cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5913181.v6
title: Protist Ribosomal Reference database (PR2) - SSU rRNA gene database

description: The Protist Ribosomal Reference database (PR<sup>2</sup>) provides a unique access to eukaryotic small sub-unit (SSU) ribosomal RNA and DNA sequences, with curated taxonomy. The database mainly consists of nuclear-encoded protistan sequences. However, metazoans, land plants, macrosporic fungi and eukaryotic organelles (mitochondrion, plastid and others) are also included because they are useful for the analysis of high-troughput sequencing data sets. Introns and putative chimeric sequences have been also carefully checked. Taxonomic assignation of sequences consists of eight unique taxonomic fields.<br><br>The database is now synchronized on <b>Github </b>for easier maintenance. Please go to the GitHub site to download the files you need.<br><br>Latest version 4.12.0 (8 August 2019)<br><b>Home page</b>https://github.com/pr2database/pr2database<br><br><b>Latest version of files</b>https://github.com/pr2database/pr2database/releases<br><br><b>Information</b>https://github.com/pr2database/pr2database/wiki<br><br><b>Reports problems and bugs</b>https://github.com/pr2database/pr2database/issues<br><br><b>Contact<br><br></b>Daniel VAULOT, Laure GUILLOU<br>DIPO team, Plankton Group, UMR 7144 CNRS-UPMC<br>Station Biologique,<br>Place G. Tessier<br>29680 Roscoff FRANCE<br>email: vaulot@sb-roscoff.fr<br><br><b>Please cite</b><br>Guillou, L., Bachar, D., Audic, S., Bass, D., Berney, C., Bittner, L., Boutte, C. et al. 2013. The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy. <i>Nucleic Acids Res.</i> 41:D597–604.<br>
DOI: 10.6084/m9.figshare.5913181.v7
title: Protist Ribosomal Reference database (PR2) - SSU rRNA gene database

description: The Protist Ribosomal Reference database (PR<sup>2</sup>) provides a unique access to eukaryotic small sub-unit (SSU) ribosomal RNA and DNA sequences, with curated taxonomy. The database mainly consists of nuclear-encoded protistan sequences. However, metazoans, land plants, macrosporic fungi and eukaryotic organelles (mitochondrion, plastid and others) are also included because they are useful for the analysis of high-troughput sequencing data sets. Introns and putative chimeric sequences have been also carefully checked. Taxonomic assignation of sequences consists of eight unique taxonomic fields.<br><br>The database is now synchronized on <b>Github </b>for easier maintenance. Please go to the GitHub site to download the files you need.<br><br>Latest version 4.12.0 (8 August 2019, updated 17 August 2019)<br><b>Home page</b>https://github.com/pr2database/pr2database<br><br><b>Latest version of files</b>https://github.com/pr2database/pr2database/releases<br><br><b>Information</b>https://github.com/pr2database/pr2database/wiki<br><br><b>Reports problems and bugs</b>https://github.com/pr2database/pr2database/issues<br><br><b>Contact<br><br></b>Daniel VAULOT, Laure GUILLOU<br>DIPO team, Plankton Group, UMR 7144 CNRS-UPMC<br>Station Biologique,<br>Place G. Tessier<br>29680 Roscoff FRANCE<br>email: vaulot@sb-roscoff.fr<br><br><b>Please cite</b><br>Guillou, L., Bachar, D., Audic, S., Bass, D., Berney, C., Bittner, L., Boutte, C. et al. 2013. The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy. <i>Nucleic Acids Res.</i> 41:D597–604.<br>
DOI: 10.6084/m9.figshare.5913136
title: Jurkat

description: ying yang one
DOI: 10.6084/m9.figshare.5913136.v1
title: Jurkat

description: ying yang one
DOI: 10.6084/m9.figshare.5913013
title: More Scalable LTL Model Checking via Discovering Design-Space Dependencies (Artifact)

description: This record contains a single artifact in compressed .tar.gz format, holding software and models to run the Discover Design-Space Dependencies (D<sup>3</sup>) algorithm for scalable Linear Temporal Logic (LTL) model checking on two benchmarks derived from real-world case studies. <br>The artifact relates to the TACAS 2018 paper:Dureja, R., Rozier, K.Y.: <i>More Scalable LTL Model Checking via Discovering Design-Space Dependencies (D<sup>3</sup>)</i>. In: TACAS (2018)<br>The artifact includes the benchmarks evaluated, source code, and scripts to efficiently reproduce the results reported in the paper. Please refer to the README contained within the artifact for more detailed information.<br>The <b>D3_Artifacts </b>subdirectory contains tools, scripts, results, plots and models for experiments to demonstrate the industrial scalability of D<sup>3</sup> on NASA’s NextGen airtraffic control system (modelled by a set of 1,620 real-life, publicly-available SMV-language benchmark models with LTL specifications) and to evaluate the property-dependence analysis on real-life models of Boeing AIR Wheel Braking System.<br>D3 is implemented as a preprocessing script in ~2,000 lines of Python code (.py files). Other file types include SMV-language (.smv), related metadata files (.xml) and mapping (.map) files, command scripts (.cmd), plots in .jpg image format and documents in .html and graphical .svg formats.<br><br>The artifact has been thoroughly tested on the Ubuntu Virtual Machine (VM) available at:<br>Hartmanns, Arnd; Wendler, Philipp (2018). figshare. https://doi.org/10.6084/m9.figshare.5896615<br><b>Background</b>Modern system design often requires comparing several models over a large design space. Different models arise out of a need to weigh different design choices, to check core capabilities of versions with varying features, or to analyze a future version against previous ones. Model checking can compare different models; however, applying model checking off-the-shelf may not scale due to the large size of the design space for today’s complex systems. We exploit relationships between different models of the same (or related) systems to optimize the modelchecking search. Our algorithm, D<sup>3</sup>, preprocesses the design space and checks fewer model-checking instances, e.g., using nuXmv. It automatically prunes the search space by reducing both the number of models to check, and the number of LTL properties that need to be checked for each model in order to provide the complete model-checking verdict for every individual model-property pair. We formalize heuristics that improve the performance of D<sup>3</sup>. We demonstrate the scalability of D<sup>3</sup> by extensive experimental evaluation, e.g., by checking 1,620 real-life models for NASA’s NextGen air traffic control system.<br>
DOI: 10.6084/m9.figshare.5913013.v1
title: More Scalable LTL Model Checking via Discovering Design-Space Dependencies (Artifact)

description: This record contains a single artifact in compressed .tar.gz format, holding software and models to run the Discover Design-Space Dependencies (D<sup>3</sup>) algorithm for scalable Linear Temporal Logic (LTL) model checking on two benchmarks derived from real-world case studies. <br>The artifact relates to the TACAS 2018 paper:Dureja, R., Rozier, K.Y.: <i>More Scalable LTL Model Checking via Discovering Design-Space Dependencies (D<sup>3</sup>)</i>. In: TACAS (2018)<br>The artifact includes the benchmarks evaluated, source code, and scripts to efficiently reproduce the results reported in the paper. Please refer to the README contained within the artifact for more detailed information.<br>The <b>D3_Artifacts </b>subdirectory contains tools, scripts, results, plots and models for experiments to demonstrate the industrial scalability of D<sup>3</sup> on NASA’s NextGen airtraffic control system (modelled by a set of 1,620 real-life, publicly-available SMV-language benchmark models with LTL specifications) and to evaluate the property-dependence analysis on real-life models of Boeing AIR Wheel Braking System.<br>D3 is implemented as a preprocessing script in ~2,000 lines of Python code (.py files). Other file types include SMV-language (.smv), related metadata files (.xml) and mapping (.map) files, command scripts (.cmd), plots in .jpg image format and documents in .html and graphical .svg formats.<br><br>The artifact has been thoroughly tested on the Ubuntu Virtual Machine (VM) available at:<br>Hartmanns, Arnd; Wendler, Philipp (2018). figshare. https://doi.org/10.6084/m9.figshare.5896615<br><b>Background</b>Modern system design often requires comparing several models over a large design space. Different models arise out of a need to weigh different design choices, to check core capabilities of versions with varying features, or to analyze a future version against previous ones. Model checking can compare different models; however, applying model checking off-the-shelf may not scale due to the large size of the design space for today’s complex systems. We exploit relationships between different models of the same (or related) systems to optimize the modelchecking search. Our algorithm, D<sup>3</sup>, preprocesses the design space and checks fewer model-checking instances, e.g., using nuXmv. It automatically prunes the search space by reducing both the number of models to check, and the number of LTL properties that need to be checked for each model in order to provide the complete model-checking verdict for every individual model-property pair. We formalize heuristics that improve the performance of D<sup>3</sup>. We demonstrate the scalability of D<sup>3</sup> by extensive experimental evaluation, e.g., by checking 1,620 real-life models for NASA’s NextGen air traffic control system.<br>
DOI: 10.6084/m9.figshare.5910220
title: NMR spectra.doc

description: NMR Spectra of compounds in a paper entitled "Selective carboxylation of substituted phenols with engineered <i>Escherichia coli </i>whole-cells"
DOI: 10.6084/m9.figshare.5910115
title: Table S1.doc

description: <b>Table S1. Corresponding affinity energy, H-bond interactions and hydrophobic interactions between substrates or corresponding products and the active site of LigW_Sp or LigW2_Sp</b>
DOI: 10.6084/m9.figshare.5910115.v1
title: Table S1.doc

description: <b>Table S1. Corresponding affinity energy, H-bond interactions and hydrophobic interactions between substrates or corresponding products and the active site of LigW_Sp or LigW2_Sp</b>
DOI: 10.6084/m9.figshare.5910088.v1
title: Determination of quinolone residues in raw cow milk. Application of polar stir-bars and ultra-high performance liquid chromatography–tandem mass spectrometry

description: Seventeen quinolone antibiotics were determined in cows’ milk. A method of high sensitivity, selectivity and accuracy was developed. Accuracy (trueness and precision), linearity, sensitivity, selectivity, decision limit and detection capability were established following the recommendations of the Commission Decision 2002/657/EC and the Food and Drug Administration (FDA) guideline. The use of polar stir-bar sorptive extraction (SBSE) prior to UHPLC-MS/MS analysis is proposed. The variables that affect SBSE were optimised using multivariate optimisation strategies. The ionic strength, the extraction time and the sample volume were studied. pH and stir-bar coating (polydimethylsiloxane, PDMS, and polyethyleneglycol modified silicone, PEG) were studied. PEG showed the best extraction yield at pH 6. For validation, a matrix-matched calibration and a recovery assay were carried out. Limits of quantification from 0.5 μg kg<sup>−1</sup> for nalidixic acid, flumequine and piromidic acid, to 4.0 μg kg<sup>−1</sup> for sarafloxacin were calculated. The precision (%, RSD) was lower than 15% for all antibiotics. Recoveries in fortified samples were between 88 and 114%.
DOI: 10.6084/m9.figshare.5910073
title: RUC(1).mp4

description: Retrograde ureteral catheterization (RUC) was performed with intravenous anesthesia combined with caudal anesthesia, continuous epidural anesthesia or laryngeal mask airway. An F7.5-10.8 cystoscope (Karl Storz, Germany) was placed through the urethra to observe the bladder and the ureteral orifice; An F3 ureteral catheter (Shanghai Kangge, China) was inversely inserted into the ureter through the cystoscope until urine was evident. Sediment-like calculi, floc, or crystals ejection from the ureteral orifice was observed during surgery after dredging with RUC through a cystoscope. On dragging the catheter back and forth, most of the calculi loosen, break, and fall into the bladder, eventually relieving the ureteral obstruction.
DOI: 10.6084/m9.figshare.5910073.v1
title: RUC(1).mp4

description: Retrograde ureteral catheterization (RUC) was performed with intravenous anesthesia combined with caudal anesthesia, continuous epidural anesthesia or laryngeal mask airway. An F7.5-10.8 cystoscope (Karl Storz, Germany) was placed through the urethra to observe the bladder and the ureteral orifice; An F3 ureteral catheter (Shanghai Kangge, China) was inversely inserted into the ureter through the cystoscope until urine was evident. Sediment-like calculi, floc, or crystals ejection from the ureteral orifice was observed during surgery after dredging with RUC through a cystoscope. On dragging the catheter back and forth, most of the calculi loosen, break, and fall into the bladder, eventually relieving the ureteral obstruction.
DOI: 10.6084/m9.figshare.5910058.v1
title: Development of an ultrasensitive PCR assay for polycyclic musk determination in fish

description: Polycyclic musks (PCMs) in the aquatic environment and organisms have become an emerging environmental issue because of their potential risk. The most used method for polycyclic musk determination is gas chromatography-mass spectrometry (GC-MS) with different sample extractions, which are somewhat expensive to operate, complex and laborious. In this study, a novel and ultrasensitive real-time polymerase chain reaction (PCR) assay with multiple signal amplification of carboxylic-DNA by gold nanoparticle-polyamidoamine conjugation (Au-PAMAM) was developed for determining polycyclic musks in fish. Hapten and immunogen were specially prepared. Polyclonal antibodies were produced based on the optimal immunisation, and the antibodies were characterised. Due to PAMAM’s unique nanostructure of numerous functional amino groups, polyclonal antibody and carboxylic-DNA were immobilised by Au-PAMAM conjugation to develop the antibody-Au-PAMAM-DNA probes, which were used as a signal DNA amplifier in the PCR system. Compared with real-time immuno-PCR, this biological probe-amplified immuno-PCR (BPAI-PCR) assay had higher sensitivity due to the probes’ higher ratio of signal DNA. Finally, the BPAI-PCR assay was applied to analyse AHTN (7-acetyl-1,1,3,4,4,6-hexamethyl-1,2,3,4-tetrahydronaphthalene,Tonalide) concentrations in fish samples in the range from 1 pg/L to 10 ng/L, giving an of LOD 0.61 pg/L. In general, due to the specificity of the antibody and novel nanoprobe design, this BPAI-PCR assay provided a potential way for trace analysis of AHTN in the aquatic organisms. The high concentrations of AHTN found in cultivated fish should encourage further toxicological studies.
DOI: 10.6084/m9.figshare.5910049
title: Patulin in fruit juices: occurrence, bioaccessibility, and risk assessment for Serbian population

description: This paper reports the first study of patulin occurrence in fruit juices and risk assessment related to patulin intake by children, adolescents and adults in Serbia. During 3 consecutive years (2013–2015), 142 fruit (apple or multi-fruit) juices were collected from the market and analysed using HPLC-UV. Patulin was found in 51.4% of juices with 0.7% of the samples in excess of the legal limit of 50 μg kg<sup>−1</sup> (mean 4.3 μg kg<sup>−1</sup>). Apple juices showed significantly higher percentage of contaminated samples (74.0% vs 27.5%), as well as higher mean patulin content (6.4 vs 2.1 μg kg<sup>−1</sup>) when compared with the multi-fruit ones. Bioaccessibility of patulin in fruit juices was studied using the standardised <i>in vitro</i> digestion method. A mean of 21.6% of the initial patulin amount reached the end of the intestinal phase showing a significant reduction of this toxin during the human digestion process. Risk assessment of patulin intake by Serbian children, adolescents and adults, conducted by deterministic and probabilistic approaches and including the bioaccessibility results, revealed no health concern. Although patulin alone does not represent risk, further research should consider its co-occurrence with other toxic substances in food and potential adverse effects of their mixtures.
DOI: 10.6084/m9.figshare.5910049.v1
title: Patulin in fruit juices: occurrence, bioaccessibility, and risk assessment for Serbian population

description: This paper reports the first study of patulin occurrence in fruit juices and risk assessment related to patulin intake by children, adolescents and adults in Serbia. During 3 consecutive years (2013–2015), 142 fruit (apple or multi-fruit) juices were collected from the market and analysed using HPLC-UV. Patulin was found in 51.4% of juices with 0.7% of the samples in excess of the legal limit of 50 μg kg<sup>−1</sup> (mean 4.3 μg kg<sup>−1</sup>). Apple juices showed significantly higher percentage of contaminated samples (74.0% vs 27.5%), as well as higher mean patulin content (6.4 vs 2.1 μg kg<sup>−1</sup>) when compared with the multi-fruit ones. Bioaccessibility of patulin in fruit juices was studied using the standardised <i>in vitro</i> digestion method. A mean of 21.6% of the initial patulin amount reached the end of the intestinal phase showing a significant reduction of this toxin during the human digestion process. Risk assessment of patulin intake by Serbian children, adolescents and adults, conducted by deterministic and probabilistic approaches and including the bioaccessibility results, revealed no health concern. Although patulin alone does not represent risk, further research should consider its co-occurrence with other toxic substances in food and potential adverse effects of their mixtures.
DOI: 10.6084/m9.figshare.5910043.v1
title: Versicolorin A is a potential indicator of aflatoxin contamination in the granary-stored corn

description: The objective of this study was to evaluate the feasibility of the predictive monitoring of aflatoxin B<sub>1</sub> (AFB<sub>1</sub>) under granary conditions, since mycotoxin contamination of the stored grain represents an important issue. Using the storage test, we investigated the relationship between versicolorin A (Ver A, an intermediate in AFB<sub>1</sub> biosynthesis) levels and the levels of aflatoxigenic fungi, and their relationship with aflatoxin production. All samples, except for one, were found to be contaminated with aflatoxigenic fungi using PCR analyses, while their AFB<sub>1</sub> levels were not detectable before the storage test using an enzyme-linked immunosorbent assay (ELISA) method with an LOD of 2 μg/kg. Aflatoxigenic fungi levels were analysed, as well as Ver A levels prior to the accumulation of AFB<sub>1</sub> (Levels were ≥5 μg/kg; the permissible levels of AFB<sub>1</sub> in corn intended for direct consumption are &lt;5 μg/kg (EC)). Statistical analyses demonstrated that aflatoxin levels after both actual storage and safe storage (AFB<sub>1</sub>˂5μg/kg) times are significantly correlated with the Ver A levels and the changes in Ver A levels (ΔVer A). Both high and variable Ver A levels were indicative of the vigorous metabolic activity of aflatoxigenic fungi. In contrast, steady Ver A levels showed that aflatoxin production by the fungi was not active. Monitoring Ver A levels and their changes may allow an earlier detection of harmful aflatoxin contamination in the stored grain. Additionally, the toxicity of Ver A should be further examined. The results of our study indicate that the monitoring of Ver A levels, even when the AFB<sub>1</sub> levels are very low, may increase the safety of grain consumption, especially considering Ver A toxicity.
DOI: 10.6084/m9.figshare.5910022
title: Rat Body Masses over the 12-Week Experiment

description: Barplot of rat body masses by group over the course of the 12-week experiment. Error bars are the standard error (SE).
DOI: 10.6084/m9.figshare.5910004
title: Spatiotemporal changes in distributions of the two dominant bivalve species in an estuarine river connecting two brackish lakes, Japan

description: Spatiotemporal changes in the biomass and abundance of the two dominant bivalve species <i>Corbicula japonica</i> and <i>Arcuatula senhousia</i> were investigated at 14 stations positioned along the Ohashi River from November 2005 to August 2007. <i>Corbicula japonica</i> predominantly inhabited the upstream section of the primary branch and Kensaki stream of the Ohashi River, whereas <i>A. senhousia</i> predominantly inhabited the downstream section of the Ohashi River. However, the distributions were highly variable among stations and seasons. Intrusions of saline water from Lake Nakaumi varied with astronomical and climatological factors, and consequently, the halocline of the Ohashi River is subject to spatiotemporal changes. Changes in distributions of <i>C. japonica</i> and <i>A. senhousia</i> occurred in relation to a flood event, indicating that environmental disturbances affect the distributions of the two bivalve species. Responses of the two species to continual saline water intrusion were also observed during the period of normal flow conditions. We suggest that the distribution of the two species is closely related to the dynamics of the ambient saline water, which is the most important factor correlated to changes in the distributions of <i>C. japonica</i> and <i>A. senhousia</i> in the Ohashi River.
DOI: 10.6084/m9.figshare.5910004.v1
title: Spatiotemporal changes in distributions of the two dominant bivalve species in an estuarine river connecting two brackish lakes, Japan

description: Spatiotemporal changes in the biomass and abundance of the two dominant bivalve species <i>Corbicula japonica</i> and <i>Arcuatula senhousia</i> were investigated at 14 stations positioned along the Ohashi River from November 2005 to August 2007. <i>Corbicula japonica</i> predominantly inhabited the upstream section of the primary branch and Kensaki stream of the Ohashi River, whereas <i>A. senhousia</i> predominantly inhabited the downstream section of the Ohashi River. However, the distributions were highly variable among stations and seasons. Intrusions of saline water from Lake Nakaumi varied with astronomical and climatological factors, and consequently, the halocline of the Ohashi River is subject to spatiotemporal changes. Changes in distributions of <i>C. japonica</i> and <i>A. senhousia</i> occurred in relation to a flood event, indicating that environmental disturbances affect the distributions of the two bivalve species. Responses of the two species to continual saline water intrusion were also observed during the period of normal flow conditions. We suggest that the distribution of the two species is closely related to the dynamics of the ambient saline water, which is the most important factor correlated to changes in the distributions of <i>C. japonica</i> and <i>A. senhousia</i> in the Ohashi River.
DOI: 10.6084/m9.figshare.5910001
title: longRange

description: HiChip
DOI: 10.6084/m9.figshare.5910001.v1
title: longRange

description: HiChip