bluuebunny/crossref_metadata_2025 huggingface dataset:
3D hybrid carbon composed of multigraphene bridged by carbon chains
Authors: Liu Lingyu , Hu Meng , Liu Chao , Shao Cancan , Pan Yilong , Ma Mengdong , Wu Yingju , Zhao Zhisheng , Gao Guoying , He Julong
Published: January 2018

The element carbon possesses various stable and metastable allotropes; some of them have been applied in diverse fields. The experimental evidences of both carbon chain and graphdiyne have been reported. Here, we reveal the mystery of an enchanting carbon allotrope with sp-, sp2-, and sp3-hybridized carbon atoms using a newly developed ab initio particle-swarm optimization algorithm for crystal structure prediction. This crystalline allotrope, namely m-C12, can be viewed as braided mesh architecture interwoven with multigraphene and carbon chains. The m-C12 meets the criteria for dynamic and mechanical stabilities and is energetically more stable than carbyne and graphdiyne. Analysis of the B/G and Poisson’s ratio indicates that this allotrope is ductile. Notably, m-C12 is a superconducting carbon with Tc of 1.13 K, which is rare in the family of carbon allotropes.
A role for P2X4 receptors in lysosome function
Authors: Murrell-Lagnado Ruth D.
Published: January 2018

Murrell-Lagnado provides insight into new research revealing the physiological role of lysosomal P2X4 channels.
Applicability of the lattice Boltzmann method to determine the ohmic resistance in equivalent resistor connections
Authors: Espinoza-Andaluz Mayken , Barzola Julio , Guarochico-Moreira Víctor H. , Andersson Martin
Published: January 2018

Knowing the ohmic resistance in the materials allow to know in advance its electrical behavior when a potential difference is applied, and therefore the prediction of the electrical performance can be achieved in a most certain manner. Although the Lattice Boltzmann method (LBM) has been applied to solve several physical phenomena in complex geometries, it has only been used to describe the fluid phase, but applicability studies of LBM on the solid-electric-conducting material have not been carried out yet. The purpose of this paper is to demonstrate the accuracy of calculating the equivalent resistor connections using LBM. Several series and parallel resistor connections are effected. All the computations are carried out with 3D models, and the domain materials are designed by the authors.
Interleukin 1α (IL-1α) Promotes Pathogenic Immature Myeloid Cells and IL-1β Favors Protective Mature Myeloid Cells During Acute Lung Infection
Authors: Periasamy Sivakumar , Harton Jonathan A
Published: January 2018

Bacterial pneumonia is a common risk factor for acute lung injury and sepsis-mediated death, but the mechanisms underlying the overt inflammation and accompanying pathology are unclear. Infiltration of immature myeloid cells and necrotizing inflammation mediate severe pathology and death during pulmonary infection with Francisella tularensis. However, eliciting mature myeloid cells provides protection. Yet, the host factors responsible for this pathologic immature myeloid cell response are unknown. Here, we report that while the influx of both mature and immature myeloid cells is strictly MyD88 dependent, the interleukin 1 (IL-1) receptor mediates an important dual function via its ligands IL-1α and IL-1β. Although IL-1β favors the appearance of bacteria-clearing mature myeloid cells, IL-1α contributes to lung infiltration by ineffective and pathologic immature myeloid cells. Finally, IL-1α and IL-1β are not the sole factors involved, but myeloid cell responses during acute pneumonia were largely unaffected by lung levels of interleukin 10, interleukin 17, CXCL1, granulocyte colony-stimulating factor, and granulocyte-macrophage colony-stimulating factor.
Effects of Celecoxib and Low-dose Aspirin on Outcomes in Adjuvant Aromatase Inhibitor–Treated Patients: CCTG MA.27
Authors: Strasser-Weippl Kathrin , Higgins Michaela J , Chapman Judith-Anne W , Ingle James N , Sledge George W , Budd George T , Ellis Matthew J , Pritchard Kathleen I , Clemons Mark J , Badovinac-Crnjevic Tanja , Han Lei , Gelmon Karen A , Rabaglio Manuela , Elliott Catherine , Shepherd Lois E , Goss Paul E
Published: January 2018

Background

Celecoxib and low-dose aspirin might decrease risk of breast cancer recurrence.

Methods

In the Canadian Cancer Trials Group MA.27, postmenopausal hormone receptor–positive breast cancer patients were randomly assigned (2 × 2) to adjuvant exemestane or anastrozole, and celecoxib or placebo. Low-dose aspirin of 81 mg or less was a stratification factor. Due to concerns about cardiac toxicity, celecoxib use was stopped in December 2004, while stratification by aspirin use was removed through protocol amendment. We examined the effects of celecoxib and low-dose aspirin on event-free survival (EFS), defined as time from random assignment to time of locoregional or distant disease recurrence, new primary breast cancer, or death from any cause; distant disease–free survival (DDFS); and overall survival (OS). All statistical tests were two-sided.

Results

Random assignment to celecoxib (n = 811, 50.0%) or placebo (n = 811, 50.0%) was discontinued after 18 months (n = 1622). At a median of 4.1 years’ follow-up, among 1622 patients, 186 (11.5%) patients had an EFS event: 80 (4.9%) had distant relapse, and 125 (7.7%) died from any cause. Celecoxib did not statistically significantly impact EFS, DDFS, or OS in univariate analysis (respectively, P = .92, P = .55, and P = .56) or multivariable analysis (respectively, P = .74, P = .60, and P = .76). Low-dose aspirin use (aspirin users n = 476, 21.5%; non–aspirin users n = 1733, 78.5%) was associated in univariate analyses with worse EFS (hazard ratio [HR] = 1.48, 95% confidence interval [CI] = 1.12 to 1.96, P = 0.006) and worse OS (HR = 1.87, 95% CI = 1.35 to 2.61, P < .001). After adjusting for baseline characteristics and treatment arm, aspirin use showed no statistical association with EFS (P = .08) and DDFS (P = .82), but was associated with statistically worse OS (HR = 1.67, 95% CI = 1.13 to 2.49, P = .01).

Conclusion

Random assignment to short-term (≤18 months) celecoxib as well as use of low-dose aspirin showed no effect on DDFS and EFS in multivariable analysis. Low-dose aspirin increased “all-cause” mortality, presumably because of higher preexisting cardiovascular risks.
A Reactive Inelasticity Theoretical Framework for modeling Viscoelasticity, Plastic Deformation, and damage in Soft Tissue
Authors: Safa Babak N. , Santare Michael H. , Elliott Dawn M.
Published: January 2018

Soft tissues are biopolymeric materials, primarily made of collagen and water. These tissues have non-linear, anisotropic, and inelastic mechanical behaviors that are often categorized into viscoelastic behavior, plastic deformation, and damage. While tissue’s elastic and viscoelastic mechanical properties have been measured for decades, there is no comprehensive theoretical framework for modeling inelastic behaviors of these tissues that is based on their structure. To model the three major inelastic mechanical behaviors of soft tissue we formulated a structurally inspired continuum mechanics framework based on the energy of molecular bonds that break and reform in response to external loading (reactive bonds). In this framework, we employed the theory of internal state variables and kinetics of molecular bonds. The number fraction of bonds, their reference deformation gradient, and damage parameter were used as internal state variables that allowed for consistent modeling of all three of the inelastic behaviors of tissue by using the same sets of constitutive relations. Several numerical examples are provided that address practical problems in tissue mechanics, including the difference between plastic deformation and damage. This model can be used to identify relationships between tissue’s mechanical response to external loading and its biopolymeric structure.
Baculovirus AC102 is a nucleocapsid protein that is crucial for nuclear actin polymerization and nucleocapsid morphogenesis
Authors: Hepp Susan E. , Borgo Gina M. , Ticau Simina , Ohkawa Taro , Welch Matthew D.
Published: January 2018

The baculovirusAutographa californicamultiple nucleopolyhedrovirus (AcMNPV), the type species of alphabaculoviruses, is an enveloped DNA virus that infects lepidopteran insects and is commonly known as a vector for protein expression and cell transduction. AcMNPV belongs to a diverse group of viral and bacterial pathogens that target the host cell actin cytoskeleton during infection. AcMNPV is unusual, however, in that it absolutely requires actin translocation into the nucleus early in infection, and actin polymerization within the nucleus late in infection coincident with viral replication. Of the six viral factors that are sufficient, when coexpressed, to induce the nuclear localization of actin, only AC102 is essential for viral replication and the nuclear accumulation of actin. We therefore sought to better understand the role of AC102 in actin mobilization in the nucleus early and late in infection. Although AC102 was thought to function early in infection, we found that AC102 is predominantly expressed as a late protein. In addition, we observed that AC102 is required for F-actin assembly in the nucleus during late infection, as well as for proper formation of viral replication structures and nucleocapsid morphogenesis. Finally, we found that AC102 is a nucleocapsid protein and a newly recognized member of a complex consisting of the viral proteins EC27, C42, and the actin polymerization protein P78/83. Taken together, our findings suggest that AC102 is necessary for nucleocapsid morphogenesis and actin assembly during late infection through its role as a component of the P78/83-C42-EC27-AC102 protein complex.

IMPORTANCE

The baculovirusAutographa californicamultiple nucleopolyhedrovirus (AcMNPV) is an important biotechnological tool for protein expression and cell transduction, and related nucleopolyhedroviruses are also employed as environmentally benign insecticides. One impact of our work is to better understand the fundamental mechanisms through which AcMNPV exploits the cellular machinery of the host for replication, which may aid in the development of improved baculovirus-based research and industrial tools. Moreover, AcMNPV’s ability to mobilize the host actin cytoskeleton within the cell’s nucleus during infection makes it a powerful cell biological tool. It is becoming increasingly clear that actin plays important roles in the cell’s nucleus, yet the regulation and function of nuclear actin is poorly understood. Our work to better understand how AcMNPV relocalizes and polymerizes actin within the nucleus may reveal fundamental mechanisms that govern nuclear actin regulation and function, even in the absence of viral infection.
Criteria for evaluating molecular markers: Comprehensive quality metrics to improve marker-assisted selection
Authors: Platten John Damien , Cobb Joshua N. , Zantua Rochelle E.
Published: January 2018

Despite strong interest over many years, the usage of quantitative trait loci in plant breeding has often failed to live up to expectations. A key weak point in the utilisation of QTLs is the “quality” of markers used during marker-assisted selection (MAS): unreliable markers result in variable outcomes, leading to a perception that MAS products fail to achieve reliable improvement. Most reports of markers used for MAS focus on markers derived from the mapping population. There are very few studies that examine the reliability of these markers in other genetic backgrounds, and critically, no metrics exist to describe and quantify this reliability. To improve the MAS process, this work proposes five core metrics that fully describe the reliability of a marker. These metrics give a comprehensive and quantitative measure of the ability of a marker to correctly classify germplasm as QTL[+]/[-], particularly against a background of high allelic diversity. Markers that score well on these metrics will have far higher reliability in breeding, and deficiencies in specific metrics give information on circumstances under which a marker may not be reliable. The metrics are applicable across different marker types and platforms, allowing an objective comparison of the performance of different markers irrespective of the platform. Evaluating markers using these metrics demonstrates that trait-specific markers consistently out-perform markers designed for other purposes. These metrics also provide a superb set of criteria for designing superior marker systems for a target QTL, enabling the selection of an optimal marker set before committing to design.
BDNF-TrkB signaling in oxytocin neurons contributes to maternal behavior
Authors: Maynard Kristen R. , Hobbs John W. , Phan Badoi N. , Gupta Amolika , Rajpurohit Sumita , Williams Courtney , Rajpurohit Nina , Shin Joo Heon , Jaffe Andrew E. , Martinowich Keri
Published: January 2018

Brain-derived neurotrophic factor (Bdnf) transcription is controlled by several promoters, which drive expression of multiple transcripts encoding an identical protein. We previously reported that BDNF derived from promoters I and II is highly expressed in hypothalamus and is critical for regulating aggression in male mice. Here we report that BDNF loss from these promoters causes reduced sexual receptivity and impaired maternal care in female mice, which is concomitant with decreased oxytocin (Oxt) expression during development. We identify a novel link between BDNF signaling, oxytocin, and maternal behavior by demonstrating that ablation of TrkB selectively in OXT neurons partially recapitulates maternal care impairments observed in BDNF-deficient females. Using translating ribosome affinity purification and RNA-sequencing we define a molecular profile for OXT neurons and delineate how BDNF signaling impacts gene pathways critical for structural and functional plasticity. Our findings highlight BDNF as a modulator of sexually-dimorphic hypothalamic circuits that govern female-typical behaviors.
The genome-wide rate and spectrum of spontaneous mutations differs between haploid and diploid yeast
Authors: Sharp Nathaniel P. , Sandell Linnea , James Christopher G. , Otto Sarah P.
Published: January 2018

By altering the dynamics of DNA replication and repair, alternative ploidy states may experience different rates and types of new mutations, leading to divergent evolutionary outcomes. We report the first direct comparison of the genome-wide spectrum of spontaneous mutations arising in haploid and diploid forms of the budding yeast. Characterizing the number, types, locations, and effects of thousands of mutations revealed that haploids were more prone to single-nucleotide and mitochondrial mutations, while larger structural changes were more common in diploids. Mutations were more likely to be detrimental in diploids, even after accounting for the large impact of structural changes, contrary to the prediction that diploidy masks the effects of recessive alleles. Haploidy is expected to reduce the opportunity for conservative DNA repair involving homologous chromosomes, increasing the insertion-deletion rate, but we found little support for this idea. Instead, haploids were more susceptible to particular single-nucleotide mutations in late-replicating genomic regions, resulting in a ploidy difference in the spectrum of substitutions. In diploids we detect mutation rate variation among chromosomes in association with centromere location, a finding that is supported by published polymorphism data. Diploids areSaccharomyces cerevisiaenot simply doubled haploids; instead, our results predict that the spectrum of spontaneous mutations will substantially shape the dynamics of genome evolution in haploid and diploid populations.
Single Cell Molecular Alterations Reveal Pathogenesis and Targets of Concussive Brain Injury
Authors: Arneson Douglas , Zhuang Yumei , Byun Hyae Ran , Ahn In Sook , Ying Zhe , Zhang Guanglin , Gomez-Pinilla Fernando , Yang Xia
Published: January 2018

The complex neuropathology of traumatic brain injury (TBI) is difficult to dissect in the hippocampus considering the convoluted hippocampal cytoarchitecture. As a major casualty of TBI, hippocampal dysfunction results in cognitive decline that may escalate to other neurological disorders, and the molecular basis is hidden in the genomic programs of individual hippocampal cells. Using the unbiased single cell sequencing method Drop-seq, we uncovered the hippocampal cell types most sensitive to concussive mild TBI (mTBI) as well as the vulnerable genes, pathways and cell-cell interactions predictive of disease pathogenesis in a cell-type specific manner, revealing hidden pathogenic mechanisms and potential targets. Targeting Ttr, encoding the thyroid hormone T4 transporter transthyretin, mitigated the genomic and behavioral abnormalities associated with mTBI. Single cell genomics provides unique evidence about altered circuits and pathogenic pathways, and pinpoints new targets amenable to therapeutics in mTBI and related disorders.
Charting the cross-functional map between transcription factors and cancer metabolism
Authors: Ortmayr Karin , Dubuis Sébastien , Zampieri Mattia
Published: January 2018

Transcriptional reprogramming of cellular metabolism is a hallmark feature of cancer. However, a systematic approach to study the role of transcription factors (TFs) in mediating cancer metabolic rewiring is missing. Here, we chart a genome-scale map of TF-metabolite associations in human using a new combined computational-experimental framework for large-scale metabolic profiling of adherent cell lines, and the integration of newly generated intracellular metabolic profiles of 54 cancer cell lines with transcriptomic and proteomic data. We unravel a large space of dependencies between TFs and central metabolic pathways, suggesting that the regulation of carbon metabolism in tumors may be more diverse and flexible than previously appreciated. This map provides an unprecedented resource to predict TFs responsible for metabolic transformation in patient-derived tumor samples, opening new opportunities in designing modulators of oncogenic TFs and in understanding disease etiology.
Evaluating Cell Identity from Transcription Profiles
Authors: Mah Nancy , Taškova Katerina , El Amrani Khadija , Hariharan Krithika , Kurtz Andreas , Andrade-Navarro Miguel A.
Published: January 2018

Induced pluripotent stem cells (iPS) and direct lineage programming offer promising autologous and patient-specific sources of cells for personalized drug-testing and cell-based therapy. Before these engineered cells can be widely used, it is important to evaluate how well the engineered cell types resemble their intended target cell types. We have developed a method to generate CellScore, a cell identity score that can be used to evaluate the success of an engineered cell type in relation to both its initial and desired target cell type, which are used as references. Of 20 cell transitions tested, the most successful transitions were the iPS cells (CellScore > 0.9), while other transitions (e.g. induced hepatocytes or motor neurons) indicated incomplete transitions (CellScore < 0.5). In principle, the method can be applied to any engineered cell undergoing a cell transition, where transcription profiles are available for the reference cell types and the engineered cell type.

Highlights

A curated standard dataset of transcription profiles from normal cell types was created.

CellScore evaluates the cell identity of engineered cell types, using the curated dataset.

CellScore considers the initial and desired target cell type.

CellScore identifies the most successfully engineered clones for further functional testing.
Predicting E. coli concentrations using limited qPCR deployments at Chicago beaches
Authors: Lucius Nick , Rose Kevin , Osborn Callin , Sweeney Matt E , Chesak Renel , Little Daniel Y. , Beslow Scott , Schenk Tom
Published: January 2018

Culture-based methods to measure Escherichia coli (E. coli) are used by beach administrators to inform whether bacteria levels represent an elevated risk to swimmers. Since results take up to 12 hours, statistical models are used to forecast bacteria levels in lieu of test results; however they underestimate days with elevated fecal indicator bacteria levels. Quantitative polymerase chain reaction (qPCR) tests return results within 3 hours but are 2 to 5 times more expensive than culture-based methods. This paper presents a prediction model which uses limited deployments of qPCR tested sites with inter-beach correlation to predict when bacteria will exceed acceptable thresholds. The model can be used to inform management decisions on when to warn residents or close beaches due to exposure to the bacteria. Using data from Chicago collected between 2006 and 2016, the model proposed in this paper increased sensitivity from 3.4 percent to 11.2 percent–a 230 percent increase. We find that the correlation between beaches are substantial enough to provide higher levels of precision and sensitivity to predictive models. Thus, limited deployments of qPCR testing can be used to deliver better predictions for beach administrators at lower cost and less complexity.
CITGeneDB: A comprehensive database of human and mouse genes enhancing or suppressing cold-induced thermogenesis validated by perturbation experiments in mice
Authors: Li Jin , Deng Su-Ping , Wei Gang , Yu Peng
Published: January 2018

Cold-induced thermogenesis increases energy expenditure and can reduce body weight in mammals, so the genes involved in it are thought to be potential therapeutic targets for treating obesity and diabetes. In the quest for more effective therapies, a great deal of research has been conducted to elucidate the regulatory mechanism of cold-induced thermogenesis. Over the last decade, a large number of genes that can enhance or suppress cold-induced thermogenesis have been discovered, but a comprehensive list of these genes is lacking. To fill this gap, we examined all of the annotated human and mouse genes and curated those demonstrated to enhance or suppress cold-induced thermogenesis by in vivo or ex vivo experiments in mice. The results of this highly accurate and comprehensive annotation are hosted on a database called CITGeneDB, which includes a searchable web interface to facilitate broad public use. The database will be updated as new genes are found to enhance or suppress cold-induced thermogenesis. It is expected that CITGeneDB will be a valuable resource in future explorations of the molecular mechanism of cold-induced thermogenesis, helping pave the way for new obesity and diabetes treatments. Database URL: http://citgenedb.yubiolab.org
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

Sister 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 Summary

In 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

Gene 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

The 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

miRNAs 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

Despite 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

Purpose

This 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/approach

The 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.

Findings

Comparative 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/value

This 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

Purpose

The 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/approach

The 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.

Findings

To 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/value

The 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

Purpose

This 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/approach

The 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.

Findings

The 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/value

The 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

Purpose

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

Design/methodology/approach

The 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.

Findings

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

Originality/value

A 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

Purpose

This 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/approach

Two 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.

Findings

Focusing 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/value

The 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.