bluuebunny/crossref_metadata_2025_split huggingface dataset:
De novo phased assembly of the Vitis riparia grape genome
Authors: Girollet Nabil , Rubio Bernadette , Lopez-Roques Céline , Valière Sophie , Ollat Nathalie , Bert Pierre-François 
Published: July 2019

AbstractGrapevine is one of the most important fruit species in the world. In order to better understand genetic basis of traits variation and facilitate the breeding of new genotypes, we sequenced, assembled, and annotated the genome of the American nativeVitis riparia, one of the main species used worldwide for rootstock and scion breeding. A total of 164 Gb raw DNA reads were obtained fromVitis ripariaresulting in a 225X depth of coverage. We generated a genome assembly of theV.ripariagrapede novousing the PacBio long-reads that was phased with the 10x Genomics Chromium linked-reads. At the chromosome level, a 500 Mb genome was generated with a scaffold N50 size of 1 Mb. More than 34% of the whole genome were identified as repeat sequences, and 37,207 protein-coding genes were predicted. This genome assembly sets the stage for comparative genomic analysis of the diversification and adaptation of grapevine and will provide a solid resource for further genetic analysis and breeding of this economically important species.
Tradeoffs and Compatibilities of Chemical Properties in CpHqFrOs System
Authors: Okamoto Yasuharu 
Published: July 2019

AbstractTo comply with the Kigali amendment to the Montreal Protocol in 2016, development of new refrigerants with low global warming potential is urgently required in addition to satisfying the conventional requirements of cooling performance, safety, and non-destructiveness to the ozone layer. Because these requirements closely correlated, the proper control of various chemical properties is necessary to fulfill the requirements. However, simultaneous satisfaction of all the requirements is extremely difficult because of the tradeoffs among the chemical properties. Hence, we must correctly recognize how chemical properties behave when the composition of molecules is changed. We performed an in-silico screening that combines quantum chemical calculations, machine learning, and database search, where 10,163 molecules were investigated exhaustively within the properly imposed constraints; subsequently we found a few candidates.
Mechanism of rift flank uplift and escarpment formation evidenced by Western Ghats, India
Authors: T. Radhakrishna , R. Mohamed Asanulla , M. Venkateshwarlu , G. S. Soumya , P. K. Prachiti 
Published: July 2019

AbstractThe Western Ghats is one of the largest escarpments on earth, containing Reunion plume derived Deccan Traps, it is an excellent example to probe epeirogenic uplift, extension and subsidence in volcanic continental margins. The most continuous unbiased stratigraphic section of basalt down to the basement within a 1250 m drill hole of the Continental Scientific Deep Drilling Project is a valuable resource to investigate the above aspects. The flows across the entire drill core are geologically subaerial in character with basement exposed ~300 m below the mean sea level; they clearly display more evolved compositions from primary melts of mantle in terms of petrology, and only a single geomagnetic polarity transition in palaeomagnetic data. These results, combined with existing geological and geophysical data, constitute a multi-method approach that demonstrates (a) igneous underplating caused uplift prior to frequently suggested flexural isostasy (b) plume impact and eruption are near-simultaneous and extension/rifting essentially followed soon after volcanism and (c) lithosphere beneath the continental margin, while returning to normal temperatures following the Seychelles-India breakup, experienced thermal collapse and subsidence causing slumping of basalt basement below sea level.
Structures of N-terminally processed KRAS provide insight into the role of N-acetylation
Authors: Dharmaiah Srisathiyanarayanan , Tran Timothy H. , Messing Simon , Agamasu Constance , Gillette William K. , Yan Wupeng , Waybright Timothy , Alexander Patrick , Esposito Dominic , Nissley Dwight V. , McCormick Frank , Stephen Andrew G. , Simanshu Dhirendra K. 
Published: July 2019

AbstractAlthough post-translational modification of the C-terminus of RAS has been studied extensively, little is known about N-terminal processing. Mass spectrometric characterization of KRAS expressed in mammalian cells showed cleavage of the initiator methionine (iMet) and N-acetylation of the nascent N-terminus. Interestingly, structural studies on GDP- and GMPPNP-bound KRAS lacking the iMet and N-acetylation resulted in Mg2+-free structures of KRAS with flexible N-termini. In the Mg2+-free KRAS-GDP structure, the flexible N-terminus causes conformational changes in the interswitch region resulting in a fully open conformation of switch I. In the Mg2+-free KRAS-GMPPNP structure, the flexible N-terminus causes conformational changes around residue A59 resulting in the loss of Mg2+ and switch I in the inactive state 1 conformation. Structural studies on N-acetylated KRAS-GDP lacking the iMet revealed the presence of Mg2+ and a conformation of switch regions also observed in the structure of GDP-bound unprocessed KRAS with the iMet. In the absence of the iMet, the N-acetyl group interacts with the central beta-sheet and stabilizes the N-terminus and the switch regions. These results suggest there is crosstalk between the N-terminus and the Mg2+ binding site, and that N-acetylation plays an important role by stabilizing the N-terminus of RAS upon excision of the iMet.
The effect of regular dental cast artifacts on the 3D superimposition of serial digital maxillary dental models
Authors: Henninger Eva , Vasilakos Georgios , Halazonetis Demetrios , Gkantidis Nikolaos 
Published: July 2019

AbstractSuperimpositions of serial 3D dental surface models comprise a powerful tool to assess morphological changes due to growth, treatment, or pathology. In this study, we evaluated the effect of artifacts on the superimposition outcome, using standard model acquisition and superimposition techniques. Ten pre- and post-orthodontic treatment plaster models were scanned with an intraoral scanner and superimposed using the iterative closest point algorithm. We repeated the whole process after manual removal of plaster artifacts, according to the current practice, as well as after re-scanning the cleaned models, to assess the effect of the model acquisition process derived artifacts on the superimposition outcome. Non-parametric multivariate models showed no mean effect on accuracy and precision by software settings, cleaning status (artifact removal), or time point. The choice of the superimposition reference area was the only factor that affected the measurements. However, assessment of individual cases revealed significant differences on the detected tooth movement, depending on artifact removal and on the model acquisition process. The effects of all factors tended to decrease with an increase in the size of the superimposition reference area. The present findings highlight the importance of accurate, artifact-free models, for valid assessment of morphological changes through serial 3D model superimpositions.
Contrasting Roles of Cannabidiol as an Insecticide and Rescuing Agent for Ethanol–induced Death in the Tobacco Hornworm Manduca sexta
Authors: Park Sang-Hyuck , Staples S. Kyle , Gostin Eric L. , Smith Jeffrey P. , Vigil Jose J. , Seifried Dustin , Kinney Chad , Pauli Christopher S. , Heuvel Brian D. Vanden 
Published: July 2019

AbstractCannabis sativa, also known as marijuana or hemp, produces a non-psychoactive compound cannabidiol (CBD). To investigate the defensive role of CBD, a feeding preference assay was performed with tobacco hornworm Manduca sexta. The larvae clearly show feeding preference towards the Cannabis tissue containing low CBD over high CBD. While the larva avoided the high CBD diet, we investigated detrimental effects of CBD in the insects’ diet. Contrasted to the performance on low CBD-infused artificial diet (AD), larvae reared on the high CBD diet suffer significantly reduced growth and increased mortality. Through testing different carriers, we found that the increase of EtOH in the diet is negatively correlated with insect development and behaviors. Notably, CBD treatment significantly improved ethanol-intoxicated larval survival rate by 40% and also improved diet searching activity, resulting in increased diet consumption. Electrophysiology results revealed that the CBD-treated ganglia had delayed but much larger response with electric stimuli in comparison to the larvae reared on AD only and EtOH-added diet. Our results show CBDs’ defensive role against pest insects, which suggests its possible use as an insecticide. We also provide evidence that CBD alleviates alcohol-induced stress; consequently, improving the performance and viability of M. sexta larvae.
Development of a quantitative method to measure EV uptake
Authors: Toribio Víctor , Morales Sara , López-Martín Soraya , Cardeñes Beatriz , Cabañas Carlos , Yáñez-Mó María 
Published: July 2019

AbstractThe outstanding potential of Extracellular Vesicles (EVs) in medicine, deserves a detailed study of the molecular aspects regulating their incorporation into target cells. However, because EV size lies below the limit of resolution of optical techniques, quantification together with discrimination between EV binding to the target cell and uptake is usually not completely achieved with current techniques. Human tetraspanins CD9 and CD63 were fused to a dual EGFP-Renilla-split tag. Subcellular localization and incorporation of these fusion proteins into EVs was assessed by western-blot and fluorescence microscopy. EV binding and uptake was measured using either a classical Renilla substrate or a cytopermeable one. Incubation of target cells expressing DSP2 with EVs containing the complementary DSP1 portion could not recover fluorescence or luciferase activity. However, using EVs carrying the fully reconstituted Dual-EGFP-Renilla protein and the cytopermeable Renilla luciferase substrate, we could distinguish EV binding from uptake. We provide proof of concept of the system by analysing the effect of different chemical inhibitors, demonstrating that this method is highly sensitive and quantitative, allowing a dynamic follow-up in a high-throughput scheme to unravel the molecular mechanisms of EV uptake in different biological systems.
Canine osteosarcoma genome sequencing identifies recurrent mutations in DMD and the histone methyltransferase gene SETD2
Authors: Gardner Heather L. , Sivaprakasam Karthigayini , Briones Natalia , Zismann Victoria , Perdigones Nieves , Drenner Kevin , Facista Salvatore , Richholt Ryan , Liang Winnie , Aldrich Jessica , Trent Jeffrey M. , Shields Peter G. , Robinson Nicholas , Johnson Jeremy , Lana Susan , Houghton Peter , Fenger Joelle , Lorch Gwendolen , Janeway Katherine A. , London Cheryl A. , Hendricks William P. D. 
Published: July 2019

AbstractOsteosarcoma (OS) is a rare, metastatic, human adolescent cancer that also occurs in pet dogs. To define the genomic underpinnings of canine OS, we performed multi-platform analysis of OS tumors from 59 dogs, including whole genome sequencing (n = 24) and whole exome sequencing (WES;n = 13) of primary tumors and matched normal tissue, WES (n = 10) of matched primary/metastatic/normal samples and RNA sequencing (n = 54) of primary tumors. We found that canine OS recapitulates features of human OS including low point mutation burden (median 1.98 per Mb) with a trend towards higher burden in metastases, high structural complexity, frequentTP53(71%), PI3K pathway (37%), and MAPK pathway mutations (17%), and low expression of immune-associated genes. We also identified novel features of canine OS including putatively inactivating somaticSETD2(42%) andDMD(50%) aberrations. These findings set the stage for understanding OS development in dogs and humans, and establish genomic contexts for future comparative analyses.
Sending messages in moving cells: mRNA localization and the regulation of cell migration
Authors: Herbert Shane P. , Costa Guilherme 
Published: July 2019

Abstract
Cell migration is a fundamental biological process involved in tissue formation and homeostasis. The correct polarization of motile cells is critical to ensure directed movement, and is orchestrated by many intrinsic and extrinsic factors. Of these, the subcellular distribution of mRNAs and the consequent spatial control of translation are key modulators of cell polarity. mRNA transport is dependent on cis-regulatory elements within transcripts, which are recognized by trans-acting proteins that ensure the efficient delivery of certain messages to the leading edge of migrating cells. At their destination, translation of localized mRNAs then participates in regional cellular responses underlying cell motility. In this review, we summarize the key findings that established mRNA targetting as a critical driver of cell migration and how the characterization of polarized mRNAs in motile cells has been expanded from just a few species to hundreds of transcripts. We also describe the molecular control of mRNA trafficking, subsequent mechanisms of local protein synthesis and how these ultimately regulate cell polarity during migration.
The commodification of TEFL in the context of tourism.
Authors: Stainton H. 
Published: July 2019

Abstract

This chapter examines the progressive changes seen within the industry of teaching English as a foreign language (TEFL) and the way in which commercial, public and NGO bodies operate within it. It is indicated that while the ideals of TEFL may lie in the likes of philanthropy and community development, this is now being replaced by profit-orientated and hedonistic motivations. Also discussed is the application of the four Ps of marketing in TEFL tourism marketing.
Introduction.
Authors: Vidal-Casellas D. , Aulet S. , Crous-Costa N. 
Published: July 2019

Abstract

This chapter recognizes tourism, and particularly religious tourism, as a form of intercultural interaction. It also offers background discussion on (i) pilgrims and religious tourists and their motivations and expectations, (ii) secularization and the loss of the notion of 'sacred'; and (iii) the role of interpretation in religious tourism.
Religious tourism, pilgrimage: manifestation of peace and enlightenment in contemporary religions with special reference to Islam.
Authors: Elhadary T. 
Published: July 2019

Abstract

This chapter claims that religious tourism or pilgrimage not only has the common advantages of tourism in general but also leads to enlightenment and peace. Focusing on the annual Islamic pilgrimage of the Hajj, the chapter explores the impact of pilgrimage on people's lives in general and Muslim lives in particular.
Pilgrimage tourism and social media: A way forward in the 21st century?
Authors: Paschinger E. 
Published: July 2019

Abstract

This chapter reveals a shift in the demand characteristics for religious/pilgrimage tourism with the advent of the "experience economy" and the proliferation of social media. The management implications of the advent of social media for religious/pilgrimage tourism are also discussed, including the use of social media marketing in the context of pilgrimage tourism development. A case study is presented of the 'Peregrino Lebaniego Digital', a project that digitalizes a part of the Way of Saint James.
Taking part in a pilgrimage by hosting pilgrims.
Authors: Ambrósio V. 
Published: July 2019

Abstract

This chapter's focus is on accommodation provided by local people without charge or for a small amount of money and how it contributes to the strengthening of the pilgrimage spirit and success. Examining three pilgrimages in Portugal, the research supports the idea that the locals who host pilgrims believe that they live the pilgrimage without walking the road and each one of them feels that they are taking part in the pilgrimage. On the other side, pilgrims feel that they are spreading the pilgrimage spirit along the way mainly when they have personal contact with locals and spend the night in their houses or in the lodgings they provide.
North Atlantic right whale (Eubalaena glacialis) and its food: (II) interannual variations in biomass of Calanus spp. on western North Atlantic shelves
Authors: Sorochan Kevin A , Plourde StÉphane , Morse Ryan , Pepin Pierre , Runge Jeffrey , Thompson Cameron , Johnson Catherine L 
Published: July 2019

AbstractThe North Atlantic right whale (NARW), Eubalaena glacialis, feeds on zooplankton, particularly copepods of the genus Calanus. We quantified interannual variation in anomalies of abundance and biomass of Calanus spp. and near-surface and near-bottom ocean temperature and salinity from 19 subregions spanning the Gulf of Maine–Georges Bank (GoM–GBK), Scotian Shelf (SS), Gulf of St. Lawrence (GSL) and Newfoundland and Labrador Shelves. We analyzed time series from 1977 to 2016 in GoM–GBK, 1982 to 2016 in southwest GSL and 1999 to 2016 in remaining areas. Calanus finmarchicus dominated abundance and biomass, except in the GSL where Calanus hyperboreus was abundant. The biomass of Calanus spp. declined in many subregions over years 1999–2016 and was negatively correlated with sea surface temperature in GoM–GBK and on the SS. We detected ``regime shifts” to lower biomass of Calanus spp. in the GoM–GBK in 2010 and on the SS in 2011. In the GoM–GBK, shifts to lower biomass of C. finmarchicus coincided with shifts to warmer ocean temperature and with published reports of changes in spatial distribution and reduced calving rate of NARW. We hypothesize that warming has negatively impacted population levels of Calanus spp. near their southern range limit, reducing the availability of prey to NARW.
ORANGE: A CRISPR/Cas9-based genome editing toolbox for epitope tagging of endogenous proteins in neurons
Authors: Willems Jelmer , de Jong Arthur P.H. , Scheefhals Nicky , MacGillavry Harold D. 
Published: July 2019

ABSTRACTThe correct subcellular distribution of protein complexes establishes the complex morphology of neurons and is fundamental to their functioning. Thus, determining the dynamic distribution of proteins is essential to understand neuronal processes. Fluorescence imaging, in particular super-resolution microscopy, has become invaluable to investigate subcellular protein distribution. However, these approaches suffer from the limited ability to efficiently and reliably label endogenous proteins. We developed ORANGE: an Open Resource for the Application of Neuronal Genome Editing, that mediates targeted genomic integration of fluorescent tags in neurons. This toolbox includes a knock-in library for in-depth investigation of endogenous protein distribution, and a detailed protocol explaining how knock-in can be developed for novel targets. In combination with super-resolution microscopy, ORANGE revealed the dynamic nanoscale organization of endogenous neuronal signaling molecules, synaptic scaffolding proteins, and neurotransmitter receptors. Thus, ORANGE enables quantitation of expression and distribution for virtually any protein in neurons at high resolution and will significantly further our understanding of neuronal cell biology.
Concurrent lipidomics and proteomics on malignant plasma cells from multiple myeloma patients: Probing the lipid metabolome
Authors: Mohamed Ahmed , Collins Joel , Jiang Hui , Molendijk Jeffrey , Stoll Thomas , Torta Federico , Wenk Markus R , Bird Robert J , Marlton Paula , Mollee Peter , Markey Kate A , Hill Michelle M 
Published: July 2019

AbstractBackgroundMultiple myeloma (MM) is a hematological malignancy characterized by the clonal expansion of malignant plasma cells. Though durable remissions are possible, MM is considered incurable, with relapse occurring in almost all patients. There has been limited data reported on the lipid metabolism changes in plasma cells during MM progression. Here, we evaluated the feasibility of concurrent lipidomics and proteomics analyses from patient plasma cells, and report these data on a limited number of patient samples, demonstrating the feasibility of the method, and establishing hypotheses to be evaluated in the future.MethodsPlasma cells were purified from fresh bone marrow aspirates using CD138 microbeads. Proteins and lipids were extracted using a bi-phasic solvent system with methanol, methyl tert-butyl ether, and water. Untargeted proteomics, untargeted and targeted lipidomics were performed on 7 patient samples using liquid chromatography-mass spectrometry. Two comparisons were conducted: high versus low risk; relapse versus newly diagnosed. Proteins and pathways enriched in the relapsed group was compared to a public transcriptomic dataset from Multiple Myeloma Research Consortium reference collection (n=222) at gene and pathways level.ResultsFrom one million purified plasma cells, we were able to extract material and complete untargeted (∼6000 and ∼3600 features in positive and negative mode respectively) and targeted lipidomics (313 lipids), as well as untargeted proteomics analysis (∼4100 reviewed proteins). Comparative analyses revealed limited differences between high and low risk groups (according to the standard clinical criteria), hence we focused on drawing comparisons between the relapsed and newly diagnosed patients. Untargeted and targeted lipidomics indicated significant down-regulation of phosphatidylcholines (PCs) in relapsed MM. Although there was limited overlap of the differential proteins/transcripts, 76 significantly enriched pathways in relapsed MM were common between proteomics and transcriptomics data. Further evaluation of transcriptomics data for lipid metabolism network revealed enriched correlation of PC, ceramide, cardiolipin, arachidonic acid and cholesterol metabolism pathways to be exclusively correlated among relapsed but not in newly-diagnosed patients.ConclusionsThis study establishes the feasibility and workflow to conduct integrated lipidomics and proteomics analyses on patient-derived plasma cells. Potential lipid metabolism changes associated with MM relapse warrant further investigation.
The laboratory domestication of zebrafish: from diverse populations to inbred substrains
Authors: Suurväli Jaanus , Whiteley Andrew R , Zheng Yichen , Gharbi Karim , Leptin Maria , Wiehe Thomas 
Published: July 2019

AbstractThe zebrafish (Danio rerio) is a model vertebrate widely used to study disease, development and other aspects of vertebrate biology. Most of the research is performed on laboratory strains, one of which has been fully sequenced in order to derive a reference genome. It is known that the laboratory strains differ genetically from each other, but so far no genome-scale survey of variation between the laboratory and wild zebrafish populations exists.Here we use Restriction-Associated DNA sequencing (RAD-seq) to characterize three different wild zebrafish lineages from a population genetic viewpoint, and to compare them to four common laboratory strains. For this purpose we combine new genome-wide sequence data obtained from natural samples in India, Nepal and Bangladesh with a previously published dataset. We measured nucleotide diversity, heterozygosity, allele frequency spectra and patterns of gene conversion, and find that wild fish are much more diverse than laboratory strains. Further, in wild zebrafish there is a clear signal of GC-biased gene conversion that is missing in laboratory strains. We also find that zebrafish populations in Nepal and Bangladesh are distinct from all the other strains studied, making them an attractive subject for future studies of zebrafish population genetics and molecular ecology. Finally, isolates of the same strains kept in different laboratories show a clear pattern of ongoing differentiation into genetically distinct substrains. Together, our findings broaden the basis for future genetic and evolutionary studies inDanio rerio.