cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5008373.v1
title: Multiple viral infections in primary effusion lymphoma: a model of viral cooperation in lymphomagenesis

description: <b>Introduction</b>: Primary effusion lymphoma (PEL) is a rare B-cell lymphoid neoplasm mainly associated with HIV infection, presenting as pleural, peritoneal, and pericardial effusions. A defining property of PEL is its consistent association with Kaposi sarcoma associated herpesvirus (KSHV) infection, and, in most cases, Epstein Barr virus (EBV) co-infection. On these grounds, a review of the literature related to viral cooperation and lymphomagenesis can help to understand the complex interplay between KSHV and EBV in PEL pathogenesis. <b>Areas covered</b>: In this review, the authors highlight clinical, pathologic, genetic and proteomic features of PEL, in the context of viral cooperation in PEL lymphomagenesis. <b>Expert commentary</b>: Tumour cells are characterized by the overexpression of genes that are involved in inflammation and invasion. Coherently, PEL secretomes are enriched in proteins probably responsible for the particular tropism (cell adhesion and migration) of PEL cells. The development of PEL in HIV+ patients is multifactorial and involves a complex interplay among co-infection with oncogenic viruses (EBV and KSHV), inflammatory factors, and environmental conditions.
DOI: 10.6084/m9.figshare.5008364
title: The response of wildtype and mutant cultivars of soybean to salt stress - comparing vegetative and reproductive phases on the basis of leaf biochemical contents, RWC, and stomatal conductance

description: Soybean, as a major oilseed crop, is cultivated in many parts of the world including saline-affected regions. A four-replicated factorial experiment based on a completely randomized design with five salinity levels (control, 50, 100, 150, and 200 mM NaCl) and five wild-type and new mutant cultivars of soybean (Williams, Clark, M-4, M-7, and M-9) was done at two vegetative and reproductive phases to study leaf oxidants, antioxidants and osmolytes under salinity stress. The vegetative phase demonstrated higher K<sup>+</sup>:Na<sup>+</sup> ratio, cell membrane stability, relative water content (RWC) and stomatal conductance to H<sub>2</sub>O (gs) accompanied with lower oxidative stress, antioxidants and osmolytes contrasting to reproductive phase. At both phenological phases, saline stress stimulated antioxidative defense owing to the enhancement of oxidative stress. The results indicated that mutants possessed a better antioxidative system than their wild-types.
DOI: 10.6084/m9.figshare.5008364.v1
title: The response of wildtype and mutant cultivars of soybean to salt stress - comparing vegetative and reproductive phases on the basis of leaf biochemical contents, RWC, and stomatal conductance

description: Soybean, as a major oilseed crop, is cultivated in many parts of the world including saline-affected regions. A four-replicated factorial experiment based on a completely randomized design with five salinity levels (control, 50, 100, 150, and 200 mM NaCl) and five wild-type and new mutant cultivars of soybean (Williams, Clark, M-4, M-7, and M-9) was done at two vegetative and reproductive phases to study leaf oxidants, antioxidants and osmolytes under salinity stress. The vegetative phase demonstrated higher K<sup>+</sup>:Na<sup>+</sup> ratio, cell membrane stability, relative water content (RWC) and stomatal conductance to H<sub>2</sub>O (gs) accompanied with lower oxidative stress, antioxidants and osmolytes contrasting to reproductive phase. At both phenological phases, saline stress stimulated antioxidative defense owing to the enhancement of oxidative stress. The results indicated that mutants possessed a better antioxidative system than their wild-types.
DOI: 10.6084/m9.figshare.5008325
title: Lipid Biomarkers and Their Stable Carbon Isotopes in Oxic and Anoxic Sediments of Lake Bled (NW Slovenia)

description: Sources of lipid biomarkers in two Lake Bled sediment cores deposited under oxic (Zaka Bay) and anoxic (WB) conditions were determined using stable carbon isotopes. Lipid biomarkers were of autochthonous origin mainly from planktonic and microbial sources. δ<sup>13</sup>C values for long-chain (LC) <i>n</i>-alkanes, short-chain (SC) and LC <i>n</i>-alcohols, SC <i>n</i>-fatty acids (FAs) were similar for both sediments, showing that identification of their sources was not related to different depositional regimes. A larger contribution of more refractory terrestrial organic matter (OM) was observed in δ<sup>13</sup>C values obtained from SC <i>n</i>-FAs in both environments and from SC <i>n</i>-alkanes in Zaka Bay. In contrast, the δ<sup>13</sup>C values observed in LC <i>n</i>-FAs, and especially in sterols, were lower in the WB than in Zaka Bay, indicating the pronounced contribution of an anaerobic, bacterial origin. Overall, the data indicated that the main source of lipids was autochthonous in both sediment environments including, LC <i>n</i>-alkanes, <i>n</i>-alcohols, <i>n</i>-FAs and C<sub>29</sub> sterols previously assigned to an allochthonous higher plant source. It further follows that isotope geochemistry gives an additional information for source assignment in aquatic systems.
DOI: 10.6084/m9.figshare.5008325.v1
title: Lipid Biomarkers and Their Stable Carbon Isotopes in Oxic and Anoxic Sediments of Lake Bled (NW Slovenia)

description: Sources of lipid biomarkers in two Lake Bled sediment cores deposited under oxic (Zaka Bay) and anoxic (WB) conditions were determined using stable carbon isotopes. Lipid biomarkers were of autochthonous origin mainly from planktonic and microbial sources. δ<sup>13</sup>C values for long-chain (LC) <i>n</i>-alkanes, short-chain (SC) and LC <i>n</i>-alcohols, SC <i>n</i>-fatty acids (FAs) were similar for both sediments, showing that identification of their sources was not related to different depositional regimes. A larger contribution of more refractory terrestrial organic matter (OM) was observed in δ<sup>13</sup>C values obtained from SC <i>n</i>-FAs in both environments and from SC <i>n</i>-alkanes in Zaka Bay. In contrast, the δ<sup>13</sup>C values observed in LC <i>n</i>-FAs, and especially in sterols, were lower in the WB than in Zaka Bay, indicating the pronounced contribution of an anaerobic, bacterial origin. Overall, the data indicated that the main source of lipids was autochthonous in both sediment environments including, LC <i>n</i>-alkanes, <i>n</i>-alcohols, <i>n</i>-FAs and C<sub>29</sub> sterols previously assigned to an allochthonous higher plant source. It further follows that isotope geochemistry gives an additional information for source assignment in aquatic systems.
DOI: 10.6084/m9.figshare.5008307
title: Supplementary Material for: Evaluating Weight Status and Sex as Moderators of the Association of Serum Leptin with Bone Mineral Density in Children and Adolescents

description: <i>Background/Aims:</i> Animal studies suggest that leptin may adversely affect bone mineral density (BMD). Clinical studies have yielded conflicting results. We therefore investigated associations between leptin and bone parameters in children. <i>Methods:</i> 830 healthy children (age = 11.4 ± 3.1 years; 75% female; BMI standard deviation score [BMIz] = 1.5 ± 1.1) had fasting serum leptin measured with ELISA and body composition by dual-energy X-ray absorptiometry. The main effects for leptin and BMIz plus leptin’s interactions with sex and BMIz were examined using hierarchical linear regressions for appendicular, pelvis, and lumbar spine BMD as well as bone mineral content (BMC), and bone area (BA). <i>Results:</i> Accounting for demographic, pubertal development, and anthropometric variables, leptin was negatively and independently associated with lumbar spine BMC and BA, pelvis BA, and leg BA (<i>p</i> &lt; 0.05 for all). Sex, but not BMIz, moderated the associations of leptin with bone parameters. In boys, leptin was negatively correlated with leg and arm BMD, BMC at all bone sites, and BA at the subtotal and lumbar spine (<i>p</i> &lt; 0.01 for all). In girls, leptin was positively correlated with leg and arm BMD (<i>p</i> &lt; 0.05 for both). <i>Conclusion:</i>Independent of body size, leptin is negatively associated with bone measures; however, these associations are moderated by sex: boys, but not girls, have a negative independent association between leptin and BMD.
DOI: 10.6084/m9.figshare.5008301
title: Recent progress in layered double hydroxides (LDH)-containing hybrids as adsorbents for water remediation

description: With rapidly growing industrial development worldwide, the need for a new class of nanoparticles and techniques for treating wastewater remains a major concern to protect the environment. Layered double hydroxides and particularly LDH-containing hybrids are emerging as potential nano-sized adsorbents for water treatment. Recent studies have demonstrated LDH-containing hybrids as promising multifunctional materials for potential utilization in various applications such as, photo-catalysis, energy storage, nanocomposites and water purification. This article reviews the recent applications of LDH-containing hybrids as adsorbents for waterremediation. The maximum adsorption capacities of various toxic heavy metals and dyes on different LDH hybrids were reported as 483 mg/g for Pb2+, 95 mg/g for Cd2+, 181 mg/g for Cu2+, 649 mg/g for Cr6+, 180 mg/g As5+, 813 mg/g for Hg2+, 450 for Ag+, 277 mg/g for U6+, 1062 mg/g for methyl orange, 185 mg/g for methylene blue, and 1250 mg/g for Congo red, which is comparatively higher than other commercial adsorbents. This review discusses the adsorption performance of manifold LDH-containing hybrids for treating various pollutants such as heavy metals and dyes. The mechanisms of interaction of LDH-containing hybrids with pollutants and the influence of key adsorption parameters such as pH, contact time, adsorbent dose andtemperature have been comprehensively discussed. Moreover, the regeneration potential and reuse of spentLDH-containing hybrids and its toxicity effects have also been reviewed.
DOI: 10.6084/m9.figshare.5008307.v1
title: Supplementary Material for: Evaluating Weight Status and Sex as Moderators of the Association of Serum Leptin with Bone Mineral Density in Children and Adolescents

description: <i>Background/Aims:</i> Animal studies suggest that leptin may adversely affect bone mineral density (BMD). Clinical studies have yielded conflicting results. We therefore investigated associations between leptin and bone parameters in children. <i>Methods:</i> 830 healthy children (age = 11.4 ± 3.1 years; 75% female; BMI standard deviation score [BMIz] = 1.5 ± 1.1) had fasting serum leptin measured with ELISA and body composition by dual-energy X-ray absorptiometry. The main effects for leptin and BMIz plus leptin’s interactions with sex and BMIz were examined using hierarchical linear regressions for appendicular, pelvis, and lumbar spine BMD as well as bone mineral content (BMC), and bone area (BA). <i>Results:</i> Accounting for demographic, pubertal development, and anthropometric variables, leptin was negatively and independently associated with lumbar spine BMC and BA, pelvis BA, and leg BA (<i>p</i> &lt; 0.05 for all). Sex, but not BMIz, moderated the associations of leptin with bone parameters. In boys, leptin was negatively correlated with leg and arm BMD, BMC at all bone sites, and BA at the subtotal and lumbar spine (<i>p</i> &lt; 0.01 for all). In girls, leptin was positively correlated with leg and arm BMD (<i>p</i> &lt; 0.05 for both). <i>Conclusion:</i>Independent of body size, leptin is negatively associated with bone measures; however, these associations are moderated by sex: boys, but not girls, have a negative independent association between leptin and BMD.
DOI: 10.6084/m9.figshare.5008283
title: White List Relations

description: It is a list of white list relations of dbpedia. It is based on page rank and manual intervention. <br>
DOI: 10.6084/m9.figshare.5008286
title: Seed Entities

description: This is the list of seed entities which were used for creating a QA dataset. These were obtained from Microsoft reading comphresion dataset (MSMacro) and WebQuestion Dataset. <br>
DOI: 10.6084/m9.figshare.5008289
title: nLDE SPARQL engine: computing diefficiency metrics based on answer traces and query processing performance benchmarking

description: Data to reproduce the results reported in the paper '''Diefficiency Metrics: Measuring the Continuous Efficiency of Query Processing Approaches'''<br>R package: https://github.com/maribelacosta/dief.git
DOI: 10.6084/m9.figshare.5008274
title: clim_rsv_Dadaab_month_up2.txt

description: Surveillance for viral respiratory illnesses, Respiratory syncytial virus (RSV) was implemented in Dadaab refugee camp in north eastern Kenya in 2007. Paediatric and adult patients who presented at a camp medical unit, and met the case definition for influenza-like illness (ILI) or severe acute respiratory infection (SARI), were enrolled into the laboratory-enhanced respiratory surveillance system and tested for all of the above disease after an informed consent form was completed by adults, older minors, and guardians of all minors &lt;15 years. The monthly counts of all RSV cases among children younger than 5 years were included in the present analysis; the main outcome of interest being monthly RSV incidence rate in this age group. Local weather and climatic data, including: the mean temperature and mean dew point for the day (both in <sup>0</sup>F); mean sea level pressure for the day in millibars; mean visibility for the day in miles; mean wind speed for the day in knots; minimum and maximum temperature (<sup>0</sup>F) reported during the day; and the total precipitation (in inches) reported during the day were obtained from the World Meteorological Organization’s (WMO’s), World Weather Watch Program, according to WMO Resolution 40 (Cg-XII) (available at http://www7.ncdc.noaa.gov/CDO/cdo).
DOI: 10.6084/m9.figshare.5008274.v1
title: clim_rsv_Dadaab_month_up2.txt

description: Surveillance for viral respiratory illnesses, Respiratory syncytial virus (RSV) was implemented in Dadaab refugee camp in north eastern Kenya in 2007. Paediatric and adult patients who presented at a camp medical unit, and met the case definition for influenza-like illness (ILI) or severe acute respiratory infection (SARI), were enrolled into the laboratory-enhanced respiratory surveillance system and tested for all of the above disease after an informed consent form was completed by adults, older minors, and guardians of all minors &lt;15 years. The monthly counts of all RSV cases among children younger than 5 years were included in the present analysis; the main outcome of interest being monthly RSV incidence rate in this age group. Local weather and climatic data, including: the mean temperature and mean dew point for the day (both in <sup>0</sup>F); mean sea level pressure for the day in millibars; mean visibility for the day in miles; mean wind speed for the day in knots; minimum and maximum temperature (<sup>0</sup>F) reported during the day; and the total precipitation (in inches) reported during the day were obtained from the World Meteorological Organization’s (WMO’s), World Weather Watch Program, according to WMO Resolution 40 (Cg-XII) (available at http://www7.ncdc.noaa.gov/CDO/cdo).
DOI: 10.6084/m9.figshare.5008289.v1
title: Diefficiency Metrics: Measuring the Continuous Efficiency of Query Processing Approaches

description: Data to reproduce the results reported in the paper '''Diefficiency Metrics: Measuring the Continuous Efficiency of Query Processing Approaches'''
DOI: 10.6084/m9.figshare.5008280.v1
title: suppl.zip

description: This is the supplemental material of the paper '<i>Evaluation of ten aerosol optical depth datasets over AERONET sites</i>'.<br><br>We select 400 AERONET sites, and use the in situ data to evaluate MODIS, MERRAero, and MERRA-2 AOD datasets. Inter-comparison among MODIS, MERRAero, and MERRA-2 is also conducted.<br><br>See the paper and ReadMe for details. <br>
DOI: 10.6084/m9.figshare.5008280.v2
title: Aerosol optical depth datasets over 400 AERONET sites

description: MODIS, MERRA, and <i>in-situ</i> AOD data extracted from 400 AERONET sites during 2002-2015. <br>
DOI: 10.6084/m9.figshare.5008289.v2
title: Diefficiency Metrics: Measuring the Continuous Efficiency of Query Processing Approaches

description: Data to reproduce the results reported in the paper '''Diefficiency Metrics: Measuring the Continuous Efficiency of Query Processing Approaches'''<br>R package: https://github.com/maribelacosta/dief.git
DOI: 10.6084/m9.figshare.5008289.v3
title: Diefficiency Metrics: Measuring the Continuous Efficiency of Query Processing Approaches

description: Data to reproduce the results reported in the paper '''Diefficiency Metrics: Measuring the Continuous Efficiency of Query Processing Approaches'''<br>R package: https://github.com/maribelacosta/dief.git
DOI: 10.6084/m9.figshare.5008280.v3
title: Aerosol optical depth datasets over 400 AERONET sites

description: MODIS, MERRA, and <i>in-situ</i> AOD data extracted from 400 AERONET sites during 2002-2015. The data here are from MODIS C6 and AERONET version 2.0, and the updated version (MODIS C6.1, AERONET version 3.0) is available upon request.<br>Please cite the following paper and the datasets if you use them.<br><br> Shi, H., Xiao, Z., Zhan, X., Ma, H., Tian, X., 2019. Evaluation of MODIS and two reanalysis aerosol optical depth products over AERONET sites. Atmos. Res. 220, 75–80. https://doi.org/10.1016/j.atmosres.2019.01.009<br>Shi, H., Xiao, Z., 2017. Aerosol optical depth datasets over 400 AERONET sites. <br>https://doi.org/10.6084/m9.figshare.5008280<br><br><br><br>
DOI: 10.6084/m9.figshare.5008289.v4
title: nLDE SPARQL engine: computing diefficiency metrics based on answer traces and query processing performance benchmarking

description: Data to reproduce the results reported in the paper '''Diefficiency Metrics: Measuring the Continuous Efficiency of Query Processing Approaches'''<br>R package: https://github.com/maribelacosta/dief.git
DOI: 10.6084/m9.figshare.5008289.v6
title: nLDE SPARQL engine: computing diefficiency metrics based on answer traces and query processing performance benchmarking

description: Data to reproduce the results reported in the paper '''Diefficiency Metrics: Measuring the Continuous Efficiency of Query Processing Approaches'''<br>R package: https://github.com/maribelacosta/dief.git
DOI: 10.6084/m9.figshare.5008289.v5
title: nLDE SPARQL engine: computing diefficiency metrics based on answer traces and query processing performance benchmarking

description: Data to reproduce the results reported in the paper '''Diefficiency Metrics: Measuring the Continuous Efficiency of Query Processing Approaches'''<br>R package: https://github.com/maribelacosta/dief.git
DOI: 10.6084/m9.figshare.5007992
title: Molecular Interaction Evidence Fragment Corpus

description: This file set showcases the first presentation of an annotated text corpus of 'evidence fragments' from biomedical papers. These are short passages of text from the results sections of papers that describe the goals, methods, results and interpretations of experiments that are reported as figures in biomedical articles. These figures typically provide the evidence and justification for any underlying scientific explanation or argument being explored in any given paper. Moreover, these fragments describe the specific findings of experimental studies and therefore comprise the 'raw material' of investigative scientific work. It is for that reason that we prioritize them within this corpus. <br><br>The file set should be considered as consisting of two parts: (1) a single archive of annotated text fragments forming the 'Molecular Interaction Evidence Fragment Corpus' (intact_evidence_fragment_corpus_07-25-17.tar.gz); and (2) other files provided for provenance and reproducibility. <br><br><b>The 'Molecular Interaction Evidence Fragment Corpus'<br></b><br>This gzipped tar archive forms the initial preparation of distant learning data corpus where we develop a method to link text to data. Here we use references to figure labels ('Fig 2a', etc) to identify (A) excerpts from the results sections of papers describing the goals, methods, results and interpretations of experiments showcased in those figures. We call these passages 'evidence fragments' and are contained in *.ttl files that use an OWL-enabled version of the National Library of Medicine's BioC standoff annotation format (http://bioc.sourceforge.org/) with additional relations from the SPAR ontologies (http://sparontologies.net/) to link these fragments to figure references. (B) We also use these same figure references to anchor manually-curated INTACT data records where noted (http://www.ebi.ac.uk/intact/). We restricted our analysis to papers from the PMC open access subset. <br><b>Provenance Data Files.<br></b><b><br></b>We provide a set of files for the purposes of provenance and reproducibility. This includes the following subsets of papers:<br>* <b>nxml</b> - INTACT open source articles processed in this paper downloaded from PMC.* <b>train+test</b> - Training and testing data for SciDT in TSV form. The articles forming this small corpus are derived from open source papers indexed in the Pathway Logic database developed by SRI International. * <b>scidt_bioc</b> - data fully processed by the SciDT pipeline and saved in BioC format* <b>gannt</b> - 'gantt' charts for each paper that show the distribution of evidence fragments over clauses in the results sections of papers. * <b>intact_evidence_fragment_corpus_10-17-17.tar.gz </b>- a tar archive of <i>*.ttl</i> files for both biopax and bioc sections of the data. We also include <i>*.jsonld</i> formatted files for the bioc annotations. <br>http://purl.org/ske/ro/semsci17 points to a research object (http://www.researchobject.org) that links to the software used to generate this data. <br>
DOI: 10.6084/m9.figshare.5007983
title: Entity Relatedness Test Dataset - V2

description: The entity relatedness problem refers to the question of computing the relationship paths that better describe the connectivity between a given entity pair. This dataset supports the evaluation of approaches that address the entity relatedness problem. It covers two familiar domains, music and movies, and uses data available in IMDb and last.fm, which are popular reference datasets in these domains. The dataset contains 20 entity pairs from each of these domains and, for each entity pair, a ranked list with 50 relationship paths. It also contains entity ratings and property relevance scores for the entities and properties used in the paths.<br><b><i>(This version supersedes the previous one)</i></b>
DOI: 10.6084/m9.figshare.5007992.v1
title: Distant Supervision of Structured Biomedical Data Based on Text Surrounding Figure References

description: Data accompanying the paper entitled "Resources for Distant Supervision of Structured Biomedical Data Based on Text Surrounding Figure References". <br>This fileset consists of the following archives:<br>* <b>nxml</b> - INTACT open source articles processed in this paper downloaded from PMC.* <b>train+test</b> - Training and testing data for SciDT in TSV form. The articles forming this small corpus are derived from open source papers indexed in the Pathway Logic database developed by SRI International. * <b>scidt_bioc</b> - data fully processed by the SciDT pipeline and saved in BioC format* <b>scidt_fries_bioc_tsv</b> - data fully processed by the SciDT pipeline and saved in TSV format* <b>biopax</b> - All open access data from INTACT reformatted into biopax and preserving figure-level meta data. * <b>w3c_annotations</b> - A linked data representation connecting Biopax Evidence instances to Web Annotations embedded in the published, open access research articles. holds five
DOI: 10.6084/m9.figshare.5007965
title: demo data for the error

description: demo data for the error for waters data