(Q36305583)

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Crucial role of dynamic linker histone binding and divalent ions for DNA accessibility and gene regulation revealed by mesoscale modeling of oligonucleosomes

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Europe PubMed Central

PMC publication ID

13 August 2017

Crucial role of dynamic linker histone binding and divalent ions for DNA accessibility and gene regulation revealed by mesoscale modeling of oligonucleosomes (English)

1 reference

Europe PubMed Central

PMC publication ID

13 August 2017

2

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Tamar Schlick

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Europe PubMed Central

PMC publication ID

13 August 2017

author name string

Rosana Collepardo-Guevara

1

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Europe PubMed Central

PMC publication ID

13 August 2017

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publication date

11 July 2012

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Europe PubMed Central

PMC publication ID

13 August 2017

Nucleic Acids Research

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Europe PubMed Central

PMC publication ID

13 August 2017

40

1 reference

Europe PubMed Central

PMC publication ID

13 August 2017

18

1 reference

Europe PubMed Central

PMC publication ID

13 August 2017

8803-8817

1 reference

Europe PubMed Central

PMC publication ID

13 August 2017

copyright license

Creative Commons Attribution-NonCommercial 3.0 Unported

8 November 2016

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April 2022 Public Data File from Crossref

copyright status

0 references

Modelling chromatin structure and dynamics: status and prospects

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

30 September 2017

Toward convergence of experimental studies and theoretical modeling of the chromatin fiber

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

30 September 2017

The effect of linker histone's nucleosome binding affinity on chromatin unfolding mechanisms.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

30 September 2017

Capturing the essence of folding and functions of biomolecules using coarse-grained models

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

30 September 2017

Histone fold modifications control nucleosome unwrapping and disassembly

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

30 September 2017

Chromodomain-mediated oligomerization of HP1 suggests a nucleosome-bridging mechanism for heterochromatin assembly.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

30 September 2017

The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

30 September 2017

The docking domain of histone H2A is required for H1 binding and RSC-mediated nucleosome remodeling.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

30 September 2017

Chromatin fiber dynamics under tension and torsion

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

30 September 2017

Multifunctionality of the linker histones: an emerging role for protein-protein interactions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

30 September 2017

Dissecting the binding mechanism of the linker histone in live cells: an integrated FRAP analysis.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

30 September 2017

Mesoscale simulations of two nucleosome-repeat length oligonucleosomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

30 September 2017

A method for genetically installing site-specific acetylation in recombinant histones defines the effects of H3 K56 acetylation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

30 September 2017

Characterization of the N-terminal tail domain of histone H3 in condensed nucleosome arrays by hydrogen exchange and NMR.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

30 September 2017

Evidence for heteromorphic chromatin fibers from analysis of nucleosome interactions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

30 September 2017

The biology of chromatin remodeling complexes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

30 September 2017

Large-scale chromatin structure of inducible genes: transcription on a condensed, linear template.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

30 September 2017

Histone H1 and its isoforms: contribution to chromatin structure and function

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

30 September 2017

Architecture of the SWI/SNF-nucleosome complex

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

30 September 2017

Nucleosome repeat length and linker histone stoichiometry determine chromatin fiber structure

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

30 September 2017

A variable topology for the 30-nm chromatin fibre

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

30 September 2017

An all-atom model of the chromatin fiber containing linker histones reveals a versatile structure tuned by the nucleosomal repeat length

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

30 September 2017

Global modulation of chromatin dynamics mediated by dephosphorylation of linker histone H1 is necessary for erythroid differentiation.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

30 September 2017

Role of histone tails in chromatin folding revealed by a mesoscopic oligonucleosome model

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

30 September 2017

Direct measurement of local chromatin fluidity using optical trap modulation force spectroscopy

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

30 September 2017

X-ray crystal structure of MENT: evidence for functional loop-sheet polymers in chromatin condensation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

30 September 2017

Determinants of histone H1 mobility and chromatin binding in living cells.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

30 September 2017

Structural plasticity of single chromatin fibers revealed by torsional manipulation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

30 September 2017

Flexible histone tails in a new mesoscopic oligonucleosome model

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

30 September 2017

Hyperdynamic plasticity of chromatin proteins in pluripotent embryonic stem cells.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

30 September 2017

H1 family histones in the nucleus. Control of binding and localization by the C-terminal domain

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

30 September 2017

Single chromatin fiber stretching reveals physically distinct populations of disassembly events

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

30 September 2017

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1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

30 September 2017

Histone H1 and the dynamic regulation of chromatin function

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

30 September 2017

Phosphorylation and an ATP-dependent process increase the dynamic exchange of H1 in chromatin

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

30 September 2017

Mechanical disruption of individual nucleosomes reveals a reversible multistage release of DNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

30 September 2017

Chromosome territories, nuclear architecture and gene regulation in mammalian cells

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

30 September 2017

DNA folding: structural and mechanical properties of the two-angle model for chromatin

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

30 September 2017

Dynamic binding of histone H1 to chromatin in living cells

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

30 September 2017

Rapid exchange of histone H1.1 on chromatin in living human cells

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

30 September 2017

Replication by a single DNA polymerase of a stretched single-stranded DNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

30 September 2017

Linker histone binding and displacement: versatile mechanism for transcriptional regulation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

30 September 2017

Single-molecule studies of the effect of template tension on T7 DNA polymerase activity.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

30 September 2017

Pulling a single chromatin fiber reveals the forces that maintain its higher-order structure

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

30 September 2017

Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

30 September 2017

A chromatin folding model that incorporates linker variability generates fibers resembling the native structures

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

30 September 2017

Three-dimensional structure of extended chromatin fibers as revealed by tapping-mode scanning force microscopy

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

30 September 2017

Structure of chromatin and the linking number of DNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

30 September 2017

Reversible dissociation of linker histone from chromatin with preservation of internucleosomal repeat

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

30 September 2017

The higher-order structure of chromatin: evidence for a helical ribbon arrangement

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

30 September 2017

Differences of supranucleosomal organization in different kinds of chromatin: cell type-specific globular subunits containing different numbers of nucleosomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

30 September 2017

Solenoidal model for superstructure in chromatin

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

30 September 2017

A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

30 September 2017

Nucleosome linker DNA contacts and induces specific folding of the intrinsically disordered H1 carboxyl-terminal domain

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

29 June 2018

Modeling studies of chromatin fiber structure as a function of DNA linker length.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

29 June 2018

Prediction of an HMG-box fold in the C-terminal domain of histone H1: insights into its role in DNA condensation.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

29 June 2018

Energy landscape analyses of disordered histone tails reveal special organization of their conformational dynamics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

22 September 2018

Force spectroscopy of chromatin fibers: extracting energetics and structural information from Monte Carlo simulations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

22 September 2018

Single-molecule force spectroscopy reveals a highly compliant helical folding for the 30-nm chromatin fiber

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

22 September 2018

A tale of tails: how histone tails mediate chromatin compaction in different salt and linker histone environments

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

22 September 2018

The effect of internucleosomal interaction on folding of the chromatin fiber

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

22 September 2018

Nucleosome geometry and internucleosomal interactions control the chromatin fiber conformation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

22 September 2018

Backtracking determines the force sensitivity of RNAP II in a factor-dependent manner

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

22 September 2018

Efficient global biopolymer sampling with end-transfer configurational bias Monte Carlo

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

22 September 2018

Characterizing fluorescence recovery curves for nuclear proteins undergoing binding events.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

22 September 2018

Constructing irregular surfaces to enclose macromolecular complexes for mesoscale modeling using the discrete surface charge optimization (DISCO) algorithm

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

22 September 2018

Chromatin: a tunable spring at work inside chromosomes.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

22 September 2018

Unfolding individual nucleosomes by stretching single chromatin fibers with optical tweezers.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

22 September 2018

Force and velocity measured for single molecules of RNA polymerase.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467040

22 September 2018

Monte Carlo Calculation of the Average Extension of Molecular Chains

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKS600

21 January 2018

Pulling chromatin fibers: computer simulations of direct physical micromanipulations

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKS600

21 January 2018

Novel scheme to study structural and thermal properties of continuously deformable molecules

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKS600

21 January 2018

Coarse-grained force field for the nucleosome from self-consistent multiscaling

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKS600

21 January 2018

Highly compact folding of chromatin induced by cellular cation concentrations. Evidence from atomic force microscopy studies in aqueous solution

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKS600

21 January 2018

Nucleosome interactions in chromatin: fiber stiffening and hairpin formation

1 reference

https://pubmed.ncbi.nlm.nih.gov/22790986

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Interactions of highly charged colloidal cylinders with applications to double-stranded

1 reference

https://pubmed.ncbi.nlm.nih.gov/22790986

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Exchange of histone H1 between segments of chromatin

1 reference

https://pubmed.ncbi.nlm.nih.gov/22790986

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Transient unfolding of trypsin-digested chromatin core particles

1 reference

https://pubmed.ncbi.nlm.nih.gov/22790986

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Transcription against an applied force

1 reference

https://pubmed.ncbi.nlm.nih.gov/22790986

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The N tails of histones H3 and H4 adopt a highly structured conformation in the nucleosome

1 reference

https://pubmed.ncbi.nlm.nih.gov/22790986

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Acetylation increases the alpha-helical content of the histone tails of the nucleosome

1 reference

https://pubmed.ncbi.nlm.nih.gov/22790986

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Monte Carlo simulation of chromatin stretching

1 reference

https://pubmed.ncbi.nlm.nih.gov/22790986

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1093/NAR/GKS600

1 reference

Europe PubMed Central

PMC publication ID

13 August 2017

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

13 August 2017

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

13 August 2017

ResearchGate publication ID

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