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Article ; Online: Reply: Adding Nontumor Radiomic Features to the Prognostic Model Is Bothersome but Useful.

Yusufaly, Tahir I / Mell, Loren K

Journal of nuclear medicine : official publication, Society of Nuclear Medicine

2022 Volume 63, Issue 3, Page(s) 495

MeSH term(s)	Humans ; Lung Neoplasms/pathology ; Prognosis ; Tomography, X-Ray Computed
Language	English
Publishing date	2022-01-13
Publishing country	United States
Document type	Journal Article ; Comment
ZDB-ID	80272-4
ISSN	1535-5667 ; 0097-9058 ; 0161-5505 ; 0022-3123
ISSN (online)	1535-5667
ISSN	0097-9058 ; 0161-5505 ; 0022-3123
DOI	10.2967/jnumed.121.263730
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Zs.A 114: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MO 328: Show issues

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Article ; Online: Optimized Atlas-Based Auto-Segmentation of Bony Structures from Whole-Body Computed Tomography.

Gao, Lei / Yusufaly, Tahir I / Williamson, Casey W / Mell, Loren K

Practical radiation oncology

2023 Volume 13, Issue 5, Page(s) e442–e450

Abstract: Purpose: To develop and test a method for fully automated segmentation of bony structures from whole-body computed tomography (CT) and evaluate its performance compared with manual segmentation.: Methods and materials: We developed a workflow for ... ...

Abstract	Purpose: To develop and test a method for fully automated segmentation of bony structures from whole-body computed tomography (CT) and evaluate its performance compared with manual segmentation. Methods and materials: We developed a workflow for automatic whole-body bone segmentation using atlas-based segmentation (ABS) method with a postprocessing module (ABS Results: The ABS Conclusions: We developed a fully automated MIM workflow for bony structure segmentation from whole-body CT, which exhibited high accuracy compared with manual delineation. The integrated postprocessing module significantly improved workflow performance.
MeSH term(s)	Humans ; Image Processing, Computer-Assisted/methods ; Tomography, X-Ray Computed/methods
Language	English
Publishing date	2023-04-06
Publishing country	United States
Document type	Journal Article
ZDB-ID	2655748-4
ISSN	1879-8519 ; 1879-8500
ISSN (online)	1879-8519
ISSN	1879-8500
DOI	10.1016/j.prro.2023.03.013
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Mapping quorum sensing onto neural networks to understand collective decision making in heterogeneous microbial communities.

Yusufaly, Tahir I / Boedicker, James Q

Physical biology

2017 Volume 14, Issue 4, Page(s) 46002

Abstract: Microbial communities frequently communicate via quorum sensing (QS), where cells produce, secrete, and respond to a threshold level of an autoinducer (AI) molecule, thereby modulating gene expression. However, the biology of QS remains incompletely ... ...

Abstract	Microbial communities frequently communicate via quorum sensing (QS), where cells produce, secrete, and respond to a threshold level of an autoinducer (AI) molecule, thereby modulating gene expression. However, the biology of QS remains incompletely understood in heterogeneous communities, where variant bacterial strains possess distinct QS systems that produce chemically unique AIs. AI molecules bind to 'cognate' receptors, but also to 'non-cognate' receptors found in other strains, resulting in inter-strain crosstalk. Understanding these interactions is a prerequisite for deciphering the consequences of crosstalk in real ecosystems, where multiple AIs are regularly present in the same environment. As a step towards this goal, we map crosstalk in a heterogeneous community of variant QS strains onto an artificial neural network model. This formulation allows us to systematically analyze how crosstalk regulates the community's capacity for flexible decision making, as quantified by the Boltzmann entropy of all QS gene expression states of the system. In a mean-field limit of complete cross-inhibition between variant strains, the model is exactly solvable, allowing for an analytical formula for the number of variants that maximize capacity as a function of signal kinetics and activation parameters. An analysis of previous experimental results on the Staphylococcus aureus two-component Agr system indicates that the observed combination of variant numbers, gene expression rates and threshold concentrations lies near this critical regime of parameter space where capacity peaks. The results are suggestive of a potential evolutionary driving force for diversification in certain QS systems.
MeSH term(s)	Bacterial Physiological Phenomena ; Bacterial Proteins/metabolism ; Decision Making ; Gene Expression Regulation, Bacterial ; Microbial Interactions ; Models, Biological ; Neural Networks (Computer) ; Quorum Sensing ; Signal Transduction ; Staphylococcus aureus/genetics ; Staphylococcus aureus/physiology
Chemical Substances	Bacterial Proteins
Language	English
Publishing date	2017--19
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2133216-2
ISSN	1478-3975 ; 1478-3967
ISSN (online)	1478-3975
ISSN	1478-3967
DOI	10.1088/1478-3975/aa7c1e
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Knowledge-Based Planning for Intact Cervical Cancer.

Yusufaly, Tahir I / Meyers, Sandra M / Mell, Loren K / Moore, Kevin L

Seminars in radiation oncology

2020 Volume 30, Issue 4, Page(s) 328–339

Abstract: Cervical cancer radiotherapy is often complicated by significant variability in the quality and consistency of treatment plans. Knowledge-based planning (KBP), which utilizes prior patient data to correlated achievable optimal dosimetry with patient- ... ...

Abstract	Cervical cancer radiotherapy is often complicated by significant variability in the quality and consistency of treatment plans. Knowledge-based planning (KBP), which utilizes prior patient data to correlated achievable optimal dosimetry with patient-specific anatomy, has demonstrated promise as a quality control tool for controlling this variability, with consequences for patient outcomes, as well as for the reliability of data from multi-institutional clinical trials. In this article we highlight the application of KBP-based quality control to cervical cancer radiotherapy. We discuss the potential impact of KBP on multi-institutional clinical trials to standardize cervical cancer treatment planning across diverse clinics, and discuss challenges and progress in the implementation of KBP for brachytherapy treatment planning. Additionally, we briefly discuss secondary applications of KBP for cervical cancer. The emerging picture from these studies indicates several exciting opportunities for increasing the utilization of KBP in day-to-day cervical cancer radiotherapy.
MeSH term(s)	Clinical Trials as Topic ; Female ; Humans ; Knowledge Bases ; Organ Sparing Treatments ; Organs at Risk ; Quality Control ; Radiotherapy Dosage ; Radiotherapy Planning, Computer-Assisted ; Tumor Burden ; Uterine Cervical Neoplasms/pathology ; Uterine Cervical Neoplasms/radiotherapy
Language	English
Publishing date	2020-08-21
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	1146999-7
ISSN	1532-9461 ; 1053-4296
ISSN (online)	1532-9461
ISSN	1053-4296
DOI	10.1016/j.semradonc.2020.05.009
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Zs.A 3654: Show issues

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Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (2.OG)
ab Jg. 2022: Lesesaal (EG)

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Article ; Online: Spatial dispersal of bacterial colonies induces a dynamical transition from local to global quorum sensing.

Yusufaly, Tahir I / Boedicker, James Q

Physical review. E

2016 Volume 94, Issue 6-1, Page(s) 62410

Abstract: Bacteria communicate using external chemical signals called autoinducers (AI) in a process known as quorum sensing (QS). QS efficiency is reduced by both limitations of AI diffusion and potential interference from neighboring strains. There is thus a ... ...

Abstract	Bacteria communicate using external chemical signals called autoinducers (AI) in a process known as quorum sensing (QS). QS efficiency is reduced by both limitations of AI diffusion and potential interference from neighboring strains. There is thus a need for predictive theories of how spatial community structure shapes information processing in complex microbial ecosystems. As a step in this direction, we apply a reaction-diffusion model to study autoinducer signaling dynamics in a single-species community as a function of the spatial distribution of colonies in the system. We predict a dynamical transition between a local quorum sensing (LQS) regime, with the AI signaling dynamics primarily controlled by the local population densities of individual colonies, and a global quorum sensing (GQS) regime, with the dynamics being dependent on collective intercolony diffusive interactions. The crossover between LQS to GQS is intimately connected to a trade-off between the signaling network's latency, or speed of activation, and its throughput, or the total spatial range over which all the components of the system communicate.
MeSH term(s)	Bacterial Physiological Phenomena ; Models, Biological ; Quorum Sensing/physiology ; Signal Transduction
Language	English
Publishing date	2016-12
Publishing country	United States
Document type	Journal Article
ZDB-ID	2844562-4
ISSN	2470-0053 ; 2470-0045
ISSN (online)	2470-0053
ISSN	2470-0045
DOI	10.1103/PhysRevE.94.062410
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Disruption of microbial communication yields a two-dimensional percolation transition.

Silva, Kalinga Pavan T / Yusufaly, Tahir I / Chellamuthu, Prithiviraj / Boedicker, James Q

Physical review. E

2019 Volume 99, Issue 4-1, Page(s) 42409

Abstract: Bacteria communicate with each other to coordinate macroscale behaviors including pathogenesis, biofilm formation, and antibiotic production. Empirical evidence suggests that bacteria are capable of communicating at length scales far exceeding the size ... ...

Abstract	Bacteria communicate with each other to coordinate macroscale behaviors including pathogenesis, biofilm formation, and antibiotic production. Empirical evidence suggests that bacteria are capable of communicating at length scales far exceeding the size of individual cells. Several mechanisms of signal interference have been observed in nature, and how interference influences macroscale activity within microbial populations is unclear. Here we examined the exchange of quorum sensing signals to coordinate microbial activity over long distances in the presence of a variable amount of interference through a neighboring signal-degrading strain. As the level of interference increased, communication over large distances was disrupted and at a critical amount of interference, large-scale communication was suppressed. We explored this transition in experiments and reaction-diffusion models, and confirmed that this transition is a two-dimensional percolation transition. These results demonstrate the utility of applying physical models to emergence in complex biological networks to probe robustness and universal quantitative features.
MeSH term(s)	Biofilms ; Diffusion ; Escherichia coli/cytology ; Escherichia coli/genetics ; Escherichia coli/physiology ; Models, Biological ; Quorum Sensing
Language	English
Publishing date	2019-05-21
Publishing country	United States
Document type	Journal Article
ZDB-ID	2844562-4
ISSN	2470-0053 ; 2470-0045
ISSN (online)	2470-0053
ISSN	2470-0045
DOI	10.1103/PhysRevE.99.042409
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Book ; Online: Spatial Dispersal of Bacterial Colonies Induces a Dynamical Transition From Local to Global Quorum Sensing

Yusufaly, Tahir I. / Boedicker, James Q.

2016

Abstract	Bacteria communicate using external chemical signals called autoinducers (AI) in a process known as quorum sensing (QS). QS efficiency is reduced by both limitations of AI diffusion and potential interference from neighboring strains. There is thus a need for predictive theories of how spatial community structure shapes information processing in complex microbial ecosystems. As a step in this direction, we apply a reaction-diffusion model to study autoinducer signaling dynamics in a single-species community as a function of the spatial distribution of colonies in the system. We predict a dynamical transition between a local quorum sensing (LQS) regime, with the AI signaling dynamics primarily controlled by the local population densities of individual colonies, and a global quorum sensing (GQS) regime, with the dynamics being dependent on collective inter-colony diffusive interactions. The crossover between LQS to GQS is intimately connected to a tradeoff between the signaling network's latency, or speed of activation, and its throughput, or the total spatial range over which all the components of the system communicate. Comment: Revised version, accepted to Phys. Rev. E
Keywords	Quantitative Biology - Molecular Networks ; Quantitative Biology - Cell Behavior
Subject code	612
Publishing date	2016-03-22
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: 5-Methylation of cytosine in CG:CG base-pair steps: a physicochemical mechanism for the epigenetic control of DNA nanomechanics.

Yusufaly, Tahir I / Li, Yun / Olson, Wilma K

The journal of physical chemistry. B

2013 Volume 117, Issue 51, Page(s) 16436–16442

Abstract: van der Waals density functional theory is integrated with analysis of a non-redundant set of protein-DNA crystal structures from the Nucleic Acid Database to study the stacking energetics of CG:CG base-pair steps, specifically the role of cytosine 5- ... ...

Abstract	van der Waals density functional theory is integrated with analysis of a non-redundant set of protein-DNA crystal structures from the Nucleic Acid Database to study the stacking energetics of CG:CG base-pair steps, specifically the role of cytosine 5-methylation. Principal component analysis of the steps reveals the dominant collective motions to correspond to a tensile "opening" mode and two shear "sliding" and "tearing" modes in the orthogonal plane. The stacking interactions of the methyl groups globally inhibit CG:CG step overtwisting while simultaneously softening the modes locally via potential energy modulations that create metastable states. Additionally, the indirect effects of the methyl groups on possible base-pair steps neighboring CG:CG are observed to be of comparable importance to their direct effects on CG:CG. The results have implications for the epigenetic control of DNA mechanics.
MeSH term(s)	Base Pairing ; Chemical Phenomena ; Cytosine/chemistry ; Cytosine/metabolism ; DNA/chemistry ; DNA/genetics ; DNA/metabolism ; DNA Methylation ; Epigenesis, Genetic ; Models, Molecular ; Quantum Theory
Chemical Substances	Cytosine (8J337D1HZY) ; DNA (9007-49-2)
Language	English
Publishing date	2013-12-16
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	1520-5207
ISSN (online)	1520-5207
DOI	10.1021/jp409887t
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: 5-Methylation of Cytosine in CG:CG Base-Pair Steps: A Physicochemical Mechanism for the Epigenetic Control of DNA Nanomechanics

Yusufaly, Tahir I / Li Yun / Olson Wilma K

Journal of physical chemistry. 2013 Dec. 27, v. 117, no. 51

2013

Abstract: van der Waals density functional theory is integrated with analysis of a non-redundant set of proteinâDNA crystal structures from the Nucleic Acid Database to study the stacking energetics of CG:CG base-pair steps, specifically the role of cytosine 5- ... ...

Abstract	van der Waals density functional theory is integrated with analysis of a non-redundant set of proteinâDNA crystal structures from the Nucleic Acid Database to study the stacking energetics of CG:CG base-pair steps, specifically the role of cytosine 5-methylation. Principal component analysis of the steps reveals the dominant collective motions to correspond to a tensile âopeningâ mode and two shear âslidingâ and âtearingâ modes in the orthogonal plane. The stacking interactions of the methyl groups globally inhibit CG:CG step overtwisting while simultaneously softening the modes locally via potential energy modulations that create metastable states. Additionally, the indirect effects of the methyl groups on possible base-pair steps neighboring CG:CG are observed to be of comparable importance to their direct effects on CG:CG. The results have implications for the epigenetic control of DNA mechanics.
Keywords	DNA ; crystal structure ; cytosine ; databases ; energy ; epigenetics ; mechanics ; methodology ; principal component analysis ; van der Waals forces
Language	English
Dates of publication	2013-1227
Size	p. 16436-16442.
Publishing place	American Chemical Society
Document type	Article
ISSN	1520-5207
DOI	10.1021%2Fjp409887t
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Arginine-phosphate salt bridges between histones and DNA: intermolecular actuators that control nucleosome architecture.

Yusufaly, Tahir I / Li, Yun / Singh, Gautam / Olson, Wilma K

The Journal of chemical physics

2014 Volume 141, Issue 16, Page(s) 165102

Abstract: Structural bioinformatics and van der Waals density functional theory are combined to investigate the mechanochemical impact of a major class of histone-DNA interactions, namely, the formation of salt bridges between arginine residues in histones and ... ...

Abstract	Structural bioinformatics and van der Waals density functional theory are combined to investigate the mechanochemical impact of a major class of histone-DNA interactions, namely, the formation of salt bridges between arginine residues in histones and phosphate groups on the DNA backbone. Principal component analysis reveals that the configurational fluctuations of the sugar-phosphate backbone display sequence-specific directionality and variability, and clustering of nucleosome crystal structures identifies two major salt-bridge configurations: a monodentate form in which the arginine end-group guanidinium only forms one hydrogen bond with the phosphate, and a bidentate form in which it forms two. Density functional theory calculations highlight that the combination of sequence, denticity, and salt-bridge positioning enables the histones to apply a tunable mechanochemical stress to the DNA via precise and specific activation of backbone deformations. The results suggest that selection for specific placements of van der Waals contacts, with high-precision control of the spatial distribution of intermolecular forces, may serve as an underlying evolutionary design principle for the structure and function of nucleosomes, a conjecture that is corroborated by previous experimental studies.
MeSH term(s)	Arginine/chemistry ; DNA/chemistry ; Histones/chemistry ; Hydrogen Bonding ; Models, Molecular ; Nucleosomes/chemistry ; Phosphates/chemistry ; Protein Conformation ; Quantum Theory
Chemical Substances	Histones ; Nucleosomes ; Phosphates ; DNA (9007-49-2) ; Arginine (94ZLA3W45F)
Language	English
Publishing date	2014-10-28
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	3113-6
ISSN	1089-7690 ; 0021-9606
ISSN (online)	1089-7690
ISSN	0021-9606
DOI	10.1063/1.4897978
Database	MEDical Literature Analysis and Retrieval System OnLINE

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