cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7476227.v1
title: Effect of a change in reactor power on response of murine solid tumors <i>in vivo</i>, referring to impact on quiescent tumor cell population.

description: <b>Purpose:</b> To examine the effect of a change in reactor power on the response of solid tumors, referring to impact on quiescent (Q) tumor cell population. <b>Materials and Methods:</b> Tumor-bearing mice received 5-bromo-2-deoxyuridine (BrdU) to label all proliferating (P) tumor cells, and were treated with boronophenylalanine-<sup>10</sup>B (BPA) or sodium mercaptododecaborate-<sup>10</sup>B (BSH). After reactor neutron beam irradiation at a power of 1 or 5 MW with an identical beam spectrum, cells from tumors were isolated and incubated with a cytokinesis blocker. The responses of BrdU-unlabeled Q and total (= P + Q) tumor cells were assessed based on the frequencies of micronucleation using immunofluorescence staining for BrdU. <b>Results:</b> After neutron irradiation with or without <b><sup>10</sup></b>B-carrier, radio-sensitivity was reduced by decreasing reactor power in both cells, especially in Q cells and after irradiation with BPA. The values of relative and compound biological effectiveness were larger at a power of 5 MW and in Q cells than at a power of 1 MW and in total cells, respectively. The sensitivity difference between total and Q cells was widened when combined with <b><sup>10</sup></b>B-carrier, especially with BPA, and through decreasing reactor power. <b>Conclusion:</b> 5 MW is more advantageous than 1 MW for boron neutron capture therapy.
DOI: 10.6084/m9.figshare.7476230.v3
title: Polyphenol Consumption.xlsx

description: This data contain age ranges,gestacional age, weight, height, IMC and polyphenol comsumption of pregnant women that participated the research in the south of Brazil.<br>
DOI: 10.7284/110830
title: pCO2 (Partial Pressure of Carbon Dioxide) data collected during research cruise MGL1305 using a LDEO pCO2 instrument system onboard the platform RV Marcus G. Langseth

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7476230.v2
title: Polyphenol Consumption.xlsx

description: This data contain age,gestacional age, weight, height, IMC and polyphenol comsumption of pregnant women that participated the research in the south of Brazil.<br>
DOI: 10.6084/m9.figshare.7476173
title: Supplementary Figures

description: Supplementation figures for research article titled 'Dietary nitrate supplementation enhances cerebral autoregulation and cerebral CO<sub>2</sub> reactivity in a sex-specific manner'
DOI: 10.7284/110833
title: Singlebeam Echosounder data collected during research cruise MGL1305 using a Knudsen 3260 instrument system onboard the platform RV Marcus G. Langseth

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7476191.v2
title: Evaluation of mature miR398 family, expression analysis and the post-transcriptional regulation evidence in gamma-irradiated and nitrogen-stressed <i>Medicago sativa</i> seedlings

description: <b>Background:</b> The miR398 (microRNA398) posttranscriptionally regulates the superoxide dismutase (Cu/Zn-SOD). <b>Materials and methods:</b> The miR398 level was quantitated in gamma-irradiated (20Gy and 200Gy) and nitrogen-stressed seedlings by stem-loop RT-PCR (Real Time-Polymerase chain reaction). The positional preference of nucleotide (nt) for miR398 families and new targets was done. The SOD enzyme was assayed in native PAGE (Polyacrylamide gel electrophoresis). <b>Results:</b> A relative increase in miR398-3p expression in the roots, and reduction in shoots for gamma-irradiated tissue and downregulation in miR398-5p in shoots is noted. The nitrogen stress shows upregulation of miR398-3p in roots and shoots, whereas the expression of miR398-5p is upregulated in roots and downregulated in shoots. Positional preference in miR398-3p for 1–14 nt is 90% conserved unlike miR398-5p where no nucleotide positional preference is seen. Targets obtained were functionally characterized. <b>Conclusions:</b> The mature miR398-5p and miR398-3p levels estimated in gamma-irradiated (20 and 200Gy) and nitrogen-stressed <i>Medicago sativa</i> seedlings show differential levels in roots and shoots. Native PAGE of Cu/Zn-SOD suggests its negative correlation with miR398 in shoots of irradiated and nitrogen-stressed samples. The nucleotide preferences for the nucleotide for a given position and functional characterization of targets are reported herein.
DOI: 10.6084/m9.figshare.7476173.v2
title: Supplementary Figures

description: Supplementation figures for research article titled 'Dietary nitrate supplementation enhances cerebral autoregulation and cerebral CO<sub>2</sub> reactivity in a sex-specific manner'
DOI: 10.6084/m9.figshare.7476191.v1
title: Evaluation of mature miR398 family, expression analysis and the post transcriptional regulation evidence in gamma-irradiated and nitrogen stressed <i>Medicago sativa</i> seedlings

description: <b>Background:</b> The miRNA398 (microRNA398) post transcriptionally regulates the superoxide dismutase (Cu/Zn-SOD). <b>Materials and methods:</b> The miRNA398 level were quantitated in gamma irradiated 20Gy and 200Gy and nitrogen stressed seedlings by stem-loop RT-PCR (Real Time- Polymerase chain reaction). The positional preference of nucleotide for miR398 families and new targets was done. The superoxide dismutase enzyme was assayed in native PAGE (Polyacrylamide gel electrophoresis). <b>Results:</b> A relative increase in miR398-3p expression in the roots, and reduction in shoots for gamma irradiated tissue and downregulation in miR398-5p in shoots is noted. The nitrogen stress shows upregulation of miR398-3p in roots and shoots, whereas the expression of miR398-5p is upregulated in roots and downregulated in shoots. Positional preference in miR398-3p for 1-14 nt (nucleotide) is 90% conserved unlike miR398-5p where no nucleotide positional preference is seen. Targets obtained were functionally characterized. <b>Conclusions:</b> The mature miR398-5p and miR398-3p levels estimated in gamma-irradiated (20 and 200Gy) and nitrogen stressed <i>Medicago sativa</i> seedlings show differential levels in roots and shoots. Native PAGE of Cu/Zn-SOD suggests its negative correlation with miR398 in shoots of irradiated and nitrogen stressed samples. The nucleotide preferences for the nucleotide for a given position and functional characterization of targets are reported herein.
DOI: 10.7284/110831
title: TSG (Thermosalinograph) data collected during research cruise MGL1305 using a Sea-Bird SBE-21 instrument system onboard the platform RV Marcus G. Langseth

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7476173.v1
title: Supplementary Figures

description: Supplementation figures for research article titled 'Dietary nitrate supplementation enhances cerebral autoregulation and cerebral CO<sub>2</sub> reactivity in a sex-specific manner'
DOI: 10.6084/m9.figshare.7476149
title: CGO19FMSA-Benchmarks/Scripts

description: Scripts used by the CGO19FMSA artifact.The scripts compile, run and produces the outputs for the SPEC CPU2006 benchmark.
DOI: 10.7284/110852
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise MGL1306 using a Hawaii UHDAS instrument system onboard the platform RV Marcus G. Langseth

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/110847
title: GNSS (Global Navigation Satellite System) data collected during research cruise MGL1306 using a C&C C-Nav 3050 instrument system onboard the platform RV Marcus G. Langseth

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7475939
title: Biological characteristics of gene expression features in pancreatic cancer cells induced by proton and X-ray irradiation

description: <b>Background:</b> Radiation therapy is an important alternative treatment for advanced cancer. The aim of the current study was to disclose distinct alterations of the biological characteristics of gene expression features in pancreatic cancer cells, MIAPaCa-2, following proton and X-ray irradiation. <b>Materials and methods:</b> Using cDNA microarray, we examined the gene expression alterations of MIAPaCa-2 cells following proton or X-ray irradiation. We also isolated the surviving MIAPaCa-2 cells after irradiation and analyzed their gene expression profiles. <b>Results:</b> Although the cytocidal effects of both types of irradiation were similar at sufficient doses in vitro and in vivo, the affected gene expression profile alterations of MIAPaCa-2 cells irradiated with protons were distinct from those irradiated with X-ray. Interestingly, clustering analysis of gene expression of the surviving MIAPaCa-2 cells was also completely discernible between the two types of irradiation. However, a similar cytocidal effect was still observed in the proton- and X-ray-irradiated surviving cells after re-irradiation, commonly showing biological effects related to apoptosis and cell cycle processes. <b>Conclusions:</b> Proton irradiation treatment for pancreatic cancer provides the distinct biological effect of steady gene expression alterations compared to X-ray irradiation; however, surviving cells from both types of irradiation were still susceptible to the cytocidal effects induced by proton re-irradiation treatment.
DOI: 10.7284/110849
title: GNSS (Global Navigation Satellite System) data collected during research cruise MGL1306 using a C&C C-Nav 2000 instrument system onboard the platform RV Marcus G. Langseth

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7475939.v1
title: Biological characteristics of gene expression features in pancreatic cancer cells induced by proton and X-ray irradiation

description: <b>Background:</b> Radiation therapy is an important alternative treatment for advanced cancer. The aim of the current study was to disclose distinct alterations of the biological characteristics of gene expression features in pancreatic cancer cells, MIAPaCa-2, following proton and X-ray irradiation. <b>Materials and methods:</b> Using cDNA microarray, we examined the gene expression alterations of MIAPaCa-2 cells following proton or X-ray irradiation. We also isolated the surviving MIAPaCa-2 cells after irradiation and analyzed their gene expression profiles. <b>Results:</b> Although the cytocidal effects of both types of irradiation were similar at sufficient doses in vitro and in vivo, the affected gene expression profile alterations of MIAPaCa-2 cells irradiated with protons were distinct from those irradiated with X-ray. Interestingly, clustering analysis of gene expression of the surviving MIAPaCa-2 cells was also completely discernible between the two types of irradiation. However, a similar cytocidal effect was still observed in the proton- and X-ray-irradiated surviving cells after re-irradiation, commonly showing biological effects related to apoptosis and cell cycle processes. <b>Conclusions:</b> Proton irradiation treatment for pancreatic cancer provides the distinct biological effect of steady gene expression alterations compared to X-ray irradiation; however, surviving cells from both types of irradiation were still susceptible to the cytocidal effects induced by proton re-irradiation treatment.
DOI: 10.6084/m9.figshare.7473374
title: Data Citation 1

description: Gene RPKM analysis for PRO-seq and ChIP-exo data
DOI: 10.7284/110850
title: Gravimeter data collected during research cruise MGL1306 using a Bell BGM-3 instrument system onboard the platform RV Marcus G. Langseth

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7473332
title: Data Set 3: Proximity ligation assay of PTEN-L:EGFP (V420) with Gab2 after control (PBS) or 50µM glutamate treatment (Fig. 4c)

description: This dataset contains 18<b> .tif</b> image files holding the results of a proximity ligation assay of PTEN-L:EGFP (V420) with Gab2 after control (PBS) or 50µM glutamate treatment. These images correspond to figure 4 of the related article: Unique properties of PTEN-L contribute to neuroprotection in response to ischemic-like stress.<br>The related study investigates the function and regulation of PTEN-L in neurons in the context of brain ischemia. Exogenous, EGFP-tagged PTEN-L or the shorter variant PTEN were expressed in primary neurons after knock out of endogenous PTEN. Oxygen-glucose deprivation or exposure to 50 µM glutamate were applied to neurons to test their response to ischemic-like stress.<br> <b>Figure 4 | Unique interaction of PTEN-L:EGFP in response to glutamate stress and cytosolic interaction with Gab2.</b><strong> <br></strong> A proximity-ligation assay with a Gab2 and PTEN-L antibody was performed in PTEN-L replaced neurons. These image data present the interaction between Gab2 and PTEN-L under PBS conditions, including changes after 50μM glutamate was applied, as described in the related research article.<b><br></b><b>Methods</b>: Primary neurons derived from conditional PTEN knockout mice were plated in 8-well microscopy dishes (Ibidi) and transduced with either cre- and PTEN-delivering lentiviral particles LVPs (Knockout and exogenous PTEN replacement condition), or mcherry- and EGFP-delivering control LVPs (Endogenous PTEN condition). At DIV 9 cells were treated with either PBS or 50 µM glutamate for 60 min and fixed with 4 % formaldehyde. To test the primary antibodies anti-GAB2 (HPA001368, Sigma-Aldrich), derived from murine origin, and anti-PTEN-L (MABS1680, Merck), derived from canine origin, cells were permeabilised with 0.25% triton X-100 , blocked with 0.2% normal donkey serum (ab7475, Abcam) and primary antibodies were applied at 1:500 dilutions over-night. Secondary antibodies alexa Fluor 647 donkey anti-rabbit IgG and alexa Fluor 647 donkey anti-mouse IgG (ThermoFisher) were applied at 1:500 dilutions for 1 h at room temperature.<br> To detect interactions between GAB2 and PTEN-L below a distance of 40 nm, permeabilisation, blocking and primary antibodies were applied like described above. Duolink® PLA PLUS targeting mouse IgGs and Duolink® PLA MINUS secondary antibodies targeting rabbit IgGs were incubated at ambient temperature overnight. Ligation, rolling circle amplification and hybridization with in the far red detectable olgionucleotides were performed according to the manufacturer’s instructions (Duolink ® PLA, Sigma Aldrich).
DOI: 10.6084/m9.figshare.7473374.v2
title: Data Citation 1

description: Gene RPKM analysis for PRO-seq and ChIP-exo data
DOI: 10.6084/m9.figshare.7473374.v1
title: Data Citation 1

description: Gene RPKM analysis for PRO-seq and ChIP-exo data
DOI: 10.7284/110843
title: Gyrocompass data collected during research cruise MGL1306 using a Kongsberg Simrad GC80 instrument system onboard the platform RV Marcus G. Langseth

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7473332.v1
title: Data Set 3: Proximity ligation assay of PTEN-L:EGFP (V420) with Gab2 after control (PBS) or 50µM glutamate treatment (Fig. 4c)

description: This dataset contains 18<b> .tif</b> image files holding the results of a proximity ligation assay of PTEN-L:EGFP (V420) with Gab2 after control (PBS) or 50µM glutamate treatment. These images correspond to figure 4 of the related article: Unique properties of PTEN-L contribute to neuroprotection in response to ischemic-like stress.<br>The related study investigates the function and regulation of PTEN-L in neurons in the context of brain ischemia. Exogenous, EGFP-tagged PTEN-L or the shorter variant PTEN were expressed in primary neurons after knock out of endogenous PTEN. Oxygen-glucose deprivation or exposure to 50 µM glutamate were applied to neurons to test their response to ischemic-like stress.<br> <b>Figure 4 | Unique interaction of PTEN-L:EGFP in response to glutamate stress and cytosolic interaction with Gab2.</b><strong> <br></strong> A proximity-ligation assay with a Gab2 and PTEN-L antibody was performed in PTEN-L replaced neurons. These image data present the interaction between Gab2 and PTEN-L under PBS conditions, including changes after 50μM glutamate was applied, as described in the related research article.<b><br></b><b>Methods</b>: Primary neurons derived from conditional PTEN knockout mice were plated in 8-well microscopy dishes (Ibidi) and transduced with either cre- and PTEN-delivering lentiviral particles LVPs (Knockout and exogenous PTEN replacement condition), or mcherry- and EGFP-delivering control LVPs (Endogenous PTEN condition). At DIV 9 cells were treated with either PBS or 50 µM glutamate for 60 min and fixed with 4 % formaldehyde. To test the primary antibodies anti-GAB2 (HPA001368, Sigma-Aldrich), derived from murine origin, and anti-PTEN-L (MABS1680, Merck), derived from canine origin, cells were permeabilised with 0.25% triton X-100 , blocked with 0.2% normal donkey serum (ab7475, Abcam) and primary antibodies were applied at 1:500 dilutions over-night. Secondary antibodies alexa Fluor 647 donkey anti-rabbit IgG and alexa Fluor 647 donkey anti-mouse IgG (ThermoFisher) were applied at 1:500 dilutions for 1 h at room temperature.<br> To detect interactions between GAB2 and PTEN-L below a distance of 40 nm, permeabilisation, blocking and primary antibodies were applied like described above. Duolink® PLA PLUS targeting mouse IgGs and Duolink® PLA MINUS secondary antibodies targeting rabbit IgGs were incubated at ambient temperature overnight. Ligation, rolling circle amplification and hybridization with in the far red detectable olgionucleotides were performed according to the manufacturer’s instructions (Duolink ® PLA, Sigma Aldrich).
DOI: 10.7284/110848
title: INS (Inertial Navigation System) data collected during research cruise MGL1306 using a Kongsberg Seapath 200 instrument system onboard the platform RV Marcus G. Langseth

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7473248
title: p = 0.0001

description: pressure = 0.0001<br>
DOI: 10.6084/m9.figshare.7473248.v1
title: p = 0.0001

description: pressure = 0.0001<br>
DOI: 10.7284/110851
title: INS (Inertial Navigation System) data collected during research cruise MGL1306 using a Applanix POS/MV-320 V3 instrument system onboard the platform RV Marcus G. Langseth

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7473218
title: Mutation list

description: list of mutations identified in these MA lines in 7 environments.
DOI: 10.6084/m9.figshare.7473221
title: Conformation-dependent dynamics of macromolecular ions in the gas phase under an electrostatic field: A molecular dynamics simulation

description: Highly charged macromolecular ions exhibit various conformations in gas. Intramolecular charge-to-charge interaction induces a transformation from a globular structure into a stretched one. The change in the molecular conformation brings a complex dynamic behavior of ions under an electrostatic field. In the present study, we visualized the movement of a monovalent and multiply charged straight chain macromolecules, polyethylene glycol (PEG), by a molecular dynamics (MD) simulation. The simulation showed that a singly charged PEG ion (899 M<sub>W</sub> &lt; 4,643) takes a globular conformation. The electrical mobilities of these ions determined from the migration distance under an electric field were compared with the experimental data and those determined by the classical Mason–Schamp theory under an assumption of spherical shape. As a result, we obtained a good agreement between the MD, theoretical, and experimental data for the monovalent ions. We also found that the MD simulation successfully predicts the electrical mobility of the multiply charged stretched PEG ions, but the classical theory fails. We were able to visualize the periodic bending and stretching motion by the MD simulation. This unique motion results from the localization of charges on the PEG molecule and may have a significant effect on the dynamic behavior of macromolecule ions in gas. Copyright © 2019 American Association for Aerosol Research
DOI: 10.6084/m9.figshare.7473218.v1
title: Mutation list

description: list of mutations identified in these MA lines in 7 environments.
DOI: 10.7284/110846
title: Meteorological Station data collected during research cruise MGL1306 using a RM Young 26700 instrument system onboard the platform RV Marcus G. Langseth

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7473221.v1
title: Conformation-dependent dynamics of macromolecular ions in the gas phase under an electrostatic field: A molecular dynamics simulation

description: Highly charged macromolecular ions exhibit various conformations in gas. Intramolecular charge-to-charge interaction induces a transformation from a globular structure into a stretched one. The change in the molecular conformation brings a complex dynamic behavior of ions under an electrostatic field. In the present study, we visualized the movement of a monovalent and multiply charged straight chain macromolecules, polyethylene glycol (PEG), by a molecular dynamics (MD) simulation. The simulation showed that a singly charged PEG ion (899 M<sub>W</sub> &lt; 4,643) takes a globular conformation. The electrical mobilities of these ions determined from the migration distance under an electric field were compared with the experimental data and those determined by the classical Mason–Schamp theory under an assumption of spherical shape. As a result, we obtained a good agreement between the MD, theoretical, and experimental data for the monovalent ions. We also found that the MD simulation successfully predicts the electrical mobility of the multiply charged stretched PEG ions, but the classical theory fails. We were able to visualize the periodic bending and stretching motion by the MD simulation. This unique motion results from the localization of charges on the PEG molecule and may have a significant effect on the dynamic behavior of macromolecule ions in gas. Copyright © 2019 American Association for Aerosol Research
DOI: 10.6084/m9.figshare.7473170
title: Download_Website_Section.zip

description: Download Website Section Data
DOI: 10.6084/m9.figshare.7473170.v1
title: Download_Website_Section.zip

description: Download Website Section Data
DOI: 10.7284/110842
title: Multibeam Echosounder data collected during research cruise MGL1306 using a Kongsberg EM122 instrument system onboard the platform RV Marcus G. Langseth

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7473164
title: 2-DE gel images of Tuber magnatum Pico samples

description: 2-DE gel images related to <i>Tuber magnatum </i>Pico samples collected from three different geographical areas (Isernia, San Miniato, Alba). Twelve (Isernia) or sixteen replicate gels (four for each year of collection, Alba, San Miniato) were performed for each biological sample, depending on the overall duration of the study for each of the sampling locations evaluated.<br>
DOI: 10.6084/m9.figshare.7473167.v1
title: superesolved light sheet microscopy of microspheres

description: 3D view of a 100 µm thick stacks of images of fluorescent 0.4-0.6 µm diameter microspheres (Spherotec Inc.) embedded in a pluronic gel excited at 355 nm with and without stimulation depletion at 532 nm.
DOI: 10.7284/110844
title: pCO2 (Partial Pressure of Carbon Dioxide) data collected during research cruise MGL1306 using a LDEO pCO2 instrument system onboard the platform RV Marcus G. Langseth

description: Original (unprocessed) data collected during a Field_expedition