bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data
Authors: McMurry Julie A , Juty Nick , Blomberg Niklas , Burdett Tony , Conlin Tom , Conte Nathalie , Courtot Mélanie , Deck John , Dumontier Michel , Fellows Donal K , Gonzalez-Beltran Alejandra , Gormanns Philipp , Grethe Jeffrey , Hastings Janna , Hermjakob Henning , Hériché Jean-Karim , Ison Jon C , Jimenez Rafael C , Jupp Simon , Kunze John , Laibe Camille , Le Novère Nicolas , Malone James , Martin Maria Jesus , McEntyre Johanna R , Morris Chris , Muilu Juha , Müller Wolfgang , Rocca-Serra Philippe , Sansone Susanna-Assunta , Sariyar Murat , Snoep Jacky L , Stanford Natalie J , Soiland-Reyes Stian , Swainston Neil , Washington Nicole , Williams Alan R , Wimalaratne Sarala , Winfree Lilly , Wolstencroft Katherine , Goble Carole , Mungall Christopher J , Haendel Melissa A , Parkinson Helen 
Published: March 2017

AbstractIn many disciplines, data is highly decentralized across thousands of online databases (repositories, registries, and knowledgebases). Wringing value from such databases depends on the discipline of data science and on the humble bricks and mortar that make integration possible; identifiers are a core component of this integration infrastructure. Drawing on our experience and on work by other groups, we outline ten lessons we have learned about the identifier qualities and best practices that facilitate large-scale data integration. Specifically, we propose actions that identifier practitioners (database providers) should take in the design, provision and reuse of identifiers; we also outline important considerations for those referencing identifiers in various circumstances, including by authors and data generators. While the importance and relevance of each lesson will vary by context, there is a need for increased awareness about how to avoid and manage common identifier problems, especially those related to persistence and web-accessibility/resolvability. We focus strongly on web-based identifiers in the life sciences; however, the principles are broadly relevant to other disciplines.
A transformation from temporal to ensemble coding in a model of piriform cortex
Authors: Stern Merav , Bolding Kevin A. , Abbott L.F. , Franks Kevin M. 
Published: March 2017

ABSTRACTDifferent coding strategies are used to represent odor information at various stages of the mammalian olfactory system. A temporal latency code represents odor identity in olfactory bulb (OB), but this temporal information is discarded in piriform cortex (PCx) where odor identity is instead encoded through ensemble membership. We developed a spiking PCx network model to understand how this transformation is implemented. In the model, the impact of OB inputs activated earliest after inhalation is amplified within PCx by diffuse recurrent collateral excitation, which then recruits strong, sustained feedback inhibition that suppresses the impact of later-responding glomeruli. Simultaneous OB-PCx recordings indicate that indeed, over a single sniff, the earliest-active OB inputs are most effective at driving PCx activity. We model increasing odor concentrations by decreasing glomerulus onset latencies while preserving their activation sequences. This produces a multiplexed cortical odor code in which activated ensembles are robust to concentration changes while concentration information is encoded through population synchrony. Our model demonstrates how PCx circuitry can implement multiplexed ensemble-identity/temporal-concentration odor coding.
Genomic inferences of domestication events are corroborated by written records inBrassica rapa
Authors: Qi Xinshuai , An Hong , Ragsdale Aaron , Hall Tara E. , Gutenkunst Ryan N. , Chris Pires J. , Barker Michael S. 
Published: March 2017

AbstractDemographic modeling is often used with population genomic data to infer the relationships and ages among populations. However, relatively few analyses are able to validate these inferences with independent data. Here, we leverage written records that describe distinctBrassica rapacrops to corroborate demographic models of domestication.Brassica rapacrops are renowned for their outstanding morphological diversity, but the relationships and order of domestication remains unclear. We generated genome-wide SNPs from 126 accessions collected globally using high-throughput transcriptome data. Analyses of more than 31,000 SNPs across theB. rapagenome revealed evidence for five distinct genetic groups and supported a European-Central Asian origin ofB. rapacrops. Our results supported the traditionally recognized South Asian and East AsianB. rapagroups with evidence that pak choi, Chinese cabbage, and yellow sarson are likely monophyletic groups. In contrast, the oil-typeB. rapasubsp.oleiferaand brown sarson were polyphyletic. We also found no evidence to support the contention that rapini is the wild type or the earliest domesticated subspecies ofB. rapa.Demographic analyses suggested thatB. rapawas introduced to Asia 2400-4100 years ago, and that Chinese cabbage originated 1200-2100 years ago via admixture of pak choi and European-Central AsianB. rapa.We also inferred significantly different levels of founder effect among theB. rapasubspecies. Written records from antiquity that document these crops are consistent with these inferences. The concordance between our age estimates of domestication events with historical records provides unique support for our demographic inferences.
MELODI - Mining Enriched Literature Objects to Derive Intermediates
Authors: Elsworth Benjamin , Dawe Karen , Vincent Emma E , Langdon Ryan , Lynch Brigid M , Martin Richard M , Relton Caroline , Higgins Julian PT , Gaunt Tom R 
Published: March 2017

AbstractMotivationThe scientific literature contains a wealth of information from different fields on potential disease mechanisms. However, prioritising mechanisms for further analytical evaluation presents enormous challenges in terms of the quantity and diversity of published research. The application of data mining approaches to the literature offers the potential to identify and prioritise mechanisms for more focused and detailed analysis.ResultsHere we present MELODI, a literature mining platform that can identify mechanistic pathways between any two biomedical concepts. Two case studies demonstrate the potential uses of MELODI and how it can generate hypotheses for further investigation. Firstly, an analysis of ERG and prostate cancer derives the intermediate transcription factor SP1, recently confirmed to be physically interacting with ERG. Secondly, examining the relationship between a new potential risk factor for pancreatic cancer identifies possible mechanistic insights which can be studiedin vitro.AvailabilityMELODI has been implemented as a Python/Django web application, and is freely available to use atwww.melodi.biocompute.org.ukContactmelodi@biocompute.org.uk
Bootstrapping and Empirical Bayes Methods Improve Rhythm Detection in Sparsely Sampled Data
Authors: Hutchison Alan L. , Allada Ravi , Dinner Aaron R. 
Published: March 2017

AbstractMotivationThere is much interest in using genome-wide expression time series to identify circadian genes. However, the cost and effort of such measurements often limits data collection. Consequently, it is difficult to assess the experimental uncertainty in the measurements and, in turn, to detect periodic patterns with statistical confidence.ResultsWe show that parametric bootstrapping and empirical Bayes methods for variance shrinkage can improve rhythm detection in genome-wide expression time series. We demonstrate these approaches by building on the empirical JTK_CYCLE method (eJTK) to formulate a method that we term BooteJTK. Our procedure rapidly and accurately detects cycling time series by combining information about measurement uncertainty with information about the rank order of the time series values. We exploit a publicly available genome-wide dataset with high time resolution to show that BooteJTK provides more consistent rhythm detection thanexisting methods at typical sampling frequencies. Then, we apply BooteJTK to genome-wide expression time series from multiple tissues and show that it reveals biologically sensible tissue relationships that eJTK misses.AvailabilityBootstrap eJTK (BooteJTK) is implemented in Python and is freely available on GitHub athttps://github.com/alanlhutchison/BooteJTK.
Correcting for Dependent P-values in Rhythm Detection
Authors: Hutchison Alan L. , Dinner Aaron R. 
Published: March 2017

AbstractThere is much interest in using genome-wide expression time series to identify circadian genes. Several methods have been developed to test for rhythmicity in sparsely sampled time series typical of such measurements. Because these methods are statistical in nature, they rely on estimating the probabilities that patterns arise by chance (i.e., p-values). Here we show that leading methods implicitly make inappropriate assumptions of independence when estimating p-values. We show how to correct for the dependence to obtain accurate estimates for statistical significance during rhythm detection.
Preservation of Chromatin Organization after Acute Loss of CTCF in Mouse Embryonic Stem Cells
Authors: Kubo Naoki , Ishii Haruhiko , Gorkin David , Meitinger Franz , Xiong Xiong , Fang Rongxin , Liu Tristin , Ye Zhen , Li Bin , Dixon Jesse R. , Desai Arshad , Zhao Huimin , Ren Bing 
Published: March 2017

SummaryThe CCCTC-binding factor (CTCF) is widely regarded as a key player in chromosome organization in mammalian cells, yet direct assessment of the impact of loss of CTCF on genome architecture has been difficult due to its essential role in cell proliferation and early embryogenesis. Here, using auxin-inducible degron techniques to acutely deplete CTCF in mouse embryonic stem cells, we show that cell growth is severely slowed yet chromatin organization remains largely intact after loss of CTCF. Depletion of CTCF reduces interactions between chromatin loop anchors, diminishes occupancy of cohesin complex genome-wide, and slightly weakens topologically associating domain (TAD) structure, but the active and inactive chromatin compartments are maintained and the vast majority of TAD boundaries persist. Furthermore, transcriptional regulation and histone marks associated with enhancers are broadly unchanged upon CTCF depletion. Our results suggest CTCF-independent mechanisms in maintenance of chromatin organization.
Accurate and Reproducible Functional Maps in 127 Human Cell Types via 2D Genome Segmentation
Authors: Zhang Yu , Hardison Ross C. 
Published: March 2017

ABSTRACTThe Roadmap Epigenomics consortium has published whole-genome functional annotation maps in 127 human cell types and cancer cell lines by integrating data from multiple epigenetic marks. These maps have thereby been widely used by the community for studying gene regulation in cell type specific contexts and predicting functional impacts of DNA mutations on disease. Here, we present a new map of functional elements produced by a recently published method called IDEAS on the same data set. The IDEAS method has several unique advantages and was shown to outperform existing methods, including the one used by the Roadmap Epigenomics consortium. We further introduce a simple but highly effective pipeline to greatly improve the reproducibility of functional annotation. Using five categories of independent experimental results, we extensively compared the annotation produced by IDEAS and the Roadmap Epigenomics consortium. While the overall concordance between the two maps was high, we observed many differences in the details and in the position-wise consistency of annotation across cell types. We show that the IDEAS annotation was uniformly and often substantially more accurate than the Roadmap Epigenomics result. This study therefore reports on the quality of an existing functional map in 127 human genomes and provides an alternative and better map to be used by the community. The annotation result can be visualized in the UCSC genome browser via the hub athttp://bx.psu.edu/~yuzhang/Roadmap_ideas/ideas_hub.txt
Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts
Authors: Bell Jason C. , Jukam David , Teran Nicole A. , Risca Viviana I. , Smith Owen K. , Johnson Whitney L. , Skotheim Jan , Greenleaf William J. , Straight Aaron F. 
Published: March 2017

AbstractRNA is a critical component of chromatin in eukaryotes, both as a product of transcription, and as an essential constituent of ribonucleoprotein complexes that regulate both local and global chromatin states. Here we present a proximity ligation and sequencing method calledChromatin-AssociatedRNAsequencing (ChAR-seq) that maps all RNA-to-DNA contacts across the genome. ChAR-seq provides unbiased,de novoidentification of targets of chromatin-bound RNAs including nascent transcripts, chromosome-specific dosage compensation ncRNAs, and genome-wide trans-associated RNAs involved in co-transcriptional RNA processing.
A new approach to steady state analysis of nonlinear electrical circuits
Authors: Sobczyk Tadeusz , Radzik Michał 
Published: March 2017

Purpose
The purpose of this study is to identify a novel methodology for direct calculation of steady-state periodic solutions for electrical circuits described by nonlinear differential equations, in the time domain.

Design/methodology/approach
An iterative algorithm was created to determine periodic steady-state solutions for circuits with nonlinear elements in a chosen set of time instants.

Findings
This study found a novel differential operator for periodic functions and its application in the steady-state analysis.

Research limitations/implications
This approach can be extended to the determination of two- or multi-periodic solutions of nonlinear dynamic systems.

Practical implications
The complexity of the steady-state analysis can be reduced in comparison with the frequency-domain approach.

Originality/value
This study identified novel difference equations for direct steady-state analysis of nonlinear electrical circuits.
Modelling anisotropy in non-oriented electrical steel sheet using vector Jiles–Atherton model
Authors: Upadhaya Brijesh , Martin Floran , Rasilo Paavo , Handgruber Paul , Belahcen Anouar , Arkkio Antero 
Published: March 2017

PurposeNon-oriented electrical steel presents anisotropic behaviour. Modelling such anisotropic behaviour has become a necessity for accurate design of electrical machines. The main aim of this study is to model the magnetic anisotropy in the non-oriented electrical steel sheet of grade M400-50A using a phenomenological hysteresis model.Design/methodology/approachThe well-known phenomenological vector Jiles–Atherton hysteresis model is modified to correctly model the typical anisotropic behaviour of the non-oriented electrical steel sheet, which is not described correctly by the original vector Jiles–Atherton model. The modification to the vector model is implemented through the anhysteretic magnetization. Instead of the commonly used classical Langevin function, the authors introduced 2D bi-cubic spline to represent the anhysteretic magnetization for modelling the magnetic anisotropy.FindingsThe proposed model is found to yield good agreement with the measurement data. Comparisons are done between the original vector model and the proposed model. Another comparison is also made between the results obtained considering two different modifications to the anhysteretic magnetization.Originality/valueThe paper presents an original method to model the anhysteretic magnetization based on projections of the anhysteretic magnetization in the principal axis, and apply such modification to the vector Jiles–Atherton model to account for the magnetic anisotropy. The replacement of the classical Langevin function with the spline resulted in better fitting. The proposed model could be used in the numerical analysis of magnetic field in an electrical application.
Effect of mechanical stress on different iron loss components up to high frequencies and magnetic flux densities
Authors: Karthaus Jan , Steentjes Simon , Leuning Nora , Hameyer Kay 
Published: March 2017

Purpose
The purpose of this paper is to study the variation of the specific iron loss components of electrical steel sheets when applying a tensile mechanical load below the yield strength of the material. The results provide an insight into the iron loss behaviour of the laminated core of electrical machines which are exposed to mechanical stresses of diverse origins.

Design/methodology/approach
The specific iron losses of electrical steel sheets are measured using a standardised single-sheet tester equipped with a hydraulic pressure cylinder which enables application of a force to the specimen under test. Based on the measured data and a semi-physical description of specific iron losses, the stress-dependency of the iron loss components can be studied.

Findings
The results show a dependency of iron loss components on the applied mechanical stress. Especially for the non-linear loss component and high frequencies, a large variation is observed, while the excess loss component is not as sensitive to high mechanical stresses. Besides, it is shown that the stress-dependent iron loss prediction approximates the measured specific iron losses in an adequate way.

Originality/value
New applications such as high-speed traction drives in electric vehicles require a suitable design of the electrical machine. These applications require particular attention to the interaction between mechanical influences and magnetic behaviour of the machine. In this regard, knowledge about the relation between mechanical stress and magnetic properties of soft magnetic material is essential for an exact estimation of the machine’s behaviour.
Impact of supply voltage variations on external magnetic field emitted by induction machines
Authors: Younsi Mohamed Omar , Ninet Olivier , Morganti Fabrice , Lecointe Jean-Philippe , Zidat Farid , Buire Matthieu 
Published: March 2017

Purpose
This paper aims to study the influence of supply voltage variations on the external magnetic field emitted by grid-powered induction machines (IMs).

Design/methodology/approach
Two models are developed in the paper to analyse, for different supply voltage values, the influence of the variations of the magnetizing voltage for which there is a link with the tangential component of the external flux. The first is an analytical model based on the IM single-phase-equivalent circuit with variable magnetizing reactance to take into account the saturation of the magnetic circuit. The second is a numerical finite element simulation to model the same phenomenon. Results of both models are analysed with experimental measures of the external flux.

Findings
The study shows that the amplitude of the external field strongly depends on supply voltage values.

Research limitations/implications
The investigation is mainly focused on the tangential component of the external magnetic field which is of high importance concerning the applicability of non-invasive methods of diagnosis, as electromagnetic torque estimation developed by the authors or internal fault determination.

Originality/value
The originality of the paper concerns the characterization of the external flux with the supply voltage for IMs. It is shown that the magnetic circuit radiates external flux differently with the load and with the supply voltage.
Eliminating short switching cycles when using hysteresis control of resistance spot welding systems
Authors: Černelič Jernej , Brezovnik Robert , Sukič Primož , Petrun Martin 
Published: March 2017

Purpose
This paper aims to present two hysteresis-control algorithms designed for medium-frequency, direct-current, resistance-spot-welding (MFDC RSW) systems. The first proposed control algorithm (MSCHC) eliminates the short switching cycles that can occur when using the existing hysteresis-control algorithms. This control minimises the number of switching cycles that are needed to generate the selected welding current. The welding-current ripple can be high when using this control algorithm. Therefore, a second algorithm (HCRR) is presented that reduces the welding-current ripple by half.

Design/methodology/approach
The proposed hysteresis controllers consist of the transformer’s magnetic-flux-density hysteresis regulator and a welding-current hysteresis regulator. Therefore, the welding current must be measured and the saturation of the iron core must be detected. The proposed hysteresis controller supplies the inverter with the signals needed to generate the supply voltage for the RSW transformer, which then generates the selected welding current.

Findings
The proposed MSCHC algorithm produces the smallest possible number of switching cycles needed to generate the selected welding current. The high welding-current ripple can be reduced if the number of switching cycles is increased. The observed number of switching cycles and the welding-current ripple change if the welding resistance and/or inductance change.

Originality/value
The number of switching cycles can be minimised when using the first proposed control algorithm (MSCHC), and so the switching power losses can be minimised. If the welding-current ripple produced by the first control algorithm is unacceptable, the second control algorithm (HCRR) can reduce it by increasing the number of switching cycles.
A computational framework for a two-scale generalized/extended finite element method
Authors: Malekan Mohammad , Barros Felício , Pitangueira Roque Luiz da Silva , Alves Phillipe Daniel , Penna Samuel Silva 
Published: March 2017

Purpose
This paper aims to present a computational framework to generate numeric enrichment functions for two-dimensional problems dealing with single/multiple local phenomenon/phenomena. The two-scale generalized/extended finite element method (G/XFEM) approach used here is based on the solution decomposition, having global- and local-scale components. This strategy allows the use of a coarse mesh even when the problem produces complex local phenomena. For this purpose, local problems can be defined where these local phenomena are observed and are solved separately by using fine meshes. The results of the local problems are used to enrich the global one improving the approximate solution.

Design/methodology/approach
The implementation of the two-scale G/XFEM formulation follows the object-oriented approach presented by the authors in a previous work, where it is possible to combine different kinds of elements and analyses models with the partition of unity enrichment scheme. Beside the extension of the G/XFEM implementation to enclose the global–local strategy, the imposition of different boundary conditions is also generalized.

Findings
The generalization done for boundary conditions is very important, as the global–local approach relies on the boundary information transferring process between the two scales of the analysis. The flexibility for the numerical analysis of the proposed framework is illustrated by several examples. Different analysis models, element formulations and enrichment functions are used, and the accuracy, robustness and computational efficiency are demonstrated.

Originality/value
This work shows a generalize imposition of different boundary conditions for global–local G/XFEM analysis through an object-oriented implementation. This generalization is very important, as the global–local approach relies on the boundary information transferring process between the two scales of the analysis. Also, solving multiple local problems simultaneously and solving plate problems using global–local G/XFEM are other contributions of this work.