cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3468890.v1
title: Early Career Research Network (Univ. Exeter) - Strategically Using Social Media to Communicate Science

description: This is the presentation I gave for the University of Exeter's Early Career Research Network on 30 June 2016.
DOI: 10.6084/m9.figshare.3468791
title: Stratigraphy of Reinga and Aotea basins, NW New Zealand: constraints from dredge samples on regional correlations and reservoir character

description: Sandstone, mudstone and limestone samples dredged in the Reinga and Aotea basins, NW New Zealand during voyage TAN1312 provide age and lithological constraints on the Cretaceous–Neogene succession. A total of 46 micropaleontology and 7 macropaleontology samples were examined along with 84 thin-sectioned petrographical samples. Some were examined by X-ray diffraction and porosity-permeability analyses. Late Cretaceous sandstones are dominated by feldspathic and lithofeldspathic compositions, with mixed granitic plutoniclastic and volcaniclastic provenance; a comparison with Pakawau Group of Taranaki Basin is appropriate. Late Cretaceous–Paleogene mudstones are widespread and display close petrographical and age similarities to the Whangai Formation facies of other parts of New Zealand and fine-grained carbonate facies of the Weber and Amuri formations of eastern North and South Islands, respectively. Cretaceous limestone and Paleogene sandstone were not recovered. Carbonates and mudstones dominate the Neogene succession of Reinga and Aotea basins; rare Neogene sandstones have feldspatholithic compositions and resemble Waitemata Group sandstones of the northern North Island. In terms of petroleum prospectivity, Cretaceous sandstones represent a potential reservoir facies but are lithic with low permeability.
DOI: 10.6084/m9.figshare.3468791.v1
title: Stratigraphy of Reinga and Aotea basins, NW New Zealand: constraints from dredge samples on regional correlations and reservoir character

description: Sandstone, mudstone and limestone samples dredged in the Reinga and Aotea basins, NW New Zealand during voyage TAN1312 provide age and lithological constraints on the Cretaceous–Neogene succession. A total of 46 micropaleontology and 7 macropaleontology samples were examined along with 84 thin-sectioned petrographical samples. Some were examined by X-ray diffraction and porosity-permeability analyses. Late Cretaceous sandstones are dominated by feldspathic and lithofeldspathic compositions, with mixed granitic plutoniclastic and volcaniclastic provenance; a comparison with Pakawau Group of Taranaki Basin is appropriate. Late Cretaceous–Paleogene mudstones are widespread and display close petrographical and age similarities to the Whangai Formation facies of other parts of New Zealand and fine-grained carbonate facies of the Weber and Amuri formations of eastern North and South Islands, respectively. Cretaceous limestone and Paleogene sandstone were not recovered. Carbonates and mudstones dominate the Neogene succession of Reinga and Aotea basins; rare Neogene sandstones have feldspatholithic compositions and resemble Waitemata Group sandstones of the northern North Island. In terms of petroleum prospectivity, Cretaceous sandstones represent a potential reservoir facies but are lithic with low permeability.
DOI: 10.6084/m9.figshare.3468734
title: Identifying the microbial taxa which consistently respond to soil warming across time and space

description: Phylotype tables (rarefied) and corresponding metadata for soil warming project, pre 0.05% cutoff filtering.<br>- Lab incubation experiment- Global grasslands dataset- US LTER dataset- Peru elevation<br><br>
DOI: 10.6084/m9.figshare.3468734.v1
title: Identifying the microbial taxa which consistently respond to soil warming across time and space

description: Phylotype tables (rarefied) and corresponding metadata for soil warming project, pre 0.05% cutoff filtering.<br>- Lab incubation experiment- Global grasslands dataset- US LTER dataset- Peru elevation<br><br>
DOI: 10.6084/m9.figshare.3468734.v2
title: Identifying the microbial taxa which consistently respond to soil warming across time and space

description: Phylotype tables (rarefied) and corresponding metadata for soil warming project, pre 0.05% cutoff filtering.<br>- Lab incubation experiment- Global grasslands dataset- US LTER dataset- Peru elevation<br><br>
DOI: 10.6084/m9.figshare.3468734.v4
title: Identifying the microbial taxa which consistently respond to soil warming across time and space

description: Phylotype tables (rarefied) and corresponding metadata for soil warming project, pre 0.05% cutoff filtering.<br>- Lab incubation experiment- Global grasslands dataset- US LTER dataset- Peru elevation<br><br>
DOI: 10.6084/m9.figshare.3468734.v3
title: Identifying the microbial taxa which consistently respond to soil warming across time and space

description: Phylotype tables (rarefied) and corresponding metadata for soil warming project, pre 0.05% cutoff filtering.<br>- Lab incubation experiment- Global grasslands dataset- US LTER dataset- Peru elevation<br><br>
DOI: 10.6084/m9.figshare.3468728
title: Juvenile Hormone Affinity Purification

description: <i>Drosophila</i> S2 cell frozen cells were pelleted by centrifugation and prepared by glass Dounce homogenizing on ice in lysis buffer (I-Per insect protein extraction reagent; Fisher Scientific) containing Halt™ protease inhibitor cocktail with EDTA (Fisher Scientific). Cell lysates were centrifuged 13.2k x g for 20 min at 4°C and the supernatant was collected and used as the initial whole cell lysate. For the JH affinity column, 10 cell pellets were homogenized and the whole cell lysate was recirculated through the control linoleate column for 1 hour at 4°C to remove non-specific binding proteins; the flow-through was transferred to the JH affinity column and recirculated for 4 hours at 4°C. The columns were washed with 20 column volumes of bead buffer (50 mM Tris pH 6.8, 5 mM sodium fluoride, 240 mM sodium chloride, 100 µM benzamidine HCL 5mM EDTA, 5 mM EGTA, 0.1% triton X-100, Halt™ protease inhibitor cocktail) until the OD<sub>280</sub> fell below 0.05. The JH affinity column was eluted by recirculating bead buffer plus 10 mg/ml methoprene for 4 hours at 4°C. The control column was eluted by adding release buffer (10% sodium dodecyl sulfate (SDS), 1% beta-mercaptoethanol) and the resin brought to 95°C. The resin was centrifuged and the supernatant collected. The process was repeated several times and the supernatants pooled. Eluted proteins were concentrated against 20% polyethylene glycol in SDS reservoir buffer, separated on Precise™ 4-20% Tris-HEPES Gels (Fisher Scientific) and visualized by non-destructive silver staining (Blum et al. 1987). Protein gels from the control and JH resins were compared; bands unique to the JH resin were identified, cut from the gel and taken to the University of Wisconsin Biotechnology Center for tryptic digest and identification by mass spectrometry. Synthesis and elution for the methoprene and linoleic affinity columns followed the same procedures but cell lysates were eluted with 8M urea, concentrated with a 10K spin column (Amicon) and exchanged to 500mM ammonium bicarbonate before the sample was sent to University of Wisconsin Biotechnology Center for tryptic digest and identification by mass spectrometry.
DOI: 10.6084/m9.figshare.3468728.v1
title: Juvenile Hormone Affinity Purification

description: <i>Drosophila</i> S2 cell frozen cells were pelleted by centrifugation and prepared by glass Dounce homogenizing on ice in lysis buffer (I-Per insect protein extraction reagent; Fisher Scientific) containing Halt™ protease inhibitor cocktail with EDTA (Fisher Scientific). Cell lysates were centrifuged 13.2k x g for 20 min at 4°C and the supernatant was collected and used as the initial whole cell lysate. For the JH affinity column, 10 cell pellets were homogenized and the whole cell lysate was recirculated through the control linoleate column for 1 hour at 4°C to remove non-specific binding proteins; the flow-through was transferred to the JH affinity column and recirculated for 4 hours at 4°C. The columns were washed with 20 column volumes of bead buffer (50 mM Tris pH 6.8, 5 mM sodium fluoride, 240 mM sodium chloride, 100 µM benzamidine HCL 5mM EDTA, 5 mM EGTA, 0.1% triton X-100, Halt™ protease inhibitor cocktail) until the OD<sub>280</sub> fell below 0.05. The JH affinity column was eluted by recirculating bead buffer plus 10 mg/ml methoprene for 4 hours at 4°C. The control column was eluted by adding release buffer (10% sodium dodecyl sulfate (SDS), 1% beta-mercaptoethanol) and the resin brought to 95°C. The resin was centrifuged and the supernatant collected. The process was repeated several times and the supernatants pooled. Eluted proteins were concentrated against 20% polyethylene glycol in SDS reservoir buffer, separated on Precise™ 4-20% Tris-HEPES Gels (Fisher Scientific) and visualized by non-destructive silver staining (Blum et al. 1987). Protein gels from the control and JH resins were compared; bands unique to the JH resin were identified, cut from the gel and taken to the University of Wisconsin Biotechnology Center for tryptic digest and identification by mass spectrometry. Synthesis and elution for the methoprene and linoleic affinity columns followed the same procedures but cell lysates were eluted with 8M urea, concentrated with a 10K spin column (Amicon) and exchanged to 500mM ammonium bicarbonate before the sample was sent to University of Wisconsin Biotechnology Center for tryptic digest and identification by mass spectrometry.
DOI: 10.6084/m9.figshare.3468704.v2
title: Uncovering the diverse cultural bases of social identity: In-group ties predict self-stereotyping amongst individualists but not among collectivists.

description: On what basis do people form their social identities? To investigate this issue, the present research investigated cross-cultural differences in self-stereotyping, a key outcome of social identification. In particular, the research tested the hypothesis that in-group ties are a stronger predictor of self-stereotyping among people from individualist cultures than among people from collectivist cultures. In Study 1, university students (<i>N</i> = 117) completed measures of in-group ties and self-stereotyping with respect to an intimacy group (family and friends). Consistent with predictions, in-group ties significantly predicted self-stereotyping among individualists but not among collectivists. Study 2 (<i>N</i> = 104) found a similar pattern of results among members of the global internet community who considered either an intimacy group (their friends), a task group (their work group), or a social category (their gender). These results indicate that people in individualist cultures are more likely than those in collectivist cultures to base their social identities on in-group ties. The implications of these results are discussed in relation to self-categorization theory’s depersonalization account of social identification.
DOI: 10.6084/m9.figshare.3468701
title: Cisuralian coals of the Mullaley Sub-basin, northern New South Wales

description: The Mullaley Sub-basin of the Gunnedah Basin extends from Quirindi in the southeast, to north of Narrabri, to west of Dunedoo in northern New South Wales. There have been more than 100 boreholes sunk to basement investigating the (lower Permian) Cisuralian coal and coal seam gas resources of the Mullaley Sub-basin since the early 1990s. A desktop review of this open file information has allowed the formal correlation and naming of six Cisuralian coal members attaining a maximum 35 m of cumulative thickness within an upward coarsening sedimentary package totalling no more than 150 m. In ascending order, the coal members are: Bibblewindi (0–10 m), Bohena (3–18 m), Collygra (0.5–3 m), Coxs (1.5–4 m), Tullamullen (0.5–4 m) and Mooki (0.5–3 m). Cisuralian coal seams in the Maules Creek Formation of the southern Mullaley Sub-basin are here correlated with those of the Greta Coal Measures at Werris Creek and Muswellbrook. It is apparent that basement paleotopography played a significant role in the Cisuralian coal development as coals are best developed where the sedimentary sequence is greater than 60 m thick, as there the thick seams (Bohena and Bibblewindi coal members) occur towards the base of the sequence. The maximum western limit of the Cisuralian coals (Rocky Glen Ridge) is further east than previously inferred with new drilling information showing the Porcupine Formation directly overlying the barren pelletoidal claystones of the Leard Formation or the underlying volcanics (Boggabri Volcanics/Werrie Basalt). Early marine transgressions at the top of the Maules Creek Formation have stopped development of the Mooki, Tullamullen and Coxs coal members in the northern and eastern Mullaley Sub-basin and allowed the development of localised paraconglomerate (diamictite) intervals up to 10 m thick. Thick (&gt;20 m cumulative) coal occurrences are localised to the Jacks Creek and Pilliga East State Forest areas southwest of Narrabri. The coal resource potential of the Mullaley Sub-basin is estimated at 13–28 billion tonnes.
DOI: 10.6084/m9.figshare.3468701.v2
title: Cisuralian coals of the Mullaley Sub-basin, northern New South Wales

description: The Mullaley Sub-basin of the Gunnedah Basin extends from Quirindi in the southeast, to north of Narrabri, to west of Dunedoo in northern New South Wales. There have been more than 100 boreholes sunk to basement investigating the (lower Permian) Cisuralian coal and coal seam gas resources of the Mullaley Sub-basin since the early 1990s. A desktop review of this open file information has allowed the formal correlation and naming of six Cisuralian coal members attaining a maximum 35 m of cumulative thickness within an upward coarsening sedimentary package totalling no more than 150 m. In ascending order, the coal members are: Bibblewindi (0–10 m), Bohena (3–18 m), Collygra (0.5–3 m), Coxs (1.5–4 m), Tullamullen (0.5–4 m) and Mooki (0.5–3 m). Cisuralian coal seams in the Maules Creek Formation of the southern Mullaley Sub-basin are here correlated with those of the Greta Coal Measures at Werris Creek and Muswellbrook. It is apparent that basement paleotopography played a significant role in the Cisuralian coal development as coals are best developed where the sedimentary sequence is greater than 60 m thick, as there the thick seams (Bohena and Bibblewindi coal members) occur towards the base of the sequence. The maximum western limit of the Cisuralian coals (Rocky Glen Ridge) is further east than previously inferred with new drilling information showing the Porcupine Formation directly overlying the barren pelletoidal claystones of the Leard Formation or the underlying volcanics (Boggabri Volcanics/Werrie Basalt). Early marine transgressions at the top of the Maules Creek Formation have stopped development of the Mooki, Tullamullen and Coxs coal members in the northern and eastern Mullaley Sub-basin and allowed the development of localised paraconglomerate (diamictite) intervals up to 10 m thick. Thick (&gt;20 m cumulative) coal occurrences are localised to the Jacks Creek and Pilliga East State Forest areas southwest of Narrabri. The coal resource potential of the Mullaley Sub-basin is estimated at 13–28 billion tonnes.
DOI: 10.6084/m9.figshare.3468695
title: Critical role of Kupffer cell CD89 expression in experimental IgA nephropathy-Supporting Information file

description: The supporting Information file of the manuscript"Critical role of Kupffer cell CD89 expression in experimental IgA nephropathy".
DOI: 10.6084/m9.figshare.3468695.v1
title: Critical role of Kupffer cell CD89 expression in experimental IgA nephropathy-Supporting Information file

description: The supporting Information file of the manuscript"Critical role of Kupffer cell CD89 expression in experimental IgA nephropathy".
DOI: 10.6084/m9.figshare.3468671
title: cyCLASS: CLASS Models for Cyclus

description: Source code for the cyCLASS package.<br>cyCLASS allows using CLASS fuel fabrication Model and Irradiation Model in the Cyclus framework<br><br>
DOI: 10.6084/m9.figshare.3468671.v4
title: cyCLASS: CLASS Models for Cyclus

description: Source code for the cyCLASS package.<br>cyCLASS allows using CLASS fuel fabrication Model and Irradiation Model in the Cyclus framework<br><br>
DOI: 10.6084/m9.figshare.3468653
title: Continuity-based approaches to seriation and the study of patterns of cultural inheritance

description: Presentation delivered at HBES 2016
DOI: 10.6084/m9.figshare.3468653.v2
title: Continuity-based approaches to seriation and the study of patterns of cultural inheritance

description: Presentation delivered at HBES 2016
DOI: 10.6084/m9.figshare.3468653.v1
title: lipomadsen2016-hbes-continuity-inheritance.pdf

description: Presentation delivered at HBES 2016
DOI: 10.6084/m9.figshare.3468566
title: Oxidative damage and chemokine production dominate days before immune cell infiltration and EAE disease debut

description: Data files on which the results presented in the manuscript 'Oxidative damage and chemokine production dominate days before immune cell infiltration and EAE disease debut' are based.
DOI: 10.6084/m9.figshare.3468566.v1
title: Oxidative damage and chemokine production dominate days before immune cell infiltration and EAE disease debut

description: Data files on which the results presented in the manuscript 'Oxidative damage and chemokine production dominate days before immune cell infiltration and EAE disease debut' are based.
DOI: 10.6084/m9.figshare.3468506
title: History of A. thaliana Atg8 isoform identifiers

description: Atg8 isoforms of <i>Arabidospis thaliana</i> were assigned multiple names in earlier publications. The presented table summarises these names with each row linking former names to the current nomenclature and coding sequence as provided by The Arabidopsis Information Resource (https://www.arabidopsis.org).<br><br>Doelling, J. H., Walker, J. M., Friedman, E. M., Thompson, A. R., & Vierstra, R. D. (2002). The APG8/12-activating enzyme APG7 is required for proper nutrient recycling and senescence in Arabidopsis thaliana. <i>Journal of Biological Chemistry</i>, <i>277</i>(36), 33105–33114. http://doi.org/10.1074/jbc.M204630200Hanaoka, H., Noda, T., Shirano, Y., Kato, T., Hayashi, H., Shibata, D., … Ohsumi, Y. (2002). Leaf senescence and starvation-induced chlorosis are accelerated by the disruption of an Arabidopsis autophagy gene. <i>Plant Physiology</i>, <i>129</i>(3), 1181–93. http://doi.org/10.1104/pp.011024Sláviková, S., Shy, G., Yao, Y., Glozman, R., Levanony, H., Pietrokovski, S., … Galili, G. (2005). The autophagy-associated Atg8 gene family operates both under favourable growth conditions and under starvation stresses in Arabidopsis plants. <i>Journal of Experimental Botany</i>, <i>56</i>(421), 2839–2849. http://doi.org/10.1093/jxb/eri276Thompson, A. R. (2005). Autophagic Nutrient Recycling in Arabidopsis Directed by the ATG8 and ATG12 Conjugation Pathways. <i>Plant Physiology</i>, <i>138</i>(4), 2097–2110. http://doi.org/10.1104/pp.105.060673Yoshimoto, K., Hanaoka, H., Sato, S., Kato, T., Tabata, S., Noda, T., & Ohsumi, Y. (2004). Processing of ATG8s, ubiquitin-like proteins, and their deconjugation by ATG4s are essential for plant autophagy. <i>The Plant Cell</i>, <i>16</i>(11), 2967–2983. http://doi.org/10.1105/tpc.104.025395
DOI: 10.6084/m9.figshare.3468470
title: Inducible RasGEF1B circular RNA is a positive regulator of ICAM-1 in the TLR4/LPS pathway

description: Circular RNAs (circRNAs) constitute a large class of RNA species formed by the back-splicing of co-linear exons, often within protein-coding transcripts. Despite much progress in the field, it remains elusive whether the majority of circRNAs are merely aberrant splicing by-products with unknown functions, or their production is spatially and temporally regulated to carry out specific biological functions. To date, the majority of circRNAs have been cataloged in resting cells. Here, we identify an LPS-inducible circRNA: <i>mcircRasGEF1B</i>, which is predominantly localized in cytoplasm, shows cell-type specific expression, and has a human homolog with similar properties, <i>hcircRasGEF1B</i>. We show that knockdown of the expression of <i>mcircRasGEF1B</i> reduces LPS-induced <i>ICAM-1</i> expression. Additionally, we demonstrate that <i>mcircRasGEF1B</i> regulates the stability of mature <i>ICAM-1</i> mRNAs. These findings expand the inventory of functionally characterized circRNAs with a novel RNA species that may play a critical role in fine-tuning immune responses and protecting cells against microbial infection.
DOI: 10.6084/m9.figshare.3468470.v2
title: Inducible RasGEF1B circular RNA is a positive regulator of ICAM-1 in the TLR4/LPS pathway

description: Circular RNAs (circRNAs) constitute a large class of RNA species formed by the back-splicing of co-linear exons, often within protein-coding transcripts. Despite much progress in the field, it remains elusive whether the majority of circRNAs are merely aberrant splicing by-products with unknown functions, or their production is spatially and temporally regulated to carry out specific biological functions. To date, the majority of circRNAs have been cataloged in resting cells. Here, we identify an LPS-inducible circRNA: <i>mcircRasGEF1B</i>, which is predominantly localized in cytoplasm, shows cell-type specific expression, and has a human homolog with similar properties, <i>hcircRasGEF1B</i>. We show that knockdown of the expression of <i>mcircRasGEF1B</i> reduces LPS-induced <i>ICAM-1</i> expression. Additionally, we demonstrate that <i>mcircRasGEF1B</i> regulates the stability of mature <i>ICAM-1</i> mRNAs. These findings expand the inventory of functionally characterized circRNAs with a novel RNA species that may play a critical role in fine-tuning immune responses and protecting cells against microbial infection.
DOI: 10.6084/m9.figshare.3468470.v1
title: Inducible RasGEF1B circular RNA is a positive regulator of <i>ICAM-1</i> in the TLR4/LPS pathway

description: Circular RNAs (circRNAs) constitute a large class of RNA species formed by the back-splicing of co-linear exons, often within protein-coding transcripts. Despite much progress in the field, it remains elusive whether the majority of circRNAs are merely aberrant splicing by-products with unknown functions, or their production is spatially and temporally regulated to carry out specific biological functions. To date, the majority of circRNAs have been catalogued in resting cells. Here, we identify an LPS-inducible circRNA: <i>mcircRasGEF1B</i>, which is predominantly localized in cytoplasm, shows cell-type specific expression, and has a human homolog with similar properties, <i>hcircRasGEF1B</i>. We show that knockdown of the expression of <i>mcircRasGEF1B</i> reduces LPS-induced <i>ICAM-1</i> expression. Additionally, we demonstrate that <i>mcircRasGEF1B</i> regulates the stability of mature <i>ICAM-1</i> mRNAs. These findings expand the inventory of functionally characterized circRNAs with a novel RNA species that may play a critical role in fine-tuning immune responses and protecting cells against microbial infection.