bluuebunny/crossref_metadata_2025_split huggingface dataset:
Temporal and spatial dimensions in the management of scientific advice to governments
Authors: Saner Marc 
Published: September 2016

AbstractScientific advice is given to governments through a variety of processes and structures. A key task is, thus, to understand the pros and cons of the various process design options. In this article, two very basic and abstract components of all process options are discussed: their temporal and spatial dimensions. The temporal axis is bracketed by processes that are either divided into entirely distinct tasks or joined into interactive processes. The spatial axis is bracketed by teams that are either physically or administratively embedded or sequestered. The separation of these two axes and their endpoints provides a foundation for a governance analysis that is highly universal and that provides some insights into all types of scientific advice to governments. This article is published as part of a collection on scientific advice to governments.
Zika: the cost of neglect
Authors: Sarkar Sahotra , Gardner Lauren 
Published: September 2016

AbstractThe Zika virus is vectored by mosquito species of the genus Aedes, particularly the yellow fever mosquito, Aedes aegypti and, very likely, the Asian tiger mosquito, Ae. albopictus. These species also vector a host of other viral diseases including dengue and chikungunya all of which are “neglected tropical diseases” (NTDs) because of the lack of attention given to them. NTDs are diseases of poverty: They have lacked due attention because they typically affect the poorest populations of the world and at the same time they are not common enough to be profitably exploited by the pharmaceutical industry. We argue that the depth of the current Zika crisis is because of the extent of neglect for NTDs: First, in spite of yellow fever, dengue, chikungunya and other diseases vectored by Aedes mosquitoes, insufficient efforts have been directed towards their population control. Second, specific drugs for combating yellow fever, dengue, or chikungunya do not exist. For the last two, vaccines are yet to be developed (though some trials are finally taking place for one for dengue). Thus the pharmaceutical knowledge base for tackling related viral diseases is lacking. Third, thanks to the neglect even the epidemiological, sociopolitical and economic data required to make credible and timely risk assessments are not available. For instance, in the case of Zika, it would be useful to have a global risk map based on projected travel to and from Brazil for the 2016 Summer Olympics in Rio de Janeiro. Yet, projected travel volumes for chartered flights for the summer of 2016 are not publicly accessible, preventing the creation of credible risk maps. In addition, there is a severe lack of publicly available case data, especially in countries of the South where NTDs have the largest impact. Without reliable and comprehensive outbreak data, risk models necessary for outbreak prediction cannot be validated. Zika has only drawn attention to these problems because of the likelihood of its spread into the affluent North. It is high time that all NTDs are rescued from their dangerous oblivion.
Listening between the lines: medieval and modern science
Authors: Gasper Giles , McLeish Tom , E Smithson Hannah 
Published: September 2016

AbstractIn this article the investigators of the Ordered Universe project will reflect on how a diverse range of disciplinary perspectives essential for effective research into medieval science have been identified, acknowledged and absorbed into a genuinely interdisciplinary methodology. The project operates with a radical interdisciplinary composition bridging science and humanities in particular. How to translate what might be termed current academic practices and expectations between disciplines and between colleagues is a key issue. The article explores the practices of collaborative discussion, collaborative reading and collaborative writing. Central to these issues is the notion of the “atmosphere of enquiry”: getting the best from disciplinary perspectives, respecting expertise and having the right to challenge disciplinary boundaries are integral elements within the process. Finally the experience of this project is set in the context of the wider discussion of what interdisciplinary research means. We discuss how the methods of the Ordered Universe might be used, by imitation or by analogy. This article is published as part of a collection on interdisciplinarity.
Hybridization can facilitate species invasions, even without enhancing local adaptation
Authors: Mesgaran Mohsen B. , Lewis Mark A. , Ades Peter K. , Donohue Kathleen , Ohadi Sara , Li Chengjun , Cousens Roger D. 
Published: September 2016

Significance
Species colonizations frequently occur in regions already occupied by other species of the same genus, or by other genotypes of the same species. When hybrid genotypes become more invasive than their parents, improved local adaptation is inevitably assumed. Here, we show that there is another way that hybridization could facilitate invasions, by temporarily overcoming pollen limitation when populations are small. We verify this conclusion using two contemporary sequential invaders, a plant analog of the Neanderthal–modern human system. Our findings indicate that it may be misleading to assume that all cases of invasive hybrids result from enhanced phenotypic suitability. Our hypothesis may be even more relevant to animal species because, unlike plants, animals can rarely escape mate limitation by self-fertilization.
Detailed H i kinematics of Tully–Fisher calibrator galaxies
Authors: Ponomareva Anastasia A. , Verheijen Marc A. W. , Bosma Albert 
Published: September 2016

Abstract
We present spatially resolved H i kinematics of 32 spiral galaxies which have Cepheid or/and tip of the red giant branch distances, and define a calibrator sample for the Tully–Fisher relation. The interferometric H i data for this sample were collected from available archives and supplemented with new Giant Metrewave Radio Telescope observations. This paper describes a uniform analysis of the H i kinematics of this inhomogeneous data set. Our main result is an atlas for our calibrator sample that presents global H i profiles, integrated H i column-density maps, H i surface-density profiles and, most importantly, detailed kinematic information in the form of high-quality rotation curves derived from highly resolved, two-dimensional velocity fields and position–velocity diagrams.
Chemo-hydrodynamic patterns in porous media
Authors: De Wit A. 
Published: September 2016

Chemical reactions can interplay with hydrodynamic flows to generate chemo-hydrodynamic instabilities affecting the spatio-temporal evolution of the concentration of the chemicals. We review here such instabilities for porous media flows. We describe the influence of chemical reactions on viscous fingering, buoyancy-driven fingering in miscible systems, convective dissolution as well as precipitation patterns. Implications for environmental systems are discussed.This article is part of the themed issue ‘Energy and the subsurface’.
Elastic and inelastic deformation of fluid-saturated rock
Authors: Makhnenko Roman Y. , Labuz Joseph F. 
Published: September 2016

In siturock is often saturated with fluid, the presence of which affects both elastic parameters and inelastic deformation processes. Techniques were developed for testing fluid-saturated porous rock under the limiting conditions of drained (long-term), undrained (short-term) and unjacketed (solid matrix) response in hydrostatic, axisymmetric and plane-strain compression. Drained and undrained poroelastic parameters, including bulk modulus, Biot and Skempton coefficients, of Berea sandstone were found to be stress dependent up to 35 MPa mean stress, and approximately constant at higher levels of loading. The unjacketed bulk modulus was measured to be constant for pressure up to 60 MPa, and it appears to be larger than the unjacketed pore bulk modulus. An elasto-plastic constitutive model calibrated with parameters from drained tests provided a first-order approximation of undrained inelastic deformation: dilatant hardening was observed due to pore pressure decrease during inelastic deformation of rock specimens with constant fluid content.This article is part of the themed issue ‘Energy and the subsurface’.
A similarity solution for reaction front propagation in a fracture–matrix system
Authors: Rajaram Harihar , Arshadi Masoud 
Published: September 2016

We propose a new composite similarity variable, based on which a similarity solution is derived for reaction front propagation in fracture–matrix systems. The similarity solution neglects diffusion/dispersion within the fracture and assumes the existence of a sharp reaction front in the rock matrix. The reaction front location in the rock matrix is shown to follow a linear decrease with distance along the fracture. The reaction front propagation along the fracture is shown to scale like diffusion (i.e. as the square root of time). The similarity solution using the composite similarity variable appears to be applicable to a broad class of reactive transport problems involving mineral reactions in fracture–matrix systems. It also reproduces the solutions for non-reactive solute and heat transport when diffusion/dispersion/conduction are neglected in the fracture. We compared our similarity solution against numerical simulations for nonlinear reactive transport of an aqueous species with a mineral in the rock matrix. The similarity solutions agree very well with the numerical solutions, especially at later times when diffusion limitations are more pronounced.
This article is part of the themed issue ‘Energy and the subsurface’.
Differential Expression Analysis for RNAseq using Poisson Mixed Models
Authors: Sun Shiquan , Hood Michelle , Scott Laura , Peng Qinke , Mukherjee Sayan , Tung Jenny , Zhou Xiang 
Published: September 2016

AbstractIdentifying differentially expressed (DE) genes from RNA sequencing (RNAseq) studies is among the most common analyses in genomics. However, RNAseq DE analysis presents several statistical and computational challenges, including over-dispersed read counts and, in some settings, sample non-independence. Previous count-based methods rely on simple hierarchical Poisson models (e.g., negative binomial) to model independent over-dispersion, but do not account for sample non-independence due to relatedness, population structure and/or hidden confounders. Here, we present a Poisson mixed model with two random effects terms that account for both independent over-dispersion and sample non-independence. We also develop a scalable sampling-based inference algorithm using a latent variable representation of the Poisson distribution. With simulations, we show that our method properly controls for type I error and is generally more powerful than other widely used approaches, except in small samples (n<15) with other unfavorable properties (e.g., small effect sizes). We also apply our method to three real data sets that contain related individuals, population stratification, or hidden confounders. Our results show that our method increases power in all three data compared to other approaches, though the power gain is smallest in the smallest sample (n=6). Our method is implemented in MACAU, freely available atwww.xzlab.org/software.html.
Comparative genomics and metagenomics analyses of endangered Père David’s deer (Elaphurus davidianus) provide insights into population recovery
Authors: Zhang Xuejing , Deng Cao , Ding Jingjing , Ren Yi , Zhao Xiang , Qin Shishang , Zhu Shilin , Wang Zhiwen , Chai Xiaoqiang , Huang Huasheng , Ding Yuhua , Lu Guoqing , Zhu Lifeng 
Published: September 2016

AbstractThe milu (Père David’s deer,Elaphurus davidianus) has become a classic example of how highly endangered animal species can be rescued. However, the mechanisms that underpinned this population recovery remain largely unknown. As part of this study, we sequenced and analyzed whole genomes from multiple captive individuals. Following this analysis, we observed that the milu experienced a prolonged population decline over the last 200,000 years, which led to an elongated history of inbreeding. This protracted inbreeding history facilitated the purging of deleterious recessive alleles, thereby ameliorating associated threats to population viability. Because of this phenomenon, milu are now believed to be less susceptible to future inbreeding depression occurrences. SNP distribution patterns confirmed inbreeding history and also indicated sign of increased and increasing diversity in the recovered milu population. A selective sweep analysis identified two outlier genes (CTSR2andGSG1) that were related to male fertility. Furthermore, we observed strong signatures of selection pertaining to the host immune system, including six genes (SERPINE1, PDIA3, CD302, IGLL1, VPREB3, andCD53 antigen), which are likely to strengthen resistance to pathogens. We also identified several adaptive features including the over-representation of gene families encoding for olfactory receptor activity, a high selection pressure pertaining to DNA repair and host immunity, and tolerance to high-salt swamp diets. Moreover, glycan biosynthesis, lipid metabolism, and cofactor and vitamin metabolism were all significantly enriched in the gut microbiomes of milu. We speculate that these characteristics play an important role in milu energy metabolism, immunity, development, and health. In conclusion, our findings provide a unique insight into animal population recovery strategies.
LoRTE: Detecting transposon-induced genomic variants using low coverage PacBio long read sequences
Authors: Disdero Eric , Filée Jonathan 
Published: September 2016

AbstractMotivationPopulation genomic analysis of transposable elements has greatly benefited from recent advances of sequencing technologies. However, the propensity of transposable elements to nest in highly repeated regions of genomes limits the efficiency of bioinformatic tools when short read sequences technology is used.ResultsLoRTE is the first tool able to use PacBio long read sequences to identify transposon deletions and insertions between a reference genome and genomes of different strains or populations. Tested against Drosophila melanogaster PacBio datasets, LoRTE appears to be a reliable and broadly applicable tools to study the dynamic and evolutionary impact of transposable elements using low coverage, long read sequences.Availability and ImplementationLoRTE is available athttp://www.egce.cnrs-gif.fr/?p=6422. It is written in Python 2.7 and only requires the NCBI BLAST + package. LoRTE can be used on standard computer with limited RAM resources and reasonable running time even with large datasets.Contactjonathan.filee@ecge.cnrs-gif.fr
Measuring MEG closer to the brain: Performance of on-scalp sensor arrays
Authors: Iivanainen Joonas , Stenroos Matti , Parkkonen Lauri 
Published: September 2016

AbstractOptically-pumped magnetometers (OPMs) have recently reached sensitivity levels required for magnetoencephalogra-phy (MEG). OPMs do not need cryogenics and can thus be placed within millimetres from the scalp into an array that adapts to the invidual head size and shape, thereby reducing the distance from cortical sources to the sensors. Here, we quantified the improvement in recording MEG with hypothetical on-scalp OPM arrays compared to a 306-channel state-of-the-art SQUID array (102 magnetometers and 204 planar gradiometers).We simulated OPM arrays that measured either normal (nOPM; 102 sensors), tangential (tOPM; 204 sensors), or all components (aOPM; 306 sensors) of the magnetic field. We built forward models based on magnetic resonance images of 10 adult heads; we employed a three-compartment boundary element model and distributed current dipoles evenly across the cortical mantle.Compared to the SQUID magnetometers, nOPM and tOPM yielded 7.5 and 5.3 times higher signal power, while the correlations between the field patterns of source dipoles were reduced by factors of 2.8 and 3.6, respectively. Values of the field-pattern correlations were similar across nOPM, tOPM and SQUID gradiometers. Volume currents reduced the signals of primary currents on average by 10%, 72% and 15% in nOPM, tOPM and SQUID magnetometers, respectively. The information capacities of the OPM arrays were clearly higher than that of the SQUID array. The dipole-localization accuracies of the arrays were similar while the minimum-norm-based point-spread functions were on average 2.4 and 2.5 times more spread for the SQUID array compared to nOPM and tOPM arrays, respectively.
Job characteristics, work involvement, and job performance of public servants
Authors: Johari Johanim , Yahya Khulida Kirana 
Published: September 2016

PurposeThe primary purpose of this study is to assess the predicting role of job characteristics on job performance. Dimensions in the job characteristics construct are skill variety, task identity, task significance, autonomy and feedback. Further, work involvement is tested as a mediator in the hypothesized link.Design/methodology/approachA total of 256 public servants reported on their job characteristics and work involvement while supervisory ratings were used to assess their level of job performance. SPSS version 14 and AMOS 16 were used for statistical analyses of the data. A hypothesized structural equation model was tested to examine both direct and indirect influence of job characteristics on job performance.FindingsThe findings revealed that task significance and feedback significantly influence job performance and the relationships are mediated by work involvement. Skill variety, however, has a significant and direct influence on public servants’ job performance.Research limitations/implicationsThe research results have provided support for the key theoretical propositions. Specifically, this study has managed to substantiate some empirical evidences in partial support of the job characteristics theory.Practical implicationsAs for practical implication, the significant and positive impact of skill variety, task significance and feedback on job performance suggests the importance of these job characteristics dimensions in promoting high level of job performance among public servants.Originality/valueThis study aims to provide additional empirical evidence in support of the job characteristics theory. The theoretical framework of this study managed to substantiate empirical evidence in partial support of the job characteristics theory.
Promoting self-directed learning in a learning organization: tools and practices
Authors: Rana Sowath , Ardichvili Alexandre , Polesello Daiane 
Published: September 2016

PurposeThe purpose of this paper is to examine a set of practices that can help promote self-directed learning (SDL) in congruence with the goals of developing and maintaining a learning organization.Design/methodology/approachFindings from this study were derived from an extensive review of the SDL and the learning organization literature, as well as the body of research that examines the connections between the two constructs.FindingsThis paper identifies the following set of practices as integral to promoting SDL in a learning organization: building and communicating a shared vision to employees at all levels; fostering collaboration, interaction and teamwork; empowering employees through participatory work practices; encouraging and providing opportunities for continuous learning; and using relevant technologies in the workplace.Originality/valueThis paper addresses the paucity of research that investigates the connections between SDL and the learning organization and that specifically examines important practicesvis-à-visthe two concepts.
Bare ownership of residential properties: insights on two segments of the Italian market
Authors: Morano Pierluigi , Tajani Francesco 
Published: September 2016

PurposeThis paper aims to deal with the sale of the bare ownership subject to the lifetime usufruct to the seller as an alternative channel for housing investments in Italian cities. The first aim of the study is to understand in greater detail the bare ownership market while also stimulating the interest of researchers in this segment of the housing market that up until now has been marginally analyzed so far. The second aim is to make the estimation of the bare ownership easier and more reliable for market investors and institutions. The third aim is to quantify on the markets investigated in this paper, the “actual” appraisal coefficients for the usufructuary presence, as well as compare these coefficients with the ones set for tax purposes to highlight either the concordance or discordance.Design/methodology/approachA hedonic price model is developed, with which it is possible to evaluate the market price of the bare ownership as a function of the determinants of value in the market segments in question, in particular the life expectancy of the usufructuary.FindingsThrough the hedonic models defined in this work, it is possible to appraise the market value of the bare ownership of residential flats in a building located in the same districts overcoming the limitations of the procedures currently used. Comparing the appraisal coefficients for the usufructuary presence estimated through the hedonic models defined in this work, with the legally defined coefficients applied countrywide for tax purpose, it is possible to conclude that the latter markedly underestimate the market value of bare ownership, thereby leading to fiscal iniquities and substantial social costs.Research limitations/implicationsIt has not been possible to know the gender of the usufructuary. Rather limited size of the apartment sales samples.Practical implicationsThe bare ownership market is currently an important sector that deserves greater attention from the institutions, market investors and real estate research. The model developed allows to estimate the “actual” coefficients for the determination of the market value of the bare ownership of residential units.Originality/valueThere are currently no studies nor descriptive investigations relating to either the bare ownership market segments or recent cases of estimates. The present study is the first in current literature that both systematically deals with the quantification of the “actual” appraisal coefficients for the usufructuary presence, as well as compares these coefficients with the ones set for tax purposes.