cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.2796886
title: Low-dose AgNPs reduce lung mechanical function and innate immune defense in the absence of cellular toxicity

description: Multiple studies have examined the direct cellular toxicity of silver nanoparticles (AgNPs). However, the lung is a complex biological system with multiple cell types and a lipid-rich surface fluid; therefore, organ level responses may not depend on direct cellular toxicity. We hypothesized that interaction with the lung lining is a critical determinant of organ level responses. Here, we have examined the effects of low dose intratracheal instillation of AgNPs (0.05 μg/g body weight) 20 and 110 nm diameter in size, and functionalized with citrate or polyvinylpyrrolidone. Both size and functionalization were significant factors in particle aggregation and lipid interaction <i>in vitro</i>. One day post-intratracheal instillation lung function was assessed, and bronchoalveolar lavage (BAL) and lung tissue collected. There were no signs of overt inflammation. There was no change in surfactant protein-B content in the BAL but there was loss of surfactant protein-D with polyvinylpyrrolidone (PVP)-stabilized particles. Mechanical impedance data demonstrated a significant increase in pulmonary elastance as compared to control, greatest with 110 nm PVP-stabilized particles. Seven days post-instillation of PVP-stabilized particles increased BAL cell counts, and reduced lung function was observed. These changes resolved by 21 days. Hence, AgNP-mediated alterations in the lung lining and mechanical function resolve by 21 days. Larger particles and PVP stabilization produce the largest disruptions. These studies demonstrate that low dose AgNPs elicit deficits in both mechanical and innate immune defense function, suggesting that organ level toxicity should be considered.
DOI: 10.6084/m9.figshare.2796886.v1
title: Low-dose AgNPs reduce lung mechanical function and innate immune defense in the absence of cellular toxicity

description: Multiple studies have examined the direct cellular toxicity of silver nanoparticles (AgNPs). However, the lung is a complex biological system with multiple cell types and a lipid-rich surface fluid; therefore, organ level responses may not depend on direct cellular toxicity. We hypothesized that interaction with the lung lining is a critical determinant of organ level responses. Here, we have examined the effects of low dose intratracheal instillation of AgNPs (0.05 μg/g body weight) 20 and 110 nm diameter in size, and functionalized with citrate or polyvinylpyrrolidone. Both size and functionalization were significant factors in particle aggregation and lipid interaction <i>in vitro</i>. One day post-intratracheal instillation lung function was assessed, and bronchoalveolar lavage (BAL) and lung tissue collected. There were no signs of overt inflammation. There was no change in surfactant protein-B content in the BAL but there was loss of surfactant protein-D with polyvinylpyrrolidone (PVP)-stabilized particles. Mechanical impedance data demonstrated a significant increase in pulmonary elastance as compared to control, greatest with 110 nm PVP-stabilized particles. Seven days post-instillation of PVP-stabilized particles increased BAL cell counts, and reduced lung function was observed. These changes resolved by 21 days. Hence, AgNP-mediated alterations in the lung lining and mechanical function resolve by 21 days. Larger particles and PVP stabilization produce the largest disruptions. These studies demonstrate that low dose AgNPs elicit deficits in both mechanical and innate immune defense function, suggesting that organ level toxicity should be considered.
DOI: 10.6084/m9.figshare.2818540
title: Antiproliferative activity of <i>Curcuma phaeocaulis</i> <i>Valeton</i> extract using ultrasonic assistance and response surface methodology

description: The objective of the study was to optimize the ultrasonic-assisted extraction of curdione, furanodienone, curcumol, and germacrone from <i>Curcuma phaeocaulis</i> <i>Valeton</i> (Val.) and investigate the antiproliferative activity of the extract. Under the suitable high-performance liquid chromatography condition, the calibration curves for these four tested compounds showed high levels of linearity and the recoveries of these four compounds were between 97.9 and 104.3%. Response surface methodology (RSM) combining central composite design and desirability function (DF) was used to define optimal extraction parameters. The results of RSM and DF revealed that the optimum conditions were obtained as 8 mL g<sup>−1</sup> for liquid–solid ratio, 70% ethanol concentration, and 20 min of ultrasonic time. It was found that the surface structures of the sonicated herbal materials were fluffy and irregular. The <i>C. phaeocaulis</i> Val. extract significantly inhibited the proliferation of RKO and HT-29 cells <i>in vitro</i>. The results reveal that the RSM can be effectively used for optimizing the ultrasonic-assisted extraction of bioactive components from <i>C. phaeocaulis</i> Val. for antiproliferative activity.
DOI: 10.6084/m9.figshare.2818540.v1
title: Anti-proliferative activity of <i>Curcuma phaeocaulis Valeton</i> extract using ultrasonic assistance and response surface methodology

description: The objective of the study was to optimize the ultrasonic-assisted extraction of curdione, furanodienone, curcumol and germacrone from <i>Curcuma phaeocaulis Valeton</i> (Val.) and investigate the anti-proliferative activity of the extract. Under the suitable high performance liquid chromatography condition, the calibration curves for these four tested compounds showed high levels of linearity and the recoveries of these four compounds were between 97.9% and 104.3%. Response surface methodology (RSM) combining central composite design and desirability function (DF) was used to define optimal extraction parameters. The results of RSM and DF revealed that the optimum conditions were obtained as 8 mL · g<sup>−1</sup> for liquid-solid ratio, 70% ethanol concentration and 20 min of ultrasonic time. It was found that the surface structures of the sonicated herbal materials were fluffy and irregular. The <i>Curcuma phaeocaulis</i> Val. extract significantly inhibited the proliferation of RKO and HT-29 cells <i>in vitro</i>. The results reveal that the response surface methodology can be effectively employed for optimizing the ultrasonic-assisted extraction of bioactive components from <i>Curcuma phaeocaulis</i> Val. for anti-proliferative activity.
DOI: 10.6084/m9.figshare.2818540.v2
title: Antiproliferative activity of <i>Curcuma phaeocaulis</i> <i>Valeton</i> extract using ultrasonic assistance and response surface methodology

description: The objective of the study was to optimize the ultrasonic-assisted extraction of curdione, furanodienone, curcumol, and germacrone from <i>Curcuma phaeocaulis</i> <i>Valeton</i> (Val.) and investigate the antiproliferative activity of the extract. Under the suitable high-performance liquid chromatography condition, the calibration curves for these four tested compounds showed high levels of linearity and the recoveries of these four compounds were between 97.9 and 104.3%. Response surface methodology (RSM) combining central composite design and desirability function (DF) was used to define optimal extraction parameters. The results of RSM and DF revealed that the optimum conditions were obtained as 8 mL g<sup>−1</sup> for liquid–solid ratio, 70% ethanol concentration, and 20 min of ultrasonic time. It was found that the surface structures of the sonicated herbal materials were fluffy and irregular. The <i>C. phaeocaulis</i> Val. extract significantly inhibited the proliferation of RKO and HT-29 cells <i>in vitro</i>. The results reveal that the RSM can be effectively used for optimizing the ultrasonic-assisted extraction of bioactive components from <i>C. phaeocaulis</i> Val. for antiproliferative activity.
DOI: 10.6084/m9.figshare.2825557
title: XMAn-A Homo sapiens Mutated Cancer Peptides Database

description: To enable the identification of mutated peptide sequences in complex
biological samples, in this work, a cancer protein database with mutation information collected from several
public resources such as COSMIC, IARC P53, OMIM and UniProtKB, was developed. In-house
developed Perl-scripts were used to search and process the data, and to
translate each gene-level mutation into a mutated peptide sequence. The
cancer mutation database comprises a total of 872,125 peptide entries from 25,642 protein IDs. A description
line for each entry provides the parent protein ID and name, the cDNA- and
protein-level mutation site and type, the originating database, and the cancer tissue type and corresponding hits. The database is FASTA
formatted to enable data retrieval by commonly used tandem MS search engines. <br>
DOI: 10.6084/m9.figshare.2825557.v1
title: XMAn – A Homo sapiens Mutated-Peptide Database

description: To enable the identification of mutated peptide sequences in complex
biological samples, in this work, a cancer protein database with mutation information collected from several
public resources such as COSMIC, IARC P53, OMIM and UniProtKB, was developed. In-house
developed Perl-scripts were used to search and process the data, and to
translate each gene-level mutation into a mutated peptide sequence. The
cancer mutation database comprises a total of 872,125 peptide entries from 25,642 protein IDs. A description
line for each entry provides the parent protein ID and name, the cDNA- and
protein-level mutation site and type, the originating database, and the cancer tissue type and corresponding hits. The database is FASTA
formatted to enable data retrieval by commonly used tandem MS search engines. <br>
DOI: 10.6084/m9.figshare.2825557.v2
title: XMAn_Homo_Sapiens_Mutated_Peptide_Database_cancer_fasta

description: To enable the identification of mutated peptide sequences in complex
biological samples, in this work, a cancer protein database with mutation information collected from several
public resources such as COSMIC, IARC P53, OMIM and UniProtKB, was developed. In-house
developed Perl-scripts were used to search and process the data, and to
translate each gene-level mutation into a mutated peptide sequence. The
cancer mutation database comprises a total of 872,125 peptide entries from 25,642 protein IDs. A description
line for each entry provides the parent protein ID and name, the cDNA- and
protein-level mutation site and type, the originating database, and the cancer tissue type and corresponding hits. The database is FASTA
formatted to enable data retrieval by commonly used tandem MS search engines. <br>
DOI: 10.6084/m9.figshare.2825557.v4
title: XMAn-A Homo sapiens Mutated Cancer Peptides Database

description: To enable the identification of mutated peptide sequences in complex
biological samples, in this work, a cancer protein database with mutation information collected from several
public resources such as COSMIC, IARC P53, OMIM and UniProtKB, was developed. In-house
developed Perl-scripts were used to search and process the data, and to
translate each gene-level mutation into a mutated peptide sequence. The
cancer mutation database comprises a total of 872,125 peptide entries from 25,642 protein IDs. A description
line for each entry provides the parent protein ID and name, the cDNA- and
protein-level mutation site and type, the originating database, and the cancer tissue type and corresponding hits. The database is FASTA
formatted to enable data retrieval by commonly used tandem MS search engines. <br>
DOI: 10.6084/m9.figshare.2825557.v3
title: XMAn_Homo_Sapiens_Mutated_Peptides_Database_Cancer_fasta

description: To enable the identification of mutated peptide sequences in complex
biological samples, in this work, a cancer protein database with mutation information collected from several
public resources such as COSMIC, IARC P53, OMIM and UniProtKB, was developed. In-house
developed Perl-scripts were used to search and process the data, and to
translate each gene-level mutation into a mutated peptide sequence. The
cancer mutation database comprises a total of 872,125 peptide entries from 25,642 protein IDs. A description
line for each entry provides the parent protein ID and name, the cDNA- and
protein-level mutation site and type, the originating database, and the cancer tissue type and corresponding hits. The database is FASTA
formatted to enable data retrieval by commonly used tandem MS search engines. <br>
DOI: 10.6084/m9.figshare.3051700
title: A Wiskott–Aldrich syndrome protein is involved in endocytosis in <i>Aspergillus nidulans</i>

description: Endocytosis is vital for hyphal tip growth in filamentous fungi and is involved in the tip localization of various membrane proteins. To investigate the function of a Wiskott–Aldrich syndrome protein (WASP) in endocytosis of filamentous fungi, we identified a WASP ortholog-encoding gene, <i>wspA</i>, in <i>Aspergillus nidulans</i> and characterized it. The <i>wspA</i> product, WspA, localized to the tips of germ tubes during germination and actin rings in the subapical regions of mature hyphae. <i>wspA</i> is essential for the growth and functioned in the polarity establishment and maintenance during germination of conidia. We also investigated its function in endocytosis and revealed that endocytosis of SynA, a synaptobrevin ortholog that is known to be endocytosed at the subapical regions of hyphal tips in <i>A</i>. <i>nidulans</i>, did not occur when <i>wspA</i> expression was repressed. These results suggest that WspA plays roles in endocytosis at hyphal tips and polarity establishment during germination. Colocalization of a WASP ortholog and actin filament in the hyphal tips of <i>Aspergillus nidulans</i>.
DOI: 10.6084/m9.figshare.3051700.v1
title: A Wiskott–Aldrich syndrome protein is involved in endocytosis in <i>Aspergillus nidulans</i>

description: Endocytosis is vital for hyphal tip growth in filamentous fungi and is involved in the tip localization of various membrane proteins. To investigate the function of a Wiskott–Aldrich syndrome protein (WASP) in endocytosis of filamentous fungi, we identified a WASP ortholog-encoding gene, <i>wspA</i>, in <i>Aspergillus nidulans</i> and characterized it. The <i>wspA</i> product, WspA, localized to the tips of germ tubes during germination and actin rings in the subapical regions of mature hyphae. <i>wspA</i> is essential for the growth and functioned in the polarity establishment and maintenance during germination of conidia. We also investigated its function in endocytosis and revealed that endocytosis of SynA, a synaptobrevin ortholog that is known to be endocytosed at the subapical regions of hyphal tips in <i>A</i>. <i>nidulans</i>, did not occur when <i>wspA</i> expression was repressed. These results suggest that WspA plays roles in endocytosis at hyphal tips and polarity establishment during germination. Colocalization of a WASP ortholog and actin filament in the hyphal tips of <i>Aspergillus nidulans</i>.
DOI: 10.6084/m9.figshare.3081211
title: A correlation between the Large Igneous Provinces and mass extinctions: constraint on the end-Guadalupian mass extinction and the Emeishan LIP in South China, eastern Tethys

description: Well-documented outcrops around the Emeishan Large Igneous Province (ELIP) in South China, eastern Tethys, encompassing the end-Guadalupian mass extinction have been investigated. Correlatable sections recording the event exhibit very similar lithological characters, positive-then-negative C isotope excursions and massive biotic demise. Detailed analyses of the fossil record and carbon isotopic variations were carried out on the Guadalupian–Wuchiapingian Boundary sections over the inner, middle, outer zones of the ELIP and its margin. Due to a pronounced decrease in marine habitat area and the environmental and ecological change over this part of the Tethys, the biota crisis records show the loss of numerous tropical invertebrate taxa, and exhibit fewer genera and smaller testing sizes and low productivity. The biota crisis was a sustainable and gradual reduction in diversity over the Capitanian. The associated carbon isotopic data reveal unusually high δ<sup>13</sup>C(carb) values before the late Capitanian, representing higher primary productivity (or buried rate) and more <sup>13</sup>C-enriched CO<sub>2</sub> released by hydrothermal carbonate breakdown from the upper crust into the sediments at that time. Subsequently, an accelerated negative excursion across the boundary and the gradual excursion with low carbon isotope amplitude favours an increased influx of light <sup>12</sup>C sourced by the volcanism around the eastern Tethys. The very similar time–space relation between the biota crisis and the Emeishan volcanism confirms that volcanic eruptions may have triggered the biota crisis event in South China. Intensive volcanism could result in detrimental environmental and ecological stresses, habitat loss, organic material splitting, or the emission of light carbon and thermal fluid (or aerosol), implying that the losses of the shallow-marine invertebrates either occurred geologically instantaneously or in a series of closely spaced crises coinciding with the initial phase of ELIP formation. These findings in South China may reveal the causal relation between mass extinctions and LIPs in a global context.
DOI: 10.6084/m9.figshare.3081211.v1
title: A correlation between the Large Igneous Provinces and mass extinctions: constraint on the end-Guadalupian mass extinction and the Emeishan LIP in South China, eastern Tethys

description: Well-documented outcrops around the Emeishan Large Igneous Province (ELIP) in South China, eastern Tethys, encompassing the end-Guadalupian mass extinction have been investigated. Correlatable sections recording the event exhibit very similar lithological characters, positive-then-negative C isotope excursions and massive biotic demise. Detailed analyses of the fossil record and carbon isotopic variations were carried out on the Guadalupian–Wuchiapingian Boundary sections over the inner, middle, outer zones of the ELIP and its margin. Due to a pronounced decrease in marine habitat area and the environmental and ecological change over this part of the Tethys, the biota crisis records show the loss of numerous tropical invertebrate taxa, and exhibit fewer genera and smaller testing sizes and low productivity. The biota crisis was a sustainable and gradual reduction in diversity over the Capitanian. The associated carbon isotopic data reveal unusually high δ<sup>13</sup>C(carb) values before the late Capitanian, representing higher primary productivity (or buried rate) and more <sup>13</sup>C-enriched CO<sub>2</sub> released by hydrothermal carbonate breakdown from the upper crust into the sediments at that time. Subsequently, an accelerated negative excursion across the boundary and the gradual excursion with low carbon isotope amplitude favours an increased influx of light <sup>12</sup>C sourced by the volcanism around the eastern Tethys. The very similar time–space relation between the biota crisis and the Emeishan volcanism confirms that volcanic eruptions may have triggered the biota crisis event in South China. Intensive volcanism could result in detrimental environmental and ecological stresses, habitat loss, organic material splitting, or the emission of light carbon and thermal fluid (or aerosol), implying that the losses of the shallow-marine invertebrates either occurred geologically instantaneously or in a series of closely spaced crises coinciding with the initial phase of ELIP formation. These findings in South China may reveal the causal relation between mass extinctions and LIPs in a global context.
DOI: 10.6084/m9.figshare.3081991
title: Modeling the response of phytoplankton to reduced external nutrient load in a subtropical Chinese reservoir using DYRESM-CAEDYM

description: Cui Y, Zhu G, Li H, Luo L, Cheng X, Jin Y, and Trolle D. Modeling the response of phytoplankton to reduced external nutrient load in a subtropical Chinese reservoir using DYRESM-CAEDYM. Lake Reserv Manage. 32: 146--157. The DYRESM-CAEDYM model was used to quantify the potential effects of reductions in external nutrient loads to the Shahe Reservoir in China, with an emphasis on effects on phytoplankton biomass. DYRESM-CAEDYM was calibrated using field data for a 2-year period and validated against a separate 1-year period. Simulated values for water temperature, dissolved oxygen, total nitrogen, total phosphorus, and chlorophyll <i>a</i> showed good agreement with field measurements. The model tended to underestimate peak values of inorganic nutrients such as ammonium, nitrate, and phosphate, with phosphate levels close to detection limits in both observed and simulated values. The model successfully captured seasonal phytoplankton succession, indicating spring peaks of diatom biomass and summer peaks of cyanophytes. Scenarios in which different reductions in external loading were applied suggest that simultaneous reductions in both external nitrogen and external phosphorus loading is more effective in controlling phytoplankton biomass than reducing input of either nutrient alone. Diatoms responded more strongly to load reductions in phosphorus input than nitrogen load, whereas cyanophytes showed the opposite pattern. A combined 25% reduction in the external loading of both nutrients could significantly decrease phytoplankton biomass in the reservoir below the 7 μg/L chlorophyll <i>a</i> required by drinking water standards, and the study indicated that DYRESM-CAEDYM can be a useful management tool for eutrophication control.
DOI: 10.6084/m9.figshare.3081991.v1
title: Modeling the response of phytoplankton to reduced external nutrient load in a subtropical Chinese reservoir using DYRESM-CAEDYM

description: Cui Y, Zhu G, Li H, Luo L, Cheng X, Jin Y, and Trolle D. Modeling the response of phytoplankton to reduced external nutrient load in a subtropical Chinese reservoir using DYRESM-CAEDYM. Lake Reserv Manage. 32: 146--157. The DYRESM-CAEDYM model was used to quantify the potential effects of reductions in external nutrient loads to the Shahe Reservoir in China, with an emphasis on effects on phytoplankton biomass. DYRESM-CAEDYM was calibrated using field data for a 2-year period and validated against a separate 1-year period. Simulated values for water temperature, dissolved oxygen, total nitrogen, total phosphorus, and chlorophyll <i>a</i> showed good agreement with field measurements. The model tended to underestimate peak values of inorganic nutrients such as ammonium, nitrate, and phosphate, with phosphate levels close to detection limits in both observed and simulated values. The model successfully captured seasonal phytoplankton succession, indicating spring peaks of diatom biomass and summer peaks of cyanophytes. Scenarios in which different reductions in external loading were applied suggest that simultaneous reductions in both external nitrogen and external phosphorus loading is more effective in controlling phytoplankton biomass than reducing input of either nutrient alone. Diatoms responded more strongly to load reductions in phosphorus input than nitrogen load, whereas cyanophytes showed the opposite pattern. A combined 25% reduction in the external loading of both nutrients could significantly decrease phytoplankton biomass in the reservoir below the 7 μg/L chlorophyll <i>a</i> required by drinking water standards, and the study indicated that DYRESM-CAEDYM can be a useful management tool for eutrophication control.