bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lilikoi: an R package for personalized pathway-based classification modeling using metabolomics data
Authors: Al-Akwaa Fadhl M. , Huang Sijia , Garmire Lana X. 
Published: March 2018

AbstractLilikoi (Hawaiian word for passion fruit) is a new and comprehensive R package for personalized pathway based classification modelling, using metabolomics data. Four basic modules are presented as the backbone of the package: 1) Feature mapping module, which standardizes the metabolite names provided by users, and map them to pathways. 2) Dimension transformation module, which transforms the metabolomic profiles to personalized pathway-based profiles using pathway deregulation scores (PDS). 3) Feature selection module which helps to select the significant pathway features related to the disease phenotypes, and 4) Classification and prediction module which offers various machine-learning classification algorithms. The package is freely available under the GPLv3 license through the github repository at: https://github.com/lanagarmire/lilikoi
Fast NeighborNet: Improving the Speed of the Neighbor-Net Phylogenetic Network Algorithm with Multithreading and a Relaxed Search Strategy
Authors: Porter Jacob 
Published: March 2018

AbstractFast Neighbor-Net is a command-line Java program that has fast implementations of the popular Neighbor-Net phylo-genetic split network approach. This allows more efficiency in computationally intensive tasks such as larger scale data analysis and bootstrapping. The canonical search phase iteratively finds a pair of connected components that minimizes a distance function in Θ(n3) time in the input taxa count. A relaxed search strategy has been implemented that has averagecase time complexity of𝒪(n2logn) but with Θ(n3) worst-case time complexity. This search strategy sacrifices some accuracy for speed. The original approach’s implementation has been improved by using good programming practice. These improvements increased run-time performance by a constant factor of approximately 2 and reduced memory requirements by a constant factor of approximately 6. These search strategies allow multithreading to better use modern CPU hardware. PFAM data of 2000–30,000 taxa were used for testing performance. The canonical implementation with three threads improved average performance by approximately 2.1. The relaxed search has good quality, and the accuracy was tested on a mammal and a eukaryote data set. Kendall tau distance was used as a rough measure of topological similarity for the relaxed and canonical search strategies.
Detecting archaic introgression without archaic reference genomes
Authors: Skov Laurits , Hui Ruoyun , Hobolth Asger , Scally Aylwyn , Schierup Mikkel Heide , Durbin Richard 
Published: March 2018

AbstractHuman populations out of Africa have experienced at least two bouts of introgression from archaic humans, from Neanderthals and Denisovans. In Papuans there is prior evidence of both these introgressions. Here we present a new approach to detect segments of individual genomes of archaic origin without using an archaic reference genome. The approach is based on a hidden Markov model that identifies genomic regions with a high density of single nucleotide variants (SNVs) not seen in unadmixed populations. We show using simulations that this provides a powerful approach to identifying segments of archaic introgression with a small rate of false detection. Furthermore our approach is able to accurately infer admixture proportions and divergence time of human and archaic populations.We apply the model to detect archaic introgression in 89 Papuans and show how the identified segments can be assigned to likely Neanderthal or Denisovan origin. We report more Denisovan admixture than previous studies and directly find a shift in size distribution of fragments of Neanderthal and Denisovan origin that is compatible with a difference in admixture time. Furthermore, we identify small amounts of Denisova ancestry in West Eurasians, South East Asians and South Asians.
P-bodies and the miRNA pathway regulate translational repression ofbicoidmRNA duringDrosophila melanogasteroogenesis
Authors: McLaughlin John M. , Smith Daniel F.Q. , Catrina Irina E. , Bratu Diana P. 
Published: March 2018

ABSTRACTEmbryonic axis patterning inDrosophila melanogasteris partly achieved by mRNAs that are maternally localized to the oocyte; the spatio-temporal regulation of these transcripts’ stability and translation is a characteristic feature of oogenesis. While protein regulatory factors are necessary for the translational regulation of some maternal transcripts (e.g.oskarandgurken), small RNA pathways are also known to regulate mRNA stability and translation in eukaryotes. MicroRNAs (miRNAs) are small RNA regulators of gene expression, widely conserved throughout eukaryotic genomes and essential for animal development. The mainD. melanogasteranterior determinant,bicoid, is maternally transcribed, but it is not translated until early embryogenesis. We investigated the possibility that its translational repression during oogenesis is mediated by miRNA activity. We found that thebicoid3’UTR contains a highly conserved, predicted binding site for miR-305. Our studies reveal that miR-305 regulates the translation of a reporter gene containing thebicoid3’UTR in cell culture, and that miR-305 only partially contributes tobicoidmRNA translational repression during oogenesis. We also found that Processing bodies (P-bodies) in the egg chamber may play a role in stabilizingbicoidand other maternal transcripts. Here, we offer insights into the possible role of P-bodies and the miRNA pathway in the translational repression ofbicoidmRNA during oogenesis.
Selection in parental species predicts hybrid evolution
Authors: Runemark Anna , Bailey Richard I , Bache-Mathiesen Lena , Sætre Glenn-Peter 
Published: March 2018

AbstractWhile hybridization is recognized as important in evolution, its contribution to adaptation and diversification remains poorly understood. Using genomically diverged island populations of the homoploid hybrid Italian sparrow, we test predictions for phenotypic trait values and evolvability based on patterns of parental species divergence in four plumage color traits. We find associations between parental divergence and trait evolution in Italian sparrows. Fixed major QTL in species differences lead to hybrids with higher trait variation, and hence evolvability, than the parent species. Back and crown plumage show no correlation between current within-parent variability and among-parent differentiation. For these traits, Italian sparrow phenotypes are biased towards axes of high parental differentiation and show greater phenotypic novelty along axes of low current parental evolvability, as predicted when major QTL are involved in species differences. Crown color has consistently evolved back towards one parent, while back color varies among islands. We also find significant among-population diversification within the Italian sparrow. Hence, hybridization of the same parent species can generate different phenotypes. In conclusion, we find support for parental phenotypic divergence patterns reflecting divergence mechanisms, and hence such patterns can be useful in predicting how hybridization alters the potential to evolve and adapt.
Nucleosome remodelling at origins of Global Genome-Nucleotide Excision Repair occurs at the boundaries of higher-order chromatin structure
Authors: van Eijk Patrick , Nandi Shuvro Prokash , Yu Shirong , Bennett Mark , Leadbitter Matthew , Teng Yumin , Reed Simon H. 
Published: March 2018

AbstractRepair of UV-induced DNA damage requires chromatin remodeling. How repair is initiated in chromatin remains largely unknown. We recently demonstrated that Global Genome Nucleotide Excision Repair (GG-NER) in chromatin is organized into domains around open reading frames. Here, we identify these domains, and by examining DNA damage-induced changes in the linear structure of nucleosomes, we demonstrate how chromatin remodeling is initiated during repair. In undamaged cells, we show that the GG-NER complex occupies chromatin at nucleosome free regions of specific gene promoters. This establishes the nucleosome structure at these genomic locations, which we refer to as GG-NER complex binding sites (GCBS’s). We demonstrate that these sites are frequently located at genomic boundaries that delineate chromasomally interacting domains (CIDs). These boundaries define domains of higher-order nucleosome-nucleosome interaction. We show that efficient repair of DNA damage in chromatin is initiated following disruption of H2A.Z-containing nucleosomes adjacent to GCBSs by the GG-NER complex.
Long-read genome sequence and assembly ofLeptopilina boulardi: a specialistDrosophilaparasitoid
Authors: Khan Shagufta , Sowpati Divya Tej , Mishra Rakesh K 
Published: March 2018

AbstractBackgroundLeptopilina boulardiis a specialist parasitoid belonging to the order Hymenoptera, which attacks the larval stages ofDrosophila. TheLeptopilinagenus has enormous value in the biological control of pests as well as in understanding several aspects of host-parasitoid biology. However, none of the members of Figitidae family has their genomes sequenced. In order to improve the understanding of the parasitoid wasps by generating genomic resources, we sequenced the whole genome ofL. boulardi.FindingsHere, we report a high-quality genome ofL. boulardi, assembled from 70Gb of Illumina reads and 10.5Gb of PacBio reads, forming a total coverage of 230X. The 375Mb draft genome has an N50 of 275Kb with 6315 scaffolds >500bp, and encompasses >95% complete BUSCOs. The GC% of the genome is 28.26%, and RepeatMasker identified 868105 repeat elements covering 43.9% of the assembly. A total of 25259 protein-coding genes were predicted using a combination ofab-initioand RNA-Seq based methods, with an average gene size of 3.9Kb. 78.11% of the predicted genes could be annotated with at least one function.ConclusionOur study provides a highly reliable assembly of this parasitoid wasp, which will be a valuable resource to researchers studying parasitoids. In particular, it can help delineate the host-parasitoid mechanisms that are part of theDrosophila–Leptopilinamodel system.
Compound signaling activates endogenous retroviruses by inducing enhancer and gene-neighborhood transcription
Authors: Azébi Saliha , Batsché Eric , Michel Fréderique , Kornobis Etienne , Muchardt Christian 
Published: March 2018

SummaryMultiple sclerosis (MS) is a neuroinflammatory and autoimmune disease, in which various immune cell types and autoreactive T cells exert a pathogenic activity. This disease is also associated with increased transcription of several endogenous retroviruses (HERVs) normally kept in check by heterochromatin. Here, we have uncovered an organic pollutant dieldrin that activates several HERVs associated with MS and allowing us to examine the mechanism of their activation. Dieldrin singles out by its ability to simultaneously activate the MAP kinase and the PI3K pathways, while also triggering calcium dependent peptidylarginine deiminase activity. It was this association of pathways that caused HERV activation, a phenomenon that was only part of more generally increased transcription of heterochromatic regions. The HERV transcripts were generally not polyadenylated. Some arose as a consequence of activation of HERV-based enhancers, while others were the result of unusually strong activation at some mostly transcription factor genes causing transcription to leak out of the HERV-free region that surrounds them. Altogether, our data emphasized the hazard associated with simultaneous activation of multiples signaling pathways by xenobiotics, while also providing a very general toolbox for the interpretation of HERV transcription.
Modeling and verification of the equivalent circuit for high temperature superconducting partial-core transformer with ReBCO-coated conductors
Authors: Hu Daoyu , Zhang Jianwen , Gu Feng , Li Zhuyong 
Published: March 2018

Purpose
The purpose of this study is to propose a modeling method of the equivalent circuit for a new type of high-temperature superconducting partial-core transformer (HTS-PCT) made of ReBCO-coated conductors.

Design/methodology/approach
The modeling process is based on the “Steinmetz” equivalent circuit. The impedance components in the circuit are obtained by the calculations of the core losses and AC losses of the HTS windings by using theoretical methods. An iterative computation is also used to decide the equivalent resistances of the AC losses of the primary and secondary HTS windings. The reactance components in the circuit are calculated from the energy stored in the magnetic fields by finite element method. The validation of the modeling method is verified by experimental results

Findings
The modeling method of the equivalent circuit of HTS-PCT is valid, and an equivalent circuit for HTS-PCT is presented.

Practical implications
The equivalent circuit of HTS-PCT could be obtained by the suggested modeling method. Then, it is easy to analyze the characteristics of the HTS-PCT by its equivalent circuit. Moreover, the modeling method could also be useful for the design of a specific HTS-PCT.

Originality/value
The study proposes a modeling method of the HTS-PCT made of the second-generation HTS tapes, i.e. ReBCO-coated conductors.
Modeling and simulation of saturated double rotor induction machine
Authors: Choobdari Omran Koosha , Mosallanejad Ali 
Published: March 2018

Purpose
Double rotor induction machine (DRIM) is a particular type of induction machine (IM) that has been introduced to improve the parameters of the conventional IM. The purpose of this study is to propose a dynamic model of the DRIM under saturated and unsaturated conditions by using the equations obtained in this paper. Also, skin and temperature effects are considered in this model.

Design/methodology/approach
First, the DRIM structure and its performance will be briefly reviewed. Then, to realize the DRIM model, the mathematical equations of the electrical and mechanical part of the DRIM will be presented by state equations in the q-d axis by using the Park transformation. In this paper, the magnetizing fluxes saturation is included in the DRIM model by considering the difference between the amplitudes of the unsaturated and saturated magnetizing fluxes. The skin and temperature effects are also considered in this model by correcting the rotor and stator resistances values during operation.

Findings
To evaluate the effects of the saturation and skin effects on DRIM performance and validate the model, the machine is simulated with/without consideration of saturation and skin effects by the proposed model. Then, the results, including torque, speed, stator and rotor currents, active and reactive power, efficiency, power factor and torque-speed characteristic, are compared. In addition, the performance of the DRIM has been investigated at different speed conditions and load variations. The proposed model is developed in Matlab/Simulink for the sake of validation.

Originality/value
This paper presents an understandable model of DRIM with and without saturation, which can be used to analyze the steady-state and transient behavior of the motor in different situations.
Miniaturized quad-band coplanar-fed monopole antenna for tablet computers
Authors: Subbaraj Sangeetha , Kanagasabai Malathi , Mohammed Gulam Nabi Alsath , Panneer Selvam Yogeshwari , Kingsly Saffrine , Yeragudipati Venkata Ramana Rao 
Published: March 2018

Purpose
This paper aims to present the design of a compact quad-band coplanar-fed monopole antenna for tablet computer applications.

Design/methodology/approach
The antenna has the smallest size of 26 × 14 mm and supports GSM, Wi-Fi, WIMAX and Bluetooth. The proposed antenna consists of a coplanar fed main radiator, c-shaped stubs and parasitic meandered stub. The inverted c-shaped stubs enhance the bandwidth of upper frequencies. The resonance at 2.4 GHz is individually controlled by the coupled meandered stub.

Findings
The percentage bandwidth in the four operating bands are 8.7/4.12/27.8/13.3%. Furthermore, the antenna is integrated with the mock-up ground plane and specific absorption rate (SAR) calculations are performed. The estimated SAR is less than 1.6 W/kg for a 1 g body tissue. The gain and efficiency of the antenna are 3.56/4.37/4.97/6 dBi and 82.4/85/97.1/89.3%, respectively. The measured impedance and radiation characteristics of the fabricated prototype are in good correlation with the simulated results.

Originality/value
In the proposed work, vias and lumped elements are not used for lower band excitation, and most of the wireless applications in the tablet computers have been covered. Further, the effect of antenna with different orientation has been tested for the estimation of SAR.
Measurements show need for transformer core joint details in finite element modelling of GIC and DC effects
Authors: Chisepo Hilary Kudzai , Borrill Leslie David , Gaunt Charles Trevor 
Published: March 2018

Purpose
This paper aims to improve the finite element modelling of transformers subjected to DC excitation, by including core joint details.

Design/methodology/approach
Geomagnetically induced currents (GICs) or leakage DC can cause part-cycle, half wave saturation of a power transformer’s core. Practical measurements and finite element matrix (FEM) simulation were carried out using three laboratory-scale, untanked single-phase four limb transformers resembling real power transformers in terms of the core steel and parallel winding assemblies. “Equivalent air gaps” at the joints, based on AC measurements, were applied to the FEM models for simultaneous AC and DC excitation.

Findings
Measurements confirm that introducing equivalent air gaps at the joints improves the FEM simulation of transformers carrying DC.

Research limitations/implications
The FEM simulations based on the laboratory transformers are exemplary, showing the difference between modelling core joints as solid or including equivalent air gaps. They show that, for more representative results, laboratory transformers used for research should have mitred core joints (like power transformers).

Originality/value
This research shows why joint details are important in FEM models for analysing transformer core saturation in the presence of DC/GICs. Extending this, other core structures of power transformers with mitred joints should improve the understanding of the leakage flux during half-wave saturation.
Governance issues constraining the deployment of flood resilience strategies in Maroua, Far North Region of Cameroon
Authors: Wanie Clarkson Mvo , Ndi Roland Akoh 
Published: March 2018

Purpose
Cities across the globe, particularly those of the less developed world, face long-term challenges associated with floods which impact negatively on the resilience of city systems and their inhabitants. In the city of Maroua, most urban management stakeholders have been unable to integrate flood resilience research into urban development issues. It is against this background that the purpose of this paper is to evaluate the governance issues constraining the deployment of flood resilience strategies implemented by residents in flood-prone zones and those used by the government via administrative authorities and institutions charged with urban development to flood-related risks in the city of Maroua, Far North Region of Cameroon.

Design/methodology/approach
Field surveys, participant observations, interviews, and on-the-spot appraisals were carried out with residents in flood-prone neighbourhoods and municipal authorities on the state of recurrent floods including mitigating strategies being implemented.

Findings
The results revealed that Maroua has a fragile ecological setting which has increased the vulnerability of the town to flood-related risks. This is further aggravated by the fact that municipal authorities are yet to have a thorough mastery of such recurrent flood incidences due to their limited planning horizons, rendering the urban poor disproportionately susceptible to flood-related stresses. This exposes them to unavoidable flood associated hazards such as water borne diseases (typhoid and cholera) as they are bogged down by physical and financial limitations. Besides, decision-making processes in relation to managing urban systems are not guided by good governance as efforts to enhance and integrate the local population for flood resilience are neither participatory nor inclusive, ushering the urban environment of Maroua into a frivolous path to profligacy.

Originality/value
For resilience to be deeply entrenched, the paper proffers for the mainstreaming of flood resilience strategies into urban development plans through multi-stakeholder involvement across different sectors and departments, as well as the setting up of a practical time table for monitoring the progress of these measures through geospatial technologies such as remote sensing and geographical information systems.
Development of a defect monitoring system (DMOSYS) for building maintenance at polytechnic
Authors: Bin Ismail Zul-Atfi 
Published: March 2018

Purpose
The current maintenance management method has affected the efficiency of the building facility management at Polytechnics. Many issues such as poor service delivery, inadequate finance, poor maintenance planning and maintenance backlogs have emerged due to the usage of conventional method application (paper-based form and unsystematic database. The purpose of this paper is to review existing literature and case studies project of the technologies in maintenance management at Polytechnic, and subsequently to identify the challenge in improving the current maintenance management technologies.

Design/methodology/approach
The purpose of this paper is to review existing literature and case studies project of the technologies in maintenance management at Polytechnic, and subsequently to identify the challenges of information and communication technology (ICT) implementation for strategic defect diagnosis and decision-making in improving the current maintenance management technologies. Eight Polytechnics are selected on the basis of the major problems of using the conventional method in the comparison to investigate the maintenance management practices in each Polytechnic. There are around 32 Polytechnics in Malaysia and most are using conventional methods.

Findings
The findings reveal the need for a more sophisticated maintenance management system that provides guidelines for decision-making processes with the implementation of ICT. The interview results also reveal irregularities within the Malaysian Polytechnics’ maintenance management database. The system architecture and the information system prototype are presented to integrate the information database and maintenance management processes in improving the building diagnosis approach and decision-making process for managing building maintenance.

Originality/value
This new system is expected to become the successful technology in assisting the maintenance contractors, clients and developer for effective management of maintenance defects at Polytechnic.