cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/dz6hpkrzm3.3
title: Code for "Gradual entry into carbon starvation decreases the death rate of Escherichia coli"

description: Code used for the simulations employed in the manuscript "Gradual entry into carbon starvation decreases the death rate of Escherichia coli"

This folder contains the code that simulates the allocation strategy during the shift to starvation, as described in the manuscript. The model is based upon the FCR model, published by Erikson, Schink et al in 2017.
In this program you can simulate the dynamics of the shift experiment by fitting the time course of the growth rate with a sigmoid (as in the manuscript) and inserting the values of the parameters of the fit in the program. You can simulate the three different dynamics that we propose: the global regulation one, the targeted towards the survival sector and the targeted towards the harmful.
Abstract:
Bacterial fitness is determined both by how fast cells grow in nutrient-rich environments and by how well they survive when nutrients are depleted. However, these behaviors are not independent, since the molecular composition of non-growing cells is affected by their prior growth history. For instance, recent work observed that the death rates of Escherichia coli cultures that rapidly entered carbon starvation depend on their prior growth rates, with faster growth leading to exponentially faster death. On the other hand, it is well known that cells adapt their molecular composition as they slow down growth and enter stationary phase, which is generally believed to improve their chance of survival. Hence, the question arises to what extent this adaptation process reduces the subsequent death rate. And how does the duration of the time window during which cells are allowed to adapt determine the reduction in death rate, and thus the fitness benefit of adaptation?
Here, we study these quantitative questions by probing the adaptation of E. coli during gradual transitions from exponential growth to carbon starvation. We monitor such transitions in cultures with different initial growth conditions and measure the resulting rates of cell death after the transition. Our experiments demonstrate that cells with the opportunity to adapt their proteome composition before entering a state of starvation exhibit lower death rates compared to those that cannot, across various substrate conditions. The quantitative data is consistent with a theoretical model built on the assumption that before starvation, cells up-regulate a specific sector of the proteome, the effect of which is to decrease the death rate in energy-limiting conditions. This work highlights the influence of the non-genetic memory of a cell, specifically in the form of inherited proteome composition, on bacterial fitness. Our results emphasize that a comprehensive understanding of bacterial fitness requires quantitative characterization of bacterial physiology in all phases of their life cycle, including growth, stationary phase, and death, as well as the transitions between them. 
Differences with v1:
- fixed the values of the parameters gamma_0, tau
DOI: 10.15468/dl.nnchfu
title: Occurrence Download

description: A dataset containing 109 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Cuba",
 "OccurrenceStatus is Present",
 "TaxonKey is Anolis paternus Hardy, 1967"
 ]
}

 The dataset includes 109 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029126-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kqwp6k
title: Occurrence Download

description: A dataset containing 237674 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is USA.5_1",
 "TaxonKey is Poaceae"
 ]
}

 The dataset includes 237674 records from 182 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029111-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uner29
title: Occurrence Download

description: A dataset containing 105390 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is USA.5_1",
 "TaxonKey is Hydrophyllaceae"
 ]
}

 The dataset includes 105390 records from 121 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029115-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8sx7dj
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Cuba",
 "OccurrenceStatus is Present",
 "TaxonKey is Anolis pigmaequestris Garrido, 1975"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029127-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6adjv2
title: Occurrence Download

description: A dataset containing 1526 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Cuba",
 "OccurrenceStatus is Present",
 "TaxonKey is Anolis porcatus Gray, 1840"
 ]
}

 The dataset includes 1526 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029128-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.s38xtn
title: Occurrence Download

description: A dataset containing 1403 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "OccurrenceStatus is Present",
 "RecordedBy is one of (Forbes, H.O., FORBES,H.O., Forbes, H O, Forbes, H. O, Forbes, H. O., Forbes, H., O.)"
 ]
}

 The dataset includes 1403 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029129-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9re378
title: Occurrence Download

description: A dataset containing 30 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Cuba",
 "OccurrenceStatus is Present",
 "TaxonKey is Anolis pumilus Garrido, 1988"
 ]
}

 The dataset includes 30 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029130-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4ym5gb
title: Occurrence Download

description: A dataset containing 112 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Cuba",
 "OccurrenceStatus is Present",
 "TaxonKey is Anolis quadriocellifer Barbour & Ramsden, 1919"
 ]
}

 The dataset includes 112 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029131-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/cgsygwyvgg.1
title: Data of the ferruginous concretions on the Sunda Shelf

description: This dataset includes four files for the ferruginous concretions of core CJB01-53 recovered from the Sunda Shelf. Four Excel files first show the variation of 14C dating results, mineral compositions, and elements composition, versus depth of core CJB01-53 from the central Sunda Shelf. The files also present the clay mineral composition of sediment from this core.
DOI: 10.17632/cgsygwyvgg.2
title: Data of the ferruginous concretions on the Sunda Shelf

description: This dataset includes four files for the ferruginous concretions of core CJB01-53 recovered from the Sunda Shelf. Four Excel files first show the variation of 14C dating results, mineral compositions, and elements composition, versus depth of core CJB01-53 from the central Sunda Shelf. The files also present the clay mineral composition of sediment from this core.
DOI: 10.15468/dl.daz95p
title: Occurrence Download

description: A dataset containing 1100371 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Salmo salar Linnaeus, 1758"
 ]
}

 The dataset includes 1100371 records from 314 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029120-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.iqhbut
title: Occurrence Download

description: A dataset containing 96 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Die Wuhle"
 ]
}

 The dataset includes 96 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017771-180131172636756/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.w9t6j5
title: Occurrence Download

description: A dataset containing 31 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Catunaregam torulosa (Dennst.) Deb & M.Gangop."
 ]
}

 The dataset includes 31 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0082285-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wiyeji
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Viburnum buddleifolium C.H.Wright",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 8 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017772-151016162008034/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rn5gyr
title: Occurrence Download

description: A dataset containing 1609 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lagerstroemia speciosa (L.) Pers.",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1609 records from 131 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039412-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cqda4p
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cardamine dubia Nicotra"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0082287-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.u6wh4x
title: Occurrence Download

description: A dataset containing 139 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is BIRDRACE Turbine Untersee"
 ]
}

 The dataset includes 139 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017772-180131172636756/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bhk7vc
title: Occurrence Download

description: A dataset containing 16 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cardamine elegantula Hook.f. & Thomson"
 ]
}

 The dataset includes 16 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0082296-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gnsdfi
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Viburnum burejaeticum Regel & Herder",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 10 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017773-151016162008034/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mzqry5
title: Occurrence Download

description: A dataset containing 96 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Goodyera nankoensis Fukuy."
 ]
}

 The dataset includes 96 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017892-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.guxwtz
title: Occurrence Download

description: A dataset containing 2080 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lagerstroemia subcostata Koehne",
 "HasCoordinate is true"
 ]
}

 The dataset includes 2080 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039413-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.j0akxt
title: Occurrence Download

description: A dataset containing 306261 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Aquila chrysaetos (Linnaeus, 1758)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 306261 records from 110 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017773-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fvwmeu
title: Occurrence Download

description: A dataset containing 80 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Helictochloa blaui (Asch. & Janka) Romero Zarco"
 ]
}

 The dataset includes 80 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017907-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zx9ayn
title: Occurrence Download

description: A dataset containing 528594 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is eButterfly Surveys"
 ]
}

 The dataset includes 528594 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022848-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pjrovi
title: Occurrence Download

description: A dataset containing 35 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Ortsrand Zandershagen"
 ]
}

 The dataset includes 35 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017773-180131172636756/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.65n9q2
title: Occurrence Download

description: A dataset containing 19 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)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Afroedura rupestris Jacobsen, Kuhn, Jackman & Bauer, 2014"
 ]
}

 The dataset includes 19 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0082358-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ch4xb9
title: Occurrence Download

description: A dataset containing 82356 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Depth 0.0-9999.0m",
 "Geometry POLYGON((145.03377 -40.73233,146.25231 -41.17356,147.92154 -40.8587,147.77131 -39.69989,147.25385 -38.66482,147.00346 -38.54742,146.16885 -38.82105,145.55123 -38.61266,144.76669 -38.4429,145.03377 -40.73233))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Animalia"
 ]
}

 The dataset includes 82356 records from 65 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025548-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ztpezr
title: Occurrence Download

description: A dataset containing 39 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Evolvulus simplex Andersson"
 ]
}

 The dataset includes 39 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017774-151016162008034/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4hf7hh
title: Occurrence Download

description: A dataset containing 2389 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is North America",
 "Country is Guatemala",
 "GadmGid is GTM.18_1",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 2389 records from 52 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025533-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5ff2cp
title: Occurrence Download

description: A dataset containing 20 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hedysarum omissum Kovalevsk."
 ]
}

 The dataset includes 20 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017969-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.w0hgp6
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is \"Ach, du dicke Eiche\", Wald an der Oste-Grundschule Heeslingen"
 ]
}

 The dataset includes 9 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017774-180131172636756/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5vt89t
title: Occurrence Download

description: A dataset containing 54 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Observation, Material sample, Material citation, Occurrence evidence)",
 "DatasetKey is one of (iNaturalist Research-grade Observations, Flora-On: occurrence data of the flora of mainland Portugal, Pl@ntNet observations, Biodiversity4all Research-Grade Observations)",
 "Geometry POLYGON((-9.44389 43.55286,-10.06503 36.83596,-6.99585 36.89443,-6.44778 43.44684,-9.44389 43.55286))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Sedum acre L.",
 "Year 1965-2023"
 ]
}

 The dataset includes 54 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028318-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.v8wsgq
title: Occurrence Download

description: A dataset containing 34 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Centella thesioides M.T.R.Schub. & B.-E.van Wyk"
 ]
}

 The dataset includes 34 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0082309-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uyfkhq
title: Occurrence Download

description: A dataset containing 3165 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is EWT: Carnivore Conservation Programme Cheetah Tracking Data"
 ]
}

 The dataset includes 3165 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017775-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.76k8ap
title: Occurrence Download

description: A dataset containing 3219 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Spartina alterniflora Loisel."
 ]
}

 The dataset includes 3219 records from 252 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027630-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9n38p4
title: Occurrence Download

description: A dataset containing 81 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Chlorophytum vestitum Baker"
 ]
}

 The dataset includes 81 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0082269-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.x4nyyp
title: Occurrence Download

description: A dataset containing 148212 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Populus nigra L.)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Geometry POLYGON ((-15 75, -15 25, 60 25, 60 75, -15 75))"
 ]
}

 The dataset includes 148212 records from 1214 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0034026-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rr8x6v
title: Occurrence Download

description: A dataset containing 4192 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Japan",
 "OccurrenceStatus is Present",
 "TaxonKey is Alcyonacea"
 ]
}

 The dataset includes 4192 records from 42 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0112850-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f5maah
title: Occurrence Download

description: A dataset containing 542 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Germany",
 "DatasetKey is one of (iNaturalist Research-grade Observations, ZFMK Mammalia collection, Observation.org, Nature data from around the World, Collection Mammalia SMF, Swiss National Mammal Databank, Mammalia fossil Kleinsäuger - SMF, The Mammalia Collection at the Staatssammlung für Anthropologie und Paläoanatomie München, Collection Mammalogie - ZSRO, Field Museum of Natural History (Zoology) Mammal Collection)",
 "TaxonKey is Glis glis (Linnaeus, 1766)"
 ]
}

 The dataset includes 542 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007511-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.