cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1621914
title: A New Music Instrument from Ancient Times: Modern Reconstruction of the Greek Lyre of Hermes using 3D Laser Scanning, Advanced Computer Aided Design and Audio Analysis

description: The current paper proposes a unique approach by examining the ancient Greek literature and antique black figure amphorae’s representations (also known as melanomorpha) for the reconstruction, after digital design processing, of a modern top-quality replica of an ancient tortoise lyre. Through the review of certain ancient Greek documents, the observation of the amphorae’s relevant representations, 3D scanning and reverse engineering as well as 3D design using advanced Computer Aided Design (CAD) software, this study illustrates the detailed drawings and the fabrication procedures followed for a modern version of the ancient musical instrument. By using only materials available in antiquity such as specific kinds of wood, tortoise carcasses and sheep strings, as well as modern carpentry technology, a high-quality musical instrument was produced suited for use by today’s professional musicians. Two variations were produced and tested utilizing the Phrygian and Lydian ancient Greek music scales in a specialized unechoic chamber, in order to define their sound properties. Typical statistics were computed in the frequency domain such as spectral centroid, spectral standard deviation, spectral skewness, spectral kurtosis along with spectral rolloff and spectral smoothness in order to justify the lyres’ quality as musical instruments. The result was a prototype music product using advanced 3D design procedures that can be produced in a rather repeatable manner.
DOI: 10.6084/m9.figshare.1621907
title: A large-scale analysis of autophagy-related gene expression identifies new regulators of autophagy

description: Autophagy is a pathway mediating vacuolar degradation and recycling of proteins and organelles, which plays crucial roles in cellular physiology. To ensure its proper cytoprotective function, the induction and amplitude of autophagy are tightly regulated, and defects in its regulation are associated with various diseases. Transcriptional control of autophagy is a critical aspect of autophagy regulation, which remains largely unexplored. In particular, very few transcription factors involved in the activation or repression of autophagy-related gene expression have been characterized. To identify such regulators, we analyzed the expression of representative <i>ATG</i> genes in a large collection of DNA-binding mutant deletion strains in growing conditions as well as after nitrogen or glucose starvation. This analysis identified several proteins involved in the transcriptional control of <i>ATG</i> genes. Further analyses showed a correlation between variations in expression and autophagy magnitude, thus identifying new positive and negative regulators of the autophagy pathway. By providing a detailed analysis of the regulatory network of the <i>ATG</i> genes our study paves the way for future research on autophagy regulation and signaling.
DOI: 10.6084/m9.figshare.1621907.v1
title: A large-scale analysis of autophagy-related gene expression identifies new regulators of autophagy

description: Autophagy is a pathway mediating vacuolar degradation and recycling of proteins and organelles, which plays crucial roles in cellular physiology. To ensure its proper cytoprotective function, the induction and amplitude of autophagy are tightly regulated, and defects in its regulation are associated with various diseases. Transcriptional control of autophagy is a critical aspect of autophagy regulation, which remains largely unexplored. In particular, very few transcription factors involved in the activation or repression of autophagy-related gene expression have been characterized. To identify such regulators, we analyzed the expression of representative <i>ATG</i> genes in a large collection of DNA-binding mutant deletion strains in growing conditions as well as after nitrogen or glucose starvation. This analysis identified several proteins involved in the transcriptional control of <i>ATG</i> genes. Further analyses showed a correlation between variations in expression and autophagy magnitude, thus identifying new positive and negative regulators of the autophagy pathway. By providing a detailed analysis of the regulatory network of the <i>ATG</i> genes our study paves the way for future research on autophagy regulation and signaling.
DOI: 10.6084/m9.figshare.1621901
title: Global and local QSPR models to predict supercooled vapour pressure for organic compounds

description: In this study, a quantitative structure–property relationship (QSPR) approach was used for estimation of logarithmic values of supercooled liquid vapour pressure (log <i>P</i><sub>L</sub>) of a large set of structurally diverse organic compounds. This set includes 12 local sets of aromatic and aliphatic hydrocarbons, polychlorinated biphenyls, ethers, polychlorinated and brominated diphenylethers, polychlorinated naphthalenes and alcohols. Some simple models based on the linear relationship between log <i>P</i><sub>L</sub> and VolSurf descriptors were developed as global models, and a general equation as a simple way to calculate the supercooled liquid vapour pressure of organic chemicals was provided. A descriptor representing the hydrophilic regions (WO<sub>1</sub>) of organic chemicals showed the highest correlation with log <i>P</i><sub>L</sub> and resulted in a one-parameter global model characterized by satisfactory statistical performance; calibration (<i>r</i><sup>2</sup><sub>c</sub>) and prediction (<i>r</i><sup>2</sup><sub>p</sub>) correlation coefficient of 0.84 and 0.85, respectively. Moreover, local QSPR models were also developed for each subset of organic compounds and, as expected, the statistical results obtained from these models were better than the global one. From the descriptors involved in the models, it is concluded that the hydrophilic and hydrophobic regions at different energy levels and polarizability usually determine the variation of supercooled liquid vapour pressure of organic compounds.
DOI: 10.6084/m9.figshare.1621898
title: Pollen records related to vegetation and climate change from northern Chhattisgarh, central India during the late Quaternary

description: Pollen records from a 1.8-m deep sediment profile from Lakadandh Swamp, Baikunthpur Forest Range of Koriya District, Chhattisgarh (C'garh, central India), show the late Quaternary vegetation and climate history. Lakadandh Swamp occurs in the core monsoon zone of India. The study revealed that between ∼12,785 and ∼9035 cal. yrs BP, tree savannah vegetation, – composed of Poaceae, Amaranthaceae, Tubuliflorae along with the tree taxa <i>Holoptelea</i> sp. and Sapotaceae; sparsely distributed <i>Acacia</i> sp., <i>Emblica officinalis, Lagerstroemia</i> sp., <i>Madhuca indica</i> and <i>Syzygium</i> sp., <i>thickets of Ricinus</i> and <i>Zizyphus</i> sp. – occurred in the region under a cool and dry climate probably indicative of reduced monsoon precipitation. The early part of this phase is comparable with the Younger Dryas (YD) cold event which occurred between ∼12,800 and ∼11,500 yrs BP. Between ∼9035 and ∼4535 cal. yrs BP, the expansion of existing taxa <i>Holoptelea</i> sp., Sapotaceae, <i>Madhuca indica</i>, <i>Ailanthus excelsa</i> and <i>Lagerstroemia</i> sp. as well as the appearance of <i>Acacia</i>, and <i>Shorea robusta</i>, Acanthaceae, <i>Rungia</i> sp., and <i>Ricinus</i> sp., shows the tree savannah vegetation was replaced by open mixed tropical deciduous forest under a regime of warm and moderately humid climate with increased monsoon precipitation. Since ∼4535 cal. yrs BP to Present, owing to the improvement of most of the forest constituents, particularly <i>Madhuca indica</i>, <i>Holoptelea</i> sp., Sapotaceae and <i>Lannea coromandelica</i>, and also with immigration of <i>Terminalia</i> sp., <i>Diospyros</i> sp., <i>Butea</i> sp. and <i>Maytenus</i> sp., mixed tropical deciduous forest has taken over the space covered by open mixed tropical deciduous forest under a warm and relatively more humid climate, with further increase in monsoon precipitation. The existing cereal-based agricultural practice increased during the latter two phases, which could be attributed to increased monsoon precipitation.
DOI: 10.6084/m9.figshare.1621898.v1
title: Pollen records related to vegetation and climate change from northern Chhattisgarh, central India during the late Quaternary

description: Pollen records from a 1.8-m deep sediment profile from Lakadandh Swamp, Baikunthpur Forest Range of Koriya District, Chhattisgarh (C'garh, central India), show the late Quaternary vegetation and climate history. Lakadandh Swamp occurs in the core monsoon zone of India. The study revealed that between ∼12,785 and ∼9035 cal. yrs BP, tree savannah vegetation, – composed of Poaceae, Amaranthaceae, Tubuliflorae along with the tree taxa <i>Holoptelea</i> sp. and Sapotaceae; sparsely distributed <i>Acacia</i> sp., <i>Emblica officinalis, Lagerstroemia</i> sp., <i>Madhuca indica</i> and <i>Syzygium</i> sp., <i>thickets of Ricinus</i> and <i>Zizyphus</i> sp. – occurred in the region under a cool and dry climate probably indicative of reduced monsoon precipitation. The early part of this phase is comparable with the Younger Dryas (YD) cold event which occurred between ∼12,800 and ∼11,500 yrs BP. Between ∼9035 and ∼4535 cal. yrs BP, the expansion of existing taxa <i>Holoptelea</i> sp., Sapotaceae, <i>Madhuca indica</i>, <i>Ailanthus excelsa</i> and <i>Lagerstroemia</i> sp. as well as the appearance of <i>Acacia</i>, and <i>Shorea robusta</i>, Acanthaceae, <i>Rungia</i> sp., and <i>Ricinus</i> sp., shows the tree savannah vegetation was replaced by open mixed tropical deciduous forest under a regime of warm and moderately humid climate with increased monsoon precipitation. Since ∼4535 cal. yrs BP to Present, owing to the improvement of most of the forest constituents, particularly <i>Madhuca indica</i>, <i>Holoptelea</i> sp., Sapotaceae and <i>Lannea coromandelica</i>, and also with immigration of <i>Terminalia</i> sp., <i>Diospyros</i> sp., <i>Butea</i> sp. and <i>Maytenus</i> sp., mixed tropical deciduous forest has taken over the space covered by open mixed tropical deciduous forest under a warm and relatively more humid climate, with further increase in monsoon precipitation. The existing cereal-based agricultural practice increased during the latter two phases, which could be attributed to increased monsoon precipitation.
DOI: 10.6084/m9.figshare.1621901.v1
title: Global and local QSPR models to predict supercooled vapour pressure for organic compounds

description: In this study, a quantitative structure–property relationship (QSPR) approach was used for estimation of logarithmic values of supercooled liquid vapour pressure (log <i>P</i><sub>L</sub>) of a large set of structurally diverse organic compounds. This set includes 12 local sets of aromatic and aliphatic hydrocarbons, polychlorinated biphenyls, ethers, polychlorinated and brominated diphenylethers, polychlorinated naphthalenes and alcohols. Some simple models based on the linear relationship between log <i>P</i><sub>L</sub> and VolSurf descriptors were developed as global models, and a general equation as a simple way to calculate the supercooled liquid vapour pressure of organic chemicals was provided. A descriptor representing the hydrophilic regions (WO<sub>1</sub>) of organic chemicals showed the highest correlation with log <i>P</i><sub>L</sub> and resulted in a one-parameter global model characterized by satisfactory statistical performance; calibration (<i>r</i><sup>2</sup><sub>c</sub>) and prediction (<i>r</i><sup>2</sup><sub>p</sub>) correlation coefficient of 0.84 and 0.85, respectively. Moreover, local QSPR models were also developed for each subset of organic compounds and, as expected, the statistical results obtained from these models were better than the global one. From the descriptors involved in the models, it is concluded that the hydrophilic and hydrophobic regions at different energy levels and polarizability usually determine the variation of supercooled liquid vapour pressure of organic compounds.
DOI: 10.6084/m9.figshare.1621894
title: A combined proteomics and metabolomics approach to assess the effects of gold nanoparticles <i>in vitro</i>.

description: Omics technologies, such as proteomics or metabolomics, have to date been applied in the field of nanomaterial safety assessment to a limited extent. To address this dearth, we developed an integrated approach combining the two techniques to study the effects of two sizes, 5 and 30 nm, of gold nanoparticles (AuNPs) in Caco-2 cells. We observed differences in cells exposed for 72 h to each size of AuNPs: 61 responsive (up/down-regulated) proteins were identified and 35 metabolites in the cell extract tentatively annotated. Several altered biological pathways were highlighted by integrating the obtained multi-omics data with bioinformatic tools. This provided a unique set of molecular information on the effects of nanomaterials at cellular level. This information was supported by complementary data obtained by immunochemistry, microscopic analysis and multiplexed assays. A part from increasing our knowledge on how the cellular processes and pathways are affected by nanomaterials (NMs), these findings could be used to identify specific biomarkers of toxicity or to support the safe-by-design concept in the development of new nanomedicines.
DOI: 10.6084/m9.figshare.1621895
title: Outburst floods of the Maly Yenisei. Part I

description: ABSTRACTThe Yenisei, the largest river flowing to the Arctic Ocean, repeatedly hosted cataclysmic floods during the Pleistocene. The largest of the known floods likely originated from palaeolakes in northern Mongolia, at the headwaters of the Little, or Maly, Yenisei. These ancient floods are among the greatest known globally. They left giant gravel dunes and wide abandoned channels in the Kyzyl basin, and high terraces in the gorges upstream. However, few detailed field studies of the flood deposits and no measurements of their ages have been made thus far. The largest palaeolakes were impounded during major glaciations by outlet glaciers from the East Sayan ice field in southern Siberia. The shorelines suggest four distinct palaeolake depths of 290, 175, 145, and 65 m. The timing and location of the glacier impounding the deepest lakes are uncertain but at its maximum, the Tengis outlet glacier was likely capable of impounding the 175 m lake. The dating of glacial deposits in and around the basin reveals that the maximum late Pleistocene glaciers were during Marine Oxygen Isotope Stage (MIS) 3. The ages for deep-lake sediments exposed in the basin behind the dam’s location support this finding. During MIS 2 the Tengis glacier was large enough to impound at least the 145 m lake. However, the existence of a deep MIS 2 palaeolake in the basin has been challenged, because no evidence has been published of MIS 2 lake sediments from the cutbank outcrops and deep drilling cores. Additionally, the end moraines of the Tengis glacier, separated from the deeply eroded lateral moraines by the Maly Yenisei, remain undated; therefore it is uncertain exactly when this glacier crossed the river. This review is part I of a two-part article; Part II presents new age data to constrain the ages of the glacial dam.
DOI: 10.6084/m9.figshare.1621894.v1
title: A combined proteomics and metabolomics approach to assess the effects of gold nanoparticles <i>in vitro</i>.

description: Omics technologies, such as proteomics or metabolomics, have to date been applied in the field of nanomaterial safety assessment to a limited extent. To address this dearth, we developed an integrated approach combining the two techniques to study the effects of two sizes, 5 and 30 nm, of gold nanoparticles (AuNPs) in Caco-2 cells. We observed differences in cells exposed for 72 h to each size of AuNPs: 61 responsive (up/down-regulated) proteins were identified and 35 metabolites in the cell extract tentatively annotated. Several altered biological pathways were highlighted by integrating the obtained multi-omics data with bioinformatic tools. This provided a unique set of molecular information on the effects of nanomaterials at cellular level. This information was supported by complementary data obtained by immunochemistry, microscopic analysis and multiplexed assays. A part from increasing our knowledge on how the cellular processes and pathways are affected by nanomaterials (NMs), these findings could be used to identify specific biomarkers of toxicity or to support the safe-by-design concept in the development of new nanomedicines.
DOI: 10.6084/m9.figshare.1621895.v1
title: Outburst floods of the Maly Yenisei. Part I

description: ABSTRACTThe Yenisei, the largest river flowing to the Arctic Ocean, repeatedly hosted cataclysmic floods during the Pleistocene. The largest of the known floods likely originated from palaeolakes in northern Mongolia, at the headwaters of the Little, or Maly, Yenisei. These ancient floods are among the greatest known globally. They left giant gravel dunes and wide abandoned channels in the Kyzyl basin, and high terraces in the gorges upstream. However, few detailed field studies of the flood deposits and no measurements of their ages have been made thus far. The largest palaeolakes were impounded during major glaciations by outlet glaciers from the East Sayan ice field in southern Siberia. The shorelines suggest four distinct palaeolake depths of 290, 175, 145, and 65 m. The timing and location of the glacier impounding the deepest lakes are uncertain but at its maximum, the Tengis outlet glacier was likely capable of impounding the 175 m lake. The dating of glacial deposits in and around the basin reveals that the maximum late Pleistocene glaciers were during Marine Oxygen Isotope Stage (MIS) 3. The ages for deep-lake sediments exposed in the basin behind the dam’s location support this finding. During MIS 2 the Tengis glacier was large enough to impound at least the 145 m lake. However, the existence of a deep MIS 2 palaeolake in the basin has been challenged, because no evidence has been published of MIS 2 lake sediments from the cutbank outcrops and deep drilling cores. Additionally, the end moraines of the Tengis glacier, separated from the deeply eroded lateral moraines by the Maly Yenisei, remain undated; therefore it is uncertain exactly when this glacier crossed the river. This review is part I of a two-part article; Part II presents new age data to constrain the ages of the glacial dam.
DOI: 10.6084/m9.figshare.1621535
title: Anvi'o files for Wagner's Nitrospira

description: This is the anvi'o essential files for the reanalysis of the genome published in http://www.nature.com/nature/journal/vnfv/ncurrent/full/nature16461.html.
DOI: 10.6084/m9.figshare.1621535.v1
title: Anvi'o files for Wagner's Nitrospira

description: This is the anvi'o essential files for the reanalysis of the genome published in http://www.nature.com/nature/journal/vnfv/ncurrent/full/nature16461.html.
DOI: 10.6084/m9.figshare.1621440
title: Group B

description: This group contains clips that doesnt contain fire
DOI: 10.6084/m9.figshare.1621441
title: Group A

description: Clips contain fire
DOI: 10.6084/m9.figshare.1621437
title: Transmigration characteristics of breast cancer and melanoma cells through the brain endothelium: role of Rac and PI3K

description: ABSTRACTBrain metastases are common and devastating complications of both breast cancer and melanoma. Although mammary carcinoma brain metastases are more frequent than those originating from melanoma, this latter has the highest tropism to the brain. Using static and dynamic in vitro approaches, here we show that melanoma cells have increased adhesion to the brain endothelium in comparison to breast cancer cells. Moreover, melanoma cells can transmigrate more rapidly and in a higher number through brain endothelial monolayers than breast cancer cells. In addition, melanoma cells have increased ability to impair tight junctions of cerebral endothelial cells. We also show that inhibition of Rac or PI3K impedes adhesion of breast cancer cells and melanoma cells to the brain endothelium. In addition, inhibition of Rac or PI3K inhibits the late phase of transmigration of breast cancer cells and the early phase of transmigration of melanoma cells. On the other hand, the Rac inhibitor EHT1864 impairs the junctional integrity of the brain endothelium, while the PI3K inhibitor LY294002 has no damaging effect on interendothelial junctions. We suggest that targeting the PI3K/Akt pathway may represent a novel opportunity in preventing the formation of brain metastases of melanoma and breast cancer.
DOI: 10.6084/m9.figshare.1621438
title: Raman spectroscopy detects melanoma and the tissue surrounding melanoma using tissue engineered melanoma models

description: ABSTRACTInvasion of melanoma cells from the primary tumour involves interaction with adjacent tissues and extracellular matrix. The extent of this interaction is not fully understood. In this study Raman spectroscopy was applied to cryo-sections of established 3D models of melanoma in human skin. Principal component analysis was used to investigate differences between the tumour and normal tissue and between the peri-tumour area and the normal skin. Two human melanoma cells lines A375SM and C8161 were investigated and compared in 3D melanoma models. Changes were found in protein conformations and tryptophan configurations across the entire melanoma samples, in tyrosine orientation and in more fluid lipid packing only in tumour dense areas, and in increased glycogen content in the peri-tumour areas of melanoma. Raman spectroscopy revealed changes around the perimeter of a melanoma tumour as well as detecting differences between the tumour and the normal tissue.
DOI: 10.6084/m9.figshare.1621437.v1
title: Transmigration characteristics of breast cancer and melanoma cells through the brain endothelium: role of Rac and PI3K

description: ABSTRACTBrain metastases are common and devastating complications of both breast cancer and melanoma. Although mammary carcinoma brain metastases are more frequent than those originating from melanoma, this latter has the highest tropism to the brain. Using static and dynamic in vitro approaches, here we show that melanoma cells have increased adhesion to the brain endothelium in comparison to breast cancer cells. Moreover, melanoma cells can transmigrate more rapidly and in a higher number through brain endothelial monolayers than breast cancer cells. In addition, melanoma cells have increased ability to impair tight junctions of cerebral endothelial cells. We also show that inhibition of Rac or PI3K impedes adhesion of breast cancer cells and melanoma cells to the brain endothelium. In addition, inhibition of Rac or PI3K inhibits the late phase of transmigration of breast cancer cells and the early phase of transmigration of melanoma cells. On the other hand, the Rac inhibitor EHT1864 impairs the junctional integrity of the brain endothelium, while the PI3K inhibitor LY294002 has no damaging effect on interendothelial junctions. We suggest that targeting the PI3K/Akt pathway may represent a novel opportunity in preventing the formation of brain metastases of melanoma and breast cancer.