bluuebunny/crossref_metadata_2025_split huggingface dataset:
SVIR epidemic model with age structure in susceptibility, vaccination effects and relapse
Authors: Wang Jinliang , Guo Min , Liu Shengqiang 
Published: May 2017

Abstract
An SVIR epidemic model with continuous age structure in the susceptibility, vaccination effects and relapse is proposed. The asymptotic smoothness, existence of a global attractor, the stability of equilibria and persistence are addressed. It is shown that if the basic reproductive number $\Re_0&lt;1$, then the disease-free equilibrium is globally asymptotically stable. If $\Re_0&gt;1$, the disease is uniformly persistent, and a Lyapunov functional is used to show that the unique endemic equilibrium is globally asymptotically stable. Combined effects of susceptibility age, vaccination age and relapse age on the basic reproductive number are discussed.
Clear Cell Renal Cell Carcinoma with Biallelic Inactivation of CDKN2A/B on 9p21 have Distinct Gene Expression Signature and are Associated with Poor Prognosis
Authors: Girgis Andrew H. 
Published: May 2017

AbstractPurposeThe clinical implications of biallelic inactivation ofCDKN2A/Bin clear cell renal cell carcinoma (ccRCC) and relevant dysregulated biological pathways and gene signatures were investigated.Materials and MethodsData were obtained from the TCGA data set and validated using Project GENIE and previously published dataset.CDKN2A/Ballelic status was classified into 3 groups, including biallelicCDKN2A/Binactivation (homozygous deletion or combined heterozygous deletion and mutation), monoallelicCDKN2A/Bloss (heterozygous deletion or mutation) and absentCDKN2A/Ballelic loss. Univariate and multivariate cancer-specific survival and disease-free survival analyses were performed. Integrated analyses of copy number, gene expression (mRNA and miRNA), protein expression and methylation changes were conducted.ResultsOf 440 patients with ccRCC 17 (3.9%) had biallelicCDKN2A/Binactivation and 116 (26.4%) had monoallelicCDKN2A/Bloss.CDKN2A/Ballelic inactivation was associated with late tumor stage, high histological grade, presence of metastasis and greater tumor size. Patients with biallelic deletion ofCDKN2A/Bshowed significantly worse cancer-specific survival and disease-free survival (p<0.0001). Significant co-occurrence ofMTAPhomozygous deletion was observed inCDKN2A/Bbiallic inactivated tumors (46.7%; p<0.001). Significant underexpression ofCDKN2A/Bwas observed in biallelic inactivated tumors at the mRNA and protein levels. miR-21 was the most highly expressed miRNA in biallelic inactivated tumors. Biallelic inactivated tumors were significantly enriched for genes related to activation ofATRin response to replication stress and miR-21 target genes.ConclusionsCDKN2A/Bbiallelic inactivation may be a prognostic marker for ccRCC and is associated with distinct dysregulation of gene expression signatures.
Biochemical adaptations of the retina and retinal pigment epithelium support a metabolic ecosystem in the vertebrate eye
Authors: Kanow Mark A. , Giarmarco Michelle M. , Jankowski Connor , Tsantilas Kristine , Engel Abbi L. , Du Jianhai , Linton Jonathan D. , Farnsworth Christopher C. , Sloat Stephanie R. , Lindsay Ken J. , Parker Edward D. , Brockerhoff Susan E. , Sadilek Martin , Chao Jennifer R. , Hurley James B. 
Published: May 2017

ABSTRACTHere we report multiple lines of evidence for a comprehensive model for retinal energy metabolism. Metabolic flux, locations of key enzymes and our finding that glucose enters the neural retina almost entirely through photoreceptors support a conceptually new model for retinal metabolism. In this model, glucose from the choroidal blood supply passes through the retinal pigment epithelium to the retina where photoreceptors convert it to lactate. Photoreceptors then export the lactate as fuel for the retinal pigment epithelium and for neighboring Müller glial cells. A key feature of this model is that aerobic glycolysis in photoreceptors produces lactate to suppress glycolysis in the neighboring retinal pigment epithelium. That enhances the flow of glucose to the retina by minimizing consumption of glucose within the retinal pigment epithelium. This framework for metabolic relationships in retina provides new insights into the underlying causes of retinal disease, age-related vision loss and metabolism-based therapies.
Metabolic constraints and quantitative design principles in gene expression during adaption of yeast to heat shock
Authors: Pereira Tania , Vilaprinyo Ester , Belli Gemma , Herrero Enric , Salvado Baldiri , Sorribas Albert , Altés Gisela , Alves Rui 
Published: May 2017

AbstractMicroorganisms evolved adaptive responses that enable them to survive stressful challenges in ever changing environments by adjusting metabolism through the modulation of gene expression, protein levels and activity, and flow of metabolites. More frequent challenges allow natural selection ampler opportunities to select from a larger number of phenotypes that are compatible with survival. Understanding the causal relationships between physiological and metabolic requirements that are needed for cellular stress adaptation and gene expression changes that are used by organisms to achieve those requirements may have a significant impact in our ability to interpret and/or guide evolution.Here, we study those causal relationships during heat shock adaptation in the yeastSaccharomyces cerevisiae. We do so by combining dozens of independent experiments measuring whole genome gene expression changes during stress response with a nonlinear simplified kinetic model of central metabolism.This combination is used to create a quantitative, multidimensional, genotype-to-phenotype mapping of the metabolic and physiological requirements that enable cell survival to the feasible changes in gene expression that modulate metabolism to achieve those requirements. Our results clearly show that the feasible changes in gene expression that enable survival to heat shock are specific for this stress. In addition, they suggest that genetic programs for adaptive responses to desiccation/rehydration and to pH shifts might be selected by physiological requirements that are qualitatively similar, but quantitatively different to those for heat shock adaptation. In contrast, adaptive responses to other types of stress do not appear to be constrained by the same qualitative physiological requirements. Our model also explains at the mechanistic level how evolution might find different sets of changes in gene expression that lead to metabolic adaptations that are equivalent in meeting physiological requirements for survival. Finally, our results also suggest that physiological requirements for heat shock adaptation might be similar between unicellular ascomycetes that live in similar environments. Our analysis is likely to be scalable to other adaptive response and might inform efforts in developing biotechnological applications to manipulate cells for medical, biotechnological, or synthetic biology purposes.
Improved transcriptome sampling pinpoints 26 paleopolyploidy events in Caryophyllales, including two paleo-allopolyploidy events
Authors: Yang Ya , Moore Michael J. , Brockington Samuel F. , Mikenas Jessica , Olivieri Julia , Walker Joseph F. , Smith Stephen A. 
Published: May 2017

SummaryStudies of the macroevolutionary legacy of paleopolyploidy are limited by an incomplete sampling of these events across the tree of life. To better locate and understand these events, we need comprehensive taxonomic sampling as well as homology inference methods that accurately reconstruct the frequency and location of gene duplications.We assembled a dataset of transcriptomes and genomes from 169 species in Caryophyllales, of which 43 were newly generated for this study, representing one of the densest sampled genomic-scale datasets yet available. We carried out phylogenomic analyses using a modified phylome strategy to reconstruct the species tree. We mapped phylogenetic distribution of paleopolyploidy events by both tree-based and distance-based methods, and explicitly tested scenarios for paleo-allopolyploidy.We identified twenty-six paleopolyploidy events distributed throughout Caryophyllales, and using novel techniques inferred two to be paleo-allopolyploidy.Through dense phylogenomic sampling, we show the propensity of paleo-polyploidy in the clade Caryophyllales. We also provide the first method for utilizing transcriptome data to detect paleo-allopolyploidy, which is important as it may have different macro-evolutionary implications compared to paleo-autopolyploidy.
nQuire: A Statistical Framework For Ploidy Estimation Using Next Generation Sequencing
Authors: Weiß Clemens L. , Pais Marina , Cano Liliana M. , Kamoun Sophien , Burbano Hernán A. 
Published: May 2017

AbstractIntraspecific variation in ploidy occurs in a wide range of species including pathogenic and nonpathogenic eukaryotes such as yeasts and oomycetes. Ploidy can be inferred indirectly - without measuring DNA content - from experiments using next-generation sequencing (NGS). We present nQuire, a statistical framework that distinguishes between diploids, triploids and tetraploids using NGS. The command-line tool models the distribution of base frequencies at variable sites using a Gaussian Mixture Model, and uses maximum likelihood to select the most plausible ploidy model. nQuire handles large genomes at high coverage efficiently and uses standard input file formats.We demonstrate the utility of nQuire analyzing individual samples of the pathogenic oomycetePhytophthora infestansand the Baker’s yeastSaccharomyces cerevisiae. Using these organisms we show the dependence between reliability of the ploidy assignment and sequencing depth. Additionally, we employ normalized maximized log-likelihoods generated by nQuire to ascertain ploidy level in a population of samples with ploidy heterogeneity. Using these normalized values we cluster samples in three dimensions using multivariate Gaussian mixtures. The cluster assignments retrieved from aS. cerevisiaepopulation recovered the true ploidy level in over 96% of samples. Finally, we show that nQuire can be used regionally to identify chromosomal aneuploidies.nQuire provides a statistical framework to study organisms with intraspecific variation in ploidy. nQuire is likely to be useful in epidemiological studies of pathogens, artificial selection experiments, and for historical or ancient samples where intact nuclei are not preserved. It is implemented as a stand-alone Linux command line tool in the C programming language and is available atgithub.com/clwgg/nQuireunder the MIT license.
An interaction between cancer progression and social environment in Drosophila
Authors: Dawson Erika H. , Bailly Tiphaine P.M. , Dos Santos Julie , Moreno Céline , Devilliers Maëlle , Maroni Brigitte , Sueur Cédric , Casali Andreu , Ujvari Beata , Thomas Frederic , Montagne Jacques , Mery Frederic 
Published: May 2017

This preprint has been reviewed and recommended by Peer Community In Evolutionary Biology (http://dx.doi.ors/10.24072/pci.evolbiol.100030)The influence of oncogenic phenomena on the ecology and evolution of animal species is fast becoming an important research topic. Similar to host-pathogen interactions, cancer negatively affects host fitness, which should lead to the selection of host control mechanisms, including behavioral traits that best minimize the proliferation of malignant cells. Social behavior is one such trait, which is suggested to influence cancer progression. While the ecological benefits of sociality in gregarious species are widely acknowledged, only limited data are available on the role of the social environment on cancer progression. Here, we exposed adultDrosophila, with colorectal-like tumors, to different social environments. First, we show that cancerous flies kept in complete isolation exhibit increased tumor progression. Yet, more surprisingly, we find that cancerous flies, kept in groups with other non-cancerous individuals, also develop tumors at a faster rate compared to those kept with other cancerous conspecifics, suggesting a strong impact of social group composition on cancer growth. Finally, we show that flies can discriminate between individuals at different stages of tumor growth and selectively choose their social environment accordingly. Control flies actively avoid flies with cancer but only at the later stages of tumor development, whereas cancerous flies display strong social interactions with cancerous flies in the early stages of tumor growth. Our study demonstrates the reciprocal links between cancer and social interactions, as well as highlighting how sociality impacts health and fitness in animals and its potential implications for disease ecology and ecosystem dynamics.
Graphene oxide-quenching-based fluorescencein situhybridization (G-FISH) to detect RNA in tissue: simple and fast tissue RNA diagnostics
Authors: Hwang Do Won , Choi Yoo Ri , Kim Dohyun , Park Hye Yoon , Kim Kyu Wan , Kim Mee Young , Park Chul-Kee , Lee Dong Soo 
Published: May 2017

AbstractFISH-based RNA detection in paraffin-embedded tissue can be challenging, with complicated procedures producing uncertain results and poor image quality. Here, we developed a robust RNA detection method based on graphene oxide (GO) quenching and recovery of fluorescence in situ hybridization (G-FISH) in formalin-fixed paraffin-embedded (FFPE) tissues. Using G-FISH technique, the long noncoding BC1 RNA, β-actin mRNA, miR-124a and miR-21 could be detected in the cytoplasm of a mouse brain, primary hippocampal neurons, and glioblastoma multiforme tumor tissues, respectively. G-FISH showed the increased BC1 RNA level in individual hippocampal neurons of Alzheimer’s disease brain. The fluorescence recovered by G-FISH correlated highly with the amount of miR-21, as measured by real time RT-PCR. We propose G-FISH as a simple, fast, inexpensive, and sensitive method for RNA detection, with very low background, which could be applied to a variety of researches or diagnostic purposes.
A robust method to estimate regional polygenic correlation identifies heterogeneity in the shared heritability between complex traits
Authors: Paré Guillaume , Mao Shihong , Deng Wei Q. 
Published: May 2017

AbstractBackgroundComplex traits can share a substantial proportion of their polygenic heritability. However, genome-wide polygenic correlations between pairs of traits can mask heterogeneity in their shared polygenic effects across loci. We propose a novel method (WML-RPC) to evaluate polygenic correlation between two complex traits in small genomic regions using summary association statistics. Our method tests for evidence that the polygenic effect at a given region affects two traits concurrently.ResultsWe show through simulations that our method is well calibrated, powerful and more robust to misspecification of linkage disequilibrium than other methods under a polygenic model. As small genomic regions are more likely to harbour specific genetic effects, our method is ideal to identify heterogeneity in shared polygenic correlation across regions. We illustrate the usefulness of our method by addressing two questions related to cardio-metabolic traits. First, we explored how regional polygenic correlation can inform on the strong epidemiological association between HDL cholesterol and coronary artery disease (CAD), suggesting a key role for triglycerides metabolism. Second, we investigated the potential role of PPARγ activators in the prevention of CAD.ConclusionsOur results provide a compelling argument that shared heritability between complex traits is highly heterogeneous across loci.
Design of novel aerial jet target
Authors: Goraj Zdobyslaw Jan , Malinowski Marek , Frydrychewicz Andrzej 
Published: May 2017

Purpose
This paper aims to present and discuss the requirements for flying targets which sometimes are contradictory to each other and to perform a trade-off analysis before the design activity is started. It also aims to demonstrate conceptual and preliminary design processes using a practical example of PW-61 configuration and to show how results of experimental flight tests using a scaled flying target will be described and analyzed before manufacturing the full scale flying target.

Design/methodology/approach
An important part of the paper consists of the selection of tailplane configuration of the flying target UAV to protect some expensive on-board systems against serious damages and to obtain a sufficient dynamic stability, independently of the amount of the petrol in fuel tank. Inverted V-tail, U-tail and H-tail configurations were considered and compared both, theoretically and in-flight experiments.

Findings
Flight dynamics models and associated computational procedures were useful both in a preliminary design phase and during the final assessment of the configuration after flight tests. Selection of the tailplane configuration for the flying target UAV is very important to protect some expensive on-board systems against serious damages and to obtain a sufficient dynamic stability, independent of the amount of the petrol in fuel tank.

Practical implications
Flying targets should be speedy, maneuverable, cheap, easy in deployment and multi-recoverable (if not destroyed by live ammunition), must have relatively low take-off weight and an endurance of at least 1 h. This paper can be useful for proper selection of requirements and preliminary design parameters to make the design process more economically effective.

Originality/value
This paper presents very efficient methods of assessing the design parameters of flying targets, especially in an early stage of the design process. Stability computations are performed based on equations of motion and are supplemented by flight tests using the scaled flying models. It can be considered as an original, not typical, but very practical approach because it delivers lots of data in the early design stages at relatively low cost.
The electric-powered motorglider AOS-71 – the study of development
Authors: Marjanowski Jędrzej , Tomasiewicz Jan , Frączek Wojciech 
Published: May 2017

Purpose
The purpose of this paper is to present the process of design and prototyping of a two-seat, electric-powered, self-launching motorglider AOS-71 closely connected with the teaching process conducted by the academic staff of Warsaw University of Technology (WUT) within a unique educational ULS – Ultra Light Sailplanes programme.

Design/methodology/approach
The selected design methods and tools used during the development of the motorglider have been described. The computer aided design/computer aided manufacturing modules of the Siemens NX software were used to work on the structural design, tools and technical documentation. The core of the ULS educational programme is to educate aerospace engineering students by providing an opportunity for them to participate in each phase of the aircraft life cycle – from conceptual drawings through structural design and prototyping to manufacturing, testing and maintenance.

Findings
The main innovations of the AOS-71 design are: retractable ecological electric propulsion, spacious cockpit where seats are located side by side and the all-composite airframe made of 90 per cent advanced carbon epoxy composites.

Practical implications
The electric motorglider can be used as a multifunctional flying laboratory for flight research and student education.

Originality/value
The AOS-71 project and its continuation are a valuable example of involving aerospace students in each phase of the aircraft life cycle. It also contributes to the research in the field of using innovative electrical propulsion systems in aircraft designs.
Implementation of the LPS using an excel spreadsheet
Authors: Zaeri Fahimeh , Rotimi James Olabode Bamidele , Hosseini M. Reza , Cox Jeff 
Published: May 2017

Purpose
The purpose of this paper is to investigate the implementation challenges of one of lean construction’s recent tools, the last planner system (LPS), by exploring issues in the New Zealand construction sector to identify potential areas for improvement. To achieve this aim, the study formulated two objectives: to present the challenges in LPS use and to explore solutions by using an Excel spreadsheet for facilitating LPS applications.

Design/methodology/approach
The study drew primarily upon a case study approach. A fieldwork study and document analysis of a New Zealand construction project were conducted with an extensive literature review undertaken on the LPS concept.

Findings
The findings revealed that although an automated spreadsheet could be a simple and inexpensive option for using the LPS, data collection, storage and transfer into the spreadsheet could significantly influence the reliability of the LPS outcomes. Most data utilisation challenges were found to occur around the three data sets included in the weekly work plan (WWP). The study presented several automation solutions which had been applied to overcome data utilisation challenges.

Originality/value
Among the first of its kind in the construction industry, this study, with its first-hand account of an organisation which uses the lean paradigm, provides an in-depth insight into LPS tool implementation. The study extends the current body of knowledge by unearthing the challenges of LPS integration into construction activities and presenting efforts undertaken in a construction case project to overcome relevant issues. This adds value by enhancing the reliability of the LPS and, consequently, the effectiveness of its implementation in practical terms.
Spanning the multilevel boundaries of construction organisations
Authors: Sackey Enoch , Akotia Julius 
Published: May 2017

Purpose
The purpose of this paper is to study the interdependent boundary-spanning activities that characterise the level of permeability of knowledge, information flow and learning among construction supply chains involved in the delivery of building information modelling (BIM)-compliant construction projects. Construction projects are mobilised through a number of interdependent processes and multi-functional activities by different practitioners with myriad specialised skills. Many of the difficulties that manifest in construction projects can be attributed to the fragmented work activities and inter-disciplinary nature of project teams. This is nevertheless becoming ever more pertinent with the rise of technology deployment in construction organisations.

Design/methodology/approach
The study combined experts’ sampling interviews and a case study research method to help offer better insights into the kind of emerging multilevel boundary practices as influenced by the rapidly evolving construction technological solutions. The experts’ sampling helped inform better understanding by unravelling the key changes in contemporary boundary configurations and related boundary-spanning practices within technology-mediated construction project settings. The case study also helped to establish the manifestation of best practices for managing multilevel boundaries in BIM-enabled construction project organisations.

Findings
The study has revealed that different generic organisational BIM strategies as developed in specialised boundaries are reconfigured as appropriate at the project level to produce project-specific BIM execution plan (BXP). The outcome of project BXP is dependent on the project organisational teams that cooperate in creating new solutions and on conceding space for negotiations and compromises which conflicting interests at the project level can find to be both desirable and feasible. The implementation effort is therefore contingent on mutual translation in which different actors with different insights instigate their practice through negotiation and persuasion which eventually are reinforced by contractual agreements and obligations.

Originality/value
The paper has presented a novel and well-timed empirical insight into BIM-enabled project delivery and best practices that span multilevel boundaries of construction organisations.