cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.26140092
title: Bayesian <i>L</i><sub>1/2</sub> Regression

description: It is well known that Bridge regression enjoys superior theoretical properties when compared to traditional LASSO. However, the current latent variable representation of its Bayesian counterpart, based on the exponential power prior, is computationally expensive in higher dimensions. In this article, we show that the exponential power prior has a closed form scale mixture of normal decomposition for α=(12)γ,γ∈{1,2,…}. We call these types of priors L12 prior for short. We develop an efficient partially collapsed Gibbs sampling scheme for computation using the L12 prior and study theoretical properties when p&gt;n. In addition, we introduce a non-separable Bridge penalty function inspired by the fully Bayesian formulation and a novel, efficient coordinate descent algorithm. We prove the algorithm’s convergence and show that the local minimizer from our optimization algorithm has an oracle property. Finally, simulation studies were carried out to illustrate the performance of the new algorithms. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.26140092.v2
title: Bayesian <i>L</i><sub>1/2</sub> Regression

description: It is well known that Bridge regression enjoys superior theoretical properties when compared to traditional LASSO. However, the current latent variable representation of its Bayesian counterpart, based on the exponential power prior, is computationally expensive in higher dimensions. In this article, we show that the exponential power prior has a closed form scale mixture of normal decomposition for α=(12)γ,γ∈{1,2,…}. We call these types of priors L12 prior for short. We develop an efficient partially collapsed Gibbs sampling scheme for computation using the L12 prior and study theoretical properties when p&gt;n. In addition, we introduce a non-separable Bridge penalty function inspired by the fully Bayesian formulation and a novel, efficient coordinate descent algorithm. We prove the algorithm’s convergence and show that the local minimizer from our optimization algorithm has an oracle property. Finally, simulation studies were carried out to illustrate the performance of the new algorithms. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.26140092.v1
title: Bayesian L12 regression

description: It is well known that Bridge regression Knight et al. (2000) enjoys superior theoretical properties when compared to traditional LASSO. However, the current latent variable representation of its Bayesian counterpart, based on the exponential power prior, is computationally expensive in higher dimensions. In this paper, we show that the Bridge prior has a closed form scale mixture of normal decomposition for α=(12)γ,γ∈{1,2,…}. We call these types of priors L12 prior for short. We develop an efficient partially collapsed Gibbs sampling scheme for computation using the L12 prior and study theoretical properties when <i>p</i> &gt; <i>n</i>. In addition, we introduce a non-separable Bridge penalty function inspired by the fully Bayesian formulation and a novel, efficient coordinate descent algorithm. We prove the algorithm’s convergence and show that the local minimizer from our optimisation algorithm has an oracle property. Finally, simulation studies were carried out to illustrate the performance of the new algorithms. Supplementary materials for this article are available online.
DOI: 10.15468/dl.cv52c3
title: Occurrence Download

description: A dataset containing 873 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Myotis auriculus Baker & Stains, 1955"
 ]
}

 The dataset includes 873 records from 48 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008767-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ufmd3f
title: Occurrence Download

description: A dataset containing 143 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Atractus duboisi (Boulenger, 1880))",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 143 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008768-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.26970694
title: Data from "Basil and Swiss chard: edible crops for use in floating treatment wetlands improving agricultural runoff"

description: We quantified plant growth (at saleable/harvestable size), nutrient partitioning, and overall nutrient removal efficiency of sweet basil (<i>Ocimum basilicum</i>) and Swiss chard (<i>Beta vulgaris</i>) over a six- or eight-week period, respectively, with exposures to simulated irrigation return flow with moderate or high concentrations of nutrients present.Worksheets within the file detail (1) Basil and swiss chard growth (shoot height and root length), over time by week, experimental unit (tank), plant, and Fertilizer. In the column variety. SCS = species Swiss Chard, SCB = Swiss chard 'Bright Lights', and SCM = mixture of species and 'Bright Lights' Swiss Chard.(2) Basil & Swiss Chard Harvest data detail fresh biomass and dry biomass along with nutrient concentration in tissues and all calculations that led to calculated nutrient uptake rates by plants(3) basil and swiss chard water detail the species (basil & swiss chard) treatments, fill days, influent/effluent, treatment volume, and concentrations of all measured analytes and then removal rates and efficiency(4) basil and swiss chard water loads: calculate loads of nutrients in vs. out.(5) comparative nutrient removal - calculations made for Table 2 when plant removal rates contrasted with other studies.
DOI: 10.15468/dl.3fz7vu
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Aspidura desilvai Wickramasinghe, Bandara, Vidanapathirana & Wickramasinghe, 2019)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008771-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.p9znjh
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Atractus microrhynchus (Cope, 1868))",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 12 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008772-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.k42sbv
title: Occurrence Download

description: A dataset containing 1617 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Bolitoglossa platydactyla (Gray, 1831)"
 ]
}

 The dataset includes 1617 records from 56 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008773-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cfu4vs
title: Occurrence Download

description: A dataset containing 556 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Gavialis gangeticus (Gmelin, 1789))",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 556 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008774-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kjky9a
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Atractus occidentalis Savage, 1955)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 13 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008775-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2rdaqr
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Monilesaurus acanthocephalus Pal, Vijayakumar, Shanker, Jayarajan & Deepak, 2018)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 8 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008778-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gksed7
title: Occurrence Download

description: A dataset containing 95 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Myrcia monteverdensis (P.E.Sánchez) A.R.Lourenço & Sánchez-Cháv."
 ]
}

 The dataset includes 95 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008777-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.p2zaub
title: Occurrence Download

description: A dataset containing 23 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Atractus paucidens (Despax, 1910))",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 23 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008781-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5khdec
title: Occurrence Download

description: A dataset containing 39 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Orthion guatemalense Lundell"
 ]
}

 The dataset includes 39 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008780-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c78rnk
title: Occurrence Download

description: A dataset containing 3206 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Neuradaceae"
 ]
}

 The dataset includes 3206 records from 108 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008779-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wtghfa
title: Occurrence Download

description: A dataset containing 16 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Parmentiera trunciflora Standl. & L.O.Williams"
 ]
}

 The dataset includes 16 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008782-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hppmg4
title: Occurrence Download

description: A dataset containing 13957 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Crateva L."
 ]
}

 The dataset includes 13957 records from 475 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008783-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.22v57k
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Cnemaspis ingerorum Batuwita, Agarwal & Bauer, 2019)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008785-240906103802322/datasets/export for details.
DOI: 10.5281/zenodo.13687774
title: CRISPRi with barcoded expression reporters dissects regulatory networks in human cells

description: Genome-wide CRISPR screens have emerged as powerful tools for uncovering the genetic underpinnings of diverse biological processes. Incisive screens often depend on directly measuring molecular phenotypes, such as regulated gene expression changes, provoked by CRISPR-mediated genetic perturbations. Here, we provide quantitative measurements of transcriptional responses in human cells across genome-scale perturbation libraries by coupling CRISPR interference (CRISPRi) with barcoded expression reporter sequencing (CiBER-seq). To enable CiBER-seq in mammalian cells, we optimize the integration of highly complex, barcoded sgRNA libraries into a defined genomic context. CiBER-seq profiling of a nuclear factor kappa B (NF-κB) reporter delineates the canonical signaling cascade linking the transmembrane TNF-alpha receptor to inflammatory gene activation and highlights cell-type-specific factors in this response. Importantly, CiBER-seq relies solely on bulk RNA sequencing to capture the regulatory circuit driving this rapid transcriptional response. Our work demonstrates the accuracy of CiBER-seq and its potential for dissecting genetic networks in mammalian cells with superior time resolution.
DOI: 10.5281/zenodo.13687775
title: CRISPRi with barcoded expression reporters dissects regulatory networks in human cells

description: Genome-wide CRISPR screens have emerged as powerful tools for uncovering the genetic underpinnings of diverse biological processes. Incisive screens often depend on directly measuring molecular phenotypes, such as regulated gene expression changes, provoked by CRISPR-mediated genetic perturbations. Here, we provide quantitative measurements of transcriptional responses in human cells across genome-scale perturbation libraries by coupling CRISPR interference (CRISPRi) with barcoded expression reporter sequencing (CiBER-seq). To enable CiBER-seq in mammalian cells, we optimize the integration of highly complex, barcoded sgRNA libraries into a defined genomic context. CiBER-seq profiling of a nuclear factor kappa B (NF-κB) reporter delineates the canonical signaling cascade linking the transmembrane TNF-alpha receptor to inflammatory gene activation and highlights cell-type-specific factors in this response. Importantly, CiBER-seq relies solely on bulk RNA sequencing to capture the regulatory circuit driving this rapid transcriptional response. Our work demonstrates the accuracy of CiBER-seq and its potential for dissecting genetic networks in mammalian cells with superior time resolution.
DOI: 10.15468/dl.ee8m7a
title: Occurrence Download

description: A dataset containing 158 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Dipsas elegans (Boulenger, 1896))",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 158 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008787-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hxwhgc
title: Occurrence Download

description: A dataset containing 859 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Persea schiedeana Nees"
 ]
}

 The dataset includes 859 records from 72 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008784-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mjsxrm
title: Occurrence Download

description: A dataset containing 80 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Psychotria matagalpensis C.M.Taylor"
 ]
}

 The dataset includes 80 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008786-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.u4zrde
title: Occurrence Download

description: A dataset containing 17811 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Muntingiaceae"
 ]
}

 The dataset includes 17811 records from 429 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008776-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qxomqa
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Amblyceps cerinum Ng & Wright, 2010"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003328-160623103540712/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qdse99
title: Occurrence Download

description: A dataset containing 58 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Sida carpinifolia L.fil.",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 58 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000333-180920211646547/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cg9xa6
title: Occurrence Download

description: A dataset containing 416 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Kinnaridae"
 ]
}

 The dataset includes 416 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032264-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.plppgl
title: Occurrence Download

description: A dataset containing 15329 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Aruncus dioicus (Walter) Fernald"
 ]
}

 The dataset includes 15329 records from 251 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003328-170714134226665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3b9ynm
title: Occurrence Download

description: A dataset containing 182 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Africa",
 {
 "or" : [
 "Country is South Africa",
 "Country is Zimbabwe",
 "Country is Mozambique"
 ]
 },
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Naja annulifera Peters, 1854"
 ]
}

 The dataset includes 182 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0336624-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4gyzxm
title: Occurrence Download

description: A dataset containing 2527 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Brongniartia Kunth"
 ]
}

 The dataset includes 2527 records from 84 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003328-170826194755519/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hr8r37
title: Occurrence Download

description: A dataset containing 2541 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Colección de Celastrales hasta Escalloniales del Museo Botánico CORD - IMBIV"
 ]
}

 The dataset includes 2541 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0163366-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yj4ywt
title: Occurrence Download

description: A dataset containing 50 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Vanilla appendiculata Rolfe"
 ]
}

 The dataset includes 50 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0183078-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hjooir
title: Occurrence Download

description: A dataset containing 5087 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Specimen",
 "BasisOfRecord is Fossil"
 ]
 },
 "TaxonKey is Gallus gallus Linnaeus, 1758"
 ]
}

 The dataset includes 5087 records from 111 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003328-171124123535762/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6fw5mn
title: Occurrence Download

description: A dataset containing 67673 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Castor canadensis Kuhl, 1820"
 ]
}

 The dataset includes 67673 records from 171 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0163365-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fwzvhr
title: Occurrence Download

description: A dataset containing 1321 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((91.33594 -1.82781,157.14844 -0.49218,135.49219 20.69856,90.21094 28.36625,91.33594 -1.82781))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Lepidodactylus lugubris (Duméril & Bibron, 1836)"
 ]
}

 The dataset includes 1321 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0336619-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.