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Article ; Online: The Role of Visual Features in Text-Based CAPTCHAs

Emre Mülazimoğlu / Murat P. Çakır / Cengiz Acartürk

Computational Intelligence and Neuroscience, Vol

An fNIRS Study for Usable Security

2021 Volume 2021

Abstract: To mitigate dictionary attacks or similar undesirable automated attacks to information systems, developers mostly prefer using CAPTCHA challenges as Human Interactive Proofs (HIPs) to distinguish between human users and scripts. Appropriate use of ... ...

Abstract	To mitigate dictionary attacks or similar undesirable automated attacks to information systems, developers mostly prefer using CAPTCHA challenges as Human Interactive Proofs (HIPs) to distinguish between human users and scripts. Appropriate use of CAPTCHA requires a setup that balances between robustness and usability during the design of a challenge. The previous research reveals that most usability studies have used accuracy and response time as measurement criteria for quantitative analysis. The present study aims at applying optical neuroimaging techniques for the analysis of CAPTCHA design. The functional Near-Infrared Spectroscopy technique was used to explore the hemodynamic responses in the prefrontal cortex elicited by CAPTCHA stimulus of varying types. The findings suggest that regions in the left and right dorsolateral and right dorsomedial prefrontal cortex respond to the degrees of line occlusion, rotation, and wave distortions present in a CAPTCHA. The systematic addition of the visual effects introduced nonlinear effects on the behavioral and prefrontal oxygenation measures, indicative of the emergence of Gestalt effects that might have influenced the perception of the overall CAPTCHA figure.
Keywords	Computer applications to medicine. Medical informatics ; R858-859.7 ; Neurosciences. Biological psychiatry. Neuropsychiatry ; RC321-571
Subject code	005
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	Hindawi Limited
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book ; Online: The Role of Visual Features in Text-Based CAPTCHAs

Mulazimoglu, Emre / Cakir, Murat P. / Acarturk, Cengiz

An fNIRS Study for Usable Security

2023

Abstract	To mitigate dictionary attacks or similar undesirable automated attacks to information systems, developers mostly prefer using CAPTCHA challenges as Human Interactive Proofs (HIPs) to distinguish between human users and scripts. Appropriate use of CAPTCHA requires a setup that balances between robustness and usability during the design of a challenge. The previous research reveals that most usability studies have used accuracy and response time as measurement criteria for quantitative analysis. The present study aims at applying optical neuroimaging techniques for the analysis of CAPTCHA design. The functional Near-Infrared Spectroscopy technique was used to explore the hemodynamic responses in the prefrontal cortex elicited by CAPTCHA stimulus of varying types. )e findings suggest that regions in the left and right dorsolateral and right dorsomedial prefrontal cortex respond to the degrees of line occlusion, rotation, and wave distortions present in a CAPTCHA. The systematic addition of the visual effects introduced nonlinear effects on the behavioral and prefrontal oxygenation measures, indicative of the emergence of Gestalt effects that might have influenced the perception of the overall CAPTCHA figure. Comment: 24 pages, 32 figures, Computational Intelligence and Neuroscience
Keywords	Computer Science - Cryptography and Security ; Computer Science - Human-Computer Interaction
Subject code	005
Publishing date	2023-11-30
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The Role of Visual Features in Text-Based CAPTCHAs: An fNIRS Study for Usable Security.

Mülazimoğlu, Emre / Çakır, Murat P / Acartürk, Cengiz

Computational intelligence and neuroscience

2021 Volume 2021, Page(s) 8842420

Abstract	To mitigate dictionary attacks or similar undesirable automated attacks to information systems, developers mostly prefer using CAPTCHA challenges as Human Interactive Proofs (HIPs) to distinguish between human users and scripts. Appropriate use of CAPTCHA requires a setup that balances between robustness and usability during the design of a challenge. The previous research reveals that most usability studies have used accuracy and response time as measurement criteria for quantitative analysis. The present study aims at applying optical neuroimaging techniques for the analysis of CAPTCHA design. The functional Near-Infrared Spectroscopy technique was used to explore the hemodynamic responses in the prefrontal cortex elicited by CAPTCHA stimulus of varying types. The findings suggest that regions in the left and right dorsolateral and right dorsomedial prefrontal cortex respond to the degrees of line occlusion, rotation, and wave distortions present in a CAPTCHA. The systematic addition of the visual effects introduced nonlinear effects on the behavioral and prefrontal oxygenation measures, indicative of the emergence of Gestalt effects that might have influenced the perception of the overall CAPTCHA figure.
MeSH term(s)	Humans ; Neuroimaging ; Prefrontal Cortex ; Spectroscopy, Near-Infrared
Language	English
Publishing date	2021-05-04
Publishing country	United States
Document type	Journal Article
ZDB-ID	2388208-6
ISSN	1687-5273 ; 1687-5265
ISSN (online)	1687-5273
ISSN	1687-5265
DOI	10.1155/2021/8842420
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Article ; Online: DNA polymerase stalling at structured DNA constrains the expansion of short tandem repeats.

Murat, Pierre / Guilbaud, Guillaume / Sale, Julian E

Genome biology

2020 Volume 21, Issue 1, Page(s) 209

Abstract: Background: Short tandem repeats (STRs) contribute significantly to de novo mutagenesis, driving phenotypic diversity and genetic disease. Although highly diverse, their repetitive sequences induce DNA polymerase slippage and stalling, leading to length ...

Abstract	Background: Short tandem repeats (STRs) contribute significantly to de novo mutagenesis, driving phenotypic diversity and genetic disease. Although highly diverse, their repetitive sequences induce DNA polymerase slippage and stalling, leading to length and sequence variation. However, current studies of DNA synthesis through STRs are restricted to a handful of selected sequences, limiting our broader understanding of their evolutionary behaviour and hampering the characterisation of the determinants of their abundance and stability in eukaryotic genomes. Results: We perform a comprehensive analysis of DNA synthesis at all STR permutations and interrogate the impact of STR sequence and secondary structure on their genomic representation and mutability. To do this, we developed a high-throughput primer extension assay that allows monitoring of the kinetics and fidelity of DNA synthesis through 20,000 sequences comprising all STR permutations in different lengths. By combining these measurements with population-scale genomic data, we show that the response of a model replicative DNA polymerase to variously structured DNA is sufficient to predict the complex genomic behaviour of STRs, including abundance and mutational constraints. We demonstrate that DNA polymerase stalling at DNA structures induces error-prone DNA synthesis, which constrains STR expansion. Conclusions: Our data support a model in which STR length in eukaryotic genomes results from a balance between expansion due to polymerase slippage at repeated DNA sequences and point mutations caused by error-prone DNA synthesis at DNA structures.
MeSH term(s)	Base Sequence ; DNA/metabolism ; DNA Replication ; DNA-Directed DNA Polymerase/genetics ; DNA-Directed DNA Polymerase/metabolism ; Evolution, Molecular ; Genetic Techniques ; Genome, Human ; Humans ; Kinetics ; Microsatellite Repeats ; Mutagenesis ; Mutation ; Point Mutation
Chemical Substances	DNA (9007-49-2) ; DNA-Directed DNA Polymerase (EC 2.7.7.7)
Language	English
Publishing date	2020-08-21
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2040529-7
ISSN	1474-760X ; 1474-760X
ISSN (online)	1474-760X
ISSN	1474-760X
DOI	10.1186/s13059-020-02124-x
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Article: DNA polymerase stalling at structured DNA constrains the expansion of short tandem repeats

Murat, Pierre / Guilbaud, Guillaume / Sale, Julian E

Genome biology. 2020 Dec., v. 21, no. 1

2020

Abstract: BACKGROUND: Short tandem repeats (STRs) contribute significantly to de novo mutagenesis, driving phenotypic diversity and genetic disease. Although highly diverse, their repetitive sequences induce DNA polymerase slippage and stalling, leading to length ... ...

Abstract	BACKGROUND: Short tandem repeats (STRs) contribute significantly to de novo mutagenesis, driving phenotypic diversity and genetic disease. Although highly diverse, their repetitive sequences induce DNA polymerase slippage and stalling, leading to length and sequence variation. However, current studies of DNA synthesis through STRs are restricted to a handful of selected sequences, limiting our broader understanding of their evolutionary behaviour and hampering the characterisation of the determinants of their abundance and stability in eukaryotic genomes. RESULTS: We perform a comprehensive analysis of DNA synthesis at all STR permutations and interrogate the impact of STR sequence and secondary structure on their genomic representation and mutability. To do this, we developed a high-throughput primer extension assay that allows monitoring of the kinetics and fidelity of DNA synthesis through 20,000 sequences comprising all STR permutations in different lengths. By combining these measurements with population-scale genomic data, we show that the response of a model replicative DNA polymerase to variously structured DNA is sufficient to predict the complex genomic behaviour of STRs, including abundance and mutational constraints. We demonstrate that DNA polymerase stalling at DNA structures induces error-prone DNA synthesis, which constrains STR expansion. CONCLUSIONS: Our data support a model in which STR length in eukaryotic genomes results from a balance between expansion due to polymerase slippage at repeated DNA sequences and point mutations caused by error-prone DNA synthesis at DNA structures.
Keywords	DNA ; DNA replication ; DNA-directed DNA polymerase ; genetic disorders ; genome ; genomics ; microsatellite repeats ; models ; monitoring ; mutagenesis ; phenotypic variation ; point mutation ; sequence diversity
Language	English
Dates of publication	2020-12
Size	p. 209.
Publishing place	BioMed Central
Document type	Article
ZDB-ID	2040529-7
ISSN	1474-760X ; 1465-6906
ISSN (online)	1474-760X
ISSN	1465-6906
DOI	10.1186/s13059-020-02124-x
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Determination of human DNA replication origin position and efficiency reveals principles of initiation zone organisation.

Guilbaud, Guillaume / Murat, Pierre / Wilkes, Helen S / Lerner, Leticia Koch / Sale, Julian E / Krude, Torsten

Nucleic acids research

2022 Volume 50, Issue 13, Page(s) 7436–7450

Abstract: Replication of the human genome initiates within broad zones of ∼150 kb. The extent to which firing of individual DNA replication origins within initiation zones is spatially stochastic or localised at defined sites remains a matter of debate. A thorough ...

Abstract	Replication of the human genome initiates within broad zones of ∼150 kb. The extent to which firing of individual DNA replication origins within initiation zones is spatially stochastic or localised at defined sites remains a matter of debate. A thorough characterisation of the dynamic activation of origins within initiation zones is hampered by the lack of a high-resolution map of both their position and efficiency. To address this shortcoming, we describe a modification of initiation site sequencing (ini-seq), based on density substitution. Newly replicated DNA is rendered 'heavy-light' (HL) by incorporation of BrdUTP while unreplicated DNA remains 'light-light' (LL). Replicated HL-DNA is separated from unreplicated LL-DNA by equilibrium density gradient centrifugation, then both fractions are subjected to massive parallel sequencing. This allows precise mapping of 23,905 replication origins simultaneously with an assignment of a replication initiation efficiency score to each. We show that origin firing within early initiation zones is not randomly distributed. Rather, origins are arranged hierarchically with a set of very highly efficient origins marking zone boundaries. We propose that these origins explain much of the early firing activity arising within initiation zones, helping to unify the concept of replication initiation zones with the identification of discrete replication origin sites.
MeSH term(s)	DNA/genetics ; DNA Replication/genetics ; Genome, Human ; Humans ; Replication Origin/genetics ; Sequence Analysis, DNA
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2022-07-06
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkac555
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Article ; Online: Development of a HS-SPME-GC-MS method for the analysis of phthalates in glycerin and liquid paraffin: application to safety evaluation of cosmetic packagings.

Murat, Pauline / Ferret, Pierre-Jacques / Coslédan, Sylvie / Simon, Valérie

Analytical and bioanalytical chemistry

2020 Volume 412, Issue 21, Page(s) 5157–5168

Abstract: Migration of molecules from packaging into products is a well-known phenomenon of which the studies in the food and medical industries are regulated in Europe by several legislations. However, for cosmetic packagings, there is no protocol nor specific ... ...

Abstract	Migration of molecules from packaging into products is a well-known phenomenon of which the studies in the food and medical industries are regulated in Europe by several legislations. However, for cosmetic packagings, there is no protocol nor specific migration limits available. The objective of this work was to use glycerin and liquid paraffin as cosmetic product simulants to perform a safety assessment on phthalates in 11 plastic packagings used in the cosmetic industry. To study these compounds in the matrices, 2 extraction techniques were compared: liquid-liquid extraction and solid-phase microextraction (SPME). The optimization of the 2 processes of extraction showed that SPME was more adapted to the study. Finally, samples of glycerin and liquid paraffin were analyzed by a SPME-GC-MS method to quantitate 10 regulated phthalates. In glycerin, only DEP was quantitated above the LOQ in 3 packagings, but the concentrations measured were under the set concentration threshold of 0.5 ppm. In liquid paraffin, DEP was quantitated above this concentration threshold. A safety evaluation was so performed by calculating the systemic exposure damage, and the results were finally considered to be safe for consumers.
MeSH term(s)	Consumer Product Safety ; Cosmetics ; Drug Packaging ; Gas Chromatography-Mass Spectrometry/methods ; Glycerol/chemistry ; Glycerol/standards ; Limit of Detection ; Paraffin/chemistry ; Paraffin/standards ; Phthalic Acids/analysis ; Reference Standards ; Reproducibility of Results ; Solid Phase Microextraction/methods
Chemical Substances	Cosmetics ; Phthalic Acids ; Paraffin (8002-74-2) ; Glycerol (PDC6A3C0OX)
Language	English
Publishing date	2020-03-27
Publishing country	Germany
Document type	Journal Article
ZDB-ID	201093-8
ISSN	1618-2650 ; 0016-1152 ; 0372-7920
ISSN (online)	1618-2650
ISSN	0016-1152 ; 0372-7920
DOI	10.1007/s00216-020-02519-6
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Article ; Online: Synthesis and biophysical analysis of modified thymine-containing DNA oligonucleotides.

Kawasaki, F / Murat, P / Li, Z / Santner, T / Balasubramanian, S

Chemical communications (Cambridge, England)

2016 Volume 53, Issue 8, Page(s) 1389–1392

Abstract: We report the synthesis of a 5-formyl-2'-deoxyuridine (5fU) phosphoramidite and the preparation of oligonucleotides comprising all known, naturally observed eukaryotic thymidine modifications. Biophysical characterization of the synthetic ... ...

Abstract	We report the synthesis of a 5-formyl-2'-deoxyuridine (5fU) phosphoramidite and the preparation of oligonucleotides comprising all known, naturally observed eukaryotic thymidine modifications. Biophysical characterization of the synthetic oligonucleotides indicates that 5fU, but not the other T-derivatives, can alter DNA structures.
MeSH term(s)	DNA/analysis ; DNA/chemical synthesis ; DNA/chemistry ; Deoxyuridine/analogs & derivatives ; Deoxyuridine/chemical synthesis ; Deoxyuridine/chemistry ; Oligonucleotides/analysis ; Oligonucleotides/chemical synthesis ; Oligonucleotides/chemistry ; Organophosphorus Compounds/chemical synthesis ; Organophosphorus Compounds/chemistry ; Thymine/chemistry
Chemical Substances	Oligonucleotides ; Organophosphorus Compounds ; phosphoramidite ; 5-formyl-2'-deoxyuridine (4494-26-2) ; DNA (9007-49-2) ; Thymine (QR26YLT7LT) ; Deoxyuridine (W78I7AY22C)
Language	English
Publishing date	2016-11-14
Publishing country	England
Document type	Journal Article
ZDB-ID	1472881-3
ISSN	1364-548X ; 1359-7345 ; 0009-241X
ISSN (online)	1364-548X
ISSN	1359-7345 ; 0009-241X
DOI	10.1039/c6cc08670e
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Article ; Online: DNA replication initiation shapes the mutational landscape and expression of the human genome.

Murat, Pierre / Perez, Consuelo / Crisp, Alastair / van Eijk, Patrick / Reed, Simon H / Guilbaud, Guillaume / Sale, Julian E

Science advances

2022 Volume 8, Issue 45, Page(s) eadd3686

Abstract: The interplay between active biological processes and DNA repair is central to mutagenesis. Here, we show that the ubiquitous process of replication initiation is mutagenic, leaving a specific mutational footprint at thousands of early and efficient ... ...

Abstract	The interplay between active biological processes and DNA repair is central to mutagenesis. Here, we show that the ubiquitous process of replication initiation is mutagenic, leaving a specific mutational footprint at thousands of early and efficient replication origins. The observed mutational pattern is consistent with two distinct mechanisms, reflecting the two-step process of origin activation, triggering the formation of DNA breaks at the center of origins and local error-prone DNA synthesis in their immediate vicinity. We demonstrate that these replication initiation-dependent mutational processes exert an influence on phenotypic diversity in humans that is disproportionate to the origins' genomic size: By increasing mutational loads at gene promoters and splice junctions, the presence of an origin significantly influences both gene expression and mRNA isoform usage. Last, we show that mutagenesis at origins not only drives the evolution of origin sequences but also contributes to sculpting regulatory domains of the human genome.
MeSH term(s)	Humans ; Genome, Human ; DNA Replication ; Replication Origin ; Mutation ; Mutagenesis
Language	English
Publishing date	2022-11-09
Publishing country	United States
Document type	Journal Article
ZDB-ID	2810933-8
ISSN	2375-2548 ; 2375-2548
ISSN (online)	2375-2548
ISSN	2375-2548
DOI	10.1126/sciadv.add3686
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Article: Development of a HS-SPME-GC-MS method for the analysis of phthalates in glycerin and liquid paraffin: application to safety evaluation of cosmetic packagings

Murat, Pauline / Ferret, Pierre-Jacques / Coslédan, Sylvie / Simon, Valérie

Analytical and bioanalytical chemistry. 2020 Aug., v. 412, no. 21

2020

Abstract	Migration of molecules from packaging into products is a well-known phenomenon of which the studies in the food and medical industries are regulated in Europe by several legislations. However, for cosmetic packagings, there is no protocol nor specific migration limits available. The objective of this work was to use glycerin and liquid paraffin as cosmetic product simulants to perform a safety assessment on phthalates in 11 plastic packagings used in the cosmetic industry. To study these compounds in the matrices, 2 extraction techniques were compared: liquid-liquid extraction and solid-phase microextraction (SPME). The optimization of the 2 processes of extraction showed that SPME was more adapted to the study. Finally, samples of glycerin and liquid paraffin were analyzed by a SPME-GC-MS method to quantitate 10 regulated phthalates. In glycerin, only DEP was quantitated above the LOQ in 3 packagings, but the concentrations measured were under the set concentration threshold of 0.5 ppm. In liquid paraffin, DEP was quantitated above this concentration threshold. A safety evaluation was so performed by calculating the systemic exposure damage, and the results were finally considered to be safe for consumers.
Keywords	cosmetics ; glycerol ; industry ; liquid-liquid extraction ; liquids ; phthalates ; safety assessment ; solid phase microextraction ; Europe
Language	English
Dates of publication	2020-08
Size	p. 5157-5168.
Publishing place	Springer Berlin Heidelberg
Document type	Article
Note	NAL-AP-2-clean
ISSN	1618-2642
DOI	10.1007/s00216-020-02519-6
Database	NAL-Catalogue (AGRICOLA)

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