cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21926518.v1
title: Bayesian Trend Filtering via Proximal Markov Chain Monte Carlo

description: Proximal Markov Chain Monte Carlo is a novel construct that lies at the intersection of Bayesian computation and convex optimization, which helped popularize the use of nondifferentiable priors in Bayesian statistics. Existing formulations of proximal MCMC, however, require hyperparameters and regularization parameters to be prespecified. In this work, we extend the paradigm of proximal MCMC through introducing a novel new class of nondifferentiable priors called epigraph priors. As a proof of concept, we place trend filtering, which was originally a nonparametric regression problem, in a parametric setting to provide a posterior median fit along with credible intervals as measures of uncertainty. The key idea is to replace the nonsmooth term in the posterior density with its Moreau-Yosida envelope, which enables the application of the gradient-based MCMC sampler Hamiltonian Monte Carlo. The proposed method identifies the appropriate amount of smoothing in a data-driven way, thereby automating regularization parameter selection. Compared with conventional proximal MCMC methods, our method is mostly tuning free, achieving simultaneous calibration of the mean, scale and regularization parameters in a fully Bayesian framework. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.20353576
title: Additional file 1 of Prognostic value of platelet count-related ratios on admission in patients with pyogenic liver abscess

description: Additional file 1. The original data presented in the study are included in the Supplementary Information.
DOI: 10.6084/m9.figshare.20353576.v1
title: Additional file 1 of Prognostic value of platelet count-related ratios on admission in patients with pyogenic liver abscess

description: Additional file 1. The original data presented in the study are included in the Supplementary Information.
DOI: 10.6084/m9.figshare.6722189
title: Additional file 1: of Transferring knowledge of bacterial protein interaction networks to predict pathogen targeted human genes and immune signaling pathways: a case study on M. tuberculosis

description: Text file contains the positive training data consisting of the derived significant interlogs. (TXT 1201 kb)
DOI: 10.6084/m9.figshare.6722189.v1
title: Additional file 1: of Transferring knowledge of bacterial protein interaction networks to predict pathogen targeted human genes and immune signaling pathways: a case study on M. tuberculosis

description: Text file contains the positive training data consisting of the derived significant interlogs. (TXT 1201 kb)
DOI: 10.6084/m9.figshare.6722201.v1
title: Additional file 2: of Transferring knowledge of bacterial protein interaction networks to predict pathogen targeted human genes and immune signaling pathways: a case study on M. tuberculosis

description: Text file contains the negative training data consisting of randomly sampled non-interlogs. (TXT 769 kb)
DOI: 10.6084/m9.figshare.6722201
title: Additional file 2: of Transferring knowledge of bacterial protein interaction networks to predict pathogen targeted human genes and immune signaling pathways: a case study on M. tuberculosis

description: Text file contains the negative training data consisting of randomly sampled non-interlogs. (TXT 769 kb)
DOI: 10.6084/m9.figshare.19305113
title: Additional file 3 of Pan-cancer analysis identifies LMNB1 as a target to redress Th1/Th2 imbalance and enhance PARP inhibitor response in human cancers

description: Additional file 3: Table S3. GESA with HALLMARK gene sets of PRAD cohort in TCGA.
DOI: 10.6084/m9.figshare.19305113.v1
title: Additional file 3 of Pan-cancer analysis identifies LMNB1 as a target to redress Th1/Th2 imbalance and enhance PARP inhibitor response in human cancers

description: Additional file 3: Table S3. GESA with HALLMARK gene sets of PRAD cohort in TCGA.
DOI: 10.6084/m9.figshare.6722207.v1
title: Additional file 3: of Transferring knowledge of bacterial protein interaction networks to predict pathogen targeted human genes and immune signaling pathways: a case study on M. tuberculosis

description: Text file contains the gene ontology analysis of the derived interlogs that get involved in drug resistance of cytochromes and other target-modifying enzymes. (TXT 1703 kb)
DOI: 10.6084/m9.figshare.6722207
title: Additional file 3: of Transferring knowledge of bacterial protein interaction networks to predict pathogen targeted human genes and immune signaling pathways: a case study on M. tuberculosis

description: Text file contains the gene ontology analysis of the derived interlogs that get involved in drug resistance of cytochromes and other target-modifying enzymes. (TXT 1703 kb)
DOI: 10.6084/m9.figshare.19305119
title: Additional file 4 of Pan-cancer analysis identifies LMNB1 as a target to redress Th1/Th2 imbalance and enhance PARP inhibitor response in human cancers

description: Additional file 4: Table S4. GESA with KEGG gene sets of PRAD cohort in TCGA.
DOI: 10.6084/m9.figshare.19305119.v1
title: Additional file 4 of Pan-cancer analysis identifies LMNB1 as a target to redress Th1/Th2 imbalance and enhance PARP inhibitor response in human cancers

description: Additional file 4: Table S4. GESA with KEGG gene sets of PRAD cohort in TCGA.
DOI: 10.6084/m9.figshare.19305125.v1
title: Additional file 5 of Pan-cancer analysis identifies LMNB1 as a target to redress Th1/Th2 imbalance and enhance PARP inhibitor response in human cancers

description: Additional file 5: Table S5. GESA with GO_BP gene sets of PRAD cohort in TCGA.
DOI: 10.6084/m9.figshare.19305125
title: Additional file 5 of Pan-cancer analysis identifies LMNB1 as a target to redress Th1/Th2 imbalance and enhance PARP inhibitor response in human cancers

description: Additional file 5: Table S5. GESA with GO_BP gene sets of PRAD cohort in TCGA.
DOI: 10.6084/m9.figshare.6722219
title: Additional file 4: of Transferring knowledge of bacterial protein interaction networks to predict pathogen targeted human genes and immune signaling pathways: a case study on M. tuberculosis

description: Text file contains the gene ontology analysis of the derived interlogs that get involved in drug resistance of SOS-response and DNA replication. (TXT 1157 kb)
DOI: 10.6084/m9.figshare.6722219.v1
title: Additional file 4: of Transferring knowledge of bacterial protein interaction networks to predict pathogen targeted human genes and immune signaling pathways: a case study on M. tuberculosis

description: Text file contains the gene ontology analysis of the derived interlogs that get involved in drug resistance of SOS-response and DNA replication. (TXT 1157 kb)
DOI: 10.6084/m9.figshare.6722231
title: Additional file 5: of Transferring knowledge of bacterial protein interaction networks to predict pathogen targeted human genes and immune signaling pathways: a case study on M. tuberculosis

description: Text file contains the predicted results on the positive independent test set consisting of less significant interlogs. (TXT 1055 kb)
DOI: 10.6084/m9.figshare.6722231.v1
title: Additional file 5: of Transferring knowledge of bacterial protein interaction networks to predict pathogen targeted human genes and immune signaling pathways: a case study on M. tuberculosis

description: Text file contains the predicted results on the positive independent test set consisting of less significant interlogs. (TXT 1055 kb)
DOI: 10.6084/m9.figshare.25287826
title: Atomistic configurations of Li<sub>2</sub>Mn<sub>1-x</sub>Ru<sub>x</sub>O<sub>3</sub> (x = 0, 0.1, 0.15, 0.2) models

description: The (131) surface model of Li<sub>2</sub>MnO<sub>3</sub> was constructed by a six-layer close-packed <i>p</i> (2*1) with 72 O atoms, 48 Li atoms and 24 Mn atoms. As the Ru and Mn doping ratio is defined as the number of doping atoms divided by the total number of atoms, the doping numbers of 2 Ru, 4 Ru, 6 Ru atoms were used to approximately simulating x = 0.1, 0.15 and 0.2 heteroatomic content in single phase Li<sub>2</sub>Mn<sub>1-x</sub>Ru<sub>x</sub>O<sub>3</sub> samples, respectively.To accurately represent the Li<sub>2</sub>RuO<sub>3</sub> model system, a new Li<sub>2</sub>RuO<sub>3</sub> model was developed based on the refined structure obtained from X-ray diffraction (XRD) data [<i>Nat. Mater.</i> <b>12</b>, 827-835 (2013);<i> Solid State lonics</i> <b>82</b>, 25-31 (1995); <i>Sci. Rep.</i> <b>9</b>, 550 (2019)], and was investigated on the strongest peak intensity of XRD pattern.
DOI: 10.6084/m9.figshare.25287826.v1
title: Atomistic configurations of Li<sub>2</sub>Mn<sub>1-x</sub>Ru<sub>x</sub>O<sub>3</sub> (x = 0, 0.1, 0.15, 0.2) models

description: The (131) surface model of Li<sub>2</sub>MnO<sub>3</sub> was constructed by a six-layer close-packed <i>p</i> (2*1) with 72 O atoms, 48 Li atoms and 24 Mn atoms. As the Ru and Mn doping ratio is defined as the number of doping atoms divided by the total number of atoms, the doping numbers of 2 Ru, 4 Ru, 6 Ru atoms were used to approximately simulating x = 0.1, 0.15 and 0.2 heteroatomic content in single phase Li<sub>2</sub>Mn<sub>1-x</sub>Ru<sub>x</sub>O<sub>3</sub> samples, respectively.To accurately represent the Li<sub>2</sub>RuO<sub>3</sub> model system, a new Li<sub>2</sub>RuO<sub>3</sub> model was developed based on the refined structure obtained from X-ray diffraction (XRD) data [<i>Nat. Mater.</i> <b>12</b>, 827-835 (2013);<i> Solid State lonics</i> <b>82</b>, 25-31 (1995); <i>Sci. Rep.</i> <b>9</b>, 550 (2019)], and was investigated on the strongest peak intensity of XRD pattern.
DOI: 10.5519/qd.4gw9yhhh
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (4 records)
DOI: 10.6084/m9.figshare.20353553.v1
title: Additional file 7 of Genetic evidence of tri-genealogy hypothesis on the origin of ethnic minorities in Yunnan

description: Additional file 7: Table S8. Annotation of major contributing SNPs for adaptive genes with extreme significance. Differential adaptive genes with extreme significance (P &lt; 0.01) with major contributing SNPs are shown in the table. Major contributing SNPs were defined as SNPs with PBS values larger than 0.1 in at least one of the other three M.Yunnan.West populations.
DOI: 10.6084/m9.figshare.20353538.v1
title: Additional file 3 of Genetic evidence of tri-genealogy hypothesis on the origin of ethnic minorities in Yunnan

description: Additional file 3: Table S1. Information of samples used in this study.
DOI: 10.6084/m9.figshare.20353547
title: Additional file 5 of Genetic evidence of tri-genealogy hypothesis on the origin of ethnic minorities in Yunnan

description: Additional file 5: Table S4. Topology test for demography model using 3-population models in dadi.
DOI: 10.6084/m9.figshare.6722249.v1
title: Additional file 6: of Transferring knowledge of bacterial protein interaction networks to predict pathogen targeted human genes and immune signaling pathways: a case study on M. tuberculosis

description: Text file contains the predicted results on the negative independent test set consisting of randomly sampled non-interlogs. (TXT 80 kb)
DOI: 10.6084/m9.figshare.20353544.v1
title: Additional file 4 of Genetic evidence of tri-genealogy hypothesis on the origin of ethnic minorities in Yunnan

description: Additional file 4: Table S3. Demographic parameters of 2-population models with 95% CI estimated by dadi. Pairwise estimations among the populations in Global Panel C were performed using three given models constructed in dadi.
DOI: 10.6084/m9.figshare.20353559
title: Additional file 9 of Genetic evidence of tri-genealogy hypothesis on the origin of ethnic minorities in Yunnan

description: Additional file 9: Table S10. Functional categories enriched from differential gene sets using metascape. Functional categories with −log10(P-value) &gt; 2 are displayed as enriched terms across input gene sets. Similar functional categories were classified into one group. Differential gene set for each M.Yunnan.West population in Additional file 8: Table S9 was used as an input gene set for functional enrichment.
DOI: 10.6084/m9.figshare.6722249
title: Additional file 6: of Transferring knowledge of bacterial protein interaction networks to predict pathogen targeted human genes and immune signaling pathways: a case study on M. tuberculosis

description: Text file contains the predicted results on the negative independent test set consisting of randomly sampled non-interlogs. (TXT 80 kb)
DOI: 10.6084/m9.figshare.20353538
title: Additional file 3 of Genetic evidence of tri-genealogy hypothesis on the origin of ethnic minorities in Yunnan

description: Additional file 3: Table S1. Information of samples used in this study.
DOI: 10.6084/m9.figshare.20353544
title: Additional file 4 of Genetic evidence of tri-genealogy hypothesis on the origin of ethnic minorities in Yunnan

description: Additional file 4: Table S3. Demographic parameters of 2-population models with 95% CI estimated by dadi. Pairwise estimations among the populations in Global Panel C were performed using three given models constructed in dadi.
DOI: 10.6084/m9.figshare.20353550
title: Additional file 6 of Genetic evidence of tri-genealogy hypothesis on the origin of ethnic minorities in Yunnan

description: Additional file 6: Table S7. List of loss-of-function (LOF) novel variants of M.Yunnan.West populations. LOF novel variants for each M.Yunnan.West were defined as a variant with a high impact classification or a missense variant whose SIFT score is lower than 0.05 and PholyPhen score is higher than 0.446.
DOI: 10.15468/dl.6kgrjz
title: Occurrence Download

description: A dataset containing 2972 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Sceloporus aeneus Wiegmann, 1828"
 ]
}

 The dataset includes 2972 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013739-171219132708484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.usrh56
title: Occurrence Download

description: A dataset containing 107 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pachycondyla tarsata (Fabricius, 1798)"
 ]
}

 The dataset includes 107 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001986-150528172251762/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5pxmcq
title: Occurrence Download

description: A dataset containing 57 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is North America",
 "Country is Mexico",
 "TaxonKey is Anas strepera Linnaeus, 1758"
 ]
}

 The dataset includes 57 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0065378-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rq773x
title: Occurrence Download

description: A dataset containing 5285 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((5.48622 49.7232,5.4734 49.6855,5.5439 49.67839,5.55092 49.7155,5.52498 49.73148,5.48622 49.7232))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 5285 records from 35 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0289973-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2skepk
title: Occurrence Download

description: A dataset containing 2614 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Guatemala",
 "DatasetKey is Harvard University Herbaria: All Records"
 ]
}

 The dataset includes 2614 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013742-190918142434337/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yeix24
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Humulus japonicus Siebold & Zucc.",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "Issue is Country mismatch"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001986-160311141623029/datasets/export for details.
DOI: 10.15468/dl.cnb48y
title: Occurrence Download

description: A dataset containing 272 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Apis cerana japonica Radoszkowski, 1887)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Human Observation, Observation, Specimen)",
 "Year is greater than 1945"
 ]
}

 The dataset includes 272 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0278174-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.b29e9x
title: Occurrence Download

description: A dataset containing 383 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hyla wrightorum Taylor, 1939"
 ]
}

 The dataset includes 383 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013743-160311141623029/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qy2vrg
title: Occurrence Download

description: A dataset containing 90 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Alsodes nodosus (Duméril & Bibron, 1841)"
 ]
}

 The dataset includes 90 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0049656-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ehgqhn
title: Occurrence Download

description: A dataset containing 2227 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Felidae",
 "Country is Mexico"
 ]
}

 The dataset includes 2227 records from 78 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001986-160822134323880/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wwyqq5
title: Occurrence Download

description: A dataset containing 271 species occurrences available in GBIF matching the query:
{
 "or" : [
 "TaxonKey is Lychnophora bahiensis Mattf.",
 "TaxonKey is Lychnophora rosmarinifolia Mart."
 ]
}

 The dataset includes 271 records from 57 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0299450-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8zecc8
title: Occurrence Download

description: A dataset containing 18 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lepidium castellanum de Lange & Heenan"
 ]
}

 The dataset includes 18 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0058031-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.1fktt5
title: Occurrence Download

description: A dataset containing 223 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ecuador",
 "HasCoordinate is true",
 "TaxonKey is Microlophus occipitalis (Peters, 1871)",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 223 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006991-180730143533302/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qphkkl
title: Occurrence Download

description: A dataset containing 51309 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "TaxonKey is Squamata",
 "TaxonKey is Reptilia"
 ]
 },
 "HasGeospatialIssue is false",
 "Geometry POLYGON((-104 -9,-104 11,-75 11,-75 -9,-104 -9))"
 ]
}

 The dataset includes 51309 records from 61 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001987-150410134957023/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6c9f84
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Chile",
 "Geometry POLYGON((-78.92578 -56.94497,-60.99609 -56.94497,-60.99609 -16.29905,-78.92578 -16.29905,-78.92578 -56.94497))",
 "HasGeospatialIssue is false",
 "TaxonKey is Hypechiniscus gladiator (Murray, 1905)",
 "Year 1970-2021"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0299453-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hlnknr
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Oryx dammah (Cretzschmar, 1827)",
 "Country is Niger"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013752-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.lu0djt
title: Occurrence Download

description: A dataset containing 5593 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Plantae",
 "DecimalLatitude is greater than 64.1921988363118",
 "DecimalLatitude is less than 65.9120892775336",
 "DecimalLongitude is greater than -144.765404904129",
 "DecimalLongitude is less than -140.354880616469"
 ]
}

 The dataset includes 5593 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006991-180824113759888/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.iaw6km
title: Occurrence Download

description: A dataset containing 18974 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Polychaeta",
 "Geometry POLYGON((-74.882812 13.923403,-74.882812 -58.813741,-2.460937 -58.813741,-2.460937 13.923403,-74.882812 13.923403))",
 "HasGeospatialIssue is false",
 "HasCoordinate is true"
 ]
}

 The dataset includes 18974 records from 40 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001987-150512124619364/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ma43a8
title: Occurrence Download

description: A dataset containing 7282 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Angelica sylvestris L.",
 "MediaType is Image",
 "BasisOfRecord is Human Observation"
 ]
}

 The dataset includes 7282 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000515-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.