cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.29042888
title: Identification of host genetic factors modulating β-lactam resistance in <i>Escherichia coli</i> harbouring plasmid-borne β-lactamase through transposon-sequencing

description: Since β-lactam antibiotics are widely used, emergence of bacteria with resistance to them poses a significant threat to society. In particular, acquisition of genes encoding β-lactamase, an enzyme that degrades β-lactam antibiotics, has been a major contributing factor in the emergence of bacteria that are resistant to β-lactam antibiotics. However, relatively few genetic targets for killing these resistant bacteria have been identified to date. Here, we used a systematic approach called transposon-sequencing (Tn-Seq), to screen the <i>Escherichia coli</i> genome for host genetic factors that, when mutated, affect resistance to ampicillin, one of the β-lactam antibiotics, in a strain carrying a plasmid that encodes β-lactamase. This approach enabled not just the isolation of genes previously known to affect β-lactam resistance, but the additional loci <i>skp</i>, <i>gshA</i>, <i>phoPQ</i> and <i>ypfN</i>. Individual mutations in these genes modestly but consistently affected antibiotic resistance. We have identified that these genes are not only implicated in β-lactam resistance by itself but also play a crucial role in conditions associated with the expression of β-lactamase. <i>GshA</i> and <i>phoPQ</i> appear to contribute to β-lactam resistance by regulating membrane integrity. Notably, the overexpression of the uncharacterized membrane-associated protein, <i>ypfN</i>, has been shown to significantly enhance β-lactam resistance. We applied the genes identified from the screening into <i>Salmonella</i> Typhimurium and <i>Pseudomonas aeruginosa</i> strains, both critical human pathogens with antibiotic resistance, and observed their significant impact on β-lactam resistance. Therefore, these genes can potentially be utilized as therapeutic targets to control the survival of β-lactamase-producing bacteria.
DOI: 10.6084/m9.figshare.29042888.v1
title: Identification of host genetic factors modulating β-lactam resistance in <i>Escherichia coli</i> harbouring plasmid-borne β-lactamase through transposon-sequencing

description: Since β-lactam antibiotics are widely used, emergence of bacteria with resistance to them poses a significant threat to society. In particular, acquisition of genes encoding β-lactamase, an enzyme that degrades β-lactam antibiotics, has been a major contributing factor in the emergence of bacteria that are resistant to β-lactam antibiotics. However, relatively few genetic targets for killing these resistant bacteria have been identified to date. Here, we used a systematic approach called transposon-sequencing (Tn-Seq), to screen the <i>Escherichia coli</i> genome for host genetic factors that, when mutated, affect resistance to ampicillin, one of the β-lactam antibiotics, in a strain carrying a plasmid that encodes β-lactamase. This approach enabled not just the isolation of genes previously known to affect β-lactam resistance, but the additional loci <i>skp</i>, <i>gshA</i>, <i>phoPQ</i> and <i>ypfN</i>. Individual mutations in these genes modestly but consistently affected antibiotic resistance. We have identified that these genes are not only implicated in β-lactam resistance by itself but also play a crucial role in conditions associated with the expression of β-lactamase. <i>GshA</i> and <i>phoPQ</i> appear to contribute to β-lactam resistance by regulating membrane integrity. Notably, the overexpression of the uncharacterized membrane-associated protein, <i>ypfN</i>, has been shown to significantly enhance β-lactam resistance. We applied the genes identified from the screening into <i>Salmonella</i> Typhimurium and <i>Pseudomonas aeruginosa</i> strains, both critical human pathogens with antibiotic resistance, and observed their significant impact on β-lactam resistance. Therefore, these genes can potentially be utilized as therapeutic targets to control the survival of β-lactamase-producing bacteria.
DOI: 10.15468/dl.3e6zym
title: Occurrence Download

description: A dataset containing 97402 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is University of Texas, Biodiversity Center, Entomology Collection (UTIC)"
 ]
}

 The dataset includes 97402 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027097-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34943/fd199398-a01b-4070-b0de-2e382ae33848
title: ROPOS Navigation System Deployed 2016-08-04

description: The ROPOS Navigation 01 was deployed on 2016-08-04 on ROPOS. This Remotely Operated Vehicle is operated by Canadian Scientific Submersible Facility (CSSF). This device is a Navigation System. Navigational instruments are used to measure and record positional information of ships, buoys, and autonomous underwater vehicles (AUVs). Typical sensors include latitude, longitude, speed, heading, pitch, roll, and depth. It was deployed on a mobile platform. Data from this deployment were archived and made available through Ocean Networks Canada's Oceans 3.0 digital infrastructure, with quality assurance and derived data products following established practices.
DOI: 10.5281/zenodo.15390482
title: Combinatorial prediction of therapeutic perturbations using causally-inspired neural networks (chemical data)

description: Dataset supporting "Combinatorial prediction of therapeutic targets using causally-inspired neural networks" (chemical data)

Abstract: Phenotype-driven approaches identify disease-counteracting compounds by analyzing the phenotypic signatures that distinguish diseased from healthy states. Here, we introduce PDGrapher, a causally inspired graph neural network (GNN) designed to predict combinatorial perturbagens (sets of therapeutic targets) capable of reversing disease phenotypes. Unlike methods that learn how perturbations alter phenotypes, PDGrapher solves the inverse problem of directly predicting the perturbagens needed to achieve a desired response by embedding disease cell states into networks, learning a latent representation of these states, and identifying optimal combinatorial perturbations. In experiments in nine cell lines with chemical perturbations, PDGrapher identified effective perturbagens in more test samples than competing methods. It also demonstrates competitive performance on ten genetic perturbation datasets. An advantage of PDGrapher is its direct prediction paradigm, in contrast to the indirect and computationally intensive models traditionally employed in phenotype-driven research. This approach accelerates training by up to 25 times compared to existing methods, providing a fast approach for identifying therapeutic perturbations and advancing phenotype-driven drug discovery.
DOI: 10.5281/zenodo.15390483
title: Combinatorial prediction of therapeutic perturbations using causally-inspired neural networks (chemical data)

description: Dataset supporting "Combinatorial prediction of therapeutic targets using causally-inspired neural networks" (chemical data)

Abstract: Phenotype-driven approaches identify disease-counteracting compounds by analyzing the phenotypic signatures that distinguish diseased from healthy states. Here, we introduce PDGrapher, a causally inspired graph neural network (GNN) designed to predict combinatorial perturbagens (sets of therapeutic targets) capable of reversing disease phenotypes. Unlike methods that learn how perturbations alter phenotypes, PDGrapher solves the inverse problem of directly predicting the perturbagens needed to achieve a desired response by embedding disease cell states into networks, learning a latent representation of these states, and identifying optimal combinatorial perturbations. In experiments in nine cell lines with chemical perturbations, PDGrapher identified effective perturbagens in more test samples than competing methods. It also demonstrates competitive performance on ten genetic perturbation datasets. An advantage of PDGrapher is its direct prediction paradigm, in contrast to the indirect and computationally intensive models traditionally employed in phenotype-driven research. This approach accelerates training by up to 25 times compared to existing methods, providing a fast approach for identifying therapeutic perturbations and advancing phenotype-driven drug discovery.
DOI: 10.34943/fdc3ce5e-9262-450d-b205-f7ce2d411df4
title: R/V Thomas G. Thompson Navigation System Deployed 2011-07-04

description: The RV T.G. Thompson Navigation 01 was deployed on 2011-07-04 on R/V Thomas G. Thompson. The Research Vessel Thomas G. Thompson is owned by the Office of Naval Research (ONR) and operated by the School of Oceanography at the University of Washington. This device is a Navigation System. Navigational instruments are used to measure and record positional information of ships, buoys, and autonomous underwater vehicles (AUVs). Typical sensors include latitude, longitude, speed, heading, pitch, roll, and depth. It was deployed on a mobile platform. Data from this deployment were archived and made available through Ocean Networks Canada's Oceans 3.0 digital infrastructure, with quality assurance and derived data products following established practices.
DOI: 10.15468/dl.58xc8t
title: Occurrence Download

description: A dataset containing 1294 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Peru",
 "OccurrenceStatus is Present",
 "TaxonKey is Phytotoma raimondii Taczanowski, 1883"
 ]
}

 The dataset includes 1294 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027105-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34943/86a51625-f569-4c18-bd3f-5f063445a1b8
title: Baynes Sound Oxygen Sensor Deployed 2025-02-28

description: The Sea-Bird SBE 63 Dissolved Oxygen Sensor 630636 was deployed on 2025-02-28 at Baynes Sound. Baynes Sound is located between Denman Island and Vancouver Island. This device is a Oxygen Sensor. Oxygen sensors measure dissolved oxygen concentration in seawater. It was deployed on a fixed platform. Data from this deployment were archived and made available through Ocean Networks Canada's Oceans 3.0 digital infrastructure, with quality assurance and derived data products following established practices.
DOI: 10.6073/pasta/671db933f173c91693678b5f56394660
title: Ecological Survey of Central Arizona: a survey of key ecological indicators in the greater Phoenix metropolitan area and surrounding Sonoran desert, ongoing since 1999

description: The Ecological Survey of Central Arizona (ESCA) is an extensive field survey and integrated inventory designed to capture key ecological indicators of the CAP LTER study area consisting of the urbanized, suburbanized, and agricultural areas of metropolitan Phoenix, and the surrounding Sonoran desert. The survey, formerly known as the survey 200 and renamed to ESCA in 2015, assesses conditions at approximately 200 sample plots (30m x 30m) that were located randomly using a tessellation-stratified dual-density sampling design. Beginning in 2000, the study is conducted every five years except the 2020 survey, which was conducted in 2023 owing to delays to due Covid. Study plots cover habitats throughout the CAP LTER study area ranging from native Sonoran desert sites to residential yards to an airport tarmac. Measurements include an inventory of all plants (identified to the lowest possible taxonomic unit, typically species), plant biovolume, soil coring for physicochemical properties, arthropod sweep-net sampling, photo documentation, and a visual survey of site and area characteristics. The objectives of the survey are to (1) characterize patches in terms of key biotic, physical, and chemical variables, and (2) examine relationships among land use, general plant diversity, native plant diversity, plant biovolume, soil nutrient status, and social-economic indices along an indirect urban gradient.

A pilot survey was conducted in 1999, and the first full ESCA was conducted in 2000. The maiden survey in 2000 featured a suite of measurements that were not assessed in later surveys, including data from a portable weather station set up during the field survey at each location, organic matter decomposition, pollen, and mycorrhizae. In 2010, the survey was expanded to include an assessment of one of the residential parcels overlapping the survey plot at sites in residential areas. Many of the same variables that are measured in the 30m x 30m survey plot are measured in the parcel, including an inventory of perennial plants, and the biovolume of trees. In addition, a detailed assessment of characteristics of the parcel is performed.

Investigators interested in the additional variables assessed in the 2000 ESCA, in parcel data collected in the 2010 and subsequent surveys, or in soil data collected during the 2000 ESCA (encapsulated in a separate data set owing to a different reporting format) should search for 'ecological survey of central arizona' (quoted!) in the Environmental Data Initiative (EDI) data catalog to locate those and other data related to the Ecological Survey of Central Arizona (ESCA).
DOI: 10.6084/m9.figshare.21656145
title: The use of recovered struvite and ammonium nitrate in fertigation in a horticultural rotation: agronomic and microbiological assessment

description: Phosphorus and nitrogen recovery from wastewater as struvite and ammonium nitrate (AN) may be viable alternative fertilizers to boost circularity in horticulture. A 2-year fertigated crop rotation in soil under greenhouse conditions was evaluated to determine the efficiency of both recovered products as raw materials for a nutrient solution (NS) manufacture. The effects of these treatments versus synthetic fertilizers were compared in terms of crop performance, plant nutrient uptake, soil chemistry and microbiota. This is the first study to implement struvite through fertigation as the sole source of P in soil crops. Results showed that both recovered products can be used as fertilizers in NS, due to the similar response to the control for different parameters and crops (tomato, lettuce, and cauliflower). However, the AN treatment showed lower yield in the first tomato crop, which results may depend on the cultivar ammonium tolerance. Besides, the concentration of heavy metals in fruits/leaves was below the permissible limits. Total and Olsen phosphorus soil analysis revealed no differences among treatments, resulting in a similar performance of P-struvite to commercial phosphate. Bulk soil bacteria structure, richness and relative dominance were increased over time, while archaea only showed lower evenness, both despite the fertilization strategy. Shannon diversity was not significantly affected. A predominance of ammonia-oxidizing bacteria (AOB) versus archaea (AOA) was observed, while nitrite-oxidizing bacteria (NOB), dominated by <i>Nitrospira</i>, increased with fertigation. Our results demonstrate that fertilizer blends for NS containing recovered nutrients are a feasible alternative to synthetic fertilizers.
DOI: 10.6084/m9.figshare.21656145.v2
title: The use of recovered struvite and ammonium nitrate in fertigation in a horticultural rotation: agronomic and microbiological assessment

description: Phosphorus and nitrogen recovery from wastewater as struvite and ammonium nitrate (AN) may be viable alternative fertilizers to boost circularity in horticulture. A 2-year fertigated crop rotation in soil under greenhouse conditions was evaluated to determine the efficiency of both recovered products as raw materials for a nutrient solution (NS) manufacture. The effects of these treatments versus synthetic fertilizers were compared in terms of crop performance, plant nutrient uptake, soil chemistry and microbiota. This is the first study to implement struvite through fertigation as the sole source of P in soil crops. Results showed that both recovered products can be used as fertilizers in NS, due to the similar response to the control for different parameters and crops (tomato, lettuce, and cauliflower). However, the AN treatment showed lower yield in the first tomato crop, which results may depend on the cultivar ammonium tolerance. Besides, the concentration of heavy metals in fruits/leaves was below the permissible limits. Total and Olsen phosphorus soil analysis revealed no differences among treatments, resulting in a similar performance of P-struvite to commercial phosphate. Bulk soil bacteria structure, richness and relative dominance were increased over time, while archaea only showed lower evenness, both despite the fertilization strategy. Shannon diversity was not significantly affected. A predominance of ammonia-oxidizing bacteria (AOB) versus archaea (AOA) was observed, while nitrite-oxidizing bacteria (NOB), dominated by <i>Nitrospira</i>, increased with fertigation. Our results demonstrate that fertilizer blends for NS containing recovered nutrients are a feasible alternative to synthetic fertilizers.
DOI: 10.6084/m9.figshare.28450280
title: Synthesis of new phenolic-containing hydroxyacyl probe and its colorimetric fluorescence detection of S<sup>2-</sup>

description: The excessive S<sup>2-</sup> can lead to a variety of serious physiological diseases, so the quickly detection of S<sup>2-</sup> is of great significance for human. In this paper, a new simple and easily probe <b>Y</b> was designed and synthesized with hydrazine and substituted salicylaldehyde. It can detect S<sup>2-</sup> with good performance in a highly water contain solution (DMSO/H<sub>2</sub>O, v/<i>v</i> = 1/9), both colorimetric and fluorescence spectroscopy have obvious changes after adding 50-folds of S<sup>2-</sup>, and other common fifteen anions have almost no influence in the detection. The detection limit and complexation constant were calculated using fluorescence titration data to be 3.88 μmol/L and 3.68×10<sup>6</sup> L/mol, respectively. Job’s plot experiment showed that the binding ratio of the host with S<sup>2-</sup> is <b>1:1</b>. The NMR titration was employed to verify the recognition mechanism, three protons in two hydroxyl groups (-OH) and one imine (-NH) are disappeared after adding excessive S<sup>2-</sup>, which shown that probe <b>Y</b> undergo a deprotonation process. Preliminary application experiments show that probe <b>Y</b> can detect S<sup>2-</sup> in water samples and soil.
DOI: 10.6084/m9.figshare.28450280.v1
title: Synthesis of new phenolic-containing hydroxyacyl probe and its colorimetric fluorescence detection of S<sup>2-</sup>

description: The excessive S<sup>2-</sup> can lead to a variety of serious physiological diseases, so the quickly detection of S<sup>2-</sup> is of great significance for human. In this paper, a new simple and easily probe <b>Y</b> was designed and synthesized with hydrazine and substituted salicylaldehyde. It can detect S<sup>2-</sup> with good performance in a highly water contain solution (DMSO/H<sub>2</sub>O, v/<i>v</i> = 1/9), both colorimetric and fluorescence spectroscopy have obvious changes after adding 50-folds of S<sup>2-</sup>, and other common fifteen anions have almost no influence in the detection. The detection limit and complexation constant were calculated using fluorescence titration data to be 3.88 μmol/L and 3.68×10<sup>6</sup> L/mol, respectively. Job’s plot experiment showed that the binding ratio of the host with S<sup>2-</sup> is <b>1:1</b>. The NMR titration was employed to verify the recognition mechanism, three protons in two hydroxyl groups (-OH) and one imine (-NH) are disappeared after adding excessive S<sup>2-</sup>, which shown that probe <b>Y</b> undergo a deprotonation process. Preliminary application experiments show that probe <b>Y</b> can detect S<sup>2-</sup> in water samples and soil.
DOI: 10.34943/fc8f2c12-a1ef-4a5c-85d8-66f6a88d07ec
title: E/V Nautilus Navigation System Deployed 2017-06-06

description: The EV Nautilus Navigation 01 was deployed on 2017-06-06 on E/V Nautilus. The Exploration Vessel Nautilus is operated by the Ocean Exploration Trust. This device is a Navigation System. Navigational instruments are used to measure and record positional information of ships, buoys, and autonomous underwater vehicles (AUVs). Typical sensors include latitude, longitude, speed, heading, pitch, roll, and depth. It was deployed on a mobile platform. Data from this deployment were archived and made available through Ocean Networks Canada's Oceans 3.0 digital infrastructure, with quality assurance and derived data products following established practices.
DOI: 10.34943/90a865ec-ee4c-43d8-b770-a9e7cd60c227
title: Baynes Sound Conductivity Temperature Depth Deployed 2025-02-28

description: The Sea-Bird SeaCAT SBE19plus V2 6001 was deployed on 2025-02-28 at Baynes Sound. Baynes Sound is located between Denman Island and Vancouver Island. This device is a Conductivity Temperature Depth. Conductivity Temperature Depth (CTD) is an instrument package that contains sensors for measuring the conductivity, temperature, and pressure of seawater. Salinity, sound velocity, depth and density are variables that can be derived from sensor measurements. CTDs can carry additional instruments and sensors such as oxygen sensors, turbidity sensors and fluorometers. It was deployed on a fixed platform. Data from this deployment were archived and made available through Ocean Networks Canada's Oceans 3.0 digital infrastructure, with quality assurance and derived data products following established practices.
DOI: 10.15468/dl.r5vgvk
title: Occurrence Download

description: A dataset containing 418 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "TaxonKey is Scytalopus iraiensis Bornschein, Reinert & Pichorim, 1998"
 ]
}

 The dataset includes 418 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027107-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h9bkqp
title: Occurrence Download

description: A dataset containing 709 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Macrothele calpeiana (Walckenaer, 1805)"
 ]
}

 The dataset includes 709 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027108-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tzwtk3
title: Occurrence Download

description: A dataset containing 21 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is North America",
 "Country is Mexico",
 "OccurrenceStatus is Present",
 "StateProvince is Querétaro",
 "TaxonKey is Arundo donax L."
 ]
}

 The dataset includes 21 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027109-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.