cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11320361.v1
title: Dataset for: Human microRNA-30 Inhibits Influenza Virus Infection by Suppressing the Expression of SOCS1, SOCS3, and NEDD4

description: Influenza A virus (IAV) has evolved multiple mechanisms to compromise type I interferon (IFN) responses. The antiviral function of interferon is mainly exerted by activating the JAK/STAT signaling and subsequently inducing interferon-stimulated genes (ISGs) production. However, the mechanism by which IAV combat the type I IFN signaling pathway is not fully elucidated. In the present study, we explored the roles of human microRNAs modulated by IAV infection in type I interferon (IFN) responses. We demonstrated that microRNA-30 (miR-30) family members were downregulated by IAV infection. Our data showed that the forced expression of miR-30 family members inhibited IAV proliferation, while miR-30 family members inhibitors promoted IAV proliferation. Mechanistically, we found that miR-30 family members targeted and reduced SOCS1 and SOCS3 expression, and thus relieved their inhibiting effects on IFN/JAK/STAT signaling pathway. In addition, miR-30 family members inhibited the expression of NEDD4, a negative regulator of IFITM3, which is important for host defense against influenza viruses. Our findings suggest that IAV utilizes a novel strategy to restrain host type I IFN-mediated antiviral immune responses by decreasing the expression of miR-30 family members, and add a new way to understand the mechanism of immune escape caused by influenza viruses.
DOI: 10.6084/m9.figshare.11320106
title: pombe

description: Supplementary
DOI: 10.6084/m9.figshare.11320109
title: ventas.xlsx

description: dataset fot the class on Time Series Forecast
DOI: 10.6084/m9.figshare.11320106.v1
title: pombe

description: Supplementary
DOI: 10.6084/m9.figshare.11319851
title: Genesis and structure of eusperm and parasperm of <i>Plicopurpura patula</i> in relation to phylogeny of Neogastropoda: proteomics of parasperm suggests role in paternity assurance

description: Eusperm and parasperm ultrastructure have been studied for the first time in the neogastropod <i>Plicopurpura patula</i>. Eusperm structure is typical of many Neogastropoda, in which an apical bleb characterizes the conical acrosome with subacrosomal granule; the nucleus is tubular and penetrated to its tip by basal body and axoneme; the mid-piece comprises spiral mitochondria that ensheath the axoneme but terminate at the annulus, defining the junction with the end-piece. In the proximal portion of the end-piece dense tracts of glycogen match the axoneme but these disappear distally. The parasperm is unusual in having no axonemes and no motility was observed. Eusperm do not attach to parasperm, as occurs in the similar nurse cells of Littorinimorpha, thus potential functions may be limited to some form of paternity assurance as occurs in some insects. The nucleus of the parasperm is eliminated during paraspermiogenesis, but there is considerable post-transcriptional secretion activity resulting in the production of a variety of granules, some rich in glycoproteins. A prominent paracrystalline rod accumulates in the centre of the parasperm also from Golgi-derived secretions. Preliminary evidence from proteomics suggests that this parasperm carries the heat shock protein HSP70 that could play a role in fertilization inside the female.
DOI: 10.6084/m9.figshare.11319842
title: MODS_Data

description: Mapping data for RNAseq of MODS patients
DOI: 10.6084/m9.figshare.11319851.v1
title: Genesis and structure of eusperm and parasperm of <i>Plicopurpura patula</i> in relation to phylogeny of Neogastropoda: proteomics of parasperm suggests role in paternity assurance

description: Eusperm and parasperm ultrastructure have been studied for the first time in the neogastropod <i>Plicopurpura patula</i>. Eusperm structure is typical of many Neogastropoda, in which an apical bleb characterizes the conical acrosome with subacrosomal granule; the nucleus is tubular and penetrated to its tip by basal body and axoneme; the mid-piece comprises spiral mitochondria that ensheath the axoneme but terminate at the annulus, defining the junction with the end-piece. In the proximal portion of the end-piece dense tracts of glycogen match the axoneme but these disappear distally. The parasperm is unusual in having no axonemes and no motility was observed. Eusperm do not attach to parasperm, as occurs in the similar nurse cells of Littorinimorpha, thus potential functions may be limited to some form of paternity assurance as occurs in some insects. The nucleus of the parasperm is eliminated during paraspermiogenesis, but there is considerable post-transcriptional secretion activity resulting in the production of a variety of granules, some rich in glycoproteins. A prominent paracrystalline rod accumulates in the centre of the parasperm also from Golgi-derived secretions. Preliminary evidence from proteomics suggests that this parasperm carries the heat shock protein HSP70 that could play a role in fertilization inside the female.
DOI: 10.6084/m9.figshare.11318627
title: precip.mon.mean.nc

description: Precipitation data that was used in a Columbia University Python class that was used to see the correlation between precipitation and anthropogenic aerosols.<br>Citation: <br>Xie, P., and P.A. Arkin, 1997: Global precipitation: A 17-year monthly analysis based on gauge observations, satellite estimates, and numerical model outputs. Bull. Amer. Meteor. Soc., 78, 2539 - 2558.<br>
DOI: 10.6084/m9.figshare.11319839
title: ROR Data Dump 2.0 (November 2019)

description: ROR data download. Based on GRID release 10.6084/m9.figshare.9963719
DOI: 10.6084/m9.figshare.11319842.v1
title: MODS_Data

description: Mapping data for RNAseq of MODS patients
DOI: 10.6084/m9.figshare.11317961
title: Drosophila suzukii tritrophic system

description: Research data used in the publication: Trichopria drosophilae parasitizes Drosophila suzukii in seven common non-crop fruits. Journal of Pest Science.<br>
DOI: 10.6084/m9.figshare.11318627.v1
title: precip.mon.mean.nc

description: Precipitation data that was used in a Columbia University Python class that was used to see the correlation between precipitation and anthropogenic aerosols.<br>Citation: <br>Xie, P., and P.A. Arkin, 1997: Global precipitation: A 17-year monthly analysis based on gauge observations, satellite estimates, and numerical model outputs. Bull. Amer. Meteor. Soc., 78, 2539 - 2558.<br>
DOI: 10.6084/m9.figshare.11317946
title: Correlation of anxiety and eye hand coordination

description: This includes the details of the data set in my study describing the an individual's level of anxiety and their Eye Hand Coordination scores. <br><br>
DOI: 10.6084/m9.figshare.11319839.v1
title: ROR Data Dump 2.0 (November 2019)

description: First ROR data download. Based on GRID release 10.6084/m9.figshare.9963719
DOI: 10.6084/m9.figshare.11319839.v3
title: ROR Data Dump 2.0 (November 2019)

description: ROR data download. Based on GRID release 10.6084/m9.figshare.9963719
DOI: 10.6084/m9.figshare.11319839.v2
title: ROR Data Dump 2.0 (November 2019)

description: First ROR data download. Based on GRID release 10.6084/m9.figshare.9963719
DOI: 10.6084/m9.figshare.11317841
title: indivPlots.tgz

description: This item contains plots of summary statistics calculated from individual simulation replicates from Dan Schrider's paper comparing patterns of variation produced by hitchhiking to those produced by background selection. For more information see the manuscript (doi: TBA), and the code used to produce these simulations (https://github.com/SchriderLab/posSelVsBgs).
DOI: 10.6084/m9.figshare.11317946.v2
title: Correlation of anxiety and eye hand coordination

description: This includes the details of the data set in my study describing the an individual's level of anxiety and their Eye Hand Coordination scores. <br><br>
DOI: 10.6084/m9.figshare.11317841.v1
title: indivPlots.tgz

description: This item contains plots of summary statistics calculated from individual simulation replicates from Dan Schrider's paper comparing patterns of variation produced by hitchhiking to those produced by background selection. For more information see the manuscript (doi: TBA), and the code used to produce these simulations (https://github.com/SchriderLab/posSelVsBgs).
DOI: 10.6084/m9.figshare.11317946.v1
title: Correlation of anxiety and eye hand coordination

description: This includes the details of the data set in my study describing the an individual's level of anxiety and their Eye Hand Coordination scores. <br>
DOI: 10.6084/m9.figshare.11317817
title: Yellowstone InSAR and GPS for modelling in JGR paper 2019JB018208

description: GPS and InSAR data used in Yellowstone deformation modeling are in the ZIP file 2019JB018208_data.zip. A description of the data (and a graphic presentation of each data set) is in the PDF file 2019JB018208_Supplemental.pdf.<br>
DOI: 10.6084/m9.figshare.11317817.v1
title: Yellowstone InSAR and GPS for modelling in JGR paper 2019JB018208

description: GPS and InSAR data used in Yellowstone deformation modeling are in the ZIP file 2019JB018208_data.zip. A description of the data (and a graphic presentation of each data set) is in the PDF file 2019JB018208_Supplemental.pdf.<br>
DOI: 10.6084/m9.figshare.11317790
title: Metadata record for: A global database for metacommunity ecology, integrating species, traits, environment and space

description: This dataset contains key characteristics about the data described in the Data Descriptor A global database for metacommunity ecology, integrating species, traits, environment and space. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format <br> <br> Versioning Note:Version 2 was generated when the metadata format was updated from JSON to JSON-LD. This was an automatic process that changed only the format, not the contents, of the metadata.<br>
DOI: 10.6084/m9.figshare.11317790.v2
title: Metadata record for: A global database for metacommunity ecology, integrating species, traits, environment and space

description: This dataset contains key characteristics about the data described in the Data Descriptor A global database for metacommunity ecology, integrating species, traits, environment and space. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format <br> <br> Versioning Note:Version 2 was generated when the metadata format was updated from JSON to JSON-LD. This was an automatic process that changed only the format, not the contents, of the metadata.<br>
DOI: 10.6084/m9.figshare.11317805.v1
title: High-Frequency Lead-Lag Effects and Cross-Asset Linkages: a Multi-Asset Lagged Adjustment Model*

description: Motivated by the empirical evidence of high-frequency lead-lag effects and cross-asset linkages, we introduce a multi-asset price formation model which generalizes standard univariate microstructure models of lagged price adjustment. Econometric inference on such model provides: (i) a unified statistical test for the presence of lead-lag correlations in the latent price process and for the existence of a multi-asset price formation mechanism; (ii) separate estimation of contemporaneous and lagged dependencies; (iii) an unbiased estimator of the integrated covariance of the efficient martingale price process that is robust to microstructure noise, asynchronous trading and lead-lag dependencies. Through an extensive simulation study, we compare the proposed estimator to alternative approaches and show its advantages in recovering the true lead-lag structure of the latent price process. Our application to a set of NYSE stocks provides empirical evidence for the existence of a multi-asset price formation mechanism and sheds light on its market microstructure determinants.
DOI: 10.6084/m9.figshare.11317778
title: Permutation Tests for Infection Graphs

description: We formulate and analyze a novel hypothesis testing problem for inferring the edge structure of an infection graph. In our model, a disease spreads over a network via contagion or random infection, where the times between successive contagion events are independent exponential random variables with unknown rate parameters. A subset of nodes is also censored uniformly at random. Given the observed infection statuses of nodes in the network, the goal is to determine the underlying graph. We present a procedure based on permutation testing, and we derive sufficient conditions for the validity of our test in terms of automorphism groups of the graphs corresponding to the null and alternative hypotheses. Our test is easy to compute and does not involve estimating unknown parameters governing the process. We also derive risk bounds for our permutation test in a variety of settings, and relate our test statistic to approximate likelihood ratio testing and maximin tests. For graphs not satisfying the necessary symmetries, we provide an additional method for testing the significance of the graph structure, albeit at a higher computational cost. We conclude with an application to real data from an HIV infection network. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.11317760
title: TGD POInT datasets and models

description: Datasets for analysis of the teleost-specific genome duplication (TGD) using POInT (Polyploidy Orthology Inference Tool; https://github.com/gconant0/POInT). Eight genome order files are included (*POInT_gene_orders.txt) corresponding to the eight genomes studied. An optimized ancestral genome order (TGD_OptOrder.txt), WGD gene loss model (WGD_fix_biasconverg_singlerate_model.txt) and assumed phylogeny (TGD_Topo.tre) are also included. All of these files are POInT inputs. POInT's optimal orthology inferences for each duplicated locus is also provided (Optimal_orthology_inferences.txt).Additionally, I provide the conditional probabilities of all possible state transitions along each branch at every duplicated locus (TGD_WGDbcnbnf_OptOrder_condprobs.xlsx). Finally, I provide a list of all inferred ohnolog pairs in zebrafish (AllDrerio_WGD_duplpairs_wtandem_merged.txt), a list which includes a number of ohnolog pairs omitted from the main dataset because homologs of the pair were lacking in at least one other teleost genome. The corresponding list of single-copy genes is AllDrerio_WGD_singls_WTANDEMS.txt.All four supplemental figures (Supplemental Figure 1-4) from the manuscript are included as fully scalable PDF files. Finally, the underlying data for Figure 2-4 are provided as MS Excel files. (Figure 1 can be constructed from the posterior probability file provided).
DOI: 10.6084/m9.figshare.11317790.v1
title: Metadata record for: A global database for metacommunity ecology, integrating species, traits, environment and space

description: This dataset contains key characteristics about the data described in the Data Descriptor A global database for metacommunity ecology, integrating species, traits, environment and space. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format
DOI: 10.6084/m9.figshare.11317778.v2
title: Permutation Tests for Infection Graphs

description: We formulate and analyze a novel hypothesis testing problem for inferring the edge structure of an infection graph. In our model, a disease spreads over a network via contagion or random infection, where the times between successive contagion events are independent exponential random variables with unknown rate parameters. A subset of nodes is also censored uniformly at random. Given the observed infection statuses of nodes in the network, the goal is to determine the underlying graph. We present a procedure based on permutation testing, and we derive sufficient conditions for the validity of our test in terms of automorphism groups of the graphs corresponding to the null and alternative hypotheses. Our test is easy to compute and does not involve estimating unknown parameters governing the process. We also derive risk bounds for our permutation test in a variety of settings, and relate our test statistic to approximate likelihood ratio testing and maximin tests. For graphs not satisfying the necessary symmetries, we provide an additional method for testing the significance of the graph structure, albeit at a higher computational cost. We conclude with an application to real data from an HIV infection network. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.11317760.v1
title: TGD POInT datasets and models

description: Datasets for analysis of the teleost-specific genome duplication (TGD) using POInT (Polyploidy Orthology Inference Tool; https://github.com/gconant0/POInT). Eight genome order files are included (*POInT_gene_orders.txt) corresponding to the eight genomes studied. An optimized ancestral genome order (TGD_OptOrder.txt), WGD gene loss model (WGD_fix_biasconverg_singlerate_model.txt) and assumed phylogeny (TGD_Topo.tre) are also included. All of these files are POInT inputs. POInT's optimal orthology inferences for each duplicated locus is also provided (Optimal_orthology_inferences.txt).
DOI: 10.6084/m9.figshare.11317676
title: Non-linear electrical measurements on Apples and Aloe Vera

description: This data contains electrical measurements on apples, aloe vera, apple juice and aloe vera liquid. The measurements were done with a three electrode system that enables monopolar recordings under the measurement electrodes. The measurements were done simultaneously with two different measurement electrodes (one silver/silver chloride electrode with a diameter of 2mm and a length of 2mm to 3mm and a clinical stainless steel needle electrode). Different voltages were applied (sinusoidal and triangular with different amplitudes and frequencies) and the resulting currents were measured. Column number one gives information about the subject number, column number 2 which type of subject, columns 3 to 5 give information which voltage was applied, number 6 is the number of measurement within one subject. Column 7 gives information about which quantity (time, applied voltage, measured current 1 (recorded with the Ag/AgCl electrode), measured current 2 (recorded with the clinical stainless steel needle electrode), the data points (from column 8 to the last column) belong to. <br>
DOI: 10.6084/m9.figshare.11317760.v2
title: TGD POInT datasets and models

description: Datasets for analysis of the teleost-specific genome duplication (TGD) using POInT (Polyploidy Orthology Inference Tool; https://github.com/gconant0/POInT). Eight genome order files are included (*POInT_gene_orders.txt) corresponding to the eight genomes studied. An optimized ancestral genome order (TGD_OptOrder.txt), WGD gene loss model (WGD_fix_biasconverg_singlerate_model.txt) and assumed phylogeny (TGD_Topo.tre) are also included. All of these files are POInT inputs. POInT's optimal orthology inferences for each duplicated locus is also provided (Optimal_orthology_inferences.txt).Additionally, I provide the conditional probabilities of all possible state transitions along each branch at every duplicated locus (TGD_WGDbcnbnf_OptOrder_condprobs.xlsx). Finally, I provide a list of all inferred ohnolog pairs in zebrafish (AllDrerio_WGD_duplpairs_wtandem_merged.txt), a list which includes a number of ohnolog pairs omitted from the main dataset because homologs of the pair were lacking in at least one other teleost genome.
DOI: 10.6084/m9.figshare.11317676.v2
title: Non-linear electrical measurements on Apples and Aloe Vera

description: This data contains electrical measurements on apples, aloe vera, apple juice and aloe vera liquid. The measurements were done with a three electrode system that enables monopolar recordings under the measurement electrodes. The measurements were done simultaneously with two different measurement electrodes (one silver/silver chloride electrode with a diameter of 2mm and a length of 2mm to 3mm and a clinical stainless steel needle electrode). Different voltages were applied (sinusoidal and triangular with different amplitudes and frequencies) and the resulting currents were measured. Column number one gives information about the subject number, column number 2 which type of subject, columns 3 to 5 give information which voltage was applied, number 6 is the number of measurement within one subject. Column 7 gives information about which quantity (time, applied voltage, measured current 1 (recorded with the Ag/AgCl electrode), measured current 2 (recorded with the clinical stainless steel needle electrode), the data points (from column 8 to the last column) belong to. <br>
DOI: 10.6084/m9.figshare.11317760.v3
title: TGD POInT datasets and models

description: Datasets for analysis of the teleost-specific genome duplication (TGD) using POInT (Polyploidy Orthology Inference Tool; https://github.com/gconant0/POInT). Eight genome order files are included (*POInT_gene_orders.txt) corresponding to the eight genomes studied. An optimized ancestral genome order (TGD_OptOrder.txt), WGD gene loss model (WGD_fix_biasconverg_singlerate_model.txt) and assumed phylogeny (TGD_Topo.tre) are also included. All of these files are POInT inputs. POInT's optimal orthology inferences for each duplicated locus is also provided (Optimal_orthology_inferences.txt).Additionally, I provide the conditional probabilities of all possible state transitions along each branch at every duplicated locus (TGD_WGDbcnbnf_OptOrder_condprobs.xlsx). Finally, I provide a list of all inferred ohnolog pairs in zebrafish (AllDrerio_WGD_duplpairs_wtandem_merged.txt), a list which includes a number of ohnolog pairs omitted from the main dataset because homologs of the pair were lacking in at least one other teleost genome. The corresponding list of single-copy genes is AllDrerio_WGD_singls_WTANDEMS.txt
DOI: 10.6084/m9.figshare.11317676.v1
title: Untitled Item

description: This data contains electrical measurements on apples, aloe vera, apple juice and aloe vera liquid. The measurements were done with a three electrode system that enables monopolar recordings under the measurement electrodes. The measurements were done simultaneously with two different measurement electrodes (one silver/silver chloride electrode with a diameter of 2mm and a length of 2mm to 3mm and a clinical stainless steel needle electrode). Different voltages were applied (sinusoidal and triangular with different amplitudes and frequencies) and the resulting currents were measured. Column number one gives information about the subject number, column number 2 which type of subject, columns 3 to 5 give information which voltage was applied, number 6 is the number of measurement within one subject. Column 7 gives information about which quantity (time, applied voltage, measured current 1 (recorded with the Ag/AgCl electrode), measured current 2 (recorded with the clinical stainless steel needle electrode), the data points (from column 8 to the last column) belong to. <br>