cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4300109.v2
title: How is Herstatin, a tumor suppressor splice variant of the oncogene <i>HER2</i>, regulated?

description: The human epidermal growth factor receptor 2 (HER2)/receptor tyrosine-protein kinasebB-2 (ERBB2) is overexpressed in 20–30% of breast tumors leading to faster growing and more aggressive tumors. Alternative splicing generates a functionally distinct HER2 variant called Herstatin, which is produced by the inclusion of intron 8. Herstatin acts as a tumor suppressor by effectively blocking HER2 activity and cell proliferation, while promoting apoptosis. In the present study we investigated HER2 pre-mRNA regulatory sequences and splicing factors which regulate the alternative splicing of Herstatin. A Herstatin minigene, comprising exon 8/intron 8/exon 9 of HER2 was generated and subsequent in vitro splicing assays revealed that RNA secondary structure and somatic mutations did not impact on inclusion of intron 8. However, using RNase-assisted RNA chromatography, followed by mass spectrometry, we identified six RNA-binding proteins (splicing factors) that bind to RNA sequences surrounding exon 8/intron 8 and intron 8/exon 9 boundaries; these included hnRNP I, H1, D, A2/B1 and hnRNPA1 plus the SR protein SRSF1. Specifically, overexpression of hnRNP A1 significantly increased retention of intron 8 resulting in higher levels of Herstatin in SKBR3 breast cancer cells whereas SRSF1 only had a marginal effect in decreasing Herstatin but increased exogenous HER2 levels under these experimental conditions. In conclusion, we have identified the first splicing factors and regulatory sequences that are involved in the production of Herstatin.
DOI: 10.6084/m9.figshare.4300109.v1
title: How is Herstatin, a tumour suppressor splice variant of the oncogene <i>HER2,</i> regulated?

description: The human epidermal growth factor receptor 2 (HER2)/receptor tyrosine-protein kinasebB-2 (ERBB2) is over-expressed in 20–30% of breast tumours leading to faster growing and more aggressive tumours. Alternative splicing generates a functionally distinct HER2 variant called Herstatin, which is produced by the inclusion of intron 8. Herstatin acts as a tumour suppressor by effectively blocking HER2 activity and cell proliferation, while promoting apoptosis. In the present study we investigated HER2 pre-mRNA regulatory sequences and splicing factors which regulate the alternative splicing of Herstatin. A Herstatin minigene, comprising exon 8/intron 8/exon 9 of HER2 was generated and subsequent in vitro splicing assays revealed that RNA secondary structure and somatic mutations did not impact on inclusion of intron 8. However, using RNase-assisted RNA chromatography, followed by mass spectrometry, we identified six RNA-binding proteins (splicing factors) that bind to RNA sequences surrounding exon 8/intron 8 and intron 8/exon 9 boundaries; these included hnRNP I, H1, D, A2/B1 and hnRNPA1 plus the SR protein SRSF1. Specifically, overexpression of hnRNP A1 significantly increased retention of intron 8 resulting in higher levels of Herstatin in SKBR3 breast cancer cells whereas SRSF1 only had a marginal effect in decreasing Herstatin but increased exogenous HER2 levels under these experimental conditions. In conclusion, we have identified the first splicing factors and regulatory sequences that are involved in the production of Herstatin.
DOI: 10.6084/m9.figshare.4300022
title: LPI_LPR2016data_public.csv

description: Data are available for use in accordance with the data policy: https://livingplanetindex.org/documents/data_agreement.pdf<br><br>Time series of population abundance data for vertebrate species spanning years between 1970 and 2012. These data were used in the Living Planet Report 2016. Confidential records that cannot be shared have been removed from this data set. A beta version of the code used in calculation of the Living Planet Index using this data set can be found here https://github.com/Zoological-Society-of-London/rlpi
DOI: 10.6084/m9.figshare.4300043.v2
title: Urai et al. (2017) Pupil-linked arousal is driven by decision uncertainty and alters serial choice bias. Nature Communications

description: This is the data to replicate all analyses from Urai AE, Braun A, Donner THD. (2017) Pupil-linked arousal is driven by decision uncertainty and alters serial choice bias.<br>See https://github.com/anne-urai/pupilUncertainty for the analysis code, including detailed instructions for replicating the figures from the manuscript.
DOI: 10.6084/m9.figshare.4299866
title: Supplementary Material for: Serum Bicarbonate Is Associated with Heart Failure in the Multi-Ethnic Study of Atherosclerosis

description: <b><i>Background:</i></b> Low serum bicarbonate concentrations are associated with mortality and kidney disease progression. Data regarding associations between bicarbonate and cardiovascular disease (CVD) are scarce. <b><i>Methods:</i></b> We performed a cohort study of 6,229 adult participants from the Multi-Ethnic Study of Atherosclerosis, a community-based cohort free of CVD at baseline. Serum bicarbonate was measured at baseline. Cardiovascular outcomes were defined as: (1) subclinical CVD (left ventricular mass [LVM] and aortic pulse pressure [PP] measured at baseline), (2) incident atherosclerotic cardiovascular events (CVE; composite of myocardial infarction, resuscitated cardiac arrest, stroke, coronary heart disease death, and stroke death), and (3) incident heart failure. <b><i>Results:</i></b> During a median (interquartile range) follow-up of 8.5 (7.7-8.6) years, 331 (5.3%) participants had an incident CVE and 174 (2.8%) developed incident heart failure. We stratified analyses by use of diuretics because we observed a significant interaction between diuretic use and bicarbonate with study outcomes. Among diuretic nonusers, with adjustment, bicarbonate ≥25 mEq/L was associated with an estimated 3.0 g greater LVM (95% CI 0.5-5.0) and 1.0 mm Hg higher aortic PP (95% CI 0.4-2.0) compared to bicarbonate 23-24 mEq/L. Each 1 mEq/L of bicarbonate increase was associated with a 13% higher risk of incident heart failure (hazards ratio 1.13, 95% CI 1.01-2.11). Among diuretic users, higher bicarbonate was not associated with CVD. Bicarbonate was not associated with incident atherosclerotic CVE irrespective of diuretic use. <b><i>Conclusion:</i></b> Among nonusers of diuretics in a large community-based study, higher serum bicarbonate concentrations are associated with subclinical CVD and new heart failure.
DOI: 10.6084/m9.figshare.4299854
title: Supplementary Material for: Interleukin-17RA Promotes Humoral Responses and Glomerular Injury in Experimental Rapidly Progressive Glomerulonephritis

description: <b><i>Background/Aims:</i></b> Interleukin (IL)-17A and IL-17F are proinflammatory cytokines, which signal through a receptor complex consisting of IL-17RA and IL-17RC subunits. We sought to define the role of IL-17RA expression by leukocytes and stromal cells in nephritogenic immunity and injury in experimental glomerulonephritis. <b><i>Methods:</i></b> Glomerulonephritis was induced in wild-type and IL-17RA-deficient (IL-17RA<sup>-/-</sup>) mice by sheep anti-mouse glomerular basement membrane globulin. Renal injury and immune responses were assessed at day 21. Glomerulonephritis was induced in bone marrow (BM) chimeric mice, with either BM or tissue cell (TC) deficiency of IL-17RA. To assess humoral responses, WT and IL-17RA<sup>-/-</sup> mice were sensitized to sheep globulin and euthanized 10 days later. <b><i>Results:</i></b> IL-17RA<sup>-/-</sup> mice had reduced glomerular crescent formation, neutrophils and macrophages compared to wild-type mice, while nephritic BM-TC+ mice developed less glomerular segmental necrosis. IL-17RA expression was required in both BM and TC for maximal systemic interferon-γ expression. Antigen-specific humoral immune responses were impaired in the absence of IL-17RA. Compared to BM+TC+ mice, glomerular IgG and C3 deposition was reduced in BM+TC- and BM-TC+ mice, respectively. Humoral immunity was also impaired in BM- and TC-deficient chimeras. BM+TC- mice had fewer B cells expressing CXCR5, while IL-17RA<sup>-/-</sup> mice had abnormal germinal centre development after immunization, with reduced follicular B cell and follicular helper T-cell CXCR5 expression, explaining the impaired humoral immunity. <b><i>Conclusion:</i></b> IL-17RA contributes to experimental glomerulonephritis, with IL-17RA expression on both leukocytes and stromal cells being required for the full expression of nephritogenic humoral immunity.
DOI: 10.6084/m9.figshare.4300043.v4
title: Urai et al. (2017) Pupil-linked arousal is driven by decision uncertainty and alters serial choice bias. Nature Communications

description: This is the data to replicate all analyses from Urai AE, Braun A, Donner THD. (2017) Pupil-linked arousal is driven by decision uncertainty and alters serial choice bias. Nature Communications, in press.<br>See https://github.com/anne-urai/pupilUncertainty for the analysis code, including detailed instructions for replicating the figures from the manuscript.
DOI: 10.6084/m9.figshare.4299842
title: Supplementary Material for: Laparoscopic versus Open Surgery for Diverticulitis: A Systematic Review and Meta-Analysis

description: <b><i>Background/Aims:</i></b> The study aimed to perform a meta-analysis comparing laparoscopic and open surgery for diverticulitis. <b><i>Methods:</i></b> Studies comparing the outcomes of laparoscopic surgery versus open surgery for diverticulitis that reported quantitative data were included. Outcome measures were mortality and morbidity rates and length of hospital stay. <b><i>Results:</i></b> Four randomized controlled trials - 3 prospective and 21 retrospective - were included in the analysis. The total numbers of patients ranged from 5 to 14,562 in the laparoscopic groups and from 4 to 110,172 in the open surgery groups, and the mean patient age ranged from 38.9 to 78 years. Overall analysis revealed that laparoscopic surgery was associated with lower mortality (pooled OR 0.40, 95% CI 0.25-0.63, p &lt; 0.001) and a lower overall morbidity rate (pooled OR 0.65, 95% CI 0.51-0.82, p &lt; 0.001) than open surgery. Laparoscopic surgery was associated with a higher anastomotic bleeding rate, but lower rates of ileus, anastomotic leakage, small bowel obstruction, wound infection, fascial dehiscence and intra-abdominal abscesses. Length of hospital stay was less with laparoscopic surgery. <b><i>Conclusions:</i></b> The current meta-analysis supports the use of laparoscopy for the treatment of diverticulitis. The results, however, should be interpreted with caution.
DOI: 10.6084/m9.figshare.4300043.v5
title: Urai et al. (2017) Pupil-linked arousal is driven by decision uncertainty and alters serial choice bias. Nature Communications

description: This is the data to replicate all analyses from Urai AE, Braun A, Donner THD. (2017) Pupil-linked arousal is driven by decision uncertainty and alters serial choice bias. Nature Communications, in press.<br>See https://github.com/anne-urai/pupilUncertainty for the analysis code, including detailed instructions for replicating the figures from the manuscript.
DOI: 10.6084/m9.figshare.4299842.v1
title: Supplementary Material for: Laparoscopic versus Open Surgery for Diverticulitis: A Systematic Review and Meta-Analysis

description: <b><i>Background/Aims:</i></b> The study aimed to perform a meta-analysis comparing laparoscopic and open surgery for diverticulitis. <b><i>Methods:</i></b> Studies comparing the outcomes of laparoscopic surgery versus open surgery for diverticulitis that reported quantitative data were included. Outcome measures were mortality and morbidity rates and length of hospital stay. <b><i>Results:</i></b> Four randomized controlled trials - 3 prospective and 21 retrospective - were included in the analysis. The total numbers of patients ranged from 5 to 14,562 in the laparoscopic groups and from 4 to 110,172 in the open surgery groups, and the mean patient age ranged from 38.9 to 78 years. Overall analysis revealed that laparoscopic surgery was associated with lower mortality (pooled OR 0.40, 95% CI 0.25-0.63, p &lt; 0.001) and a lower overall morbidity rate (pooled OR 0.65, 95% CI 0.51-0.82, p &lt; 0.001) than open surgery. Laparoscopic surgery was associated with a higher anastomotic bleeding rate, but lower rates of ileus, anastomotic leakage, small bowel obstruction, wound infection, fascial dehiscence and intra-abdominal abscesses. Length of hospital stay was less with laparoscopic surgery. <b><i>Conclusions:</i></b> The current meta-analysis supports the use of laparoscopy for the treatment of diverticulitis. The results, however, should be interpreted with caution.
DOI: 10.6084/m9.figshare.4300043.v6
title: Urai et al. (2017) Pupil-linked arousal is driven by decision uncertainty and alters serial choice bias. Nature Communications

description: This is the data to replicate all analyses from Urai AE, Braun A, Donner THD. (2017) Pupil-linked arousal is driven by decision uncertainty and alters serial choice bias. Nature Communications, 8: 14637. http://www.nature.com/articles/ncomms14637<br>See https://github.com/anne-urai/pupilUncertainty for the analysis code, including detailed instructions for replicating the figures from the manuscript.
DOI: 10.6084/m9.figshare.4300043.v7
title: Urai AE, Braun A, Donner THD. (2017) Pupil-linked arousal is driven by decision uncertainty and alters serial choice bias. Nature Communications, 8: 14637.

description: This is the data to replicate all analyses from Urai AE, Braun A, Donner THD. (2017) Pupil-linked arousal is driven by decision uncertainty and alters serial choice bias. Nature Communications, 8: 14637.<br>See https://github.com/anne-urai/pupilUncertainty for the analysis code, including detailed instructions for replicating the figures from the manuscript.
DOI: 10.6084/m9.figshare.4299737
title: Markers of lipid oxidative damage in the exhaled breath condensate of nano TiO<sub>2</sub> production workers

description: Nanoscale titanium dioxide (nanoTiO<sub>2</sub>) is a commercially important nanomaterial. Animal studies have documented lung injury and inflammation, oxidative stress, cytotoxicity and genotoxicity. Yet, human health data are scarce and quantitative risk assessments and biomonitoring of exposure are lacking. NanoTiO<sub>2</sub> is classified by IARC as a group 2B, possible human carcinogen. In our earlier studies we documented an increase in markers of inflammation, as well as DNA and protein oxidative damage, in exhaled breath condensate (EBC) of workers exposed nanoTiO<sub>2</sub>. This study focuses on biomarkers of lipid oxidation. Several established lipid oxidative markers (malondialdehyde, 4-hydroxy-trans-hexenal, 4-hydroxy-trans-nonenal, 8-isoProstaglandin F2α and aldehydes C<sub>6</sub>–C<sub>12</sub>) were studied in EBC and urine of 34 workers and 45 comparable controls. The median particle number concentration in the production line ranged from 1.98 × 10<sup>4</sup> to 2.32 × 10<sup>4</sup> particles/cm<sup>3</sup> with ∼80% of the particles<i> </i>&lt;100 nm in diameter. Mass concentration varied between 0.40 and 0.65 mg/m<sup>3</sup>. All 11 markers of lipid oxidation were elevated in production workers relative to the controls (<i>p</i> 2 and markers of lipid oxidation in the EBC. These markers were not elevated in the urine samples. Lipid oxidation in the EBC of workers exposed to (nano)TiO<sub>2</sub> complements our earlier findings on DNA and protein damage. These results are consistent with the oxidative stress hypothesis and suggest lung injury at the molecular level. Further studies should focus on clinical markers of potential disease progression. EBC has reemerged as a sensitive technique for noninvasive monitoring of workers exposed to engineered nanoparticles.
DOI: 10.6084/m9.figshare.4299737.v1
title: Markers of lipid oxidative damage in the exhaled breath condensate of nano TiO<sub>2</sub> production workers

description: Nanoscale titanium dioxide (nanoTiO<sub>2</sub>) is a commercially important nanomaterial. Animal studies have documented lung injury and inflammation, oxidative stress, cytotoxicity and genotoxicity. Yet, human health data are scarce and quantitative risk assessments and biomonitoring of exposure are lacking. NanoTiO<sub>2</sub> is classified by IARC as a group 2B, possible human carcinogen. In our earlier studies we documented an increase in markers of inflammation, as well as DNA and protein oxidative damage, in exhaled breath condensate (EBC) of workers exposed nanoTiO<sub>2</sub>. This study focuses on biomarkers of lipid oxidation. Several established lipid oxidative markers (malondialdehyde, 4-hydroxy-trans-hexenal, 4-hydroxy-trans-nonenal, 8-isoProstaglandin F2α and aldehydes C<sub>6</sub>–C<sub>12</sub>) were studied in EBC and urine of 34 workers and 45 comparable controls. The median particle number concentration in the production line ranged from 1.98 × 10<sup>4</sup> to 2.32 × 10<sup>4</sup> particles/cm<sup>3</sup> with ∼80% of the particles<i> </i>&lt;100 nm in diameter. Mass concentration varied between 0.40 and 0.65 mg/m<sup>3</sup>. All 11 markers of lipid oxidation were elevated in production workers relative to the controls (<i>p</i> 2 and markers of lipid oxidation in the EBC. These markers were not elevated in the urine samples. Lipid oxidation in the EBC of workers exposed to (nano)TiO<sub>2</sub> complements our earlier findings on DNA and protein damage. These results are consistent with the oxidative stress hypothesis and suggest lung injury at the molecular level. Further studies should focus on clinical markers of potential disease progression. EBC has reemerged as a sensitive technique for noninvasive monitoring of workers exposed to engineered nanoparticles.
DOI: 10.6084/m9.figshare.4299734
title: Source Datasets for the paper: High Resolution Mapping of Soil Properties Using Remote Sensing Variables in South-Western Burkina Faso: a Comparison of Machine Learning and Multiple Regression Models

description: Climate and topographic remote sensing variables
DOI: 10.6084/m9.figshare.4299734.v1
title: Source Datasets for the paper: High Resolution Mapping of Soil Properties Using Remote Sensing Variables in South-Western Burkina Faso: a Comparison of Machine Learning and Multiple Regression Models

description: Climate and topographic remote sensing variables
DOI: 10.6084/m9.figshare.4299725
title: Data Availability.rar

description: Data made available for PlusOne article. It contains code and raw data to fully reproduce the results found in the manuscript.
DOI: 10.6084/m9.figshare.4299725.v1
title: Data Availability.rar

description: Data made available for PlusOne article. It contains code and raw data to fully reproduce the results found in the manuscript.
DOI: 10.6084/m9.figshare.4299701
title: Electric field induced alignment of multiwalled carbon nanotubes in polymers and multiscale composites

description: Carbon fiber reinforced polymers (CFRPs) have a highly anisotropic electrical resistivity, which limits their use in electrical applications. In this contribution, an electric field was used to align multiwalled carbon nanotubes (MWCNTs) to create preferential conductive pathways within a nanocomposite and a multiscale composite in order to reduce their resistivity. Investigation on epoxy containing MWCNTs have shown that an electric field of 40 V mm<sup>−1</sup> or higher applied for 2 h can lead to a reduction of the resistivity parallel to the field up to four orders of magnitude with only 0·01 wt-% loading. In the case of CFRPs reinforced with 0·01 and 0·1 wt-% of MWCNTs, we observed reductions of the through the thickness resistivity of 36 and 99% respectively, when an electric field of 60 V mm<sup>−1</sup> was applied for 2 h during the fabrication of the samples.
DOI: 10.6084/m9.figshare.4299701.v1
title: Electric field induced alignment of multiwalled carbon nanotubes in polymers and multiscale composites

description: Carbon fiber reinforced polymers (CFRPs) have a highly anisotropic electrical resistivity, which limits their use in electrical applications. In this contribution, an electric field was used to align multiwalled carbon nanotubes (MWCNTs) to create preferential conductive pathways within a nanocomposite and a multiscale composite in order to reduce their resistivity. Investigation on epoxy containing MWCNTs have shown that an electric field of 40 V mm<sup>−1</sup> or higher applied for 2 h can lead to a reduction of the resistivity parallel to the field up to four orders of magnitude with only 0·01 wt-% loading. In the case of CFRPs reinforced with 0·01 and 0·1 wt-% of MWCNTs, we observed reductions of the through the thickness resistivity of 36 and 99% respectively, when an electric field of 60 V mm<sup>−1</sup> was applied for 2 h during the fabrication of the samples.
DOI: 10.6084/m9.figshare.4299680
title: <i>Tris</i>-<i>N</i>-alkylpyridinium-functionalised cyclotriguaiacylene hosts as axles in branched [4]pseudorotaxane formation

description: A series of [4]pseudorotaxanes composed of three-way axle threads based on the cyclotriguaiacylene family of crown-shaped cavitands and three threaded macrocyclic components has been achieved. These exploit the strong affinity for electron-poor alkyl-pyridinium units to reside within the electron-rich cavity of macrocycles, in this case dimethoxypillar[5]arene (DMP). The branched [4]pseudorotaxane assemblies {(DMP)<sub>3</sub>∙<i>L</i>}<sup>3+</sup>,where <i>L</i> = <i>N</i>-alkylated derivatives of the host molecule (±)-<i>tris</i>-(isonicotinoyl)cyclotriguaiacylene, were characterised by NMR spectroscopy and mass spectrometry, and an energy-minimised structure of {(DMP)<sub>3</sub>∙(<i>tris</i>-(<i>N</i>-propyl-isonicotinoyl)cyclotriguaiacylene)}<sup>3+</sup> was calculated. Crystal structures of <i>N</i>-ethyl-isonicotinoyl)cyclotriguaiacylene hexafluorophosphate and <i>N</i>-propyl-isonicotinoyl)cyclotriguaiacylene hexafluorophosphate each show ‘hand-shake’ self-inclusion motifs occurring between the individual cavitands.
DOI: 10.6084/m9.figshare.4299680.v1
title: <i>Tris</i>-<i>N</i>-alkylpyridinium-functionalised cyclotriguaiacylene hosts as axles in branched [4]pseudorotaxane formation

description: A series of [4]pseudorotaxanes composed of three-way axle threads based on the cyclotriguaiacylene family of crown-shaped cavitands and three threaded macrocyclic components has been achieved. These exploit the strong affinity for electron-poor alkyl-pyridinium units to reside within the electron-rich cavity of macrocycles, in this case dimethoxypillar[5]arene (DMP). The branched [4]pseudorotaxane assemblies {(DMP)<sub>3</sub>∙<i>L</i>}<sup>3+</sup>,where <i>L</i> = <i>N</i>-alkylated derivatives of the host molecule (±)-<i>tris</i>-(isonicotinoyl)cyclotriguaiacylene, were characterised by NMR spectroscopy and mass spectrometry, and an energy-minimised structure of {(DMP)<sub>3</sub>∙(<i>tris</i>-(<i>N</i>-propyl-isonicotinoyl)cyclotriguaiacylene)}<sup>3+</sup> was calculated. Crystal structures of <i>N</i>-ethyl-isonicotinoyl)cyclotriguaiacylene hexafluorophosphate and <i>N</i>-propyl-isonicotinoyl)cyclotriguaiacylene hexafluorophosphate each show ‘hand-shake’ self-inclusion motifs occurring between the individual cavitands.