authors: Ranajee Ranajee , Pathak Rajesh , Saxena Akanksha 
Published: January 2018

Purpose
The purpose of this paper is to test the stickiness of payout policy across times for Indian firms, by identifying the determinants of dividend payout (for amount of dividends as well as probability of dividends) and examine their predictive consistency through good and bad times, affiliation categories, amid controls for idiosyncratic characteristics. The authors also examine the scantly explored effects of financial constraints on firms’ dividend decisions.

Design/methodology/approach
The authors use various regression models, i.e. panel, Tobit and logit models; and amid control for firm-specific characteristics throughout the analysis.

Findings
The authors observe payout levels on average increasing with time for Indian firms. Further, group firms pay higher dividends compared to standalone firms. Firms’ leverage, profitability, non-promoters holdings, growth prospects and dividend event are apparently the important determinants of payout ratio and are mostly, but not always, consistent through times and firms’ categories, for both the amount as well as the likelihood of dividend payments. Financial constraints have an overall negative impact on dividends with significantly varying magnitude across periods of stability, crisis and recovery. Firms’ age and size are positive and significant factors for dividends level decisions in Indian firms, which is consistent with the life-cycle theory. However, inconsistent size and age effect is observed in determining the likelihood of dividend payment.

Research limitations/implications
This study adds to the growing literature on the changing trends and contributing factors of firms’ dividend payout policy.

Originality/value
This study provides evidence on predictive consistency of payout policy of firms and its determination with the change in the external economic condition.
What drives consumer choice of Islamic banking services in the United Arab Emirates?
Authors: Shome Anamitra , Jabeen Fauzia , Rajaguru Rajesh 
Published: January 2018

Purpose
Islamic banking (IB) has witnessed remarkable growth in the past decade. The purpose of this study is to explore some factors that are influencing the choice of Islamic banking and finance (IBF) products and services in the United Arab Emirates (UAE), a predominantly Muslim country.

Design/methodology/approach
Students enrolled at a university located in a major emirate in the UAE were asked to respond to a survey on factors underlying their decision to open an account at an Islamic bank. Responses were analyzed using descriptive statistics, analysis of variance and regression analysis.

Findings
Results indicate that the decision to open an account with an Islamic bank is influenced by consumer expectations regarding the conformity of the bank’s operations with Islamic principles, as well as consumers’ Arab language skills. Variables such as consumers’ nationality, gender, education and familiarity with IB do not have a significant influence on the decision to open an account at an Islamic bank.

Research limitations/implications
The study focuses on university students from a certain Emirate only, which somewhat limits the generalizability of the research results. Nevertheless, the findings of this study may potentially provide some practical insights for further improving and promoting IB, with special reference to the UAE youth market segment.

Originality/value
The research is original in nature, particularly as there have not been many instances where the choice of potential consumers (university students) regarding IB and finance services has been explored within the IB sector in a predominantly Muslim nation such as the UAE, an emerging Gulf economy. Consequently, the research findings have important implications for Islamic banks operating in a predominantly Islamic environment.
Healthcare assistants’ experiences on forensic mental health wards
Authors: Boardman Stacey , Clarbour Jane , Rayner Kelly 
Published: January 2018

Purpose
In forensic mental health wards, patients spend more time with healthcare assistants (HCAs) than qualified nurses. Despite this, there is no universally utilised standardised HCA training. The purpose of this paper is to assess the HCAs’ experiences in the HCA role in order to better understand how to build on the HCA role to ensure safe practice, and enhance staff well-being.

Design/methodology/approach
HCAs working on low and medium secure NHS forensic mental health units were recruited through purposive methods. HCAs engaged in a semi-structured interview, with questions surrounding their support needs, clinical decision making and perception of risks in the role. Template analysis was used, applying an a priori template based on the existing literature to interview transcripts.

Findings
The participants described the HCA experience to be defined by two master themes: “HCA factors” and “organisational factors”. HCAs valued a holistic patient view which prized patients’ experiences. The participants described a lack of role clarity which may be defined through ward expectations and professional experience.

Originality/value
HCAs seek a holistic view of the patient; however, some overlooked patient offences in order to do their job. Future research should address how looking past offences impacts security and HCAs’ well-being long term.