cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20337603
title: PCR assay for rapid taxonomic differentiation of virulent Staphylococcus aureus and Klebsiella pneumoniae bacteriophages

description: Phage therapy is now seen as a promising way to overcome the current global crisis in the spread of multidrug-resistant bacteria. However, phages are highly strain specific and, in most cases, one will have to isolate a new phage, or search for a suitable for therapeutic application phage in existing libraries. At an early stage of the isolation process, rapid screening techniques are needed to identify and type potential virulent phage. Here, we proposed a simple PCR approach to differentiate between two families of virulent <em>Staphylococci</em> phages (<em>Herelleviridae</em> and <em>Rountreeviridae</em>) and eleven genera of virulent <em>Klebsiella</em> phages (<em>Przondovirus, Taipeivirus, Drulisvirus, Webervirus, Jiaodavirus, Sugarlandvirus, Slopekvirus, Jedunavirus, Marfavirus, Mydovirus</em>, and <em>Yonseivirus</em>). This assay included a thorough search for specific genes, that are highly conserved at the taxonomic group level, on a dataset comprising <em>S. aureus</em> (<em>n</em> = 269) and <em>K. pneumoniae</em> (<em>n</em> = 480) phage genomes available in the NCBI RefSeq/GenBank database. The selected primers showed high sensitivity and specificity for both isolated DNA and crude phage lysates, which allows circumventing the DNA purification protocols. Our approach can be extended and applied to any group of phages, given the large number of available genomes in the databases.
DOI: 10.6084/m9.figshare.20337603.v1
title: PCR assay for rapid taxonomic differentiation of virulent Staphylococcus aureus and Klebsiella pneumoniae bacteriophages

description: Phage therapy is now seen as a promising way to overcome the current global crisis in the spread of multidrug-resistant bacteria. However, phages are highly strain specific and, in most cases, one will have to isolate a new phage, or search for a suitable for therapeutic application phage in existing libraries. At an early stage of the isolation process, rapid screening techniques are needed to identify and type potential virulent phage. Here, we proposed a simple PCR approach to differentiate between two families of virulent <em>Staphylococci</em> phages (<em>Herelleviridae</em> and <em>Rountreeviridae</em>) and eleven genera of virulent <em>Klebsiella</em> phages (<em>Przondovirus, Taipeivirus, Drulisvirus, Webervirus, Jiaodavirus, Sugarlandvirus, Slopekvirus, Jedunavirus, Marfavirus, Mydovirus</em>, and <em>Yonseivirus</em>). This assay included a thorough search for specific genes, that are highly conserved at the taxonomic group level, on a dataset comprising <em>S. aureus</em> (<em>n</em> = 269) and <em>K. pneumoniae</em> (<em>n</em> = 480) phage genomes available in the NCBI RefSeq/GenBank database. The selected primers showed high sensitivity and specificity for both isolated DNA and crude phage lysates, which allows circumventing the DNA purification protocols. Our approach can be extended and applied to any group of phages, given the large number of available genomes in the databases.
DOI: 10.5287/bodleian:r5xedr18r
title: database CTS GAP-43 study
DOI: 10.6084/m9.figshare.17000071.v3
title: Bankuptcy

description: This dataset includes stata sintax: Sintaxis for figshare.docxstata data: Bankruptcy.dta
DOI: 10.5281/zenodo.6862522
title: Model output dataset for Ardyna et al. (2022) Wildfire aerosol deposition likely amplified a summertime Arctic phytoplankton bloom

description: Daily July and August 2014 aerosol optical depth (AODVIS) and nitrogen deposition (NDEP) output from simulations using Community Earth System Model. Data owner: Diana Bernstein (diana.bernstein@usm.edu).
DOI: 10.5281/zenodo.6862521
title: Model output dataset for Ardyna et al. (2022) Wildfire aerosol deposition likely amplified a summertime Arctic phytoplankton bloom

description: Daily July and August 2014 aerosol optical depth (AODVIS) and nitrogen deposition (NDEP) output from simulations using Community Earth System Model. Data owner: Diana Bernstein (diana.bernstein@usm.edu).
DOI: 10.5519/qd.6l25j1wt
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (638 records)
DOI: 10.5519/qd.gcyzi7qk
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (658 records)
DOI: 10.5203/14y1-3f90
title: fish-com
DOI: 10.5281/zenodo.6862671
title: Dataset for "MicrographCleaner: A python package for cryo-EM micrograph cleaning using deep learning"

description: The dataset used for the Publicaton "MicrographCleaner: A python package for cryo-EM micrograph cleaning using deep learning" https://doi.org/10.1016/j.jsb.2020.107498
DOI: 10.6073/pasta/0d90c63700f164241074d1f5835c43cb
title: ASD06 Stream discharge measured at the flumes on watershed N02B at Konza Prairie

description: Stream discharge is measured on a catchment (N02B), with 2-year fire return interval and grazed by bison since 1992. Measurements are taken at 5 minute intervals at a triangular throated flume. The prairie streams are 3rd-order and are intermittent. Daily and stormflow discharge records are available.
DOI: 10.6073/pasta/5794ee6297c6cabca6169aa2c7cf082c
title: ASD05 Stream discharge measured at the flumes on watershed N01B at Konza Prairie

description: Stream discharge is measured on a catchment (N01B), with 1-year fire return interval and grazed by bison since 1992. Measurements are taken at 5 minute intervals at a triangular throated flume. The prairie streams are 3rd-order and are intermittent. Daily and stormflow discharge records are available.
DOI: 10.6073/pasta/03fa19934fafebe716f3bfd791a4d3d9
title: ASD04 Stream discharge measured at the flumes on watershed N20B at Konza Prairie

description: Stream discharge is measured on a catchment (N20B), with 20-year fire return interval and grazed by bison since 1992. Measurements are taken at 5 minute intervals at a triangular throated flume. The prairie streams are 3rd-order and are intermittent. Daily and stormflow discharge records are available.
DOI: 10.6073/pasta/1fb12b7396226b8cb6f785140be36c4c
title: ASD02 Stream discharge measured at the flumes on watershed N04D at Konza Prairie

description: Stream discharge is measured on a catchment (N04D), with 4-year fire return interval and grazed by bison since 1992. Measurements are taken at 5 minute intervals at a triangular throated flume. The prairie streams are 3rd-order and are intermittent. Daily and stormflow discharge records are available.
DOI: 10.6084/m9.figshare.20338893.v1
title: Impact of mature tertiary lymphoid structures on prognosis of Epstein-Barr virus-associated gastric cancer

description: EBVaGC tumors were sequenced on a targeted panel.
DOI: 10.18112/openneuro.ds003176.v2.0.1
title: Neurophysiological indicators of internal attention: An fMRI–eye-tracking coregistration study
DOI: 10.6084/m9.figshare.20338863
title: EBVaGC tumors were sequenced on a targeted panel..docx

description: EBVaGC tumors were sequenced on a targeted panel
DOI: 10.6084/m9.figshare.20338863.v2
title: EBVaGC tumors were sequenced on a targeted panel..docx

description: EBVaGC tumors were sequenced on a targeted panel
DOI: 10.6084/m9.figshare.20338863.v1
title: EBVaGC tumors were sequenced on a targeted panel..docx

description: EBVaGC tumors were sequenced on a targeted panel
DOI: 10.6073/pasta/5f29f3e04e78922879fcca5932ddc54f
title: Water Quality Data from Bethel and Stephens Lakes, Columbia, Missouri 2017-2019

description: This data set encompasses approximately weekly to biweekly water quality samples from Bethel and Stephens Lakes in Columbia, Missouri. The samples were collected as part of the Reservoir Observer Student Scientists Program to examine year-round water quality parameters in these urban reservoirs. Samples were collected by high school students, college students, and staff of the University of Missouri Limnology Laboratrory. Six samples at Stephens Lake were collected by volunteer community scientists as part of the Lakes of Missouri Volunteer Program. Bethel Lake was sampled November 2017 through November 2019, and Stephens Lake was sampled November 2018 through November 2019. Temperature data was obtained from Onset HOBO temperature data loggers that were deployed in 0.5-m increments from the bottom of the reservoirs to within 1 m of the surface.
DOI: 10.6084/m9.figshare.20338677.v1
title: RNA-seq data from TCGA database

description: RNA-seq data from TCGA database
DOI: 10.6084/m9.figshare.20338677.v2
title: RNA-seq data from TCGA database

description: RNA-seq data from TCGA database
DOI: 10.5517/ccdc.csd.cc29hft2
title: CCDC 2130004: Experimental Crystal Structure Determination

description: Related Article: Marion Graf, Hans‐Christian Böttcher, Peter Mayer, Nils Metzler‐Nolte, Sugina Thavalingam, Rafał Czerwieniec|2022|Z.Anorg.Allg.Chem.|648|e202200047|doi:10.1002/zaac.202200047
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.11571/upei-roblib-data/researchdata:780
title: Oral Interview - Emmanuelle LeBlanc and Pascal Miousse: Charlottetown, Prince Edward Island, February 23, 2022.
DOI: 10.11571/upei-roblib-data/researchdata:776
title: Oral Interview - Ward MacDonald: Charlottetown, Prince Edward Island, February 18, 2022.
DOI: 10.5281/zenodo.6862750
title: Cyprinella venusta decontaminated gx

description: .
DOI: 10.5281/zenodo.6862749
title: Cyprinella venusta decontaminated gx

description: .
DOI: 10.11571/upei-roblib-data/researchdata:775
title: Oral Interview - Mike Pendergast: Tracadie, Prince Edward Island, February 6, 2022.
DOI: 10.11571/upei-roblib-data/researchdata:779
title: Oral Interview - Chuck Arsenault: Charlottetown, Prince Edward Island, February 20, 2022.
DOI: 10.6084/m9.figshare.20339112.v1
title: Canopy openness drives insect-mediated ecosystem functions in oil palm biodiversity enrichment experiment in Indonesia

description: As the extent of oil palm (<em>Elaeis guineensis</em>) cultivation has expanded at the expense of tropical rainforests, enriching conventional large-scale oil palm plantations with native trees has been proposed as a strategy for restoring biodiversity and ecosystem function. However, how tree enrichment affects insect-mediated ecosystem functions is unknown. We investigated impacts on insect herbivory and pollination functions in the fourth year of a plantation-scale, long-term oil palm biodiversity enrichment experiment in Jambi, Sumatra, Indonesia. Within 48 plots systematically varying in size (25-1600 m2) and planted tree species richness (1-6 species), we collected data on vegetation structure, understory insect abundances, and pollinator and herbivore activity on chili peppers (<em>Capsicum annuum</em>), a widespread home garden crop, as phytometer plants to quantify insect-mediated ecosystem functions. We examined the independent effects of plot size, tree species richness, and tree identity using the linear model for random partition design. These experimental treatments had the most relationships with vegetation structure: the tree species <em>Peronema canescens</em> strongly decreased (by approximately one standard deviation) both canopy openness and understory vegetation cover; the smallest plots had the lowest understory flower density and richness; and total planted tree species richness decreased flower density. Enrichment influenced herbivorous insects and natural enemies in the understory to a lesser extent: both groups had higher abundances in plots with two enrichment species planted, while herbivores decreased with increasing tree species richness. We found no strong direct relationships between experimental treatments and pollinator activity or most phytometer plant variables, except for lower leaf damage in the smallest plot size. Linking relationships in structural equation models shows that the negative association between <em>P. canescens</em> and understory vegetation cover was mediated through canopy openness. Likewise, canopy openness mediated increases in herbivore and pollinator insect abundances. Higher pollinator visitation increased phytometer yield, while impacts of insect herbivores on yield were not apparent. Our results demonstrate that even at an early stage, ecological restoration influences insect-mediated ecosystem functions, mainly through canopy openness. These findings suggest that maintaining some canopy gaps while enrichment plots develop may be beneficial for increasing habitat heterogeneity and insect-mediated ecosystem functions.
DOI: 10.6084/m9.figshare.20339112
title: Canopy openness drives insect-mediated ecosystem functions in oil palm biodiversity enrichment experiment in Indonesia

description: As the extent of oil palm (<em>Elaeis guineensis</em>) cultivation has expanded at the expense of tropical rainforests, enriching conventional large-scale oil palm plantations with native trees has been proposed as a strategy for restoring biodiversity and ecosystem function. However, how tree enrichment affects insect-mediated ecosystem functions is unknown. We investigated impacts on insect herbivory and pollination functions in the fourth year of a plantation-scale, long-term oil palm biodiversity enrichment experiment in Jambi, Sumatra, Indonesia. Within 48 plots systematically varying in size (25-1600 m2) and planted tree species richness (1-6 species), we collected data on vegetation structure, understory insect abundances, and pollinator and herbivore activity on chili peppers (<em>Capsicum annuum</em>), a widespread home garden crop, as phytometer plants to quantify insect-mediated ecosystem functions. We examined the independent effects of plot size, tree species richness, and tree identity using the linear model for random partition design. These experimental treatments had the most relationships with vegetation structure: the tree species <em>Peronema canescens</em> strongly decreased (by approximately one standard deviation) both canopy openness and understory vegetation cover; the smallest plots had the lowest understory flower density and richness; and total planted tree species richness decreased flower density. Enrichment influenced herbivorous insects and natural enemies in the understory to a lesser extent: both groups had higher abundances in plots with two enrichment species planted, while herbivores decreased with increasing tree species richness. We found no strong direct relationships between experimental treatments and pollinator activity or most phytometer plant variables, except for lower leaf damage in the smallest plot size. Linking relationships in structural equation models shows that the negative association between <em>P. canescens</em> and understory vegetation cover was mediated through canopy openness. Likewise, canopy openness mediated increases in herbivore and pollinator insect abundances. Higher pollinator visitation increased phytometer yield, while impacts of insect herbivores on yield were not apparent. Our results demonstrate that even at an early stage, ecological restoration influences insect-mediated ecosystem functions, mainly through canopy openness. These findings suggest that maintaining some canopy gaps while enrichment plots develop may be beneficial for increasing habitat heterogeneity and insect-mediated ecosystem functions.
DOI: 10.6084/m9.figshare.20338782
title: Acute illness phenotypes - public datasets

description: The repository is used to hold the public datasets helping identify acute illness phenotypes
DOI: 10.6084/m9.figshare.20338782.v4
title: Acute illness phenotypes - public datasets

description: The repository is used to hold the public datasets helping identify acute illness phenotypes
DOI: 10.6084/m9.figshare.20338782.v3
title: Acute illness phenotypes - public datasets

description: The repository is used to hold the public datasets helping identify acute illness phenotypes
DOI: 10.6084/m9.figshare.20085178
title: Fused-Lasso Regularized Cholesky Factors of Large Nonstationary Covariance Matrices of Replicated Time Series

description: The smoothness of subdiagonals of the Cholesky factor of large covariance matrices is closely related to the degree of nonstationarity of autoregressive models for time series data. Heuristically, one expects for nearly stationary covariance matrix entries in each subdiagonal of the Cholesky factor of its inverse to be approximately the same in the sense that the sum of the absolute values of successive differences is small. Statistically, such smoothness is achieved by regularizing each subdiagonal using fused-type lasso penalties. We rely on the standard Cholesky factor as the new parameter within a regularized normal likelihood setup which guarantees: (a) joint convexity of the likelihood function, (b) strict convexity of the likelihood function restricted to each subdiagonal even when <i>n</i> &lt; <i>p</i>, and (c) positive-definiteness of the estimated covariance matrix. A block coordinate descent algorithm, where each block is a subdiagonal, is proposed, and its convergence is established under mild conditions. Lack of decoupling of the penalized likelihood function into a sum of functions involving individual subdiagonals gives rise to some computational challenges and advantages relative to two recent algorithms for sparse estimation of the Cholesky factor, which decouple row-wise. Simulation results and real data analysis show the scope and good performance of the proposed methodology. Software for our method is freely available in R language. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.20085178.v1
title: Fused-Lasso Regularized Cholesky Factors of Large Nonstationary Covariance Matrices of Replicated Time Series

description: The smoothness of subdiagonals of the Cholesky factor of large covariance matrices is closely related to the degree of nonstationarity of autoregressive models for time series data. Heuristically, one expects for nearly stationary covariance matrix entries in each subdiagonal of the Cholesky factor of its inverse to be approximately the same in the sense that the sum of the absolute values of successive differences is small. Statistically, such smoothness is achieved by regularizing each subdiagonal using fused-type lasso penalties. We rely on the standard Cholesky factor as the new parameter within a regularized normal likelihood setup which guarantees: (a) joint convexity of the likelihood function, (b) strict convexity of the likelihood function restricted to each subdiagonal even when <i>n</i> &lt; <i>p</i>, and (c) positive-definiteness of the estimated covariance matrix. A block coordinate descent algorithm, where each block is a subdiagonal, is proposed, and its convergence is established under mild conditions. Lack of decoupling of the penalized likelihood function into a sum of functions involving individual subdiagonals gives rise to some computational challenges and advantages relative to two recent algorithms for sparse estimation of the Cholesky factor, which decouple row-wise. Simulation results and real data analysis show the scope and good performance of the proposed methodology. Software for our method is freely available in R language. Supplementary materials for this article are available online.
DOI: 10.5281/zenodo.6862771
title: Palythoa mutuki decontaminated gx

description: .
DOI: 10.5281/zenodo.6862770
title: Palythoa mutuki decontaminated gx

description: .
DOI: 10.5281/zenodo.6862789
title: Geo-Locations of 203 Iranian Caravanserai

description: Geo-Locations dataset: Geo-Locations of 203 Iranian Caravanserai [interactive map in this link].
DOI: 10.5281/zenodo.6862788
title: Geo-Locations of 203 Iranian Caravanserai

description: Geo-Locations dataset: Geo-Locations of 203 Iranian Caravanserai [interactive map in this link].
DOI: 10.6084/m9.figshare.20338941
title: Acute illness phenotype - public datasets

description: The repository is used to hold the public datasets helping identify acute illness phenotypes
DOI: 10.6084/m9.figshare.20338941.v2
title: Acute illness phenotype - public datasets

description: The repository is used to hold the public datasets helping identify acute illness phenotypes
DOI: 10.6084/m9.figshare.20338941.v1
title: Acute illness phenotype - public datasets

description: The repository is used to hold the public datasets helping identify acute illness phenotypes
DOI: 10.34740/kaggle/dsv/3961696
title: Autocars pricing
DOI: 10.5517/ccdc.csd.cc2bqztw
title: CCDC 2167049: Experimental Crystal Structure Determination

description: Related Article: Rehan Basta, Atta M. Arif, Richard D. Ernst|2022|Polyhedron|224|115993|doi:10.1016/j.poly.2022.115993
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5281/zenodo.6862839
title: Simulated tracks for the TrackMate-ExTrack module.

description: Simulated tracks, used in a tutorial on TrackMate-ExTrack, a Java port of the ExTrack software. See this page for more information on ExTrack and the tutorial: https://imagej.net/plugins/trackmate/actions/trackmate-extrack
DOI: 10.5281/zenodo.6862838
title: Simulated tracks for the TrackMate-ExTrack module.

description: Simulated tracks, used in a tutorial on TrackMate-ExTrack, a Java port of the ExTrack software. See this page for more information on ExTrack and the tutorial: https://imagej.net/plugins/trackmate/actions/trackmate-extrack
DOI: 10.6084/m9.figshare.20090004
title: High-Dimensional Multi-Task Learning using Multivariate Regression and Generalized Fiducial Inference

description: Over the past decades, the Multi-Task Learning (MTL) problem has attracted much attention in the artificial intelligence and machine learning communities. However, most published work in this area focuses on point estimation; that is, estimating model parameters and/or making predictions. This article studies another important aspect of the MTL problem: uncertainty quantification for model choices and predictions. To be more specific, this article approaches the MTL problem with multivariate regression and develops a novel method for deriving a probability density function on the space of all potential regression models. With this density function, point estimates, as well as confidence and prediction ellipsoids, can be obtained for quantities of interest, such as future observations. The proposed method, termed GMTask, is based on the generalized fiducial inference (GFI) framework and is shown to enjoy desirable theoretical properties. Its promising empirical properties are illustrated via a sequence of numerical experiments and applications to two real datasets. Supplementary materials for this article are available online.