cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15156/bio/sh031424.07fu
title: SH031424.07FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh031425.07fu
title: SH031425.07FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15468/dl.t7kfx8
title: Occurrence Download

description: A dataset containing 29824 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "SpeciesKey is Leptinotarsa decemlineata (Say, 1824)",
 "Year is greater than or equal to 2004",
 "Year is less than or equal to 2023"
 ]
}

 The dataset includes 29824 records from 222 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083617-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xzmu87
title: Occurrence Download

description: A dataset containing 29824 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "SpeciesKey is Leptinotarsa decemlineata (Say, 1824)",
 "Year is greater than or equal to 2004",
 "Year is less than or equal to 2023"
 ]
}

 The dataset includes 29824 records from 222 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083619-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mykh5e
title: Occurrence Download

description: A dataset listing the 638 species recorded in GBIF matching the query:
{
 "TaxonKey" : [
 "is Juniperus L."
 ]
}

 The dataset's 638 records were derived from 2449 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083594-240626123714530/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.6864497
title: Additional file 3: of SWATH-MS based quantitative proteomics analysis reveals that curcumin alters the metabolic enzyme profile of CML cells by affecting the activity of miR-22/IPO7/HIF-1Îą axis

description: Table S2. SWATH-MS Data. (XLSX 884 kb)
DOI: 10.6084/m9.figshare.6864497.v1
title: Additional file 3: of SWATH-MS based quantitative proteomics analysis reveals that curcumin alters the metabolic enzyme profile of CML cells by affecting the activity of miR-22/IPO7/HIF-1Îą axis

description: Table S2. SWATH-MS Data. (XLSX 884 kb)
DOI: 10.6084/m9.figshare.6864479
title: Additional file 2: of SWATH-MS based quantitative proteomics analysis reveals that curcumin alters the metabolic enzyme profile of CML cells by affecting the activity of miR-22/IPO7/HIF-1Îą axis

description: Table S1. MS Data of Protein ID. (XLSX 2197 kb)
DOI: 10.6084/m9.figshare.6864479.v1
title: Additional file 2: of SWATH-MS based quantitative proteomics analysis reveals that curcumin alters the metabolic enzyme profile of CML cells by affecting the activity of miR-22/IPO7/HIF-1Îą axis

description: Table S1. MS Data of Protein ID. (XLSX 2197 kb)
DOI: 10.6084/m9.figshare.6864467
title: Additional file 4: of Extracting proteins involved in disease progression using temporally connected networks

description: Ranking of proteins using algorithm made in the paper and collective influence algorithm and results from controllability algorithm. (XLSX 140 kb)
DOI: 10.6084/m9.figshare.6864467.v1
title: Additional file 4: of Extracting proteins involved in disease progression using temporally connected networks

description: Ranking of proteins using algorithm made in the paper and collective influence algorithm and results from controllability algorithm. (XLSX 140 kb)
DOI: 10.6084/m9.figshare.6864446
title: Additional file 1: of Association between education and television viewing among older working and retired people: a comparative study of Finland and Japan

description: Table S3. Association between educational attainment and TV viewing durations (≥3 h and ≥ 2 h per day) for each cohort and each current working status. The additional table presents the results of the sensitivity analyses with outcomes set to TV viewing durations of ≥3 h and ≥ 2 h per day. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.6864446.v1
title: Additional file 1: of Association between education and television viewing among older working and retired people: a comparative study of Finland and Japan

description: Table S3. Association between educational attainment and TV viewing durations (≥3 h and ≥ 2 h per day) for each cohort and each current working status. The additional table presents the results of the sensitivity analyses with outcomes set to TV viewing durations of ≥3 h and ≥ 2 h per day. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.6864431
title: Additional file 1: of Extracting proteins involved in disease progression using temporally connected networks

description: Text S1. Mathematical representation of traversing a directed network. Validation of ranked lists from other temporal datasets. (ZIP 302 kb)
DOI: 10.6084/m9.figshare.6864431.v1
title: Additional file 1: of Extracting proteins involved in disease progression using temporally connected networks

description: Text S1. Mathematical representation of traversing a directed network. Validation of ranked lists from other temporal datasets. (ZIP 302 kb)
DOI: 10.6084/m9.figshare.6864413
title: Additional file 2: of Functional characterization of enhancer evolution in the primate lineage

description: Table S1. Tiling Scores. Table S2. TF motif enrichment. Table S3. gkm-SVM Prediction of Tiles. Table S4. Ortholog Scores. Table S5. Orthologs normalized to Human. Table S6. gkm-SVM Predictions of Orthologs. Table S7. Orthologs normalized to N2. Table S8. Enhancer Groups from Fig.Â 4. Table S9. Prioritized Mutations. (XLSX 974 kb)
DOI: 10.6084/m9.figshare.6864413.v1
title: Additional file 2: of Functional characterization of enhancer evolution in the primate lineage

description: Table S1. Tiling Scores. Table S2. TF motif enrichment. Table S3. gkm-SVM Prediction of Tiles. Table S4. Ortholog Scores. Table S5. Orthologs normalized to Human. Table S6. gkm-SVM Predictions of Orthologs. Table S7. Orthologs normalized to N2. Table S8. Enhancer Groups from Fig.Â 4. Table S9. Prioritized Mutations. (XLSX 974 kb)
DOI: 10.6084/m9.figshare.6864395
title: MOESM1 of Host factors determine the evolution of infection with Staphylococcus aureus to gangrenous mastitis in goats

description: Additional file 1. Antibody titers to the leukotoxin component LukM and α-toxin and concentration of α-toxin or LukM in milk. Antibody titers to LukM and α-toxin in serum and milk were calculated with reference to an immune goat serum arbitrarily given 1000 or 200 antibody units, respectively. Concentrations of LukM in mammary gland secretions were determined by sandwich ELISA, and of α-toxin by competitive ELISA.
DOI: 10.6084/m9.figshare.6864395.v1
title: MOESM1 of Host factors determine the evolution of infection with Staphylococcus aureus to gangrenous mastitis in goats

description: Additional file 1. Antibody titers to the leukotoxin component LukM and α-toxin and concentration of α-toxin or LukM in milk. Antibody titers to LukM and α-toxin in serum and milk were calculated with reference to an immune goat serum arbitrarily given 1000 or 200 antibody units, respectively. Concentrations of LukM in mammary gland secretions were determined by sandwich ELISA, and of α-toxin by competitive ELISA.
DOI: 10.6084/m9.figshare.6864305
title: Additional file 2 of DNA methylation analysis on purified neurons and glia dissects age and Alzheimer’s disease-specific changes in the human cortex

description: Additional file 2. Supplementary Tables.
DOI: 10.6084/m9.figshare.6864305.v2
title: Additional file 2 of DNA methylation analysis on purified neurons and glia dissects age and Alzheimer’s disease-specific changes in the human cortex

description: Additional file 2. Supplementary Tables.
DOI: 10.6084/m9.figshare.6864305.v1
title: MOESM2 of DNA methylation analysis on purified neurons and glia dissects age and Alzheimerâ s disease-specific changes in the human cortex

description: Additional file 2. Supplementary Tables.
DOI: 10.6084/m9.figshare.6864293
title: Additional file 3: of Wnt evolution and function shuffling in liberal and conservative chordate genomes

description: Wnt sequence alignment for Additional file 1: Figure S4. (FASTA 99 kb)
DOI: 10.6084/m9.figshare.6864293.v1
title: Additional file 3: of Wnt evolution and function shuffling in liberal and conservative chordate genomes

description: Wnt sequence alignment for Additional file 1: Figure S4. (FASTA 99 kb)
DOI: 10.6084/m9.figshare.6864284
title: Additional file 2: of Wnt evolution and function shuffling in liberal and conservative chordate genomes

description: Wnt sequence alignment for Fig. 1. (FASTA 307 kb)
DOI: 10.6084/m9.figshare.6864284.v1
title: Additional file 2: of Wnt evolution and function shuffling in liberal and conservative chordate genomes

description: Wnt sequence alignment for Fig. 1. (FASTA 307 kb)
DOI: 10.6084/m9.figshare.6864254
title: Additional file 1: of Drug utilization in neonatal setting of Pakistan: focus on unlicensed and off label drug prescribing

description: Nursery all cases. File contains all the data which has been analyzed for this manuscript. (XLSX 584 kb)
DOI: 10.6084/m9.figshare.6864254.v1
title: Additional file 1: of Drug utilization in neonatal setting of Pakistan: focus on unlicensed and off label drug prescribing

description: Nursery all cases. File contains all the data which has been analyzed for this manuscript. (XLSX 584 kb)
DOI: 10.6084/m9.figshare.6864227
title: Additional file 1: of Effect of decompressive laparotomy on organ function in patients with abdominal compartment syndrome: a systematic review and meta-analysis

description: Effect of decompressive laparotomy on organ function in adults with grades III and IV ACS. IAP Intra-abdominal pressure, HR Heart rate, MAP Mean arterial pressure, CVP Central venous pressure, PCWP Pulmonary capillary wedge pressure, CI Cardiac index, PIP Peak inspiratory pressure, PEEP Positive end-expiratory pressure, P/F ratio Ratio of partial pressure arterial oxygen and fraction of inspired oxygen, UO Urinary output. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.6864224
title: Additional file 2: of Effect of decompressive laparotomy on organ function in patients with abdominal compartment syndrome: a systematic review and meta-analysis

description: Effect of decompressive laparotomy on organ function in adults with grade IV ACS. IAP Intra-abdominal pressure, HR Heart rate, MAP Mean arterial pressure, CVP Central venous pressure, PCWP Pulmonary capillary wedge pressure, CI Cardiac index, SVRI Systemic vascular resistance index, PIP Peak inspiratory pressure, PEEP Positive end-expiratory pressure, P/F ratio Ratio of partial pressure arterial oxygen and fraction of inspired oxygen, UO Urinary output. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.6864227.v1
title: Additional file 1: of Effect of decompressive laparotomy on organ function in patients with abdominal compartment syndrome: a systematic review and meta-analysis

description: Effect of decompressive laparotomy on organ function in adults with grades III and IV ACS. IAP Intra-abdominal pressure, HR Heart rate, MAP Mean arterial pressure, CVP Central venous pressure, PCWP Pulmonary capillary wedge pressure, CI Cardiac index, PIP Peak inspiratory pressure, PEEP Positive end-expiratory pressure, P/F ratio Ratio of partial pressure arterial oxygen and fraction of inspired oxygen, UO Urinary output. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.6864224.v1
title: Additional file 2: of Effect of decompressive laparotomy on organ function in patients with abdominal compartment syndrome: a systematic review and meta-analysis

description: Effect of decompressive laparotomy on organ function in adults with grade IV ACS. IAP Intra-abdominal pressure, HR Heart rate, MAP Mean arterial pressure, CVP Central venous pressure, PCWP Pulmonary capillary wedge pressure, CI Cardiac index, SVRI Systemic vascular resistance index, PIP Peak inspiratory pressure, PEEP Positive end-expiratory pressure, P/F ratio Ratio of partial pressure arterial oxygen and fraction of inspired oxygen, UO Urinary output. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.6863984.v1
title: Data from Environmentally induced changes to brain morphology predict cognitive performance

description: Data used to conduct the analyses reported in this paper
DOI: 10.6084/m9.figshare.6863819
title: Parametric-Rate Inference for One-Sided Differentiable Parameters

description: Suppose one has a collection of parameters indexed by a (possibly infinite dimensional) set. Given data generated from some distribution, the objective is to estimate the maximal parameter in this collection evaluated at the distribution that generated the data. This estimation problem is typically nonregular when the maximizing parameter is nonunique, and as a result standard asymptotic techniques generally fail in this case. We present a technique for developing parametric-rate confidence intervals for the quantity of interest in these nonregular settings. We show that our estimator is asymptotically efficient when the maximizing parameter is unique so that regular estimation is possible. We apply our technique to a recent example from the literature in which one wishes to report the maximal absolute correlation between a prespecified outcome and one of <i>p</i> predictors. The simplicity of our technique enables an analysis of the previously open case where <i>p</i> grows with sample size. Specifically, we only require that log <i>p</i> grows slower than n, where <i>n</i> is the sample size. We show that, unlike earlier approaches, our method scales to massive datasets: the point estimate and confidence intervals can be constructed in <i>O</i>(<i>np</i>) time. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.6863813
title: Genomes used to infer a tree of life in Hug et al. (2016) - manually downloaded

description: This directory contains 108 genomes manually downloaded from NCBI and JGI. Genome IDs and raw names from Hug et al.'s supplementary table 1 were used as queries.<br>These genomes had to be downloaded manually because they would not be automatically downloaded with Christopher Brown's script (https://github.com/christophertbrown/bioscripts). <br><br>Hug et al. 2016: http://dx.doi.org/10.1038/nmicrobiol.2016.48<br>Christopher Brown and Laura Hug assisted us with the download of this dataset.<br>manualDownload_taxIDmap.txt shows the key from genome ID to taxon ID.
DOI: 10.6084/m9.figshare.6863819.v1
title: Parametric-Rate Inference for One-Sided Differentiable Parameters

description: Suppose one has a collection of parameters indexed by a (possibly infinite dimensional) set. Given data generated from some distribution, the objective is to estimate the maximal parameter in this collection evaluated at the distribution that generated the data. This estimation problem is typically nonregular when the maximizing parameter is nonunique, and as a result standard asymptotic techniques generally fail in this case. We present a technique for developing parametric-rate confidence intervals for the quantity of interest in these nonregular settings. We show that our estimator is asymptotically efficient when the maximizing parameter is unique so that regular estimation is possible. We apply our technique to a recent example from the literature in which one wishes to report the maximal absolute correlation between a prespecified outcome and one of <i>p</i> predictors. The simplicity of our technique enables an analysis of the previously open case where <i>p</i> grows with sample size. Specifically, we only require that log <i>p</i> grows slower than n, where <i>n</i> is the sample size. We show that, unlike earlier approaches, our method scales to massive datasets: the point estimate and confidence intervals can be constructed in <i>O</i>(<i>np</i>) time. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.6863798
title: Genomes of taxa analyzed in Burgess et al. (2012) from two hot springs in Kamchatka, Russia

description: Burgess et al. did a comparative geochemical and microbial characterization of two hot springs in the Uzon Caldera, Kamchatka peninsula, Russia. They described bacteria and archaea in two pools based on 16S rRNA amplicon sequencing. Here, we searched NCBI for representative genomes for all of the 16S taxa they had found. The 16S reads were first re-analyzed with the current version of the RDP database. <br>Original publication: https://link.springer.com/article/10.1007/s00248-011-9979-4
DOI: 10.6084/m9.figshare.6863813.v2
title: Genomes used to infer a tree of life in Hug et al. (2016) - manually downloaded

description: This directory contains 108 genomes manually downloaded from NCBI and JGI. Genome IDs and raw names from Hug et al.'s supplementary table 1 were used as queries.<br>These genomes had to be downloaded manually because they would not be automatically downloaded with Christopher Brown's script (https://github.com/christophertbrown/bioscripts). <br><br>Hug et al. 2016: http://dx.doi.org/10.1038/nmicrobiol.2016.48<br>Christopher Brown and Laura Hug assisted us with the download of this dataset.<br>manualDownload_taxIDmap.txt shows the key from genome ID to taxon ID.
DOI: 10.6084/m9.figshare.6863813.v1
title: Genomes in the tree of life of Hug et al. (2016) - manually downloaded

description: This directory contains 108 genomes manually downloaded from NCBI and JGI. Genome IDs and raw names from Hug et al.'s supplementary table 1 were used as queries.<br>These genomes had to be downloaded manually because they would not be automatically downloaded with Christopher Brown's script (https://github.com/christophertbrown/bioscripts). <br><br>Hug et al. 2016: http://dx.doi.org/10.1038/nmicrobiol.2016.48<br>Christopher Brown and Laura Hug assisted us with the download of this dataset.<br>manualDownload_taxIDmap.txt shows the key from genome ID to taxon ID.
DOI: 10.6084/m9.figshare.6863780.v1
title: Malaria Incidents by Municipalities

description: Malaria incidents by municipality from 2007 to 2015 for species: <i>Plasmodium falciparum </i>and<i> Plasmodium vivax.</i>
DOI: 10.6084/m9.figshare.6863798.v2
title: Genomes of taxa analyzed in Burgess et al. (2012) from two hot springs in Kamchatka, Russia

description: Burgess et al. did a comparative geochemical and microbial characterization of two hot springs in the Uzon Caldera, Kamchatka peninsula, Russia. They described bacteria and archaea in two pools based on 16S rRNA amplicon sequencing. Here, we searched NCBI for representative genomes for all of the 16S taxa they had found. The 16S reads were first re-analyzed with the current version of the RDP database. <br>Original publication: https://link.springer.com/article/10.1007/s00248-011-9979-4
DOI: 10.6084/m9.figshare.6863798.v1
title: Genomes from Burgess et al. (2012) from two hot springs in Kamchatka, Russia

description: Burgess et al. did a comparative geochemical and microbial characterization of two hot springs in the Uzon Caldera, Kamchatka peninsula, Russia. They described bacteria and archaea in two pools based on 16S rRNA amplicon sequencing. Here, we searched NCBI for representative genomes for all of the 16S taxa they had found. The 16S reads were first re-analyzed with the current version of the RDP database. <br>Original publication: https://link.springer.com/article/10.1007/s00248-011-9979-4
DOI: 10.6084/m9.figshare.6863744
title: Genomes used to infer a tree of life in Hug et al. (2016) II

description: This directory contains 2000 genomes downloaded from NCBI. There are 3859 genomes in total. The other 1859 genomes can be found in part I. Genome IDs from Hug et al.'s supplementary table 1 were used as queries. <br>Hug et al. 2016: http://dx.doi.org/10.1038/nmicrobiol.2016.48<br>A script of Christopher Brown was used to download the genomes. It is publicly available on GitHub: https://github.com/christophertbrown/bioscripts<br>Christopher Brown and Laura Hug assisted us with the download of this dataset.<br>Hug_taxIDmap.txt shows the key from genome ID to taxon ID.
DOI: 10.6084/m9.figshare.6863747
title: Standardizing the evaluation of community-based conservation success (Ecological Applications)

description: Community-based conservation, which strives to simultaneously improve nature conservation and alleviate poverty, must provide biological and socio-economic benefits that are linked through effective resilience mechanisms. To date, few community-based conservation initiatives have published comprehensive assessments that track performance in these elements of success. With 45% of the world’s protected areas in co-management with local communities, standardized measures to effectively evaluate the dual goals of community-based conservation are needed. To address this need, we developed SPECCS, a user-friendly Standardized Protocol for Evaluating Community Conservation Success that incorporates an appraisal of data quality to responsibly assess progress over time or to compare effectiveness among different initiatives (www.calgaryzoo.com/why-we-matter/our-approach). In <strong>Brichieri-Colombi et al. </strong>Standardizing the evaluation of community-based conservation success, <i>Ecological Applications,</i> we illustrate SPECCS’s use by evaluating the Wechiau Community Hippo Sanctuary (WCHS) of northern Ghana 10 and 20 years after its inception. Presented here are additional (raw) data used to evaluate the WCHS. For additional data and more information, please see our published works.