cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17182/hepdata.150998.v1/t52
title: "Upper limits on $\mathcal{B}(t\to Hu)$ per final state" of "Search for flavour-changing neutral-current couplings between the top quark and the Higgs boson in multi-lepton final states in 13 TeV $pp$ collisions with the ATLAS detector"

description: Expected upper exclusion limits on the branching ratio $\mathcal{B}(t\to Hu)$ for each individual final state and the full analysis.
description: - CERN-LHC. A search is presented for flavour-changing neutral-current interactions involving the top quark, the Higgs boson and an up-type quark ($q=u,c$) with the ATLAS detector at the Large Hadron Collider. The analysis considers leptonic decays of the top quark along with Higgs boson decays into two $W$ bosons, two $Z$ bosons or a $\tau^{+}\tau^{-}$ pair. It focuses on final states containing either two leptons (electrons or muons) of the same charge or three leptons. The considered processes are $t\bar{t}$ and $Ht$ production. For the $t\bar{t}$ production, one top quark decays via $t\to Hq$. The proton-proton collision data set analysed amounts to 140 fb$^{-1}$ at $\sqrt{s}=13$ TeV. No significant excess beyond Standard Model expectations is observed and upper limits are set on the $t\to Hq$ branching ratios at 95\,\% confidence level, amounting to observed (expected) limits of $\mathcal{B}(t\to Hu)&lt;2.8\,(3.0) \times 10^{-4}$ and $\mathcal{B}(t\to Hc)&lt;3.3\,(3.8) \times 10^{-4}$. Combining this search with other searches for $tHq$ flavour-changing neutral-current interactions previously conducted by ATLAS, considering $H\to b\bar{b}$ and $H\to\gamma\gamma$ decays, as well as $H\to\tau^{+}\tau^{-}$ decays with one or two hadronically decaying $\tau$-leptons, yields observed (expected) upper limits on the branching ratios of $\mathcal{B}(t\to Hu)&lt;2.6\,(1.8) \times 10^{-4}$ and $\mathcal{B}(t\to Hc)&lt;3.4\,(2.3) \times 10^{-4}$.
DOI: 10.17182/hepdata.150998.v1/t53
title: "Upper limits on $\mathcal{B}(t\to Hc)$ per final state" of "Search for flavour-changing neutral-current couplings between the top quark and the Higgs boson in multi-lepton final states in 13 TeV $pp$ collisions with the ATLAS detector"

description: Expected upper exclusion limits on the branching ratio $\mathcal{B}(t\to Hc)$ for each individual final state and the full analysis.
description: - CERN-LHC. A search is presented for flavour-changing neutral-current interactions involving the top quark, the Higgs boson and an up-type quark ($q=u,c$) with the ATLAS detector at the Large Hadron Collider. The analysis considers leptonic decays of the top quark along with Higgs boson decays into two $W$ bosons, two $Z$ bosons or a $\tau^{+}\tau^{-}$ pair. It focuses on final states containing either two leptons (electrons or muons) of the same charge or three leptons. The considered processes are $t\bar{t}$ and $Ht$ production. For the $t\bar{t}$ production, one top quark decays via $t\to Hq$. The proton-proton collision data set analysed amounts to 140 fb$^{-1}$ at $\sqrt{s}=13$ TeV. No significant excess beyond Standard Model expectations is observed and upper limits are set on the $t\to Hq$ branching ratios at 95\,\% confidence level, amounting to observed (expected) limits of $\mathcal{B}(t\to Hu)&lt;2.8\,(3.0) \times 10^{-4}$ and $\mathcal{B}(t\to Hc)&lt;3.3\,(3.8) \times 10^{-4}$. Combining this search with other searches for $tHq$ flavour-changing neutral-current interactions previously conducted by ATLAS, considering $H\to b\bar{b}$ and $H\to\gamma\gamma$ decays, as well as $H\to\tau^{+}\tau^{-}$ decays with one or two hadronically decaying $\tau$-leptons, yields observed (expected) upper limits on the branching ratios of $\mathcal{B}(t\to Hu)&lt;2.6\,(1.8) \times 10^{-4}$ and $\mathcal{B}(t\to Hc)&lt;3.4\,(2.3) \times 10^{-4}$.
DOI: 10.15468/dl.jsbcgn
title: Occurrence Download

description: A dataset containing 5938735 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Falco sparverius"
 ]
}

 The dataset includes 5938735 records from 677 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016001-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/rbm-c58-15153
title: Nude child running

description: Nude child running. This is plate 470, captioned "Child running after a man" from Eadweard Muybridge. Animal locomotion: an electro-photographic investigation of consecutive phases of animal movements. 1872-1885 / published under the auspices of the University of Pennsylvania. Plates. The plates printed by the Photo-Gravure Company. Philadelphia, 1887.
DOI: 10.5281/zenodo.12622026
title: Linked collectors and determiners for: CATA - Catalina Island Conservancy Herbarium Vascular Plants.

description: Natural history specimen data linked to collectors and determiners held within, "CATA - Catalina Island Conservancy Herbarium Vascular Plants". Claims or attributions were made on Bionomia by volunteer Scribes, https://bionomia.net/dataset/7122c31d-d37a-4fb8-ac1e-d17760ba7edf using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, https://gbif.org/dataset/7122c31d-d37a-4fb8-ac1e-d17760ba7edf. Formatted as a Frictionless Data package.
DOI: 10.5281/zenodo.18695328
title: Linked collectors and determiners for: CATA - Catalina Island Conservancy Herbarium Vascular Plants.

description: Natural history specimen data linked to collectors and determiners held within, "CATA - Catalina Island Conservancy Herbarium Vascular Plants". Claims or attributions were made on Bionomia by volunteer Scribes, https://bionomia.net/dataset/7122c31d-d37a-4fb8-ac1e-d17760ba7edf using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, https://gbif.org/dataset/7122c31d-d37a-4fb8-ac1e-d17760ba7edf. Formatted as a Frictionless Data package.
DOI: 10.15468/dl.na9hh9
title: Occurrence Download

description: A dataset containing 10448030 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Phaeophyceae, Ulvophyceae, Rhodophyta)",
 "BasisOfRecord is one of (Observation, Human Observation, Material sample, Specimen, Unknown evidence, Machine Observation, Occurrence evidence)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 10448030 records from 2002 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029056-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rfhzps
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Iris pallida subsp. pallida)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 6 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0094315-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ns28du
title: Occurrence Download

description: A dataset containing 23045 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Dactylorhiza majalis subsp. lapponica (Laest. ex Hartm.) H.Sund.)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 23045 records from 197 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0094316-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qzcwyh
title: Occurrence Download

description: A dataset containing 1328 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Maianthemum racemosum subsp. racemosum)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1328 records from 66 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0094317-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nvtdmk
title: Occurrence Download

description: A dataset containing 108 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Kniphofia ensifolia subsp. ensifolia)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 108 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0094318-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10356920
title: Influence of cation concentration and valence on the structure and texture of spray-dried supraparticles from colloidal silica dispersions

description: These datasets display the raw data for the manuscript: Huanhuan Zhou, Philipp Groppe, Thomas Zimmermann, Susanne Wintzheimer, Karl Mandel, Influence of cation concentration and valence on the structure and texture of spray-dried supraparticles from colloidal silica dispersions, Journal of Colloid and Interface Science, Volume 658,2024, Pages 199-208, https://doi.org/10.1016/j.jcis.2023.12.051.

The data connection file serves as an explanation for all datasets and their connection to the data displayed in the manuscript.
DOI: 10.5281/zenodo.10356921
title: Influence of cation concentration and valence on the structure and texture of spray-dried supraparticles from colloidal silica dispersions

description: These datasets display the raw data for the manuscript: Huanhuan Zhou, Philipp Groppe, Thomas Zimmermann, Susanne Wintzheimer, Karl Mandel, Influence of cation concentration and valence on the structure and texture of spray-dried supraparticles from colloidal silica dispersions, Journal of Colloid and Interface Science, Volume 658,2024, Pages 199-208, https://doi.org/10.1016/j.jcis.2023.12.051.

The data connection file serves as an explanation for all datasets and their connection to the data displayed in the manuscript.
DOI: 10.6084/m9.figshare.26104741
title: Supplementary Material for: Tumor-intrinsic perinuclear LOXL2: Prognostic relevance and relationship with YAP1 activation status in oral squamous cell carcinoma

description: Introduction. Lysyl Oxidase-Like 2 (LOXL2) expression and function is frequently altered in different cancers, but scarcely explored in oral squamous cell carcinoma (OSCC). This prompted us to investigate the clinical relevance of LOXL2 expression pattern in OSCC and also a possible crosstalk with Hippo/YAP1 pathway signaling. 
Methods. Immunohistochemical analysis of LOXL2 protein expression was performed in 158 OSCC patient samples, together with Yes-associated protein 1 (YAP1) activation status. Correlations with clinicopathological parameters and patient survival were assessed. 
Results. Tumor cell-intrinsic LOXL2 expression showed two distinct expression patterns: diffuse cytoplasmic staining (64.6%), and heterogeneous perinuclear staining (35.4%). Remarkably, perinuclear LOXL2 staining was significantly associated with lymph node metastasis, advanced clinical stage and perineural invasion. Moreover, patients harboring tumors with perinuclear LOXL2 expression exhibited significantly poorer disease-specific survival (DSS) rates. Strikingly, we also found that perinuclear LOXL2 positivity gradually increased in relation to YAP1 activation, and patients harboring tumors with concomitant perinuclear LOXL2 and fully active YAP1 exhibited the worst DSS. Multivariate Cox analysis further revealed combined perinuclear LOXL2 and fully active YAP1 as a significant independent predictor of poor DSS. 
Conclusion. Tumor-intrinsic perinuclear LOXL2 emerges as a clinically and biologically relevant feature associated with advanced disease, tumor aggressiveness, and poor prognosis in OSCC. Moreover, this study unprecedentedly uncovers a functional relationship between perinuclear LOXL2 and YAP1 activation with major prognostic implications. Notably, combined perinuclear LOXL2 and fully active YAP1 was revealed as independent predictor of poor prognosis. These findings encourage targeting oncogenic LOXL2 functions for personalized treatment regimens.
DOI: 10.15468/dl.uve677
title: Occurrence Download

description: A dataset containing 5751 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Costa Rica",
 "OccurrenceStatus is Present",
 "TaxonKey is Oophaga pumilio (Schmidt, 1857)"
 ]
}

 The dataset includes 5751 records from 42 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0094320-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rvfg9h
title: Occurrence Download

description: A dataset containing 68 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Philodendron ensifolium subsp. ensifolium)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 68 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0094321-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.35xppf
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "DatasetKey is one of (Herpetofauna de la reserva de la biósfera Valle de Tehuacán-Cuicatlán (etapa final), UCM Amphibian and Reptile Collection (Arctos))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "PublishingOrg is one of (ff90b050-c256-11db-b71b-b8a03c50a862, 4cadac10-3e7b-11d9-8439-b8a03c50a862)",
 "TaxonKey is Barisia planifrons (Bocourt, 1878)"
 ]
}

 The dataset includes 5 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0094322-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9datrr
title: Occurrence Download

description: A dataset containing 5204 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Arum italicum subsp. italicum)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 5204 records from 106 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0094324-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nfnf8t
title: Occurrence Download

description: A dataset containing 109499 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Succineidae"
 ]
}

 The dataset includes 109499 records from 762 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0094291-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15151/esrf-es-1581828213
title: Crystallographic projects at Structural Biology Core Facility, JU - bringing the state of art support to the users in need. Continuation.

description: Structural biology is very informative discipline providing strong support to virtually any biochemistry related project, however in many cases a lack of expertise is a barrier limiting application of structural biology techniques in the most exciting projects. Foundation of Structural Biology Core Facility (SBCF) at Jagiellonian University (JU, Krakow, Poland) was motivated by a need of providing a support of local experts to biochemists who could potentially benefit from detailed knowledge of their proteins of interest. SBCF is based on two pillars - cryo-EM and macromolecular crystallography. The later being conducted with the use of state-of-art beamlines at European synchrotron radiation sources. Since 2019 SBCF assisted in over 55 peer-reviewed publications. With this proposal we'd like to apply for an access to state of the art crystallographic bemlines at ESRF to help our user community to benefit from the brightest and most advanced X-ray sources in Europe.
DOI: 10.15151/esrf-es-1602272939
title: NORWAY BAG

description: The fourteen PIs associated to this proposal represent the entire crystallography community in Norway and are affiliated to the major Norwegian universities. The research interests of the PIs and their collaborators revolves around topics linked to structural biology and material sciences.

We apply for beam time for single- and multi-wavelength MX, Bio-SAXS and Cryo-EM, in support of our research projects funded e.g. by the Research Council of Norway and the ERC. Examples of research projects or topics are carbohydrate-active proteins of medical or bioeconomic relevance, inhibition of DNA repair enzymes, metalloprotein function and catalysis, regulation of cell-cycle processes, enzyme discovery, antibiotic resistance/drug-discovery and neurological diseases.

Our overarching aim is to use bright synchrotron sources to produce high quality science.
DOI: 10.15151/esrf-es-1602273227
title: NORWAY BAG

description: The fourteen PIs associated to this proposal represent the entire crystallography community in Norway and are affiliated to the major Norwegian universities. The research interests of the PIs and their collaborators revolves around topics linked to structural biology and material sciences.

We apply for beam time for single- and multi-wavelength MX, Bio-SAXS and Cryo-EM, in support of our research projects funded e.g. by the Research Council of Norway and the ERC. Examples of research projects or topics are carbohydrate-active proteins of medical or bioeconomic relevance, inhibition of DNA repair enzymes, metalloprotein function and catalysis, regulation of cell-cycle processes, enzyme discovery, antibiotic resistance/drug-discovery and neurological diseases.

Our overarching aim is to use bright synchrotron sources to produce high quality science.
DOI: 10.15468/dl.65aeb7
title: Occurrence Download

description: A dataset containing 155638 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Neritidae"
 ]
}

 The dataset includes 155638 records from 589 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0094292-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.12685951
title: Cell growth dataset for "Suppression of bacterial cell death underlies the antagonistic interaction between ciprofloxacin and tetracycline in Escherichia coli"

description: This dataset contains growth data of E. coli cells measured by optical density at a wavelenght of 600 nm (OD600) to determine the conditions where the combination of ciprofloxacin (CIP) and tetracycline (TET) is antagonistic (or suppressive), using a medium that supports fast, intermediate and slow growth (M9 based medium supplemented with: glucose and amino acid, glucose, and glycerol, respectively).

Two types of assays were performed: a checkerboard assay with a 2-dimension gradient of antibiotic concentrations shown in "Fig-S1-Growth_rates-Checkerboard_assay.zip", and bulk growth rates assay  shown in "Fig-S2-Bulk_doubling_rates-Bioreactor.zip". 

These experiments are presented in the supplementary figures of the following manuscript published as preprint in bioRxiv:  https://doi.org/10.1101/2024.04.18.590101.

 

Fig-S1-Growth_rates-Checkerboard_assay.zip:

- growth-OD600-Blank_correct.xlsx: contains the blank corrected (subtracted by initial OD of sterile medium) OD600 data for each well measured in the checkerboard assay. The negative control is named as "Blank B" in the spreasheet and the antibiotic concentrations for each well is defined in column C (Content).

- growth_data.xlsx: contains the processed data from "Growth-OD600-Blank_correct.xlsx":growth curves were smoothed with a 5-window moving median and outliers corrected using the filloutliers function in MATLAB. Outliers that were missed were manually corrected.

- time_h.xlsx: contains the time in hours used by the matlab function to build the dose response figure S1B.

- analysis_code_checkerboard_assay.m: matlab function used to build the dose response figure S1B.

 

Fig-S2-Bulk_doubling_rates-Bioreactor.zip:

- "bulk_doubling rates_gly/glu/gluaa.csv": contains the calculated doubling rates for each of three experimental replicates (rows) and for each antibiotic treatment (columns: Ctrl, CIP, TET, CIP-TET) as shown in Figure S2. These values were used to calculated the Bliss independence (for further details see https://gitlab.com/MEKlab/single-cell-suppression-2024/figure plotting.ipynb   - Folders containing OD600 measurements and calculated growth rates for each growth medium, which are further separated into folders for each experimental replicate. Each replicate folder is labelled as the date the experiment was performed (denoted as "*" hereon). Each contains the following: raw optical density data (*.txt files), summary of experiment and results (*.docx file), the function compute_growth_rates.m, and the script Growth_curves_*.m.

For more information on methods, strains used and table header descriptions, please refer to the README.txt.
DOI: 10.5281/zenodo.12685952
title: Cell growth dataset for "Suppression of bacterial cell death underlies the antagonistic interaction between ciprofloxacin and tetracycline in Escherichia coli"

description: This dataset contains growth data of E. coli cells measured by optical density at a wavelenght of 600 nm (OD600) to determine the conditions where the combination of ciprofloxacin (CIP) and tetracycline (TET) is antagonistic (or suppressive), using a medium that supports fast growth (M9 based medium supplemented with glucose and amino acid).

Two types of assays were performed: a checkerboard assay with a 2-dimension gradient of antibiotic concentrations shown in "Fig-S1AB-Growth_rates-Checkerboard_assay.zip", and bulk growth rates assay  shown in "Fig-S1C-Bulk_doubling_rates-Bioreactor.zip". 

These experiments are presented in the supplementary figures of the following manuscript published as preprint in bioRxiv:  https://doi.org/10.1101/2024.04.18.590101.

 

Fig-S1AB-Growth_rates-Checkerboard_assay.zip:

- growth-OD600-Blank_correct.xlsx: contains the blank corrected (subtracted by initial OD of sterile medium) OD600 data for each well measured in the checkerboard assay. The negative control is named as "Blank B" in the spreasheet and the antibiotic concentrations for each well is defined in column C (Content).

- growth_data.xlsx: contains the processed data from "Growth-OD600-Blank_correct.xlsx":growth curves were smoothed with a 5-window moving median and outliers corrected using the filloutliers function in MATLAB. Outliers that were missed were manually corrected.

- time_h.xlsx: contains the time in hours used by the matlab function to build the dose response figure S1B.

- analysis_code_checkerboard_assay.m: matlab function used to build the dose response figure S1B.

 

Fig-S1C-Bulk_doubling_rates-Bioreactor.zip:

- OD600 measurements for each sample in the format "Growth-OD600-treatment-sample_number" (e.g. "Growth-OD600-Ctrl-2.xlsx" refers to no drug control, sample 2). - "Doubl_rate-Bliss_indep-mean.xlsx": contains the mean and standard deviation of doubling rate and bliss independence for the three samples of each treatment (Ctrl, CIP, TET, CIP-TET) as shown in Figure S1C. - "Growth_data-all_samples.xlsx": contains calculations for growth rates, doubling rate, doublig time and Bliss independence for all samples. 

For more information on methods, strains used and table header descriptions, please refer to the README.txt.