cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5135536.v1
title: Insights into unbound–bound states of GPR142 receptor in a membrane-aqueous system using molecular dynamics simulations

description: G protein coupled receptors (GPCRs) are source machinery in signal transduction pathways and being one of the major therapeutic targets play a significant in drug discovery. GPR142, an orphan GPCR, has been implicated in the regulation of insulin, thereby having a crucial role in Type II diabetes management. Deciphering of the structures of orphan, GPCRs (O-GPCRs) offer better prospects for advancements in research in ion translocation and transduction of extracellular signals. As the crystallographic structure of GPR142 is not available in PDB, therefore, threading and <i>ab initio</i>-based approaches were used for 3D modeling of GPR142. Molecular dynamic simulations (900 ns) were performed on the 3D model of GPR142 and complexes of GPR142 with top five hits, obtained through virtual screening, embedded in lipid bilayer with aqueous system using OPLS force field. Compound 1, 3, and 4 may act as scaffolds for designing potential lead agonists for GPR142. The finding of GPR142 MD simulation study provides more comprehensive representation of the functional properties. The concern for Type II diabetes is increasing worldwide and successful treatment of this disease demands novel drugs with better efficacy.
DOI: 10.6084/m9.figshare.5135404
title: Encounter histories.txt

description: This file contains the capture-recapture encounter histories of the White-lined Tanager <i>Tachyphonus rufus</i>, a Neotropical passerine bird. It follows a robust design structure and presents 32 occasions (four occasions x eight primary sessions). With this data set is possible to create and reproduce all design models contained in our article. <br><sup></sup>
DOI: 10.6084/m9.figshare.5135392
title: KOWALSKI Apache Lucene call graph Neo4j database

description: Neo4j database of Apache Lucene clients and call graphs to Lucene.
DOI: 10.6084/m9.figshare.5135404.v1
title: Encounter histories.txt

description: This file contains the capture-recapture encounter histories of the White-lined Tanager <i>Tachyphonus rufus</i>, a Neotropical passerine bird. It follows a robust design structure and presents 32 occasions (four occasions x eight primary sessions). With this data set is possible to create and reproduce all design models contained in our article. <br><sup></sup>
DOI: 10.6084/m9.figshare.5135392.v1
title: KOWALSKI Apache Lucene call graph Neo4j database

description: Neo4j database of Apache Lucene clients and call graphs to Lucene.
DOI: 10.6084/m9.figshare.5135314
title: Supplementary Material for: Prenatal Diagnosis of Dextrocardia with Complex Congenital Heart Disease Using Fetal Intelligent Navigation Echocardiography (FINE) and a Literature Review

description: Fetal dextrocardia is a type of cardiac malposition where the major axis from base to apex points to the right side. This condition is usually associated with a wide spectrum of complex cardiac defects. As a result, dextrocardia is conceptually difficult to understand and diagnose on prenatal ultrasound. The advantage of four-dimensional sonography with spatiotemporal image correlation (STIC) is that this modality can facilitate fetal cardiac examination. A novel method known as fetal intelligent navigation echocardiography (FINE) allows automatic generation of nine standard fetal echocardiography views in normal hearts by applying intelligent navigation technology to STIC volume datasets. In fetuses with congenital heart disease, FINE is also able to demonstrate abnormal cardiac anatomy and relationships when there is normal cardiac axis and position. However, this technology has never been applied to cases of cardiac malposition. We report herein for the first time, a case of fetal dextrocardia and situs solitus with complex congenital heart disease in which the FINE method was invaluable in diagnosing multiple abnormalities and defining complex anatomic relationships. We also review the literature on prenatal sonographic diagnosis of dextrocardia (with an emphasis on situs solitus), as well as tricuspid atresia with its associated cardiac features.
DOI: 10.6084/m9.figshare.5135242
title: Supplementary Material for: Generation of a DNA-Launched Reporter Replicon Based on Dengue Virus Type 2 as a Multipurpose Platform

description: Dengue viruses (DENV) have become the most important arthropod-borne viruses, causing dengue and severe dengue fever in at least 50-100 million cases each year, mainly in tropical and subtropical countries. During recent years, important advances in the molecular biology concerning the life cycle of these viruses have allowed the manipulation and generation of recombinant viruses and replicons with multiple applications, mainly in viral biology and the screening of antiviral compounds. In the present study, we describe the construction of an enhanced green fluorescent protein-bearing DENV replicon under the control of the cytomegalovirus immediate early promoter. Following a rational in silico design and cloning by standard molecular biology techniques, a reporter DENV-2 replicon and a replication-deficient mutant were constructed, and characterized by confocal microscopy and real-time RT-PCR. The results showed successful transcription, translation, and autonomous viral RNA replication of the DENV replicon from its DNA clone. This novel DENV replicon will allow the study of viral replication and testing of antiviral candidates without the need for in vitro transcription.
DOI: 10.6084/m9.figshare.5135257
title: Grayling draft genome dataset

description: ###### Description<br><br>Tthymallus_scaffolds.fasta - Assembled scaffold sequences<br>Tthymallus_RepeatLibrary_deNovo.fasta - De novo repeat library sequences<br>Tthymallus_transcriptome_DeNovo.fasta - De novo transcriptome assembly using Trinity (followed by RSEM based filtering)<br>Tthymallus_transcriptome_ReferenceBased.fasta - Reference-based transcriptome using STAR-Cufflinks-transdecoder pipeline (followed by filtering based on homology to known proteins from zebrafish and stickleback proteins.<br>Tthymallus_ScaffoldAnnotation.gff3 - MAKER pipeline based annotation for the scaffolds.<br>Tthymallus_proteins.fasta - Grayling protein sequences used for inferring orthologous groups (based on MAKER annotations)<br>Tthymallus_maker_fullOutput.gff - Full output from MAKER<br>Tthymallus_CPMcounts.txt - Expression counts for grayling<br>OrthologousGroups.txt - Inferred orthologous groups using Orthofinder<br><br><br>
DOI: 10.6084/m9.figshare.5135188
title: q_funcs.npy from A methodology to assess the economic impact of power storage technologies

description: We present a methodology for assessing the economic impact of power storage technologies. The methodology is founded on classical approaches to the optimal stopping of stochastic processes but involves an innovation that circumvents the need to, ex ante, identify the form of a driving process and works directly on observed data, avoiding model risks. Power storage is regarded as a complement to the intermittent output of renewable energy generators and is therefore important in contributing to the reduction of carbon-intensive power generation. Our aim is to present a methodology suitable for use by policy makers that is simple to maintain, adaptable to different technologies and easy to interpret. The methodology has benefits over current techniques and is able to value, by identifying a viable optimal operational strategy, a conceived storage facility based on compressed air technology operating in the UK.
DOI: 10.6084/m9.figshare.5135185
title: Comparison of optimal and candidate solutions from A methodology to assess the economic impact of power storage technologies

description: Details of the NPV generated by implementing the candidate strategy
DOI: 10.6084/m9.figshare.5135185.v1
title: Comparison of optimal and candidate solutions from A methodology to assess the economic impact of power storage technologies

description: Details of the NPV generated by implementing the candidate strategy
DOI: 10.6084/m9.figshare.5135188.v1
title: q_funcs.npy from A methodology to assess the economic impact of power storage technologies

description: We present a methodology for assessing the economic impact of power storage technologies. The methodology is founded on classical approaches to the optimal stopping of stochastic processes but involves an innovation that circumvents the need to, ex ante, identify the form of a driving process and works directly on observed data, avoiding model risks. Power storage is regarded as a complement to the intermittent output of renewable energy generators and is therefore important in contributing to the reduction of carbon-intensive power generation. Our aim is to present a methodology suitable for use by policy makers that is simple to maintain, adaptable to different technologies and easy to interpret. The methodology has benefits over current techniques and is able to value, by identifying a viable optimal operational strategy, a conceived storage facility based on compressed air technology operating in the UK.
DOI: 10.6084/m9.figshare.5135173
title: Appendix of mathematical details from A methodology to assess the economic impact of power storage technologies

description: Appendix of mathematical details
DOI: 10.6084/m9.figshare.5135164
title: Construction of F, phi and psi from A methodology to assess the economic impact of power storage technologies

description: Details of functional parameters, Figures 1 and 2
DOI: 10.6084/m9.figshare.5135173.v1
title: Appendix of mathematical details from A methodology to assess the economic impact of power storage technologies

description: Appendix of mathematical details
DOI: 10.6084/m9.figshare.5135164.v1
title: Construction of F, phi and psi from A methodology to assess the economic impact of power storage technologies

description: Details of functional parameters, Figures 1 and 2
DOI: 10.6084/m9.figshare.5135113
title: Panax plastid genome matrix

description: Full plastid alignment of 61 Araliaceae plastid genomes. <br><br>Plastome phylogenomics resolves relationships in Panax and identifies markers for molecular identification<br><br>Manzanilla V.1, Kool A. 1, Nguyen Nhat L. 2, Nong Van H. 2, Le Thi Thu H.2§, de Boer H.J.1§<br><br>1. The Natural History Museum, University of Oslo, Oslo, Norway<br>2. Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam<br>§ These authors are co-last authors.<br><br>Abstract<br>The economic value of ginseng in the global medicinal plant trade is estimated to be in excess of US$2.1 billion. At the same time the evolutionary placement of ginseng (Panax ginseng) and the complex evolutionary history of the genus is poorly understood despite several molecular phylogenetic studies. In this study we use a full plastome phylogenomic framework to resolve relationships among Panax genus and to identify molecular markers for species discrimination. We used high-throughput sequencing of MBD2-Fc fractionated Panax DNA to supplement publicly available plastid genomes to create a phylogeny based on fully assembled and annotated plastid genomes from 60 accessions of 8 species. The plastome phylogeny is based on a 163 kbp matrix and resolves the sister relationship of Panax ginseng with P. quinquefolius. The closely related species, P. vietnamensis, described in 1985, is supported as the sister of P. japonicus. The plastome matrix also shows that the markers trnC-rps16, trnS-trnG, and trnE-trnM could be used for unambiguous molecular identification of all the represented species in the genus. MBD2 depletion reduces the cost of plastome sequencing, which makes it a cost-effective alternative to Sanger sequencing based DNA barcoding for molecular identification. The plastome phylogeny provides a robust framework that can be used to study the evolution of morphological characters and biosynthesis pathways of ginsengosides for phylogenetic bioprospecting. Molecular identification of ginseng species is essential for authenticating ginseng in international trade and provides an incentive for manufacturers to create authentic products with verified ingredients.<br>
DOI: 10.6084/m9.figshare.5135092
title: Supplementary Material for: Factor Analysis and Psychometric Properties of the Minnesota Nicotine Withdrawal Scale and the Minnesota Nicotine Withdrawal Scale-Revised: Italian Version

description: <b><i>Background/Aims:</i></b> We run<b> </b>Exploratory and Confirmatory Factor Analyses of the Minnesota Nicotine Withdrawal Scale (MNWS) and of the MNWS-Revised (MNWS-R). Psychometric properties were also explored. <b><i>Methods:</i></b> Adult Italian smokers, 366 in all, were assessed via the MNWS-R together with rating scales measuring cigarette dependence, alcohol use, anxiety sensitivity and negative affect at baseline and after 3 months. <b><i>Results:</i></b> The MNWS showed good psychometric properties (α = 0.85; rtt = 0.59) and a unidimensional factor structure. The 2-factor model of MNWS-R had the best fit and the factors were labelled psychological symptoms (α = 0.86; rtt = 0.59) and associated somatic features (α = 0.64; rtt = 0.45). <b><i>Conclusions:</i></b> MNWS showed 1 factor; MNWS-R showed 2 relatively dependent factors. The results need to be replicated in smokers in withdrawal.
DOI: 10.6084/m9.figshare.5135101
title: Raw data from "A Deterministic Approach to Locating Series Flow-Controllers Within Transmission Systems to Alleviate Congestion"

description: Some raw data for this paper which is still under review. All very rough and ready here I'm afraid, but messy public data is better than no data!<br><br>Dr. Andrew Keane was my colloborator on this work.<br>
DOI: 10.6084/m9.figshare.5135113.v1
title: Panax plastid genome matrix

description: Full plastid alignment of 61 Araliaceae plastid genomes. <br><br>Plastome phylogenomics resolves relationships in Panax and identifies markers for molecular identification<br><br>Manzanilla V.1, Kool A. 1, Nguyen Nhat L. 2, Nong Van H. 2, Le Thi Thu H.2§, de Boer H.J.1§<br><br>1. The Natural History Museum, University of Oslo, Oslo, Norway<br>2. Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam<br>§ These authors are co-last authors.<br><br>Abstract<br>The economic value of ginseng in the global medicinal plant trade is estimated to be in excess of US$2.1 billion. At the same time the evolutionary placement of ginseng (Panax ginseng) and the complex evolutionary history of the genus is poorly understood despite several molecular phylogenetic studies. In this study we use a full plastome phylogenomic framework to resolve relationships among Panax genus and to identify molecular markers for species discrimination. We used high-throughput sequencing of MBD2-Fc fractionated Panax DNA to supplement publicly available plastid genomes to create a phylogeny based on fully assembled and annotated plastid genomes from 60 accessions of 8 species. The plastome phylogeny is based on a 163 kbp matrix and resolves the sister relationship of Panax ginseng with P. quinquefolius. The closely related species, P. vietnamensis, described in 1985, is supported as the sister of P. japonicus. The plastome matrix also shows that the markers trnC-rps16, trnS-trnG, and trnE-trnM could be used for unambiguous molecular identification of all the represented species in the genus. MBD2 depletion reduces the cost of plastome sequencing, which makes it a cost-effective alternative to Sanger sequencing based DNA barcoding for molecular identification. The plastome phylogeny provides a robust framework that can be used to study the evolution of morphological characters and biosynthesis pathways of ginsengosides for phylogenetic bioprospecting. Molecular identification of ginseng species is essential for authenticating ginseng in international trade and provides an incentive for manufacturers to create authentic products with verified ingredients.<br>
DOI: 10.6084/m9.figshare.5135083
title: A.LAMBERT - Data - Pericardial effusion with Bleomycin.xlsx

description: Overall survival since intrapericardial instillation of 60mg of Bleomycin among patient with malignant pericardial effusion.
DOI: 10.6084/m9.figshare.5135089
title: Public documents regarding The Svendborgproject - Implementing three times more physical education in primary schools

description: This is a compilation of public documents from the Svendborgproject. The documents contain descriptions on the implementation of more PE in the schools of the municipality of Svendborg, Denmark. All documents has been published on the official website of the municipality of Svendborg. The project coordinators are informed that the documents are compiled and shared through this link.
DOI: 10.6084/m9.figshare.5135101.v1
title: Raw data from "A Deterministic Approach to Locating Series Flow-Controllers Within Transmission Systems to Alleviate Congestion"

description: Some raw data for this paper which is still under review. All very rough and ready here I'm afraid, but messy public data is better than no data!<br><br>Dr. Andrew Keane was my colloborator on this work.<br>
DOI: 10.6084/m9.figshare.5135083.v2
title: A.LAMBERT - Data - Pericardial effusion with Bleomycin.xlsx

description: Overall survival since intrapericardial instillation of 60mg of Bleomycin among patient with malignant pericardial effusion.
DOI: 10.6084/m9.figshare.5135083.v1
title: A.LAMBERT - Data - Pericardial effusion with Bleomycin.xlsx

description: Overall survival since intrapericardial instillation of 60mg of Bleomycin among patient with malignant pericardial effusion.
DOI: 10.6084/m9.figshare.5135056
title: Supporting information.xlsx

description: We exploit ePGA, a web-based electronic Pharmacogenomics Assistant and publicly available genetic data from the 1000 Genomes Project to explore genotype to phenotype associations among the 1000 Genomes Project populations
DOI: 10.6084/m9.figshare.5135035
title: Metabolite BridgeDb ID Mapping Database (20170621)

description: BridgeDb ID mapping database for metabolites, using HMDB 3.6, ChEBI 152, and Wikidata (21 June 2017) as data sources. No significant changes, and just updated mappings. See the attached QC for more details on the changes.
DOI: 10.6084/m9.figshare.5135053
title: Supplementary Material for: Role of Glycyrrhizin in the Reduction of Inflammation in Diabetic Kidney Disease

description: <b><i>Background:</i></b> Diabetic kidney disease (DKD) is one of the most debilitating complications of type 2 diabetes. Recent evidence suggests chronic inflammation to be one of the causal factors of DKD. The mechanisms entailed are not completely elucidated except that a variety of cytokines play a major role in this process. High mobility group box 1 (HMGB1) is a pro-inflammatory toll-like receptor-4 (TLR4)-binding cytokine that is involved in inflammation-associated gene expression. This investigation was designed to assess the involvement of HMGB1, TLR-4, and nuclear factor (NF)-κB in the development of DKD and to evaluate that whether blocking HMGB1 by its natural inhibitor Glycyrrhizin (GLC) can reduce the progression of the disease. <b><i>Methods:</i></b> Studies were carried out in 8-10-weeks old Zucker diabetic fatty (ZDF) and lean, age- and gender-matched rats. At 10 weeks of age, ZDF rats as compared to controls, showed hyperglycemia, without proteinuria. After 8-10 weeks of the development of diabetes, ZDF animals that showed proteinuria were treated with GLC for 4 weeks. In addition, normal rat kidney (NRK-52E) cells with epithelial-like morphology were comparatively treated with GLC under hyperglycemic condition in vitro. <b><i>Results:</i></b> Substantial increase in the expression of HMGB1, TLR4, and NF-κB in vivo and in vitro under hyperglycemic conditions was observed as compared to normoglycemic conditions. The overexpression of HMGB1, TLR4, NF-κB, and glomerular injury marker nestin was significantly ameliorated by GLC administration. <b><i>Conclusion:</i></b> Our findings suggest that hyperglycemia-induced HMGB1 activation in ZDF rats may contribute to the progression of DKD.
DOI: 10.6084/m9.figshare.5135056.v1
title: Supporting information.xlsx

description: We exploit ePGA, a web-based electronic Pharmacogenomics Assistant and publicly available genetic data from the 1000 Genomes Project to explore genotype to phenotype associations among the 1000 Genomes Project populations
DOI: 10.6084/m9.figshare.5135086
title: Data used in "Turbulent mixing within the Kuroshio in the Tokara Strait"

description: Data from "Turbulent mixing within the Kuroshio in the Tokara Strait" by E. Tsutsumi, T. Matsuno, R.-C. Lien, H. Nakamura, T. Senjyu, and X. Guo,, J. Geophys. Res. Oceans, 122, 7082-7094, doi:10.1002/2017JC013049.
DOI: 10.6084/m9.figshare.5135011
title: a cross-sectional survey among 1,616 Vietnamese high school students

description: This dataset contains data about 1,616 high school students who participated in a survey in Hanoi, Vietnam in 2012-13. The data provides important information about the participants' demographic characteristics, academic perspectives, family characteristics, experiences of poly-victimisation, involvement in health risk behaviours, suicidal behaviours, mental health symptoms and quality of life.
DOI: 10.6084/m9.figshare.5135035.v2
title: Metabolite BridgeDb ID Mapping Database (20170621)

description: BridgeDb ID mapping database for metabolites, using HMDB 3.6, ChEBI 152, and Wikidata (21 June 2017) as data sources. No significant changes, and just updated mappings. See the attached QC for more details on the changes.
DOI: 10.6084/m9.figshare.5135053.v2
title: Supplementary Material for: Role of Glycyrrhizin in the Reduction of Inflammation in Diabetic Kidney Disease

description: <b><i>Background:</i></b> Diabetic kidney disease (DKD) is one of the most debilitating complications of type 2 diabetes. Recent evidence suggests chronic inflammation to be one of the causal factors of DKD. The mechanisms entailed are not completely elucidated except that a variety of cytokines play a major role in this process. High mobility group box 1 (HMGB1) is a pro-inflammatory toll-like receptor-4 (TLR4)-binding cytokine that is involved in inflammation-associated gene expression. This investigation was designed to assess the involvement of HMGB1, TLR-4, and nuclear factor (NF)-κB in the development of DKD and to evaluate that whether blocking HMGB1 by its natural inhibitor Glycyrrhizin (GLC) can reduce the progression of the disease. <b><i>Methods:</i></b> Studies were carried out in 8-10-weeks old Zucker diabetic fatty (ZDF) and lean, age- and gender-matched rats. At 10 weeks of age, ZDF rats as compared to controls, showed hyperglycemia, without proteinuria. After 8-10 weeks of the development of diabetes, ZDF animals that showed proteinuria were treated with GLC for 4 weeks. In addition, normal rat kidney (NRK-52E) cells with epithelial-like morphology were comparatively treated with GLC under hyperglycemic condition in vitro. <b><i>Results:</i></b> Substantial increase in the expression of HMGB1, TLR4, and NF-κB in vivo and in vitro under hyperglycemic conditions was observed as compared to normoglycemic conditions. The overexpression of HMGB1, TLR4, NF-κB, and glomerular injury marker nestin was significantly ameliorated by GLC administration. <b><i>Conclusion:</i></b> Our findings suggest that hyperglycemia-induced HMGB1 activation in ZDF rats may contribute to the progression of DKD.
DOI: 10.6084/m9.figshare.5135035.v1
title: Metabolite BridgeDb ID Mapping Database (20170621)

description: BridgeDb ID mapping database for metabolites, using HMDB 3.6, ChEBI 152, and Wikidata (21 June 2017) as data sources. No significant changes, and just updated mappings. See the attached QC for more details on the changes.