cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7604843
title: Flame flutter due to g-jitter

description: We consider a laminar diffusion flame as a result of reaction between methane and oxygen, which enter our computational domain from an inner and annular region, respectively.We have added a (sinusoidal) time-dependent source term, signifying 'g-jitter', in the across the flow momentum equation.The two films attached here were made at two different time speeds. The source term changes direction every half cycle, which in turn changes the flame direction. Due to these sudden changes, we observed significant flame flutter. <br>
DOI: 10.6084/m9.figshare.7604846
title: A combination of bioactive and nonbioactive alkyl-peptides form a more stable nanofiber structure for differentiating neural stem cells: a molecular dynamics simulation survey

description: Self-assembling alkyl-peptides are important molecules due to their ability to construct nano-level structures such as nanofibers to be utilized as tissue engineering scaffolds. The bioactive epitope of FAQRVPP which acts as neural stem cells (NSCs) outgrowth inducing factor is used in nanofiber structures. Based on previous experimental studies the density and distribution pattern of the epitopes on the surface of the nanofibers plays an important role in the differentiation function efficiency. We decided to survey and compare the stability of two pre-constructed fiber structures in the forms of all-functionalized nanofiber (containing only bioactive alkyl-peptides) and distributed functionalized nanofiber (a combination of nonbioactive and bioactive alkyl-peptides with ratio 2:1). Our findings reveal that the all-functionalized fiber shows an unstable structure and is split into intermediate micelle-like structures to reduce compactness and steric hindrance of functional epitopes whereas the distributed functionalized fiber shows an integrated stable nanofiber with a more amount of beta sheets that are well-organized and oriented around the hydrophobic core. The hydrogen bonds and energy profiles of the structures indicate the role of hydrophobic interactions during the alkyl-chain core formation and the important role of electrostatic interactions and hydrogen bond network in the stability of the final structures. Finally, it seems that the possibility of the presence of intermediate structure is increased in the all-functionalized nanofiber environment, and it can reduce functional efficiency of the scaffolds. These findings can help to design more efficient nanofiber structures with different goals in scaffolds for tissue engineering. AbbreviationsMDMolecular DynamicsNSCsNeural Stem CellsPMEParticle mesh EwaldRDFRadial Distribution FunctionRGRadius of gyrationRASARelative Accessible Surface AreaRMSDRoot Mean Square DeviationsSASASolvent Accessible Surface Area. Molecular Dynamics Neural Stem Cells Particle mesh Ewald Radial Distribution Function Radius of gyration Relative Accessible Surface Area Root Mean Square Deviations Solvent Accessible Surface Area. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.7604831
title: Effects of agriculture, climate, and policy on NDVI change in a semi-arid river basin of the Chinese Loess Plateau

description: In 1999, the Grain for Green Project was implemented by the Chinese government. Since then, the vegetation of Zuli River Basin, a semi-arid river basin of the Chinese Loess Plateau, has been greatly changed. Clearly understanding the impact of natural and artificial factors on vegetation change is important for policy making and ecosystem management. In this study, spatio-temporal variations in vegetation cover in Chinese Zuli River Basin during 1999–2016 were investigated using Landsat normalized difference vegetation index (NDVI) data. Analyses of several indicators, including changes in NDVI in different slopes and land use changes and the relationships between climatic factors and NDVI change, were presented to quantitatively evaluate the effects of agriculture, climate, and policy on NDVI change. The NDVI in the Zuli River Basin increased during the study period, and the main contributors to this change were forest in 1999–2011, cropland, abandoned farmland, and grassland in 2009–2016, and land with slopes ≤ 15°. Land with slope &gt; 15°, where the “Project” was implemented, slightly contributed to the increase in regional NDVI. In 1999–2011, the project (−98.16%) combined with climate change (−68.18%) showed negative effects on the increase in NDVI in the Zuli River Basin, but agriculture (22.28%) played a positive role in increasing this index. In 2009–2016 and 1999–2016, the project (38.45% and 35.25%, respectively), the project combined with climate change (49.83% and 46.30%, respectively), agriculture (18.61% and 23.30%, respectively), promoted increases in NDVI in the basin.
DOI: 10.6084/m9.figshare.7604843.v1
title: Flame flutter due to g-jitter

description: We consider a laminar diffusion flame as a result of reaction between methane and oxygen, which enter our computational domain from an inner and annular region, respectively.We have added a (sinusoidal) time-dependent source term, signifying 'g-jitter', in the across the flow momentum equation.The two films attached here were made at two different time speeds. The source term changes direction every half cycle, which in turn changes the flame direction. Due to these sudden changes, we observed significant flame flutter. <br>
DOI: 10.6084/m9.figshare.7604846.v1
title: A combination of bioactive and nonbioactive alkyl-peptides form a more stable nanofiber structure for differentiating neural stem cells: a molecular dynamics simulation survey

description: Self-assembling alkyl-peptides are important molecules due to their ability to construct nano-level structures such as nanofibers to be utilized as tissue engineering scaffolds. The bioactive epitope of FAQRVPP which acts as neural stem cells (NSCs) outgrowth inducing factor is used in nanofiber structures. Based on previous experimental studies the density and distribution pattern of the epitopes on the surface of the nanofibers plays an important role in the differentiation function efficiency. We decided to survey and compare the stability of two pre-constructed fiber structures in the forms of all-functionalized nanofiber (containing only bioactive alkyl-peptides) and distributed functionalized nanofiber (a combination of nonbioactive and bioactive alkyl-peptides with ratio 2:1). Our findings reveal that the all-functionalized fiber shows an unstable structure and is split into intermediate micelle-like structures to reduce compactness and steric hindrance of functional epitopes whereas the distributed functionalized fiber shows an integrated stable nanofiber with a more amount of beta sheets that are well-organized and oriented around the hydrophobic core. The hydrogen bonds and energy profiles of the structures indicate the role of hydrophobic interactions during the alkyl-chain core formation and the important role of electrostatic interactions and hydrogen bond network in the stability of the final structures. Finally, it seems that the possibility of the presence of intermediate structure is increased in the all-functionalized nanofiber environment, and it can reduce functional efficiency of the scaffolds. These findings can help to design more efficient nanofiber structures with different goals in scaffolds for tissue engineering. AbbreviationsMDMolecular DynamicsNSCsNeural Stem CellsPMEParticle mesh EwaldRDFRadial Distribution FunctionRGRadius of gyrationRASARelative Accessible Surface AreaRMSDRoot Mean Square DeviationsSASASolvent Accessible Surface Area. Molecular Dynamics Neural Stem Cells Particle mesh Ewald Radial Distribution Function Radius of gyration Relative Accessible Surface Area Root Mean Square Deviations Solvent Accessible Surface Area. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.7604855.v1
title: The structure of viral cathepsin from <i>Bombyx mori Nuclear Polyhedrosis Virus</i> as a target against grasserie: docking and molecular dynamics simulations

description: The viral cathepsin from <i>Bombyx mori <i>Nuclear Polyhedrosis Virus</i></i> (<i>Bm</i>NPV-<i>Cath</i>) is a broad-spectrum protease that participates in the horizontal transmission of this virus in silkworm by facilitating solubilization of the integument of infected caterpillars. When a <i>B. mori</i> farm is attacked by <i>Bm</i>NPV, there are significant sericultural losses because no drugs or therapies are available. In this work, the structure of viral cathepsin <i>Bm</i>NPV-<i>Cath</i> was used as a target for virtual screening simulations, aiming to identify potential molecules that could be used to treat the infection. Virtual screening of the Natural Products library from the Zinc Database selected four molecules. Theoretical calculations of Δ<i>G</i><sub>binding</sub> by the molecular mechanics Poisson–Boltzmann surface analysis (MM-PBSA) method indicated that the molecule Zinc12888007 (Bm5) would have high affinity for the enzyme. The <i>in vivo</i> infection models of <i>B. mori</i> caterpillars with <i>Bm</i>NPV showed that treatment with a dose of 100 μg Bm5 dissolved in Pluronic-F127 0.02% was able to reduce the mortality of caterpillars in 22.6%, however, it did not impede the liquefaction of dead bodies. Our results suggest a role of <i>Bm</i>NPV-<i>Cath</i> in generating a pool of amino acids necessary for viral replication and indicate a mechanism to be exploited in the search for treatments for grasserie disease of the silkworm.
DOI: 10.6084/m9.figshare.7604855.v2
title: The structure of viral cathepsin from <i>Bombyx mori Nuclear Polyhedrosis Virus</i> as a target against grasserie: docking and molecular dynamics simulations

description: The viral cathepsin from <i>Bombyx mori <i>Nuclear Polyhedrosis Virus</i></i> (<i>Bm</i>NPV-<i>Cath</i>) is a broad-spectrum protease that participates in the horizontal transmission of this virus in silkworm by facilitating solubilization of the integument of infected caterpillars. When a <i>B. mori</i> farm is attacked by <i>Bm</i>NPV, there are significant sericultural losses because no drugs or therapies are available. In this work, the structure of viral cathepsin <i>Bm</i>NPV-<i>Cath</i> was used as a target for virtual screening simulations, aiming to identify potential molecules that could be used to treat the infection. Virtual screening of the Natural Products library from the Zinc Database selected four molecules. Theoretical calculations of Δ<i>G</i><sub>binding</sub> by the molecular mechanics Poisson–Boltzmann surface analysis (MM-PBSA) method indicated that the molecule Zinc12888007 (Bm5) would have high affinity for the enzyme. The <i>in vivo</i> infection models of <i>B. mori</i> caterpillars with <i>Bm</i>NPV showed that treatment with a dose of 100 μg Bm5 dissolved in Pluronic-F127 0.02% was able to reduce the mortality of caterpillars in 22.6%, however, it did not impede the liquefaction of dead bodies. Our results suggest a role of <i>Bm</i>NPV-<i>Cath</i> in generating a pool of amino acids necessary for viral replication and indicate a mechanism to be exploited in the search for treatments for grasserie disease of the silkworm.
DOI: 10.7284/134096
title: Speedlog data collected during research cruise EN635 using a Furuno DS-50 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7604849.v1
title: Data and code De Frenne et al. Nature Ecol Evol

description: Data and code for figures and statistics reported in Pieter De Frenne, Florian Zellweger, Francisco Rodríguez-Sánchez, Brett Scheffers, Kristoffer Hylander, Miska Luoto, Mark Vellend, Kris Verheyen & Jonathan Lenoir (2019) Global buffering of temperatures under forest canopies. Nature Ecology & Evolution.<br>
DOI: 10.6084/m9.figshare.7604831.v1
title: Effects of agriculture, climate, and policy on NDVI change in a semi-arid river basin of the Chinese Loess Plateau

description: In 1999, the Grain for Green Project was implemented by the Chinese government. Since then, the vegetation of Zuli River Basin, a semi-arid river basin of the Chinese Loess Plateau, has been greatly changed. Clearly understanding the impact of natural and artificial factors on vegetation change is important for policy making and ecosystem management. In this study, spatio-temporal variations in vegetation cover in Chinese Zuli River Basin during 1999–2016 were investigated using Landsat normalized difference vegetation index (NDVI) data. Analyses of several indicators, including changes in NDVI in different slopes and land use changes and the relationships between climatic factors and NDVI change, were presented to quantitatively evaluate the effects of agriculture, climate, and policy on NDVI change. The NDVI in the Zuli River Basin increased during the study period, and the main contributors to this change were forest in 1999–2011, cropland, abandoned farmland, and grassland in 2009–2016, and land with slopes ≤ 15°. Land with slope &gt; 15°, where the “Project” was implemented, slightly contributed to the increase in regional NDVI. In 1999–2011, the project (−98.16%) combined with climate change (−68.18%) showed negative effects on the increase in NDVI in the Zuli River Basin, but agriculture (22.28%) played a positive role in increasing this index. In 2009–2016 and 1999–2016, the project (38.45% and 35.25%, respectively), the project combined with climate change (49.83% and 46.30%, respectively), agriculture (18.61% and 23.30%, respectively), promoted increases in NDVI in the basin.
DOI: 10.7284/134098
title: Timeserver data collected during research cruise EN635 using a Spectracom SecureSync instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7604849.v2
title: Global buffering of temperatures under forest canopies Data and Code

description: Data and code for figures and statistics reported in Pieter De Frenne, Florian Zellweger, Francisco Rodríguez-Sánchez, Brett Scheffers, Kristoffer Hylander, Miska Luoto, Mark Vellend, Kris Verheyen & Jonathan Lenoir (2019) Global buffering of temperatures under forest canopies. Nature Ecology & Evolution.<br>
DOI: 10.7284/134092
title: TSG (Thermosalinograph) data collected during research cruise EN635 using a Sea-Bird SBE-45 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7604849.v3
title: Global buffering of temperatures under forest canopies: Data and Code

description: Data and code for figures and statistics reported in Pieter De Frenne, Florian Zellweger, Francisco Rodríguez-Sánchez, Brett Scheffers, Kristoffer Hylander, Miska Luoto, Mark Vellend, Kris Verheyen & Jonathan Lenoir (2019) Global buffering of temperatures under forest canopies. Nature Ecology & Evolution.<br>
DOI: 10.6084/m9.figshare.7604825.v1
title: calderon-manual.pdf

description: User manual for calderon HPC cluster
DOI: 10.7284/134100
title: TSG (Thermosalinograph) data collected during research cruise EN635 using a Sea-Bird SBE-21 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7604762
title: Plant core DNA barcode performance at a local scale: identification of the conifers of the state of Hidalgo, Mexico

description: DNA barcoding constitutes a fundamental tool for species identification, especially for highly diverse geographic regions. Here, we characterize and evaluate the plant core barcoding regions <i>matK</i> and <i>rbcL</i> to identify the 25 conifer species from the state of Hidalgo, Mexico, including 10 species in various threat categories. Sequence quality, linguistic complexity, and the presence of the barcode gap were estimated. Two methods were compared for successful species identification: BRONX (Barcode Recognition Obtained with Nucleotide eXposés) and the least inclusive clade. We generated 77 sequences for <i>matK</i> and 88 for <i>rbcL</i>. The <i>matK</i> region had higher haplotype diversity and nucleotide diversity (Π), including six indels. The analysis of 77 specimens with complete sequences (<i>matK</i> + <i>rbcL</i>) resulted in 21 nonspecies-specific unique haplotypes for the 25 conifer species. Higher sequence quality and linguistic complexity were observed in <i>rbcL</i> than in <i>matK</i>. Every diagnosable species had a barcode gap. Ninety-seven specimens were assigned unambiguously to family and genus, regardless of the marker or method employed. The analysis of <i>matK</i> with BRONX produced the highest species level identification success (44%). Despite the low specimen identification success at the specific level, it will be possible to establish local management, conservation, and monitoring projects for at least half of the threatened species even when specimens do not exhibit diagnostic morphological characters. The low divergence between closely related species may result from the slow rate of molecular evolution of the core barcoding markers or from hybridization or incomplete lineage sorting. Similar identification success is expected for groups with comparable life history traits under similar conditions as this study. A reduction in the geographic area will not necessarily translate into higher identification success, especially for high-diversity regions and centres of diversification.
DOI: 10.6084/m9.figshare.7604762.v2
title: Plant core DNA barcode performance at a local scale: identification of the conifers of the state of Hidalgo, Mexico

description: DNA barcoding constitutes a fundamental tool for species identification, especially for highly diverse geographic regions. Here, we characterize and evaluate the plant core barcoding regions <i>matK</i> and <i>rbcL</i> to identify the 25 conifer species from the state of Hidalgo, Mexico, including 10 species in various threat categories. Sequence quality, linguistic complexity, and the presence of the barcode gap were estimated. Two methods were compared for successful species identification: BRONX (Barcode Recognition Obtained with Nucleotide eXposés) and the least inclusive clade. We generated 77 sequences for <i>matK</i> and 88 for <i>rbcL</i>. The <i>matK</i> region had higher haplotype diversity and nucleotide diversity (Π), including six indels. The analysis of 77 specimens with complete sequences (<i>matK</i> + <i>rbcL</i>) resulted in 21 nonspecies-specific unique haplotypes for the 25 conifer species. Higher sequence quality and linguistic complexity were observed in <i>rbcL</i> than in <i>matK</i>. Every diagnosable species had a barcode gap. Ninety-seven specimens were assigned unambiguously to family and genus, regardless of the marker or method employed. The analysis of <i>matK</i> with BRONX produced the highest species level identification success (44%). Despite the low specimen identification success at the specific level, it will be possible to establish local management, conservation, and monitoring projects for at least half of the threatened species even when specimens do not exhibit diagnostic morphological characters. The low divergence between closely related species may result from the slow rate of molecular evolution of the core barcoding markers or from hybridization or incomplete lineage sorting. Similar identification success is expected for groups with comparable life history traits under similar conditions as this study. A reduction in the geographic area will not necessarily translate into higher identification success, especially for high-diversity regions and centres of diversification.
DOI: 10.7284/134102
title: Winch data collected during research cruise EN635 using a PHE Endeavor instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7604762.v1
title: Plant core DNA barcode performance at a local scale: identification of the conifers of the state of Hidalgo, Mexico

description: DNA barcoding constitutes a fundamental tool for species identification, especially for highly diverse geographic regions. Here, we characterize and evaluate the plant core barcoding regions <i>matK</i> and <i>rbcL</i> to identify the 25 conifer species from the state of Hidalgo, Mexico, including 10 species in various threat categories. Sequence quality, linguistic complexity, and the presence of the barcode gap were estimated. Two methods were compared for successful species identification: BRONX (Barcode Recognition Obtained with Nucleotide eXposés) and the least inclusive clade. We generated 77 sequences for <i>matK</i> and 88 for <i>rbcL</i>. The <i>matK</i> region had higher haplotype diversity and nucleotide diversity (Π), including six indels. The analysis of 77 specimens with complete sequences (<i>matK</i> + <i>rbcL</i>) resulted in 21 nonspecies-specific unique haplotypes for the 25 conifer species. Higher sequence quality and linguistic complexity were observed in <i>rbcL</i> than in <i>matK</i>. Every diagnosable species had a barcode gap. Ninety-seven specimens were assigned unambiguously to family and genus, regardless of the marker or method employed. The analysis of <i>matK</i> with BRONX produced the highest species level identification success (44%). Despite the low specimen identification success at the specific level, it will be possible to establish local management, conservation, and monitoring projects for at least half of the threatened species even when specimens do not exhibit diagnostic morphological characters. The low divergence between closely related species may result from the slow rate of molecular evolution of the core barcoding markers or from hybridization or incomplete lineage sorting. Similar identification success is expected for groups with comparable life history traits under similar conditions as this study. A reduction in the geographic area will not necessarily translate into higher identification success, especially for high-diversity regions and centres of diversification.
DOI: 10.7284/134104
title: Winch data collected during research cruise EN635 using a Markey DUSH-5 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/134106
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise EN636 using a Hawaii UHDAS instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7604696
title: Supplementary Material for: Lack of Response to Imatinib in Melanoma Carrying Rare <b><i>KIT</i></b> Mutation р.T632I

description: Approximately 15% of acral and mucous melanomas carry activating mutations in <i>KIT</i> oncogene. There is a diversity of spectrum of <i>KIT</i> mutations, with some of them rendering tumors responsive to imatinib, while others being imatinib-resistant or not studied yet. Here we present an acral melanoma patient with <i>KIT</i> р.T632I mutation, who failed to respond to imatinib.
DOI: 10.6084/m9.figshare.7604696.v1
title: Supplementary Material for: Lack of Response to Imatinib in Melanoma Carrying Rare <b><i>KIT</i></b> Mutation р.T632I

description: Approximately 15% of acral and mucous melanomas carry activating mutations in <i>KIT</i> oncogene. There is a diversity of spectrum of <i>KIT</i> mutations, with some of them rendering tumors responsive to imatinib, while others being imatinib-resistant or not studied yet. Here we present an acral melanoma patient with <i>KIT</i> р.T632I mutation, who failed to respond to imatinib.
DOI: 10.7284/134121
title: Anemometer data collected during research cruise EN636 using a Gill Windsonic instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition