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Showing NP-Card for Cytosine (NP0000973)

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Record Information
Version1.0
Created at2005-11-16 15:48:42 UTC
Updated at2022-01-12 19:57:31 UTC
NP-MRD IDNP0000973
Secondary Accession NumbersNone
Natural Product Identification
Common NameCytosine
DescriptionCytosine, also known as C, belongs to the class of organic compounds known as pyrimidones. Pyrimidones are compounds that contain a pyrimidine ring, which bears a ketone. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions. Cytosine is also classified as a pyrimidine derivative, with a heterocyclic aromatic ring and two substituents attached (an amine group at position 4 and a keto group at position 2). Cytosine is one of the four main bases found in DNA and RNA, along with adenine, guanine, and thymine (uracil in RNA). The nucleoside of cytosine is cytidine. In Watson-Crick base pairing, cytosine forms three hydrogen bonds with guanine. Cytosine was discovered and named by Albrecht Kossel and Albert Neumann in 1894 when it was hydrolyzed from calf thymus tissues. Cytosine exists in all living species, ranging from bacteria to plants to humans. Within cells, cytosine can undergo several enzymatic reactions. It can be methylated into 5-methylcytosine by an enzyme called DNA methyltransferase (DNMT) or be methylated and hydroxylated to make 5-hydroxymethylcytosine. The DNA methyltransferase (DNMT) family of enzymes transfer a methyl group from S-adenosyl-l-methionine (SAM) to the 5’ carbon of cytosine in a molecule of DNA. High levels of cytosine can be found in the urine of individuals with severe combined immunodeficiency syndrome (SCID). Cytosine concentrations as high as (23-160 mmol/mol creatinine) were detected in SCID patients compared to normal levels of <2 mmol/mol creatinine (PMID: 262183 ).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0000973 (Cytosine)

Cytosine.mol
  Mrv1652305271900072D          

  8  8  0  0  0  0            999 V2000
    0.7145    0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  2  0  0  0  0
  7  8  1  0  0  0  0
  1  8  2  0  0  0  0
M  END
Download

3D MOL for NP0000973 (Cytosine)

HMDB0000630
     RDKit          3D
Cytosine
 13 13  0  0  0  0  0  0  0  0999 V2000
   -2.0368   -0.5045   -0.0051 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6575   -0.1295   -0.0033 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2525    1.1775   -0.0764 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1043    1.4704   -0.0700 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0191    0.4872    0.0071 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6169   -0.7910    0.0785 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4942   -1.6999    0.1502 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2947   -1.0774    0.0722 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7741    0.1651    0.2299 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2946   -1.4684   -0.2479 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0015    1.9600   -0.1381 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4585    2.4825   -0.1258 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0293   -2.0721    0.1287 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  8  2  1  0
  1  9  1  0
  1 10  1  0
  3 11  1  0
  4 12  1  0
  8 13  1  0
M  END
Download

3D SDF for NP0000973 (Cytosine)

Cytosine.mol
  Mrv1652305271900072D          

  8  8  0  0  0  0            999 V2000
    0.7145    0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  2  0  0  0  0
  7  8  1  0  0  0  0
  1  8  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0000973

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NC1=CC=NC(=O)N1

> <INCHI_IDENTIFIER>
InChI=1S/C4H5N3O/c5-3-1-2-6-4(8)7-3/h1-2H,(H3,5,6,7,8)

> <INCHI_KEY>
OPTASPLRGRRNAP-UHFFFAOYSA-N

> <FORMULA>
C4H5N3O

> <MOLECULAR_WEIGHT>
111.102

> <EXACT_MASS>
111.043261797

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
13

> <JCHEM_AVERAGE_POLARIZABILITY>
9.883975778125984

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
6-amino-1,2-dihydropyrimidin-2-one

> <ALOGPS_LOGP>
-0.94

> <JCHEM_LOGP>
-1.1476057916666667

> <ALOGPS_LOGS>
-0.56

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.82715733969699

> <JCHEM_PKA_STRONGEST_BASIC>
-0.05985282344880383

> <JCHEM_POLAR_SURFACE_AREA>
67.48

> <JCHEM_REFRACTIVITY>
38.0148

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.09e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2(1H)-pyrimidinone, 6-amino-

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0000973 (Cytosine)

HMDB0000630
     RDKit          3D
Cytosine
 13 13  0  0  0  0  0  0  0  0999 V2000
   -2.0368   -0.5045   -0.0051 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6575   -0.1295   -0.0033 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2525    1.1775   -0.0764 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1043    1.4704   -0.0700 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0191    0.4872    0.0071 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6169   -0.7910    0.0785 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4942   -1.6999    0.1502 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2947   -1.0774    0.0722 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7741    0.1651    0.2299 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2946   -1.4684   -0.2479 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0015    1.9600   -0.1381 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4585    2.4825   -0.1258 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0293   -2.0721    0.1287 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  8  2  1  0
  1  9  1  0
  1 10  1  0
  3 11  1  0
  4 12  1  0
  8 13  1  0
M  END
Download

PDB for NP0000973 (Cytosine)

HEADER    PROTEIN                                 27-MAY-19   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: Cytosine.mol                                      
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-19         0                                  
HETATM    1  N   UNK     0       1.334   0.770   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       2.667  -1.540   0.000  0.00  0.00           O+0
HETATM    4  N   UNK     0       0.000  -1.540   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0      -2.667  -1.540   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0      -1.334   0.770   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
CONECT    1    2    8                                                       
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8                                                       
CONECT    8    7    1                                                       
MASTER        0    0    0    0    0    0    0    0    8    0   16    0
END
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3D PDB for NP0000973 (Cytosine)

COMPND    HMDB0000630
HETATM    1  N1  UNL     1      -2.037  -0.505  -0.005  1.00  0.00           N  
HETATM    2  C1  UNL     1      -0.657  -0.130  -0.003  1.00  0.00           C  
HETATM    3  C2  UNL     1      -0.252   1.178  -0.076  1.00  0.00           C  
HETATM    4  C3  UNL     1       1.104   1.470  -0.070  1.00  0.00           C  
HETATM    5  N2  UNL     1       2.019   0.487   0.007  1.00  0.00           N  
HETATM    6  C4  UNL     1       1.617  -0.791   0.078  1.00  0.00           C  
HETATM    7  O1  UNL     1       2.494  -1.700   0.150  1.00  0.00           O  
HETATM    8  N3  UNL     1       0.295  -1.077   0.072  1.00  0.00           N  
HETATM    9  H1  UNL     1      -2.774   0.165   0.230  1.00  0.00           H  
HETATM   10  H2  UNL     1      -2.295  -1.468  -0.248  1.00  0.00           H  
HETATM   11  H3  UNL     1      -1.001   1.960  -0.138  1.00  0.00           H  
HETATM   12  H4  UNL     1       1.458   2.483  -0.126  1.00  0.00           H  
HETATM   13  H5  UNL     1       0.029  -2.072   0.129  1.00  0.00           H  
CONECT    1    2    9   10
CONECT    2    3    3    8
CONECT    3    4   11
CONECT    4    5    5   12
CONECT    5    6
CONECT    6    7    7    8
CONECT    8   13
END
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SMILES for NP0000973 (Cytosine)

NC1=CC=NC(=O)N1
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INCHI for NP0000973 (Cytosine)

InChI=1S/C4H5N3O/c5-3-1-2-6-4(8)7-3/h1-2H,(H3,5,6,7,8)
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View in JSmol
Synonyms
ValueSource
4-Amino-2(1H)-pyrimidinoneChEBI
4-Amino-2-hydroxypyrimidineChEBI
CChEBI
CytChEBI
CytosinChEBI
ZytosinChEBI
4-Amino-2-oxo-1,2-dihydropyrimidineHMDB
4-AminouracilHMDB
CytosinimineHMDB
Chemical FormulaC4H5N3O
Average Mass111.1020 Da
Monoisotopic Mass111.04326 Da
IUPAC Name6-amino-1,2-dihydropyrimidin-2-one
Traditional Name2(1H)-pyrimidinone, 6-amino-
CAS Registry Number71-30-7
SMILES
NC1=CC=NC(=O)N1
InChI Identifier
InChI=1S/C4H5N3O/c5-3-1-2-6-4(8)7-3/h1-2H,(H3,5,6,7,8)
InChI KeyOPTASPLRGRRNAP-UHFFFAOYSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, simulated)Ahselim2022-01-12View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, experimental)Ahselim2022-01-12View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 400 MHz, H2O, simulated)Varshavi.d262021-08-03View Spectrum
Species
Species of Origin
Species NameSourceReference
Anas platyrhynchosFooDB
AnatidaeFooDB
Anser anserFooDB
Apis ceranaLOTUS Database
Bison bisonFooDB
Bos taurusFooDB
Bos taurus X Bison bisonFooDB
Bubalus bubalisFooDB
Capra aegagrus hircusFooDB
CervidaeFooDB
Cervus canadensisFooDB
ColumbaFooDB
ColumbidaeFooDB
Dromaius novaehollandiaeFooDB
Equus caballusFooDB
Gallus gallusFooDB
Homo sapiensLOTUS Database
Lagopus mutaFooDB
LeporidaeFooDB
Lepus timidusFooDB
Maackia amurensisLOTUS Database
Melanitta fuscaFooDB
Meleagris gallopavoFooDB
Mus musculusLOTUS Database
Numida meleagrisFooDB
OdocoileusFooDB
OryctolagusFooDB
Ovis ariesFooDB
PhasianidaeFooDB
Phasianus colchicusFooDB
Salmonella entericaLOTUS Database
Struthio camelusFooDB
Sus scrofaFooDB
Sus scrofa domesticaFooDB
Synechococcus elongatusLOTUS Database
Trypanosoma bruceiLOTUS Database
Species Where Detected
Species NameSourceReference
Homo sapiens (Urine)KNApSAcK Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pyrimidones. Pyrimidones are compounds that contain a pyrimidine ring, which bears a ketone. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassDiazines
Sub ClassPyrimidines and pyrimidine derivatives
Direct ParentPyrimidones
Alternative Parents
Substituents
  • Pyrimidone
  • Aminopyrimidine
  • Hydropyrimidine
  • Heteroaromatic compound
  • Azacycle
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Amine
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point> 300 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility8 mg/mLNot Available
LogP-1.73Hansch CH, Leo A and Hoekman DH. "Exploring QSAR: Hydrophobic, Electronic, and Steric Constraints. Volume 1" ACS Publications (1995).
Predicted Properties
PropertyValueSource
Water Solubility30.9 g/LALOGPS
logP-0.94ALOGPS
logP-1.1ChemAxon
logS-0.56ALOGPS
pKa (Strongest Acidic)9.83ChemAxon
pKa (Strongest Basic)-0.06ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area67.48 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity38.01 m³·mol⁻¹ChemAxon
Polarizability9.88 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0000630
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB022151
KNApSAcK IDC00001498
Chemspider ID577
KEGG Compound IDC00380
BioCyc IDCYTOSINE
BiGG ID34812
Wikipedia LinkCytosine
METLIN ID283
PubChem Compound597
PDB IDNot Available
ChEBI ID16040
Good Scents IDrw1233541
References
General References
  1. Mills GC, Schmalstieg FC, Newkirk KE, Goldblum RM: Cytosine and orotic acid in urine of immunodeficient children. Clin Chem. 1979 Mar;25(3):419-24. [PubMed:262183 ]
  2. Rodriguez Ortner E, Hayes RB, Weissfeld J, Gelmann EP: Effect of homeodomain protein NKX3.1 R52C polymorphism on prostate gland size. Urology. 2006 Feb;67(2):311-5. Epub 2006 Jan 25. [PubMed:16442598 ]
  3. Harvey BG, Maroni J, O'Donoghue KA, Chu KW, Muscat JC, Pippo AL, Wright CE, Hollmann C, Wisnivesky JP, Kessler PD, Rasmussen HS, Rosengart TK, Crystal RG: Safety of local delivery of low- and intermediate-dose adenovirus gene transfer vectors to individuals with a spectrum of morbid conditions. Hum Gene Ther. 2002 Jan 1;13(1):15-63. [PubMed:11779412 ]
  4. Cheng JC, Yoo CB, Weisenberger DJ, Chuang J, Wozniak C, Liang G, Marquez VE, Greer S, Orntoft TF, Thykjaer T, Jones PA: Preferential response of cancer cells to zebularine. Cancer Cell. 2004 Aug;6(2):151-8. [PubMed:15324698 ]
  5. Carotti D, Funiciello S, Lavia P, Caiafa P, Strom R: Different effects of histone H1 on de novo DNA methylation in vitro depend on both the DNA base composition and the DNA methyltransferase. Biochemistry. 1996 Sep 10;35(36):11660-7. [PubMed:8794746 ]
  6. Tawa R, Ueno S, Yamamoto K, Yamamoto Y, Sagisaka K, Katakura R, Kayama T, Yoshimoto T, Sakurai H, Ono T: Methylated cytosine level in human liver DNA does not decline in aging process. Mech Ageing Dev. 1992 Mar 1;62(3):255-61. [PubMed:1583911 ]
  7. Tsuchiya K, Tajima H, Yamada M, Takahashi H, Kuwae T, Sunaga K, Katsube N, Ishitani R: Disclosure of a pro-apoptotic glyceraldehyde-3-phosphate dehydrogenase promoter: anti-dementia drugs depress its activation in apoptosis. Life Sci. 2004 May 14;74(26):3245-58. [PubMed:15094325 ]
  8. Putta MR, Zhu F, Li Y, Bhagat L, Cong Y, Kandimalla ER, Agrawal S: Novel oligodeoxynucleotide agonists of TLR9 containing N3-Me-dC or N1-Me-dG modifications. Nucleic Acids Res. 2006 Jun 23;34(11):3231-8. Print 2006. [PubMed:16798912 ]
  9. Bawdon RE, Sobhi S, Dax J: The transfer of anti-human immunodeficiency virus nucleoside compounds by the term human placenta. Am J Obstet Gynecol. 1992 Dec;167(6):1570-4. [PubMed:1335207 ]
  10. Sawamura D, Abe R, Goto M, Akiyama M, Hemmi H, Akira S, Shimizu H: Direct injection of plasmid DNA into the skin induces dermatitis by activation of monocytes through toll-like receptor 9. J Gene Med. 2005 May;7(5):664-71. [PubMed:15655803 ]
  11. Thajeb P, Ma YS, Tzen CY, Chuang CK, Wu TY, Chen SC, Wei YH: Oculopharyngeal somatic myopathy in a patient with a novel large-scale 3,399 bp deletion and a homoplasmic T5814C transition of the mitochondrial DNA. Clin Neurol Neurosurg. 2006 Jun;108(4):407-10. [PubMed:16644408 ]
  12. Sigalotti L, Coral S, Nardi G, Spessotto A, Cortini E, Cattarossi I, Colizzi F, Altomonte M, Maio M: Promoter methylation controls the expression of MAGE2, 3 and 4 genes in human cutaneous melanoma. J Immunother. 2002 Jan-Feb;25(1):16-26. [PubMed:11924907 ]
  13. Costa E, Grayson DR, Mitchell CP, Tremolizzo L, Veldic M, Guidotti A: GABAergic cortical neuron chromatin as a putative target to treat schizophrenia vulnerability. Crit Rev Neurobiol. 2003;15(2):121-42. [PubMed:14977367 ]
  14. Machwe A, Orren DK, Bohr VA: Accelerated methylation of ribosomal RNA genes during the cellular senescence of Werner syndrome fibroblasts. FASEB J. 2000 Sep;14(12):1715-24. [PubMed:10973920 ]
  15. Arslan H: COVID-19 prediction based on genome similarity of human SARS-CoV-2 and bat SARS-CoV-like coronavirus. Comput Ind Eng. 2021 Nov;161:107666. doi: 10.1016/j.cie.2021.107666. Epub 2021 Sep 8. [PubMed:34511707 ]