bluuebunny/crossref_metadata_2025_split huggingface dataset:
Artificial Intelligence for Ecological and Evolutionary Synthesis
Authors: Desjardins-Proulx Philippe , Poisot Timothée , Gravel Dominique 
Published: July 2017

AbstractThe grand ambition of theorists studying ecology and evolution is to discover the logical and mathematical rules driving the world’s biodiversity at every level from genetic diversity within species to differences between populations, communities, and ecosystems. This ambition has been difficult to realize in great part because of the complexity of biodiversity. Theoretical work has led to a complex web of theories, each having non-obvious consequences for other theories. Case in point, the recent realization that genetic diversity involves a great deal of temporal and spatial stochasticity forces theoretical population genetics to consider abiotic and biotic factors generally reserved to ecosystem ecology. This interconnectedness may require theoretical scientists to adopt new techniques adapted to reason about large sets of theories. Mathematicians have solved this problem by using formal languages based on logic to manage theorems. However, theories in ecology and evolution are not mathematical theorems, they involve uncertainty. Recent work in Artificial Intelligence in bridging logic and probability theory offers the opportunity to build rich knowledge bases that combine logic’s ability to represent complex mathematical ideas with probability theory’s ability to model uncertainty. We describe these hybrid languages and explore how they could be used to build a unified knowledge base of theories for ecology and evolution.case study you explore using the Salix tritrophic system.
Why are tropical mountain passes ‘low’ for some species? Genetic and stable-isotope tests for differentiation, migration, and expansion in elevational generalist songbirds
Authors: Gadek Chauncey R. , Newsome Seth D. , Beckman Elizabeth J. , Chavez Andrea C. , Galen Spencer C. , Bautista Emil , Witt Christopher C. 
Published: July 2017

AbstractMost tropical bird species have narrow elevational ranges, likely reflecting climatic specialization. This is consistent with Janzen’s Rule, the tendency for mountain passes to be effectively ‘higher’ in the tropics. Hence, those few tropical species that occur across broad elevational gradients raise questions. Are they being sundered by diversifying selection along the gradient? Does elevational movement cause them to resist diversification or specialization? Have they recently expanded, suggesting that elevational generalism is short-lived in geological time? Here we tested for differentiation, movement, and expansion in four elevational generalist songbird species on the Andean west slope. We used morphology and mtDNA to test for genetic differentiation between high- and low-elevation populations. Morphology differed for House Wren (Troglodytes aedon) and Hooded Siskin (Spinus magellanicus), but not for Cinereous Conebill (Conirostrumcinereum) and Rufous-collared Sparrow (Zonotrichia capensis), respectively. mtDNA was structured by elevation only inZ. capensis. To test for elevational movements, we measured hydrogen isotope (δ2H) values of metabolically inert feathers and metabolically active liver. δ2H data indicated elevational movements by two tree- and shrub-foraging species with moderate-to-high vagility (C. cinereumandS. magellanicus), and sedentary behavior by two terrestrial-foraging species with low-to-moderate vagility (T. aedonandZ. capensis). InS. magellanicus, elevational movements and lack of mtDNA structure contrast with striking morphological divergence, suggesting strong diversifying selection on body proportions across the ∼50 km gradient. All species exceptC. cinereumexhibited mtDNA-haplotype variation consistent with recent population expansion across the elevational gradient.In sum,three out of four elevational generalist species underwent genetic divergence despite gene flow, two of four make seasonal elevational movements, and three of four have recently expanded. In different ways, each species defies the tendency for tropical birds to have long-term stable distributions and sedentary habits. We conclude that tropical elevational generalism is rare due to evolutionary instability.
SRSF shape analysis for sequencing data reveal new differentiating patterns
Authors: Wesolowski Sergiusz , Vera Daniel , Wu Wei 
Published: July 2017

AbstractMotivationSequencing-based methods to examine fundamental features of the genome, such as gene expression and chromatin structure, rely on inferences from the abundance and distribution of reads derived from Illumina sequencing. Drawing sound inferences from such experiments relies on appropriate mathematical methods to model the distribution of reads along the genome, which has been challenging due to the scale and nature of these data.ResultsWe propose a new framework (SRSFseq) based on Square Root Slope Functions shape analysis to analyse Illumina sequencing data. In the new approach the basic unit of information is the density of mapped reads over region of interest located on the known reference genome. The densities are interpreted as shapes and a new shape analysis model is proposed. An equivalent of a Fisher test is used to quantify the significance of shape differences in read distribution patterns between groups of density functions in different experimental conditions. We evaluated the performance of this new framework to analyze RNA-seq data at the exon level, which enabled the detection of variation in read distributions and abundances between experimental conditions not detected by other methods. Thus, the method is a suitable supplement to the state of the are count based techniques. The variety of density representations and flexibility of mathematical design allow the model to be easily adapted to other data types or problems in which the distribution of reads is to be tested. The functional interpretation and SRSF phase-amplitude separation technique gives an efficient noise reduction procedure improving the sensitivity and specificity of the method.
Imprinted loci may be more widespread in humans than previously appreciated and enable limited assignment of parental allelic transmissions in unrelated individuals
Authors: Partida Gabriel Cuellar , Laurin Charles , Ring Susan M. , Gaunt Tom R. , Relton Caroline L. , Smith George Davey , Evans David M. 
Published: July 2017

AbstractGenomic imprinting is an epigenetic mechanism leading to parent-of-origin dependent gene expression. So far, the precise number of imprinted genes in humans is uncertain. In this study, we leveraged genome-wide DNA methylation in whole blood measured longitudinally at 3 time points (birth, childhood and adolescence) and GWAS data in 740 Mother-Child duos from the Avon Longitudinal Study of Parents and Children (ALSPAC) to systematically identify imprinted loci. We reasoned thatcis-meQTLs at genomic regions that were imprinted would show strong evidence of parent-of-origin associations with DNA methylation, enabling the detection of imprinted regions. Using this approach, we identified genome-wide significantcis-meQTLs that exhibited parent-of-origin effects (POEs) at 35 novel and 50 known imprinted regions (10−10< P <10−300). Among the novel loci, we observed signals near genes implicated in cardiovascular disease (PCSK9), and Alzheimer’s disease (CR1), amongst others. Most of the significant regions exhibited imprinting patterns consistent with uniparental expression, with the exception of twelve loci (including theIGF2, IGF1R,andIGF2Rgenes), where we observed a bipolar-dominance pattern. POEs were remarkably consistent across time points and were so strong at some loci that methylation levels enabled good discrimination of parental transmissions at these and surrounding genomic regions. The implication is that parental allelic transmissions could be modelled at many imprinted (and linked) loci and hence POEs detected in GWAS of unrelated individuals given a combination of genetic and methylation data. Our results indicate that modelling POEs on DNA methylation is effective to identify loci that may be affected by imprinting.
Climate-driven shifts in sediment chemistry enhance methane production in northern lakes
Authors: Emilson E.J.S , Carson M.A. , Yakimovich K.M. , Gunn J.M. , Mykytczuk N.C.S , Basiliko N. , Tanentzap A.J. 
Published: July 2017

AbstractFreshwater ecosystems are a major source of methane (CH4), contributing 0.65 Pg (in CO2equivalents) yr-1towards global carbon (C) emissions and thereby offsetting ∼25% of the terrestrial carbon sink. Most CH4emissions come from littoral sediments, where large quantities of plant material are decomposed. As climate change is predicted to shift plant community composition, and thus change the quality of inputs into detrital food webs, this can affect CH4production and have far-reaching consequences for global C emissions. Here we find that variation in polyphenol availability from decomposing organic matter underlies large differences in CH4production in lake sediments. Production was at least 400-times higher from sediments composed of macrophyte litter compared to terrestrial sources (coniferous and deciduous), which we link to the inhibition of methanogenesis by polyphenol leachates. Applying our estimates to projected northward advances in the distribution ofTypha latifolia, a widespread and dominant macrophyte, we find that CH4production could increase by at least 73% in the lake-rich Boreal Shield ecozone solely due to increases in this one macrophyte species. Our results now suggest that earth system models and carbon budgets should consider the effects of plant communities on sediment chemistry and ultimately CH4emissions at a global scale.One-sentence summaryProduction of methane from lakes is at least 400-times lower when 24 sediments receive forest- as opposed to macrophyte-derived (Typha latifolia) litterfall.
Parallel pattern of differentiation at a genomic island shared between clinal and mosaic hybrid zones in a complex of cryptic seahorse lineages
Authors: Riquet Florentine , Liautard-Haag Cathy , Woodall Lucy , Bouza Carmen , Louisy Patrick , Hamer Bojan , Otero-Ferrer Francisco , Aublanc Philippe , Béduneau Vickie , Briard Olivier , Ayari Tahani El , Hochscheid Sandra , Belkhir Khalid , Arnaud-Haond Sophie , Gagnaire Pierre-Alexandre , Bierne Nicolas 
Published: July 2017

AbstractDiverging semi-isolated lineages either meet in narrow clinal hybrid zones, or have a mosaic distribution associated with environmental variation. Intrinsic reproductive isolation is often emphasized in the former and local adaptation in the latter, although both can contribute to isolation. Rarely these two patterns of spatial distribution are reported in the same study system. Here we report that the long-snouted seahorseHippocampus guttulatusis subdivided into discrete panmictic entities by both types of hybrid zones. Along the European Atlantic coasts, a northern and a southern lineage meet in the southwest of France where they coexist in sympatry with little hybridization. In the Mediterranean Sea, two lineages have a mosaic distribution, associated with lagoon-like and marine habitats. A fifth lineage was identified in the Black Sea. Genetic homogeneity over large spatial scales contrasts with isolation maintained in sympatry or close parapatry at a fine scale. A high variation in locus-specific introgression rates provides additional evidence that partial reproductive isolation must be maintaining the divergence. Surprisingly, fixed differences between lagoon and marine populations in the Mediterranean Sea belong to the most differentiated SNPs between the two Atlantic lineages, against the genome-wide pattern of structure. These parallel outlier SNPs cluster on a single chromosome-wide island of differentiation. Since Atlantic lineages do not match the lagoon-sea habitat variation, genetic parallelism at the genomic island suggests a shared genetic barrier contributes to reproductive isolation in contrasting contexts -i.e.spatialvs. ecological. We discuss how a genomic hotspot of parallel differentiation could have evolved and become associated either with space or with a patchy environment in a single study system.
Sequential regulatory activity prediction across chromosomes with convolutional neural networks
Authors: Kelley David R. , Reshef Yakir A. , Bileschi Maxwell , Belanger David , McLean Cory Y. , Snoek Jasper 
Published: July 2017

AbstractModels for predicting phenotypic outcomes from genotypes have important applications to understanding genomic function and improving human health. Here, we develop a machine-learning system to predict cell type-specific epigenetic and transcriptional profiles in large mammalian genomes from DNA sequence alone. Using convolutional neural networks, this system identifies promoters and distal regulatory elements and synthesizes their content to make effective gene expression predictions. We show that model predictions for the influence of genomic variants on gene expression align well to causal variants underlying eQTLs in human populations and can be useful for generating mechanistic hypotheses to enable fine mapping of disease loci.
A modification of DMVs based state space model of variation propagation for multistage machining processes
Authors: Yang Fuyong , Jin Sun , Li Zhimin 
Published: July 2017

Purpose
Complicated workpiece, such as an engine block, has special rough locating datum features (i.e. six independent datum features) due to its complex structure. This locating datum error cannot be handled by current variation propagation model based on differential motion vectors. To extend variation prediction fields, this paper aims to solve the unaddressed variation sources to modify current model for multistage machining processes.

Design/methodology/approach
To overcome the limitation of current variation propagation model based on differential motion vectors caused by the unaddressed variation sources, this paper will extend the current model by handling the unaddressed datum-induced variation and its corresponding fixture variation.

Findings
The measurement results of the rear face with respect to the rough datum W and the pan face with respect to the hole Q by coordinate measuring machine (CMM) are −0.006 mm and 0.031 mm. The variation results for rear face and pan face predicted by the modified model are −0.009 mm and 0.025 mm, respectively. The discrepancy of model prediction and measurement is very small.

Originality/value
This paper modifies the variation propagation model based on differential motion vectors by solving the unaddressed variation sources, which can extend the variation prediction fields for some complicated workpiece and is useful in the future work for many fields, such as process monitoring, fault diagnosis, quality-assured setup planning and process-oriented tolerancing.
A novel LLSDPso method for nonlinear dynamic parameter identification
Authors: Yuan Jian-jun , Wan Weiwei , Fu Xiajun , Wang Shuai , Wang Ning 
Published: July 2017

Purpose
This paper aims to propose a novel method to identify the parameters of robotic manipulators using the torque exerted by the robot joint motors (measured by current sensors).

Design/methodology/approach
Previous studies used additional sensors like force sensor and inertia measurement unit, or additional payload mounted on the end-effector to perform parameter identification. The settings of these previous works were complicated. They could only identify part of the parameters. This paper uses the torque exerted by each joint while performing Fourier periodic excited trajectories. It divides the parameters into a linear part and a non-linear part, and uses linear least square (LLS) parameter estimation and dual-swarm-based particle swarm optimization (DPso) to compute the linear and non-linear parts, respectively.

Findings
The settings are simpler and can identify the dynamic parameters, the viscous friction coefficients and the Coulomb friction coefficients of two joints at the same time. A SIASUN 7-Axis Flexible Robot is used to experimentally validate the proposal. Comparison between the predicted torque values and ground-truth values of the joints confirms the effectiveness of the method.

Originality/value
The proposed method identifies two joints at the same time with satisfying precision and high efficiency. The identification errors of joints do not accumulate.
Financing agricultural cooperatives with retained earnings
Authors: Royer Jeffrey 
Published: July 2017

Purpose
The purpose of this paper is to explore the advantages equity capitalization programs based on retained earnings from patronage sources may provide cooperatives and their patrons that traditional equity financing methods do not offer.

Design/methodology/approach
The analysis is based on a model used to assess patron benefits from a cooperative that is financed by a combination of allocated equity acquired from noncash patronage refunds and unallocated equity acquired from retained earnings. The level of patron benefits is represented by the present value of the after-tax cash flow patrons receive from the cooperative, and the model is used to determine the combination of noncash patronage refunds and retained earnings that provides the greatest present value given the levels of those parameters that affect capitalization of the cooperative and the distribution of cash benefits to patrons.

Findings
The analysis demonstrates that only pure plans, i.e., plans based entirely on retained patronage refunds or entirely on retained earnings, will be associated with the greatest present value for any particular set of parameter values. Cooperatives that are characterized by low marginal tax rates and growth rates and whose patrons are characterized by high marginal tax rates and discount rates are those most likely to benefit from equity capitalization programs based on retained earnings.

Research limitations/implications
The model is based on the assumption of constant parameter values and does not account for the existence of nonpatronage income.

Practical implications
A useful extension of this work would be the development of a decision aid capable of generating basic operating statement and balance sheet data and enabling cooperative decision makers to conduct experiments concerning alternative financing strategies based on retained earnings.

Originality/value
The analysis contained in this paper is based on an explicit model and extends across a broad range of values for various parameters that affect the level, timing, and present value of cash distributions from cooperatives. Because the cash flow received by patrons is determined after the cooperative’s planned equity growth is met, cash flow comparisons are equivalent with respect to the capital provided the cooperative. In addition, the revolving period is endogenously determined.
Uncovering transfer – a cross-national comparative analysis
Authors: Sinell Anna , Iffländer Vivien , Muschner Antonia 
Published: July 2017

PurposeSuccessful knowledge and technology transfer (KTT) is necessary to ensure the competitiveness and growth of national innovation systems. In this regard, technology transfer offices (TTOs) are becoming indispensable in their capacity as intermediaries between science, policy, industry, and the public. The purpose of this paper is to examine the strategies and operations of particularly productive transfer offices in five different countries in order to account for the high levels of transfer activity.Design/methodology/approachTo this end, the authors interviewed 34 senior KTT managers in these offices. The collected protocols were analysed in three phases. First, the authors extracted and organised the key characteristics of the transfer practices by applying rigorous method of open-end, qualitative content analysis. The authors then enhanced the thus gathered descriptive statistics and ultimately developed a transfer office typology by building on the concept of attribute space.FindingsThe analysis suggests two ideal types of transfer offices, distinguishable in terms of their intertwined characteristics such as their goals, practices, sources of income, and positions within their associated organisations. While the primarily state-funded common good type would seek benefits to the public, the self-financed entrepreneurial type would pursue commercial success. The former would therefore create opportunities for disseminating knowledge and strengthening the local innovation ecosystem, while the latter would scout for promising ideas and cultivate relationships with industry.Originality/valueThe goal was to uncover the individual characteristics of the offices under study, and the relationships between these characteristics, that can help explain these offices’ exceptional productivity. This study is the first to propose a TTO typology, which can support interorganisational and international transfer collaboration. The findings provide empirical evidence for the theoretical Quadruple Helix model of the innovation system and have implications for research and practice.
Survey process quality: a question of healthcare manager approach
Authors: Nilsson Petra , Blomqvist Kerstin 
Published: July 2017

Purpose
The purpose of this paper is to explore how healthcare first-line managers think about and act regarding workplace survey processes.

Design/methodology/approach
This interview study was performed at a hospital in south Sweden. First-line healthcare managers (n=24) volunteered. The analysis was inspired by phenomenography, which aims to describe the ways in which different people experience a phenomenon. The phenomenon was a workplace health promotion (WHP) survey processes.

Findings
Four main WHP survey process approaches were identified among the managers: as a possibility, as a competition, as a work task among others and as an imposition. For each, three common subcategories emerged; how managers: stated challenges and support from hospital management; described their own work group and collaboration with other managers; and expressed themselves and their situation in their roles as first-line managers.

Practical implications
Insights into how hospital management can understand their first-line managers’ motivation for survey processes and practical suggestions and how managers can work proactively at organizational, group and individual level are presented.

Originality/value
Usually these studies focus on those who should respond to a survey; not those who should run the survey process. Focusing on managers and not co-workers can lead to more committed and empowered managers and thereby success in survey processes.
Applying adult development theories to improvement science
Authors: Kjellström Sofia , Andersson Ann-Christine 
Published: July 2017

Purpose
The purpose of this paper is to address how adult development (AD) theories can contribute to quality improvement (QI).

Design/methodology/approach
A theoretical analysis and discussion on how personal development empirical findings can relate to QI and Deming’s four improvement knowledge domains.

Findings
AD research shows that professionals have qualitatively diverse ways of meaning-making and ways to approach possibilities in improvement efforts. Therefore, professionals with more complex meaning-making capacities are needed to create successful transformational changes and learning, with the recognition that system knowledge is a developmental capacity.

Practical implications
In QI and improvement science there is an assumption that professionals have the skills and competence needed for improvement efforts, but AD theories show that this is not always the case, which suggests a need for facilitating improvement initiatives, so that everyone can contribute based on their capacity.

Originality/value
This study illustrates that some competences in QI efforts are a developmental challenge to professionals, and should be considered in practice and research.