cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5091334
title: Identification of potential inhibitors for HCV NS3 genotype 4a by combining protein–ligand interaction fingerprint, 3D pharmacophore, docking, and dynamic simulation

description: HCV NS3 protease domain has been one of the most attractive targets for developing new drugs for HCV infection and many drugs were successfully developed, but all of them were designed for targeting HCV genotype 1 infection. HCV genotype 4a dominant in Egypt has paid less attention. Here, we describe our protocol of virtual screening in identification of novel potential potent inhibitors for HCV NS3 of genotype 4a using homology modeling, PLIF (protein–ligand interaction fingerprint), docking, pharmacophore, and dynamic simulation. A high-quality 3D model of HCV NS3 protease of genotype 4a was constructed using crystal structure of HCV NS3 protease of genotype 1b (PDB ID: 4u01) as a template. PLIF was generated using five crystal structures of HCV NS3 (PDB ID: 4u01, 3kee, 4ktc, 4i33, and 5epn) which revealed the most important residues and their interactions with the co-crystalized ligands. A 3D pharmacophore model consisting of six features was developed from the generated PLIF data and then used as a screening filter for 11,244 compounds. Only 423 compounds passed the pharmacophore filter and entered the docking-based virtual screening stage. The highest ranked five hits from docking result (compound (C1–C5)) were selected for further analysis. They exhibited stronger interaction and higher binding affinity than HCV NS3 protease ligands. Dynamic simulation of the protein–best lead complex was performed to validate and augment the virtual screening results and it showed that these compounds have a strong binding affinity and could be very effective in treating HCV genotype 4a infections.
DOI: 10.6084/m9.figshare.5091331
title: Macrofungal diversity of holm-oak forests at the northern limit of their distribution range in the Iberian Peninsula

description: Given the current gap in knowledge concerning the macrofungal diversity of holm-oak forests at the northern limit of their distribution range and in the Basque Country, a mycocoenological study was conducted by sampling 23 randomly selected permanent plots from 6 holm-oak forests. To obtain a better understanding of the macrofungal diversity distribution pattern on a regional scale, forests from both the temperate and Mediterranean-type climate regions of the Basque Country were selected, covering all their phytocoenological variation. After 4 years of sampling, a total of 377 macrofungal species were collected: 209 ectomycorrhizal species, 86 humicolous saprotrophs, 40 saprotrophs on litter, 36 lignicolous saprotrophs, 3 coprophilous saprotrophs and 3 parasitic species. Species considered characteristic of this kind of forest, such as <i>Cortinarius aurilicis</i>, <i>Cortinarius callochrous</i>, <i>Cortinarius ionochlorus</i>, <i>Hygrophorus leucophaeo-ilicis</i>, <i>Hygrophorus persoonii</i>, <i>Hygrophorus russula</i>, <i>Lactarius atlanticus</i>, <i>Lactarius ilicis</i>, <i>Leccinellum lepidum</i>, were recorded all over the territory, but Mediterranean forests were richer in species and more productive in sporocarps than temperate ones. Species assemblage was found to change gradually at local scale from temperate to Mediterranean climate zones, and was distinct to each phytocoenological association with all species, with ectomycorrhizal species and with saprotrophs.
DOI: 10.6084/m9.figshare.5091331.v2
title: Macrofungal diversity of holm-oak forests at the northern limit of their distribution range in the Iberian Peninsula

description: Given the current gap in knowledge concerning the macrofungal diversity of holm-oak forests at the northern limit of their distribution range and in the Basque Country, a mycocoenological study was conducted by sampling 23 randomly selected permanent plots from 6 holm-oak forests. To obtain a better understanding of the macrofungal diversity distribution pattern on a regional scale, forests from both the temperate and Mediterranean-type climate regions of the Basque Country were selected, covering all their phytocoenological variation. After 4 years of sampling, a total of 377 macrofungal species were collected: 209 ectomycorrhizal species, 86 humicolous saprotrophs, 40 saprotrophs on litter, 36 lignicolous saprotrophs, 3 coprophilous saprotrophs and 3 parasitic species. Species considered characteristic of this kind of forest, such as <i>Cortinarius aurilicis</i>, <i>Cortinarius callochrous</i>, <i>Cortinarius ionochlorus</i>, <i>Hygrophorus leucophaeo-ilicis</i>, <i>Hygrophorus persoonii</i>, <i>Hygrophorus russula</i>, <i>Lactarius atlanticus</i>, <i>Lactarius ilicis</i>, <i>Leccinellum lepidum</i>, were recorded all over the territory, but Mediterranean forests were richer in species and more productive in sporocarps than temperate ones. Species assemblage was found to change gradually at local scale from temperate to Mediterranean climate zones, and was distinct to each phytocoenological association with all species, with ectomycorrhizal species and with saprotrophs.
DOI: 10.5281/zenodo.4011649
title: Stressor-induced ecdysis and thecate cyst formation in the armoured dinoflagellates Prorocentrum cordatum

description: The culture of the dinoflagellates Prorocentrum cordatum was subjected to various stressors to induce the process of ecdysis. The stressors were centrifugation, vortexing, changes in temperature, salinity and pH, application of 2,3-dichlorobenzonitrile and tetracycline. The rates of complete ecdysis and ecdysis initiation, as well as mortality rate were calculated following the treatments. Rate of ecdysis induced by centrifugation was additionally estimated in the cultures at the different growth phases.
DOI: 10.5281/zenodo.4011648
title: Stressor-induced ecdysis and thecate cyst formation in the armoured dinoflagellates Prorocentrum cordatum

description: The culture of the dinoflagellates Prorocentrum cordatum was subjected to various stressors to induce the process of ecdysis. The stressors were centrifugation, vortexing, changes in temperature, salinity and pH, application of 2,3-dichlorobenzonitrile and tetracycline. The rates of complete ecdysis and ecdysis initiation, as well as mortality rate were calculated following the treatments. Rate of ecdysis induced by centrifugation was additionally estimated in the cultures at the different growth phases.
DOI: 10.6084/m9.figshare.5090608
title: The data of Figure 5

description: Differential co-expression network between co-expression networks (CEN) of acute lung injury (ALI) group and spesis group.
DOI: 10.6084/m9.figshare.5090608.v1
title: The data of Figure 5

description: Differential co-expression network between co-expression networks (CEN) of acute lung injury (ALI) group and spesis group.
DOI: 10.6084/m9.figshare.5090533
title: Modified atmosphere packaging as a method to extend postharvest life of tulip flowers

description: Tulip is one of the most important cut flowers in the world market and abscission of the tepals is this species’ most common symptom during vase life. To prevent these symptoms and extend postharvest life, passive and active modified atmosphere packaging (MAP) was applied at 0°C. Respiratory rate (CO<sub>2</sub> Kg<sup>−1</sup>h<sup>−1</sup>), ethylene production (µL kg<sup>−1</sup>h<sup>−1</sup>) and concentration of CO2 and O2 (%) inside the packaging were evaluated during storage, while fresh weight loss (FWL) (%) and vase life (days) were assessed. Flowers stored using MAP performed significantly better than conventional packaging. A lower FWL (only up to 0.3%) was observed on MAP while FWL was as high as 18 to 21% for conventional packaging after 20 and 31 days, respectively. Vase life was 5.7 and 6.0 days for active and passive MAP, respectively compared to 3.3 days for conventional packing. Thus, MAP successfully extended postharvest life of tulip flowers.
DOI: 10.25442/hku.12756458
title: Shape-control growth of 2D-In2Se3 with out-of-plane ferroelectricity by chemical vapor deposition

description: For the potential applications in ferroelectric switching and piezoelectric nano-generator device, the promising ferroelectric properties of two dimensional (2D) layered In2Se3 attracted much attention. In the present study, 2D In2Se3 flakes down to monolayers are grown by chemical vapor deposition (CVD) technique on mica substrate with the structural, optical and ferroelectric properties being studied. The effect of growth parameter (time of growth and Ar flow rate) on the shape and size of the deposited flakes was studied. Optical microscopy study revealed that the flake changed from a circular shape to a sharp face triangle as the Ar flow rate and growth time increased. The Raman spectroscopy and high-resolution scanning transmission electron microscopy (HR-STEM) studies revealed that the flakes were of the α and β phases, each of which has a hexagonal crystal structure. Strong second harmonic generation (SHG) was observed from α-In2Se3, demonstrating its non-centrosymmetric structure. Piezo-force microscopic (PFM) study showed the presence of out of plane (OOP) ferroelectricity with no in Plane (IP) ferroelectricity in CVD grown α-In2Se3 indicating its vertically confined piezoresponse, which was tuned by the applied electric bias and the flake thickness. The present result of shape-controlled growth of In2Se3 with OOP ferroelectricity would open new pathways in the field of 2D ferroelectric switching devices. <br>
DOI: 10.25442/hku.12756458.v1
title: Shape-control growth of 2D-In2Se3 with out-of-plane ferroelectricity by chemical vapor deposition

description: For the potential applications in ferroelectric switching and piezoelectric nano-generator device, the promising ferroelectric properties of two dimensional (2D) layered In2Se3 attracted much attention. In the present study, 2D In2Se3 flakes down to monolayers are grown by chemical vapor deposition (CVD) technique on mica substrate with the structural, optical and ferroelectric properties being studied. The effect of growth parameter (time of growth and Ar flow rate) on the shape and size of the deposited flakes was studied. Optical microscopy study revealed that the flake changed from a circular shape to a sharp face triangle as the Ar flow rate and growth time increased. The Raman spectroscopy and high-resolution scanning transmission electron microscopy (HR-STEM) studies revealed that the flakes were of the α and β phases, each of which has a hexagonal crystal structure. Strong second harmonic generation (SHG) was observed from α-In2Se3, demonstrating its non-centrosymmetric structure. Piezo-force microscopic (PFM) study showed the presence of out of plane (OOP) ferroelectricity with no in Plane (IP) ferroelectricity in CVD grown α-In2Se3 indicating its vertically confined piezoresponse, which was tuned by the applied electric bias and the flake thickness. The present result of shape-controlled growth of In2Se3 with OOP ferroelectricity would open new pathways in the field of 2D ferroelectric switching devices. <br>
DOI: 10.25442/hku.12752597
title: Exosomal Complement Factor H Promotes Liver Cancer Metastasis by Inhibiting Complement-dependent Cytotoxicity of Tumor Cells

description: Hepatocellular carcinoma (HCC), the seventh most common malignancy in the world, can cause deaths of approximately 780,000 patients each year. Although a large number of studies have been conducted for a long time, the current treatment level of HCC is very limited, and many treatments are only effective for early HCC. However, most HCC are diagnosed in the advanced stage. Usually, patients with advanced stage have extrahepatic metastasis. This metastasis is not a random process. Therefore, studying the mechanism of HCC metastasis is beneficial to the early diagnosis of patients and the development of novel therapeutic strategy.<br> <br>Many recent studies have found that exosomes play an important role in intercellular communication. Exosomes transfer their contents, causing localized effects of cancer cells on surrounding cells and systemic effects on distant cells. Our results indicate that exosomes derived from metastatic HCC cells increased the migratory and invasive potentials of liver cancer cells and metastasis in animal models. Further analysis of exosomal proteins by proteomic analysis revealed that complement factor H (CFH) is highly expressed in exosomes of metastatic HCC cells.<br> <br>CFH is a major inhibitor of the immune defense complement system. We generated stable CFH knockdown clones in metastatic HCC cells. It was confirmed that reduced CFH expression was observed in the total cell lysates and exosomes of the stable clones, resulting in the decreased oncogenic properties of cells and exosomes. We also showed that HCC cells treated with exosomes of non-target control cells had a decrease in complement-mediated cytotoxicity when compared to the cells treated with exosomes derived from CFH knockdown cells suggesting that CFH protects HCC cells by evading complement attack.<br> <br>Based on the above, we hypothesize that exosomal CFH inhibits complement activation in the tumor microenvironment to promote HCC tumorigenesis and metastasis. Although we do not fully understand the role of CFH in tumor development, our study provides new insights into the functional role of CFH in HCC and provides a basis for further study of other potential roles of CFH in carcinogenesis.<br><br>
DOI: 10.25442/hku.12752597.v1
title: Exosomal Complement Factor H Promotes Liver Cancer Metastasis by Inhibiting Complement-dependent Cytotoxicity of Tumor Cells

description: Hepatocellular carcinoma (HCC), the seventh most common malignancy in the world, can cause deaths of approximately 780,000 patients each year. Although a large number of studies have been conducted for a long time, the current treatment level of HCC is very limited, and many treatments are only effective for early HCC. However, most HCC are diagnosed in the advanced stage. Usually, patients with advanced stage have extrahepatic metastasis. This metastasis is not a random process. Therefore, studying the mechanism of HCC metastasis is beneficial to the early diagnosis of patients and the development of novel therapeutic strategy.<br> <br>Many recent studies have found that exosomes play an important role in intercellular communication. Exosomes transfer their contents, causing localized effects of cancer cells on surrounding cells and systemic effects on distant cells. Our results indicate that exosomes derived from metastatic HCC cells increased the migratory and invasive potentials of liver cancer cells and metastasis in animal models. Further analysis of exosomal proteins by proteomic analysis revealed that complement factor H (CFH) is highly expressed in exosomes of metastatic HCC cells.<br> <br>CFH is a major inhibitor of the immune defense complement system. We generated stable CFH knockdown clones in metastatic HCC cells. It was confirmed that reduced CFH expression was observed in the total cell lysates and exosomes of the stable clones, resulting in the decreased oncogenic properties of cells and exosomes. We also showed that HCC cells treated with exosomes of non-target control cells had a decrease in complement-mediated cytotoxicity when compared to the cells treated with exosomes derived from CFH knockdown cells suggesting that CFH protects HCC cells by evading complement attack.<br> <br>Based on the above, we hypothesize that exosomal CFH inhibits complement activation in the tumor microenvironment to promote HCC tumorigenesis and metastasis. Although we do not fully understand the role of CFH in tumor development, our study provides new insights into the functional role of CFH in HCC and provides a basis for further study of other potential roles of CFH in carcinogenesis.<br><br>
DOI: 10.25442/hku.12752534
title: Atomic Force Microscopy Enabled Analysis and Modeling for Micro Bubble Mechanical Properties

description: This dataset mainly involves the raw data about bubble measurement result, the Matlab processed data and the Matlab-programming codebook, which are applied in the final thesis.
DOI: 10.25442/hku.12752534.v1
title: Atomic Force Microscopy Enabled Analysis and Modeling for Micro Bubble Mechanical Properties

description: This dataset mainly involves the raw data about bubble measurement result, the Matlab processed data and the Matlab-programming codebook, which are applied in the final thesis.
DOI: 10.6084/m9.figshare.12612797
title: Genomic sequence of Alternaria alternata B3 causing leaf blight on Ophiopogon japonicus

description: Genomic sequence resource of Alternaria alternata strain B3 causing leaf blight on Ophiopogon japonicus
DOI: 10.6084/m9.figshare.12612797.v1
title: Genomic sequence of Alternaria alternata B3 causing leaf blight on Ophiopogon japonicus

description: Genomic sequence resource of Alternaria alternata strain B3 causing leaf blight on Ophiopogon japonicus
DOI: 10.6084/m9.figshare.5089990
title: Ecological drivers of soil microbial diversity and soil biological networks in the Southern Hemisphere

description: Data from "Manuel Delgado-Baquerizo, Frank Reith, Paul G. Dennis, Kelly Hamonts, Jeff R. Powell, Andrew Young, Brajesh K. Singh, Andrew Bissett. Latitudinal patterns in multitrophic soil biodiversity and soil biological networks across the Southern Hemisphere: Insights from two continents.” There are two spreadsheets with data. The spreadsheets "Dataset" contains the raw data used in this paper. The spreadsheet "Metadata" contains the associated metadata, where a description of all the variables and units can be found.
DOI: 10.6084/m9.figshare.5089990.v1
title: Ecological drivers of soil microbial diversity and soil biological networks in the Southern Hemisphere

description: Data from "Manuel Delgado-Baquerizo, Frank Reith, Paul G. Dennis, Kelly Hamonts, Jeff R. Powell, Andrew Young, Brajesh K. Singh, Andrew Bissett. Latitudinal patterns in multitrophic soil biodiversity and soil biological networks across the Southern Hemisphere: Insights from two continents.” There are two spreadsheets with data. The spreadsheets "Dataset" contains the raw data used in this paper. The spreadsheet "Metadata" contains the associated metadata, where a description of all the variables and units can be found.
DOI: 10.6084/m9.figshare.5089945
title: Forensic cartography with Hochstetter’s 1859 Pink and White Terraces survey: Te Otukapuarangi and Te Tarata

description: The 1859 field diaries of Ferdinand von Hochstetter (1829–1884) include raw data from a compass survey of Lake Rotomahana. The azimuth array is reverse engineered to identify Hochstetter’s survey baseline. Survey iterations are performed to reconstruct the historic Lake Rotomahana over today’s topographic map. Hochstetter’s papers include a method-of-squares survey map of Lake Rotomahana, providing scale and orientation to the reverse engineered projection. The forensic cartography delivers control points which enabled the authors to georeference Hochstetter’s survey map over the new Lake Rotomahana map. Black Terrace Crater and Te Ariki datum are derived. Validation by waterways, valleys and vegetation lines is undertaken, a biological bathymetry completed and three-point resection performed on the key survey station. The cartography shows the Pink, Black and White Terrace spring locations, Te Otukapuarangi, Te Ngāwhā a Te Tuhi and Te Tarata lie buried on land. From novel lake altimetry the plotted terrace spring locations lie buried 10–15 m. A full archaeological site investigation including imaging and core drilling is indicated to examine the three terrace locations. Excavation on one or more of the Pink, Black and White Terrace sites may then be determined.
DOI: 10.6084/m9.figshare.5089945.v1
title: Forensic cartography with Hochstetter’s 1859 Pink and White Terraces survey: Te Otukapuarangi and Te Tarata

description: The 1859 field diaries of Ferdinand von Hochstetter (1829–1884) include raw data from a compass survey of Lake Rotomahana. The azimuth array is reverse engineered to identify Hochstetter’s survey baseline. Survey iterations are performed to reconstruct the historic Lake Rotomahana over today’s topographic map. Hochstetter’s papers include a method-of-squares survey map of Lake Rotomahana, providing scale and orientation to the reverse engineered projection. The forensic cartography delivers control points which enabled the authors to georeference Hochstetter’s survey map over the new Lake Rotomahana map. Black Terrace Crater and Te Ariki datum are derived. Validation by waterways, valleys and vegetation lines is undertaken, a biological bathymetry completed and three-point resection performed on the key survey station. The cartography shows the Pink, Black and White Terrace spring locations, Te Otukapuarangi, Te Ngāwhā a Te Tuhi and Te Tarata lie buried on land. From novel lake altimetry the plotted terrace spring locations lie buried 10–15 m. A full archaeological site investigation including imaging and core drilling is indicated to examine the three terrace locations. Excavation on one or more of the Pink, Black and White Terrace sites may then be determined.
DOI: 10.6084/m9.figshare.5089942
title: Soil microbial communities drive the resistance of ecosystem multifunctionality to global change in drylands across the globe

description: Data from "Manuel Delgado-Baquerizo, David J. Eldridge, Victoria Ochoa, Beatriz Gozalo, Brajesh K. Singh & Fernando T. Maestre. Soil microbial communities drive the resistance of ecosystem multifunctionality to global change in drylands across the globe ” There are four spreadsheets with data. The spreadsheets " Multiresistance" and “Multifunctionality” contain the raw data used in this paper. The spreadsheets "Dataset_metadata" contain the associated metadata, where a description of all the variables and units can be found.
DOI: 10.6084/m9.figshare.5089939
title: Epistasis mediated alleviation of the cost of antibiotic resistance for MRSA

description: Assembled genomes of mupirocin resistance mutant strain MY40 and the SH1000 parental strain.
DOI: 10.6084/m9.figshare.5089942.v1
title: Soil microbial communities drive the resistance of ecosystem multifunctionality to global change in drylands across the globe

description: Data from "Manuel Delgado-Baquerizo, David J. Eldridge, Victoria Ochoa, Beatriz Gozalo, Brajesh K. Singh & Fernando T. Maestre. Soil microbial communities drive the resistance of ecosystem multifunctionality to global change in drylands across the globe ” There are four spreadsheets with data. The spreadsheets " Multiresistance" and “Multifunctionality” contain the raw data used in this paper. The spreadsheets "Dataset_metadata" contain the associated metadata, where a description of all the variables and units can be found.
DOI: 10.6084/m9.figshare.5089864
title: local_climate.csv

description: Local, daily climate data for parameterising NicheMapR. Include: min/max air temperatures (current, minimum warming, maximum warming), max relative humidity, max wind speed, daily rainfall.
DOI: 10.6084/m9.figshare.5089798
title: Skeleto_L._latrans

description: Analysis of "Age structure, growth pattern, sexual maturity, and longevity of <i>Leptodactylus latrans</i> (Anura: Leptodactylidae) in temperate wetlands"Authors: Javier A. López, Carolina E. Antoniazzi, Roxana E. Llanes, Romina Ghirardi
DOI: 10.6084/m9.figshare.5089867
title: Rumor-mongers as reliable sources: Communicating threat-related information suggests source reliability even for unlikely threats

description: Data for Studies 1-5 and Pretests 1-2 from our paper: "Rumor-mongers as reliable sources: Communicating threat-related information suggests source reliability even for unlikely threats".
DOI: 10.6084/m9.figshare.5089864.v1
title: local_climate.csv

description: Local, daily climate data for parameterising NicheMapR. Include: min/max air temperatures (current, minimum warming, maximum warming), max relative humidity, max wind speed, daily rainfall.