(Q35033035)

English

Transcription factors and genetic circuits orchestrating the complex, multilayered response of Clostridium acetobutylicum to butanol and butyrate stress.

scientific article

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scholarly article

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Europe PubMed Central

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24196194%20AND%20SRC:MED&resulttype=core&format=json

29 February 2020

Transcription factors and genetic circuits orchestrating the complex, multilayered response of Clostridium acetobutylicum to butanol and butyrate stress (English)

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24196194%20AND%20SRC:MED&resulttype=core&format=json

29 February 2020

Clostridium acetobutylicum

object named as

Clostridium acetobutylicum

1 reference

based on heuristic

inferred from title

author name string

Qinghua Wang

1

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24196194%20AND%20SRC:MED&resulttype=core&format=json

29 February 2020

Hongzhan Huang

3

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24196194%20AND%20SRC:MED&resulttype=core&format=json

29 February 2020

Eleftherios T Papoutsakis

4

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24196194%20AND%20SRC:MED&resulttype=core&format=json

29 February 2020

publication date

6 November 2013

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24196194%20AND%20SRC:MED&resulttype=core&format=json

29 February 2020

BMC Systems Biology

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24196194%20AND%20SRC:MED&resulttype=core&format=json

29 February 2020

7

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24196194%20AND%20SRC:MED&resulttype=core&format=json

29 February 2020

120

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24196194%20AND%20SRC:MED&resulttype=core&format=json

29 February 2020

The Clostridium small RNome that responds to stress: the paradigm and importance of toxic metabolite stress in C. acetobutylicum

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

8 July 2018

Genomic reconstruction of the transcriptional regulatory network in Bacillus subtilis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

8 July 2018

High-throughput approaches to understanding gene function and mapping network architecture in bacteria

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

8 July 2018

Butyrate-producing Clostridium cluster XIVa species specifically colonize mucins in an in vitro gut model

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

8 July 2018

STRING v9.1: protein-protein interaction networks, with increased coverage and integration

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

8 July 2018

Update on activities at the Universal Protein Resource (UniProt) in 2013

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

8 July 2018

Clostridium thermocellum ATCC27405 transcriptomic, metabolomic and proteomic profiles after ethanol stress

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

8 July 2018

Improved acid stress survival of Lactococcus lactis expressing the histidine decarboxylation pathway of Streptococcus thermophilus CHCC1524.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

8 July 2018

The branched-chain amino acid aminotransferase encoded by ilvE is involved in acid tolerance in Streptococcus mutans

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

8 July 2018

CtsR regulation in mcsAB-deficient Gram-positive bacteria.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

8 July 2018

Transcriptional regulation of central carbon and energy metabolism in bacteria by redox-responsive repressor Rex

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

8 July 2018

KEGG for integration and interpretation of large-scale molecular data sets

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

8 July 2018

Clostridia: the importance of their exceptional substrate and metabolite diversity for biofuel and biorefinery applications

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

8 July 2018

Deciphering the regulatory codes in bacterial genomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

8 July 2018

Reconstructing genome-wide regulatory network of E. coli using transcriptome data and predicted transcription factor activities

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

8 July 2018

OMA 2011: orthology inference among 1000 complete genomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

8 July 2018

A proteomic and transcriptional view of acidogenic and solventogenic steady-state cells of Clostridium acetobutylicum in a chemostat culture

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

8 July 2018

A comparative view of metabolite and substrate stress and tolerance in microbial bioprocessing: From biofuels and chemicals, to biocatalysis and bioremediation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

8 July 2018

Physiological and transcriptional response of Lactobacillus casei ATCC 334 to acid stress

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

8 July 2018

A genomic-library based discovery of a novel, possibly synthetic, acid-tolerance mechanism in Clostridium acetobutylicum involving non-coding RNAs and ribosomal RNA processing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

8 July 2018

Metabolite stress and tolerance in the production of biofuels and chemicals: gene-expression-based systems analysis of butanol, butyrate, and acetate stresses in the anaerobe Clostridium acetobutylicum

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

8 July 2018

RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

8 July 2018

The role of PerR in O2-affected gene expression of Clostridium acetobutylicum

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

8 July 2018

MEME SUITE: tools for motif discovery and searching

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

8 July 2018

MOTIFATOR: detection and characterization of regulatory motifs using prokaryote transcriptome data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

8 July 2018

The CymR regulator in complex with the enzyme CysK controls cysteine metabolism in Bacillus subtilis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

8 July 2018

Engineering solventogenic clostridia

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

8 July 2018

The transcriptional program underlying the physiology of clostridial sporulation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

8 July 2018

PerR acts as a switch for oxygen tolerance in the strict anaerobe Clostridium acetobutylicum

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

8 July 2018

Evaluation of phylogenetic footprint discovery for predicting bacterial cis-regulatory elements and revealing their evolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

8 July 2018

Transcriptomic and phenotypic analyses suggest a network between the transcriptional regulators HrcA and sigmaB in Listeria monocytogenes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

8 July 2018

Identification of target genes conferring ethanol stress tolerance to Saccharomyces cerevisiae based on DNA microarray data analysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

8 July 2018

A general framework for designing and validating oligomer-based DNA microarrays and its application to Clostridium acetobutylicum

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

8 July 2018

FIVA: Functional Information Viewer and Analyzer extracting biological knowledge from transcriptome data of prokaryotes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

8 July 2018

RegTransBase--a database of regulatory sequences and interactions in a wide range of prokaryotic genomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

8 July 2018

Global control of cysteine metabolism by CymR in Bacillus subtilis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

8 July 2018

Arginine-dependent gene regulation via the ArgR repressor is species specific in chlamydia

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

8 July 2018

Effect of Butanol Challenge and Temperature on Lipid Composition and Membrane Fluidity of Butanol-Tolerant Clostridium acetobutylicum

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

8 July 2018

Genetic composition of the Bacillus subtilis SOS system

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

8 July 2018

A comparative genomic view of clostridial sporulation and physiology

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

8 July 2018

Transcriptional program of early sporulation and stationary-phase events in Clostridium acetobutylicum

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

8 July 2018

After 30 years of study, the bacterial SOS response still surprises us

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

8 July 2018

Escherichia coli acid resistance: tales of an amateur acidophile

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

8 July 2018

WebLogo: A Sequence Logo Generator

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

8 July 2018

Transcriptional organization of the Clostridium acetobutylicum genome.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

8 July 2018

Transcriptional analysis of butanol stress and tolerance in Clostridium acetobutylicum

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

8 July 2018

Transcriptional analysis of spo0A overexpression in Clostridium acetobutylicum and its effect on the cell's response to butanol stress

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

8 July 2018

The Bacillus subtilis heat shock stimulon

1 reference

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8 July 2018

Cytoscape: a software environment for integrated models of biomolecular interaction networks

1 reference

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8 July 2018

TM4: a free, open-source system for microarray data management and analysis

1 reference

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8 July 2018

A segmental nearest neighbor normalization and gene identification method gives superior results for DNA-array analysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

8 July 2018

Role for radA/sms in recombination intermediate processing in Escherichia coli

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

8 July 2018

Significance analysis of microarrays applied to the ionizing radiation response

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

8 July 2018

Conservation of the binding site for the arginine repressor in all bacterial lineages

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

8 July 2018

When protons attack: microbial strategies of acid adaptation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

8 July 2018

Cluster analysis and display of genome-wide expression patterns

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

8 July 2018

Expression of heat shock genes inClostridium acetobutylicum

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

8 July 2018

The uvrB gene of Escherichia coli has both lexA-repressed and lexA-independent promoters

1 reference

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8 July 2018

Nucleotide sequence of the argR gene of Escherichia coli K-12 and isolation of its product, the arginine repressor

1 reference

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8 July 2018

Sequence logos: a new way to display consensus sequences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

8 July 2018

SOS-inducible DNA repair proteins, RuvA and RuvB, of Escherichia coli: functional interactions between RuvA and RuvB for ATP hydrolysis and renaturation of the cruciform structure in supercoiled DNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

8 July 2018

A shift in the dominant phenotype governs the pH-induced metabolic switch of Clostridium acetobutylicumin phosphate-limited continuous cultures

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

25 October 2018

Workflow for quantitative proteomic analysis of Clostridium acetobutylicum ATCC 824 using iTRAQ tags

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

25 October 2018

A transcriptional study of acidogenic chemostat cells of Clostridium acetobutylicum--solvent stress caused by a transient n-butanol pulse

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

25 October 2018

Global transcriptional changes of Clostridium acetobutylicum cultures with increased butanol:acetone ratios.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828012

25 October 2018

RSAT 2011: regulatory sequence analysis tools.

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25 October 2018

Microarray analysis of the transcriptional responses of Clostridium difficile to environmental and antibiotic stress

1 reference

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25 October 2018

OMA Browser--exploring orthologous relations across 352 complete genomes

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25 October 2018

A checkpoint protein that scans the chromosome for damage at the start of sporulation in Bacillus subtilis.

1 reference

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25 October 2018

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25 October 2018

Comparative genomics reveal novel heat shock regulatory mechanisms in Staphylococcus aureus and other Gram-positive bacteria.

1 reference

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25 October 2018

The redox-sensing protein Rex, a transcriptional regulator of solventogenesis in Clostridium acetobutylicum

1 reference

https://pubmed.ncbi.nlm.nih.gov/24196194

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Post-transcriptional regulation of the Bacillus subtilis dnaK operon

1 reference

https://pubmed.ncbi.nlm.nih.gov/24196194

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A transcriptional study of acidogenic chemostat cells of Clostridium acetobutylicum--cellular behavior in adaptation to n-butanol

1 reference

https://pubmed.ncbi.nlm.nih.gov/24196194

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1186/1752-0509-7-120

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24196194%20AND%20SRC:MED&resulttype=core&format=json

29 February 2020

DBLP publication ID

journals/bmcsb/WangVHPW13

1 reference

DBLP Dataset 2021-01-02

28 January 2021

Dimensions Publication ID

0 references

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24196194%20AND%20SRC:MED&resulttype=core&format=json

29 February 2020

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24196194%20AND%20SRC:MED&resulttype=core&format=json

29 February 2020

ResearchGate publication ID

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