cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1586944.v1
title: A benchmark study of numerical schemes for one-dimensional arterial blood flow modelling

description: Hæmodynamical simulations using one-dimensional (1D) computational models exhibit many of the features of the systemic circulation under normal and diseased conditions. Recent interest in verifying 1D numerical schemes has led to the development of alternative experimental setups and the use of three-dimensional numerical models to acquire data not easily measured in vivo. In most studies to date, only one particular 1D scheme is tested. In this paper, we present a systematic comparison of six commonly used numerical schemes for 1D blood flow modelling: discontinuous Galerkin, locally conservative Galerkin, Galerkin least-squares finite element method, finite volume method, finite difference MacCormack method and a simplified trapezium rule method. Comparisons are made in a series of six benchmark test cases with an increasing degree of complexity. The accuracy of the numerical schemes is assessed by comparison with theoretical results, three-dimensional numerical data in compatible domains with distensible walls or experimental data in a network of silicone tubes. Results show a good agreement among all numerical schemes and their ability to capture the main features of pressure, flow and area waveforms in large arteries. All the information used in this study, including the input data for all benchmark cases, experimental data where available and numerical solutions for each scheme, is made publicly available online, providing a comprehensive reference data set to support the development of 1D models and numerical schemes.
DOI: 10.6084/m9.figshare.1586943
title: Uncovering seasonal patterns of 56 pesticides in surface coastal waters of the Ria Formosa lagoon (Portugal), using a GC-MS method

description: ABSTRACTThis study describes the simultaneous quantification of 56 pesticides in surface coastal water, supported by the development and validation of a gas chromatography (GC)–ion trap (IT) mass spectrometry (MS) method. Samples (500 mL) were pre-concentrated 2500 times by solid phase extraction (OASISTMHLB). The compounds were identified and quantified, within 35 minutes, by GC tandem mass spectrometry (GC-MS/MS) and GC-MS, respectively. The methodology proved to be highly specific for all target pesticides, with an average linearity of 0.99. Detection limits and recovery rates ranged from 0.4 to 1.3 ng L<sup>−</sup><sup>1</sup> and 71% to 120%, respectively. The performance of the method was checked using water samples collected from nine sampling sites along the Ria Formosa Lagoon Natural Park (south of Portugal, n = 54) in each season (2010). The total annual concentrations of all pesticides in each category (fungicides, herbicides and insecticides) were 1.4, 0.6 and 9.0 µg L<sup>−1</sup>, respectively. Moreover, 89% of the pesticides tested for were detected, 84% could be quantified and 25% had concentrations above the European recommended levels (2013/39/EU). The highest total loads of pesticides were found in the spring, which is in agreement with their seasonal application. Physicochemical parameters such as, nitrites, nitrates, ammonia and phosphates, also indicate poor water quality, supporting the fact that the Ria Formosa lagoon actually needs an effective monitoring programme for effective preservation of its natural reserve status.
DOI: 10.6084/m9.figshare.1586773
title: The Geoscience Paper of the Future: OntoSoft Training

description: This presentation was developed to train scientists on best practices for digital scholarship, reproducibility, and data and software sharing. It was developed as part of the NSF EarthCube Initiative and funded under the OntoSoft project. More details about the project can be found at http://www.ontosoft.org/gpf. A powerpoint version of the slides is available upon request from ontosoft@gmail.com. These OntoSoft GPF training materials were developed and edited by Yolanda Gil (USC), with contributions from the OntoSoft team including Chris Duffy (PSU), Chris Mattmann (JPL), Scott Pechkam (CU), Ji-Hyun Oh (USC), Varun Ratnakar (USC), Erin Robinson (ESIP). They were significantly improved through input from GPF pioneers Cedric David (JPL), Ibrahim Demir (UI), Bakinam Essawy (UV), Robinson W. Fulweiler (BU), Jon Goodall (UV), Leif Karlstrom (UO), Kyo Lee (JPL), Heath Mills (UH), Suzanne Pierce (UT), Allen Pope (CU), Mimi Tzeng (DISL), Karan Venayagamoorthy (CSU), Sandra Villamizar (UC), and Xuan Yu (UD). Others contributed with feedback on best practices, including Ruth Duerr (NSIDC), James Howison (UT), Matt Jones (UCSB), Lisa Kempler (Matworks), Kerstin Lehnert (LDEO), Matt Meyernick (NCAR), and Greg Wilson (Software Carpentry). These materials were also improved thanks to the many scientists and colleagues that have taken the training and asked hard questions about GPFs.
DOI: 10.6084/m9.figshare.1586943.v2
title: Uncovering seasonal patterns of 56 pesticides in surface coastal waters of the Ria Formosa lagoon (Portugal), using a GC-MS method

description: ABSTRACTThis study describes the simultaneous quantification of 56 pesticides in surface coastal water, supported by the development and validation of a gas chromatography (GC)–ion trap (IT) mass spectrometry (MS) method. Samples (500 mL) were pre-concentrated 2500 times by solid phase extraction (OASISTMHLB). The compounds were identified and quantified, within 35 minutes, by GC tandem mass spectrometry (GC-MS/MS) and GC-MS, respectively. The methodology proved to be highly specific for all target pesticides, with an average linearity of 0.99. Detection limits and recovery rates ranged from 0.4 to 1.3 ng L<sup>−</sup><sup>1</sup> and 71% to 120%, respectively. The performance of the method was checked using water samples collected from nine sampling sites along the Ria Formosa Lagoon Natural Park (south of Portugal, n = 54) in each season (2010). The total annual concentrations of all pesticides in each category (fungicides, herbicides and insecticides) were 1.4, 0.6 and 9.0 µg L<sup>−1</sup>, respectively. Moreover, 89% of the pesticides tested for were detected, 84% could be quantified and 25% had concentrations above the European recommended levels (2013/39/EU). The highest total loads of pesticides were found in the spring, which is in agreement with their seasonal application. Physicochemical parameters such as, nitrites, nitrates, ammonia and phosphates, also indicate poor water quality, supporting the fact that the Ria Formosa lagoon actually needs an effective monitoring programme for effective preservation of its natural reserve status.
DOI: 10.6084/m9.figshare.1585894
title: Quantitative analysis of autophagic flux by confocal pH-imaging of autophagic intermediates

description: Although numerous techniques have been developed to monitor autophagy and to probe its cellular functions, these methods cannot evaluate in sufficient detail the autophagy process, and suffer limitations from complex experimental setups and/or systematic errors. Here we developed a method to image, contextually, the number and pH of autophagic intermediates by using the probe mRFP-GFP-LC3B as a ratiometric pH sensor. This information is expressed functionally by AIPD, the pH distribution of the number of autophagic intermediates per cell. AIPD analysis reveals how intermediates are characterized by a continuous pH distribution, in the range 4.5–6.5, and therefore can be described by a more complex set of states rather than the usual biphasic one (autophagosomes and autolysosomes). AIPD shape and amplitude are sensitive to alterations in the autophagy pathway induced by drugs or environmental states, and allow a quantitative estimation of autophagic flux by retrieving the concentrations of autophagic intermediates.
DOI: 10.6084/m9.figshare.1586943.v1
title: Uncovering seasonal patterns of 56 pesticides in surface coastal waters of the Ria Formosa lagoon (Portugal), using a GC-MS method

description: ABSTRACTThis study describes the simultaneous quantification of 56 pesticides in surface coastal water, supported by the development and validation of a gas chromatography (GC)–ion trap (IT) mass spectrometry (MS) method. Samples (500 mL) were pre-concentrated 2500 times by solid phase extraction (OASISTMHLB). The compounds were identified and quantified, within 35 minutes, by GC tandem mass spectrometry (GC-MS/MS) and GC-MS, respectively. The methodology proved to be highly specific for all target pesticides, with an average linearity of 0.99. Detection limits and recovery rates ranged from 0.4 to 1.3 ng L<sup>−</sup><sup>1</sup> and 71% to 120%, respectively. The performance of the method was checked using water samples collected from nine sampling sites along the Ria Formosa Lagoon Natural Park (south of Portugal, n = 54) in each season (2010). The total annual concentrations of all pesticides in each category (fungicides, herbicides and insecticides) were 1.4, 0.6 and 9.0 µg L<sup>−1</sup>, respectively. Moreover, 89% of the pesticides tested for were detected, 84% could be quantified and 25% had concentrations above the European recommended levels (2013/39/EU). The highest total loads of pesticides were found in the spring, which is in agreement with their seasonal application. Physicochemical parameters such as, nitrites, nitrates, ammonia and phosphates, also indicate poor water quality, supporting the fact that the Ria Formosa lagoon actually needs an effective monitoring programme for effective preservation of its natural reserve status.
DOI: 10.6084/m9.figshare.1585894.v2
title: Quantitative analysis of autophagic flux by confocal pH-imaging of autophagic intermediates

description: Although numerous techniques have been developed to monitor autophagy and to probe its cellular functions, these methods cannot evaluate in sufficient detail the autophagy process, and suffer limitations from complex experimental setups and/or systematic errors. Here we developed a method to image, contextually, the number and pH of autophagic intermediates by using the probe mRFP-GFP-LC3B as a ratiometric pH sensor. This information is expressed functionally by AIPD, the pH distribution of the number of autophagic intermediates per cell. AIPD analysis reveals how intermediates are characterized by a continuous pH distribution, in the range 4.5–6.5, and therefore can be described by a more complex set of states rather than the usual biphasic one (autophagosomes and autolysosomes). AIPD shape and amplitude are sensitive to alterations in the autophagy pathway induced by drugs or environmental states, and allow a quantitative estimation of autophagic flux by retrieving the concentrations of autophagic intermediates.
DOI: 10.6084/m9.figshare.1585894.v1
title: Quantitative analysis of autophagic flux by confocal pH-imaging of autophagic intermediates

description: Although numerous techniques have been developed to monitor autophagy and to probe its cellular functions, these methods cannot evaluate in sufficient detail the autophagy process, and suffer limitations from complex experimental setups and/or systematic errors. Here we developed a method to image, contextually, the number and pH of autophagic intermediates by using the probe mRFP-GFP-LC3B as a ratiometric pH sensor. This information is expressed functionally by AIPD, the pH distribution of the number of autophagic intermediates per cell. AIPD analysis reveals how intermediates are characterized by a continuous pH distribution, in the range 4.5–6.5, and therefore can be described by a more complex set of states rather than the usual biphasic one (autophagosomes and autolysosomes). AIPD shape and amplitude are sensitive to alterations in the autophagy pathway induced by drugs or environmental states, and allow a quantitative estimation of autophagic flux by retrieving the concentrations of autophagic intermediates.
DOI: 10.6084/m9.figshare.1585891
title: Epigenetic instability at imprinting control regions in a Kras<sup>G12D</sup>-induced T-cell neoplasm

description: Although aberrant DNA methylation within imprinted domains has been reported in a variety of neoplastic diseases, it remains largely uncharacterized in the context of carcinogenesis. In this study, we induced T-cell lymphoma in mice by employing a breeding scheme involving mouse strains, <i>LSL-Kras</i><sup><i>G12D</i></sup> and <i>MMTV-Cre</i>. We then systematically surveyed imprinted domains for DNA methylation changes during tumor progression using combined bisulfite restriction analysis and NGS-based bisulfite sequencing. We detected hyper- or hypo-methylation at the imprinting control regions (ICRs) of the <i>Dlk1</i>, <i>Peg10</i>, <i>Peg3</i>, <i>Grb10,</i> and <i>Gnas</i> domains. These DNA methylation changes at ICRs were more prevalent and consistent than those observed at the promoter regions of well-known tumor suppressors, such as <i>Mgmt</i>, <i>Fhit,</i> and <i>Mlh1</i>. Thus, the changes observed at these imprinted domains are the outcome of isolated incidents affecting DNA methylation settings. Within imprinted domains, DNA methylation changes tend to be restricted to ICRs as nearby somatic differentially methylated regions and promoter regions experience no change. Furthermore, detailed analyses revealed that small <i>cis</i>-regulatory elements within ICRs tend to be resistant to DNA methylation changes, suggesting potential protection by unknown <i>trans</i>-factors. Overall, this study demonstrates that DNA methylation changes at ICRs are dynamic during carcinogenesis and advocates that detection of aberrant DNA methylation at ICRs may serve as a biomarker to enhance diagnostic procedures.
DOI: 10.6084/m9.figshare.1585891.v1
title: Epigenetic instability at imprinting control regions in a Kras<sup>G12D</sup>-induced T-cell neoplasm

description: Although aberrant DNA methylation within imprinted domains has been reported in a variety of neoplastic diseases, it remains largely uncharacterized in the context of carcinogenesis. In this study, we induced T-cell lymphoma in mice by employing a breeding scheme involving mouse strains, <i>LSL-Kras</i><sup><i>G12D</i></sup> and <i>MMTV-Cre</i>. We then systematically surveyed imprinted domains for DNA methylation changes during tumor progression using combined bisulfite restriction analysis and NGS-based bisulfite sequencing. We detected hyper- or hypo-methylation at the imprinting control regions (ICRs) of the <i>Dlk1</i>, <i>Peg10</i>, <i>Peg3</i>, <i>Grb10,</i> and <i>Gnas</i> domains. These DNA methylation changes at ICRs were more prevalent and consistent than those observed at the promoter regions of well-known tumor suppressors, such as <i>Mgmt</i>, <i>Fhit,</i> and <i>Mlh1</i>. Thus, the changes observed at these imprinted domains are the outcome of isolated incidents affecting DNA methylation settings. Within imprinted domains, DNA methylation changes tend to be restricted to ICRs as nearby somatic differentially methylated regions and promoter regions experience no change. Furthermore, detailed analyses revealed that small <i>cis</i>-regulatory elements within ICRs tend to be resistant to DNA methylation changes, suggesting potential protection by unknown <i>trans</i>-factors. Overall, this study demonstrates that DNA methylation changes at ICRs are dynamic during carcinogenesis and advocates that detection of aberrant DNA methylation at ICRs may serve as a biomarker to enhance diagnostic procedures.
DOI: 10.6084/m9.figshare.1585889
title: Regioselective Synthesis of Indolizines, Pyrrolo[2,1-<i>a</i>]isoquinolines, and Quinolines

description: Convenient and regioselective synthesis of indolizine and pyrrolo[2,1-<i>a</i>]isoquinoline/quinoline derivatives by one-pot multicomponent reaction of <i>N</i>-substituted pyridinium and isoquinolinum/quinolinium salts with alkyl propiolates in the presence triphenylphosphine is described.
DOI: 10.6084/m9.figshare.1585889.v1
title: Regioselective Synthesis of Indolizines, Pyrrolo[2,1-<i>a</i>]isoquinolines, and Quinolines

description: Convenient and regioselective synthesis of indolizine and pyrrolo[2,1-<i>a</i>]isoquinoline/quinoline derivatives by one-pot multicomponent reaction of <i>N</i>-substituted pyridinium and isoquinolinum/quinolinium salts with alkyl propiolates in the presence triphenylphosphine is described.
DOI: 10.6084/m9.figshare.1585884
title: WK5 - Experimental Design - How Distance from a Pond Impacts Insect Abundance

description: Methods: This experiment took place over a two day period: Tuesday, October 13th, 2015 (from 2:30-4:30 pm), and Tuesday, October 20th, 2015 (from 230-4:00 pm). To execute this experiment, we began by selecting the unmowed grassland that runs parallel to the Stong pond as our sampling area. This pond is found on the Southeast corner of York University’s Keele campus. This experiment was designed on our own in order to study the impact of the Stong pond on insect abundance in the unmowed grassland. In order to study this, we selected sampling areas at distances of 1, 10 and 20 meters from the pond. This distance was measured using a transect in order to ensure accurate execution. Once at these distances, we placed a quadrat in order to count both plant density and insect abundance. We placed 20 quadrats at each distance running parallel with the pond. The quadrats were placed one meter apart from each other in order to ensure we sampled a sufficient area.
DOI: 10.6084/m9.figshare.1585884.v1
title: WK5 - Experimental Design - How Distance from a Pond Impacts Insect Abundance

description: Methods: This experiment took place over a two day period: Tuesday, October 13th, 2015 (from 2:30-4:30 pm), and Tuesday, October 20th, 2015 (from 230-4:00 pm). To execute this experiment, we began by selecting the unmowed grassland that runs parallel to the Stong pond as our sampling area. This pond is found on the Southeast corner of York University’s Keele campus. This experiment was designed on our own in order to study the impact of the Stong pond on insect abundance in the unmowed grassland. In order to study this, we selected sampling areas at distances of 1, 10 and 20 meters from the pond. This distance was measured using a transect in order to ensure accurate execution. Once at these distances, we placed a quadrat in order to count both plant density and insect abundance. We placed 20 quadrats at each distance running parallel with the pond. The quadrats were placed one meter apart from each other in order to ensure we sampled a sufficient area.
DOI: 10.6084/m9.figshare.1585880
title: Biofidelity assessment of the 6-year-old ATDs in lateral impact

description: <b>Objectives</b>: The objective of this study was to assess and compare the current lateral impact biofidelity of the shoulder, thorax, abdomen, and pelvis of the Q6, Q6s, and Hybrid III (HIII) 6-year-old anthropomorphic test devices (ATDs) through lateral impact testing. <b>Methods</b>: A series of lateral impact pendulum tests, vertical drop tests, and Wayne State University (WSU) sled tests was performed, based on the procedures detailed in ISO/TR 9790 (1999) and scaling to the 6-year-old using Irwin et al. (2002). The HIII used in this study was tested with the Ford-designed abdomen described in Rouhana (2006) and Elhagediab et al. (2006). The data collected from the 3 different ATDs were filtered using SAE J211 (SAE International 2003), aligned using the methodology described by Donnelly and Moorhouse (2012), and compared for each body region tested (shoulder, thorax, abdomen, and pelvis). The biofidelity performance in lateral impact for the 3 ATDs was assessed against the scaled biofidelity targets published in Irwin et al. (2002), the abdominal biofidelity target suggested in van Ratingen et al. (1997), and the biofidelity targets published in Rhule et al. (2013). Regional and overall biofidelity rankings for each of the 3 ATDs were performed using both the ISO 9790 biofidelity rating system (ISO/TR 9790 1999) and the NHTSA's external biofidelity ranking system (BRS; Rhule et al. 2013). <b>Results</b>: All 3 6-year-old ATD's pelvises were rated as least biofidelic of the 4 body regions tested, based on both the ISO and BRS biofidelity rating systems, followed by the shoulder and abdomen, respectively. The thorax of all 3 ATDs was rated as the most biofidelic body region using the aforementioned biofidelity rating systems. The HIII 6-year-old ATD was rated last in overall biofidelity of the 3 tested ATDs, based on both rating systems. The Q6s ATD was rated as having the best overall biofidelity using both rating systems. <b>Conclusions</b>: All 3 ATDs are more biofidelic in the thorax and abdomen than the shoulder and pelvis, with the pelvis being the least biofidelic of all 4 tested body regions. None of the 3 tested 6-year-old ATDs had an overall ranking of 2.0 or less, based on the BRS ranking. Therefore, it is expected that none of the 3 ATDs would mechanically respond like a postmortem human subject (PMHS) in a lateral impact crash test based on this ranking system. With respect to the ISO biofidelity rating, the HIII dummy would be considered unsuitable and the Q-series dummies would be considered marginal for assessing side impact occupant protection.
DOI: 10.6084/m9.figshare.1585880.v2
title: Biofidelity assessment of the 6-year-old ATDs in lateral impact

description: <b>Objectives</b>: The objective of this study was to assess and compare the current lateral impact biofidelity of the shoulder, thorax, abdomen, and pelvis of the Q6, Q6s, and Hybrid III (HIII) 6-year-old anthropomorphic test devices (ATDs) through lateral impact testing. <b>Methods</b>: A series of lateral impact pendulum tests, vertical drop tests, and Wayne State University (WSU) sled tests was performed, based on the procedures detailed in ISO/TR 9790 (1999) and scaling to the 6-year-old using Irwin et al. (2002). The HIII used in this study was tested with the Ford-designed abdomen described in Rouhana (2006) and Elhagediab et al. (2006). The data collected from the 3 different ATDs were filtered using SAE J211 (SAE International 2003), aligned using the methodology described by Donnelly and Moorhouse (2012), and compared for each body region tested (shoulder, thorax, abdomen, and pelvis). The biofidelity performance in lateral impact for the 3 ATDs was assessed against the scaled biofidelity targets published in Irwin et al. (2002), the abdominal biofidelity target suggested in van Ratingen et al. (1997), and the biofidelity targets published in Rhule et al. (2013). Regional and overall biofidelity rankings for each of the 3 ATDs were performed using both the ISO 9790 biofidelity rating system (ISO/TR 9790 1999) and the NHTSA's external biofidelity ranking system (BRS; Rhule et al. 2013). <b>Results</b>: All 3 6-year-old ATD's pelvises were rated as least biofidelic of the 4 body regions tested, based on both the ISO and BRS biofidelity rating systems, followed by the shoulder and abdomen, respectively. The thorax of all 3 ATDs was rated as the most biofidelic body region using the aforementioned biofidelity rating systems. The HIII 6-year-old ATD was rated last in overall biofidelity of the 3 tested ATDs, based on both rating systems. The Q6s ATD was rated as having the best overall biofidelity using both rating systems. <b>Conclusions</b>: All 3 ATDs are more biofidelic in the thorax and abdomen than the shoulder and pelvis, with the pelvis being the least biofidelic of all 4 tested body regions. None of the 3 tested 6-year-old ATDs had an overall ranking of 2.0 or less, based on the BRS ranking. Therefore, it is expected that none of the 3 ATDs would mechanically respond like a postmortem human subject (PMHS) in a lateral impact crash test based on this ranking system. With respect to the ISO biofidelity rating, the HIII dummy would be considered unsuitable and the Q-series dummies would be considered marginal for assessing side impact occupant protection.