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Article: Evaluation of a Bayesian penalized likelihood reconstruction algorithm for low-count clinical

Te Riet, Joost / Rijnsdorp, Sjoerd / Roef, Mark J / Arends, Albert J

2019 Volume 6, Issue 1, Page(s) 32

Abstract: Background: Recently, a Bayesian penalized likelihood (BPL) reconstruction algorithm was introduced for a commercial PET/CT with the potential to improve image quality. We compared the performance of this BPL algorithm with conventional reconstruction ... ...

Abstract	Background: Recently, a Bayesian penalized likelihood (BPL) reconstruction algorithm was introduced for a commercial PET/CT with the potential to improve image quality. We compared the performance of this BPL algorithm with conventional reconstruction algorithms under realistic clinical conditions such as daily practiced at many European sites, i.e. low Results: To study the performance of the BPL algorithm, regular clinical Conclusions: The BPL algorithm performs better than the standard OSEM+PSF algorithm on small lesion detectability, SUV recovery, and noise suppression. Increase of the percentage of bed overlap, time per BP, administered activity, or the β-value, all have a direct positive impact on image quality, though the latter with some loss of small lesion detectability. Thus, BPL algorithms are very interesting for improving image quality, especially in small lesion detectability.
Language	English
Publishing date	2019-12-30
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2768912-8
ISSN	2197-7364
ISSN	2197-7364
DOI	10.1186/s40658-019-0262-y
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Correction to 'Cell migration through three-dimensional confining pores: speed accelerations by deformation and recoil of the nucleus'.

Krause, Marina / Wei Yang, Feng / Te Lindert, Mariska / Isermann, Philipp / Schepens, Jan / Maas, Ralph J A / Venkataraman, Chandrasekhar / Lammerding, Jan / Madzvamuse, Anotida / Hendriks, Wiljan / Te Riet, Joost / Wolf, Katarina

Philosophical transactions of the Royal Society of London. Series B, Biological sciences

2019 Volume 374, Issue 1786, Page(s) 20190657

Language	English
Publishing date	2019-10-07
Publishing country	England
Document type	Journal Article ; Published Erratum
ZDB-ID	208382-6
ISSN	1471-2970 ; 0080-4622 ; 0264-3839 ; 0962-8436
ISSN (online)	1471-2970
ISSN	0080-4622 ; 0264-3839 ; 0962-8436
DOI	10.1098/rstb.2019.0657
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Article ; Online: Evaluation of a Bayesian penalized likelihood reconstruction algorithm for low-count clinical 18F-FDG PET/CT

Joost te Riet / Sjoerd Rijnsdorp / Mark J. Roef / Albert J. Arends

EJNMMI Physics, Vol 6, Iss 1, Pp 1-

2019 Volume 14

Abstract: Abstract Background Recently, a Bayesian penalized likelihood (BPL) reconstruction algorithm was introduced for a commercial PET/CT with the potential to improve image quality. We compared the performance of this BPL algorithm with conventional ... ...

Abstract	Abstract Background Recently, a Bayesian penalized likelihood (BPL) reconstruction algorithm was introduced for a commercial PET/CT with the potential to improve image quality. We compared the performance of this BPL algorithm with conventional reconstruction algorithms under realistic clinical conditions such as daily practiced at many European sites, i.e. low 18F-FDG dose and short acquisition times. Results To study the performance of the BPL algorithm, regular clinical 18F-FDG whole body PET scans were made. In addition, two types of phantoms were scanned with 4-37 mm sized spheres filled with 18F-FDG at sphere-to-background ratios of 10-to-1, 4-to-1, and 2-to-1. Images were reconstructed using standard ordered-subset expectation maximization (OSEM), OSEM with point spread function (PSF), and the BPL algorithm using β-values of 450, 550 and 700. To quantify the image quality, the lesion detectability, activity recovery, and the coefficient of variation (COV) within a single bed position (BP) were determined. We found that when applying the BPL algorithm both smaller lesions in clinical studies as well as spheres in phantom studies can be detected more easily due to a higher SUV recovery, especially for higher contrast ratios. Under standard clinical scanning conditions, i.e. low number of counts, the COV is higher for the BPL (β=450) than the OSEM+PSF algorithm. Increase of the β-value to 550 or 700 results in a COV comparable to OSEM+PSF, however, at the cost of contrast, though still better than OSEM+PSF. At the edges of the axial field of view (FOV) where BPs overlap, COV can increase to levels at which bands become visible in clinical images, related to the lower local axial sensitivity of the PET/CT, which is due to the limited bed overlap of 23% such as advised by the manufacturer. Conclusions The BPL algorithm performs better than the standard OSEM+PSF algorithm on small lesion detectability, SUV recovery, and noise suppression. Increase of the percentage of bed overlap, time per BP, administered activity, or the β-value, all have a direct positive impact on image quality, though the latter with some loss of small lesion detectability. Thus, BPL algorithms are very interesting for improving image quality, especially in small lesion detectability.
Keywords	Bayesian penalized likelihood ; NEMA image quality phantom ; Micro Hollow Sphere phantom ; image quality ; image reconstruction ; optimization ; Medical physics. Medical radiology. Nuclear medicine ; R895-920
Subject code	006
Language	English
Publishing date	2019-12-01T00:00:00Z
Publisher	SpringerOpen
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: N-glycan mediated adhesion strengthening during pathogen-receptor binding revealed by cell-cell force spectroscopy.

Te Riet, Joost / Joosten, Ben / Reinieren-Beeren, Inge / Figdor, Carl G / Cambi, Alessandra

Scientific reports

2017 Volume 7, Issue 1, Page(s) 6713

Abstract: Glycan-protein lateral interactions have gained increased attention as important modulators of receptor function, by regulating surface residence time and endocytosis of membrane glycoproteins. The pathogen-recognition receptor DC-SIGN is highly ... ...

Abstract	Glycan-protein lateral interactions have gained increased attention as important modulators of receptor function, by regulating surface residence time and endocytosis of membrane glycoproteins. The pathogen-recognition receptor DC-SIGN is highly expressed at the membrane of antigen-presenting dendritic cells, where it is organized in nanoclusters and binds to different viruses, bacteria and fungi. We recently demonstrated that DC-SIGN N-glycans spatially restrict receptor diffusion within the plasma membrane, favoring its internalization through clathrin-coated pits. Here, we investigated the involvement of the N-glycans of DC-SIGN expressing cells on pathogen binding strengthening when interacting with Candida fungal cells by using atomic force microscope (AFM)-assisted single cell-pathogen adhesion measurements. The use of DC-SIGN mutants lacking the N-glycans as well as blocking glycan-mediated lateral interactions strongly impaired cell stiffening during pathogen binding. Our findings demonstrate for the first time the direct involvement of the cell membrane glycans in strengthening cell-pathogen interactions. This study, therefore, puts forward a possible role for the glycocalyx as extracellular cytoskeleton contributing, possibly in connection with the intracellular actin cytoskeleton, to optimize strengthening of cell-pathogen interactions in the presence of mechanical forces.
MeSH term(s)	Animals ; Binding Sites ; Biomechanical Phenomena ; CHO Cells ; Candida albicans/chemistry ; Candida albicans/metabolism ; Cell Adhesion ; Cell Adhesion Molecules/chemistry ; Cell Adhesion Molecules/genetics ; Cell Adhesion Molecules/metabolism ; Cricetulus ; Dendritic Cells/metabolism ; Dendritic Cells/microbiology ; Dendritic Cells/ultrastructure ; Gene Expression ; Glycocalyx/chemistry ; Glycocalyx/metabolism ; Host-Pathogen Interactions ; Humans ; Lectins, C-Type/chemistry ; Lectins, C-Type/genetics ; Lectins, C-Type/metabolism ; Microscopy, Atomic Force ; Mutation ; Polysaccharides/chemistry ; Polysaccharides/metabolism ; Primary Cell Culture ; Protein Domains ; Receptors, Cell Surface/chemistry ; Receptors, Cell Surface/genetics ; Receptors, Cell Surface/metabolism ; Transgenes
Chemical Substances	Cell Adhesion Molecules ; DC-specific ICAM-3 grabbing nonintegrin ; Lectins, C-Type ; Polysaccharides ; Receptors, Cell Surface
Language	English
Publishing date	2017-07-27
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-017-07220-w
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Probing the compressibility of tumor cell nuclei by combined atomic force-confocal microscopy.

Krause, Marina / Te Riet, Joost / Wolf, Katarina

Physical biology

2013 Volume 10, Issue 6, Page(s) 65002

Abstract: The cell nucleus is the largest and stiffest organelle rendering it the limiting compartment during migration of invasive tumor cells through dense connective tissue. We here describe a combined atomic force microscopy (AFM)-confocal microscopy approach ... ...

Abstract	The cell nucleus is the largest and stiffest organelle rendering it the limiting compartment during migration of invasive tumor cells through dense connective tissue. We here describe a combined atomic force microscopy (AFM)-confocal microscopy approach for measurement of bulk nuclear stiffness together with simultaneous visualization of the cantilever-nucleus contact and the fate of the cell. Using cantilevers functionalized with either tips or beads and spring constants ranging from 0.06-10 N m(-1), force-deformation curves were generated from nuclear positions of adherent HT1080 fibrosarcoma cell populations at unchallenged integrity, and a nuclear stiffness range of 0.2 to 2.5 kPa was identified depending on cantilever type and the use of extended fitting models. Chromatin-decondensating agent trichostatin A (TSA) induced nuclear softening of up to 50%, demonstrating the feasibility of our approach. Finally, using a stiff bead-functionalized cantilever pushing at maximal system-intrinsic force, the nucleus was deformed to 20% of its original height which after TSA treatment reduced further to 5% remaining height confirming chromatin organization as an important determinant of nuclear stiffness. Thus, combined AFM-confocal microscopy is a feasible approach to study nuclear compressibility to complement concepts of limiting nuclear deformation in cancer cell invasion and other biological processes.
MeSH term(s)	Cell Line, Tumor ; Cell Nucleus/chemistry ; Cell Nucleus/drug effects ; Cell Nucleus/pathology ; Elasticity/drug effects ; Equipment Design ; Fibrosarcoma/chemistry ; Fibrosarcoma/pathology ; Histone Deacetylase Inhibitors/pharmacology ; Humans ; Hydroxamic Acids/pharmacology ; Microscopy, Atomic Force/instrumentation ; Microscopy, Atomic Force/methods
Chemical Substances	Histone Deacetylase Inhibitors ; Hydroxamic Acids ; trichostatin A (3X2S926L3Z)
Language	English
Publishing date	2013-12
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2133216-2
ISSN	1478-3975 ; 1478-3967
ISSN (online)	1478-3975
ISSN	1478-3967
DOI	10.1088/1478-3975/10/6/065002
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Article ; Online: Cell migration through three-dimensional confining pores: speed accelerations by deformation and recoil of the nucleus.

Krause, Marina / Yang, Feng Wei / Te Lindert, Mariska / Isermann, Philipp / Schepens, Jan / Maas, Ralph J A / Venkataraman, Chandrasekhar / Lammerding, Jan / Madzvamuse, Anotida / Hendriks, Wiljan / Te Riet, Joost / Wolf, Katarina

Philosophical transactions of the Royal Society of London. Series B, Biological sciences

2019 Volume 374, Issue 1779, Page(s) 20180225

Abstract: Directional cell migration in dense three-dimensional (3D) environments critically depends upon shape adaptation and is impeded depending on the size and rigidity of the nucleus. Accordingly, the nucleus is primarily understood as a physical obstacle; ... ...

Abstract	Directional cell migration in dense three-dimensional (3D) environments critically depends upon shape adaptation and is impeded depending on the size and rigidity of the nucleus. Accordingly, the nucleus is primarily understood as a physical obstacle; however, its pro-migratory functions by stepwise deformation and reshaping remain unclear. Using atomic force spectroscopy, time-lapse fluorescence microscopy and shape change analysis tools, we determined the nuclear size, deformability, morphology and shape change of HT1080 fibrosarcoma cells expressing the Fucci cell cycle indicator or being pre-treated with chromatin-decondensating agent TSA. We show oscillating peak accelerations during migration through 3D collagen matrices and microdevices that occur during shape reversion of deformed nuclei (recoil), and increase with confinement. During G1 cell-cycle phase, nucleus stiffness was increased and yielded further increased speed fluctuations together with sustained cell migration rates in confinement when compared to interphase populations or to periods of intrinsic nuclear softening in the S/G2 cell-cycle phase. Likewise, nuclear softening by pharmacological chromatin decondensation or after lamin A/C depletion reduced peak oscillations in confinement. In conclusion, deformation and recoil of the stiff nucleus contributes to saltatory locomotion in dense tissues. This article is part of a discussion meeting issue 'Forces in cancer: interdisciplinary approaches in tumour mechanobiology'.
MeSH term(s)	Acceleration ; Biophysical Phenomena ; Cell Cycle/physiology ; Cell Line, Tumor ; Cell Movement/physiology ; Cell Nucleus/metabolism ; Chromatin/metabolism ; Collagen/metabolism ; Humans
Chemical Substances	Chromatin ; Collagen (9007-34-5)
Language	English
Publishing date	2019-07-01
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	208382-6
ISSN	1471-2970 ; 0080-4622 ; 0264-3839 ; 0962-8436
ISSN (online)	1471-2970
ISSN	0080-4622 ; 0264-3839 ; 0962-8436
DOI	10.1098/rstb.2018.0225
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Article ; Online: N-glycan mediated adhesion strengthening during pathogen-receptor binding revealed by cell-cell force spectroscopy

Joost te Riet / Ben Joosten / Inge Reinieren-Beeren / Carl G. Figdor / Alessandra Cambi

Scientific Reports, Vol 7, Iss 1, Pp 1-

2017 Volume 12

Abstract: Abstract Glycan-protein lateral interactions have gained increased attention as important modulators of receptor function, by regulating surface residence time and endocytosis of membrane glycoproteins. The pathogen-recognition receptor DC-SIGN is highly ...

Abstract	Abstract Glycan-protein lateral interactions have gained increased attention as important modulators of receptor function, by regulating surface residence time and endocytosis of membrane glycoproteins. The pathogen-recognition receptor DC-SIGN is highly expressed at the membrane of antigen-presenting dendritic cells, where it is organized in nanoclusters and binds to different viruses, bacteria and fungi. We recently demonstrated that DC-SIGN N-glycans spatially restrict receptor diffusion within the plasma membrane, favoring its internalization through clathrin-coated pits. Here, we investigated the involvement of the N-glycans of DC-SIGN expressing cells on pathogen binding strengthening when interacting with Candida fungal cells by using atomic force microscope (AFM)-assisted single cell-pathogen adhesion measurements. The use of DC-SIGN mutants lacking the N-glycans as well as blocking glycan-mediated lateral interactions strongly impaired cell stiffening during pathogen binding. Our findings demonstrate for the first time the direct involvement of the cell membrane glycans in strengthening cell-pathogen interactions. This study, therefore, puts forward a possible role for the glycocalyx as extracellular cytoskeleton contributing, possibly in connection with the intracellular actin cytoskeleton, to optimize strengthening of cell-pathogen interactions in the presence of mechanical forces.
Keywords	Medicine ; R ; Science ; Q
Subject code	571
Language	English
Publishing date	2017-07-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Nanometer-grooved topography stimulates trabecular bone regeneration around a concave implant in a rat femoral medulla model.

Klymov, Alexey / Te Riet, Joost / Mulder, Peter / Gardeniers, Johannes G E / Jansen, John A / Walboomers, X Frank

Nanomedicine : nanotechnology, biology, and medicine

2016 Volume 12, Issue 8, Page(s) 2283–2290

Abstract: In the present study, a method was developed to reproduce two nanogrooved patterns (groove width/ridge width/depth: 150/150/50 nm and 200/800/70 nm) into cylindrical epoxy resin implants, which were subsequently coated with 20 nm of titanium. Also, ... ...

Abstract	In the present study, a method was developed to reproduce two nanogrooved patterns (groove width/ridge width/depth: 150/150/50 nm and 200/800/70 nm) into cylindrical epoxy resin implants, which were subsequently coated with 20 nm of titanium. Also, implants with a conventional surface roughness (R
MeSH term(s)	Animals ; Bone Regeneration ; Cancellous Bone ; Femur ; Nanotechnology ; Osseointegration ; Prostheses and Implants ; Rats ; Regeneration ; Surface Properties ; Titanium
Chemical Substances	Titanium (D1JT611TNE)
Language	English
Publishing date	2016-11
Publishing country	United States
Document type	Journal Article
ZDB-ID	2183417-9
ISSN	1549-9642 ; 1549-9634
ISSN (online)	1549-9642
ISSN	1549-9634
DOI	10.1016/j.nano.2016.06.013
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Article ; Online: Bone marrow-derived mesenchymal cells feature selective migration behavior on submicro- and nano-dimensional multi-patterned substrates.

Klymov, Alexey / Bronkhorst, Ewald M / Te Riet, Joost / Jansen, John A / Walboomers, X Frank

Acta biomaterialia

2015 Volume 16, Page(s) 117–125

Abstract: This study investigated whether cells have an intrinsic ability to recognize nanopatterns, which could lead to their accumulation or diminution on a biomaterial. A multi-patterned "biochip" was made, containing 36 differently designed surfaces, including ...

Abstract	This study investigated whether cells have an intrinsic ability to recognize nanopatterns, which could lead to their accumulation or diminution on a biomaterial. A multi-patterned "biochip" was made, containing 36 differently designed surfaces, including squares and grooves varying in feature sizes between 10 and 1000 nm. The grooved patterns could additionally be subdivided into three groups having ridge to groove ratios of 1:1, 1:3 and 3:1. These substrates were used for culture of rat bone marrow derived mesenchymal cells. In time cells should accumulate on patterns of preference, while migrating away from patterns of disfavor. A regression analysis model was designed for the analysis of the obtained data. Results showed that strong differences existed between the tested patterns regarding the cellular affinity. All sizes of squares showed strong cell-repelling capacity, with the biggest sized squares displaying up to 40% less cells compared to the smooth surface. Among the nano-grooved patterns cell repelling was seen for the grooves with the ridge to groove ratio of 1:3, while grooves with the ridge to groove ratio of 3:1 partially showed cell attraction. Such effects were shown to be based on selective migration rather than proliferation. In conclusion, the use of a multi-patterned biochip setup allows for enhanced evaluation of cell behavior, as compared to uniformly patterned setups. Cells exhibit the ability to actively avoid or migrate to surfaces featuring certain topographies on nanometric scale. Such phenomena may be utilized for the development of biomaterials in regenerative medicine.
MeSH term(s)	Animals ; Biocompatible Materials/chemistry ; Biocompatible Materials/pharmacology ; Bone Marrow Cells/cytology ; Bone Marrow Cells/drug effects ; Cell Membrane/drug effects ; Cell Membrane/metabolism ; Cell Movement/drug effects ; Cell Proliferation/drug effects ; Male ; Mesenchymal Stromal Cells/cytology ; Mesenchymal Stromal Cells/drug effects ; Mesenchymal Stromal Cells/ultrastructure ; Microscopy, Fluorescence ; Nanoparticles/chemistry ; Particle Size ; Rats, Wistar
Chemical Substances	Biocompatible Materials
Language	English
Publishing date	2015-04
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2173841-5
ISSN	1878-7568 ; 1742-7061
ISSN (online)	1878-7568
ISSN	1742-7061
DOI	10.1016/j.actbio.2015.01.016
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Article ; Online: AFM force spectroscopy reveals how subtle structural differences affect the interaction strength between Candida albicans and DC-SIGN.

te Riet, Joost / Reinieren-Beeren, Inge / Figdor, Carl G / Cambi, Alessandra

Journal of molecular recognition : JMR

2015 Volume 28, Issue 11, Page(s) 687–698

Abstract: The fungus Candida albicans is the most common cause of mycotic infections in immunocompromised hosts. Little is known about the initial interactions between Candida and immune cell receptors, such as the C-type lectin dendritic cell-specific ... ...

Abstract	The fungus Candida albicans is the most common cause of mycotic infections in immunocompromised hosts. Little is known about the initial interactions between Candida and immune cell receptors, such as the C-type lectin dendritic cell-specific intracellular cell adhesion molecule-3 (ICAM-3)-grabbing non-integrin (DC-SIGN), because a detailed characterization at the structural level is lacking. DC-SIGN recognizes specific Candida-associated molecular patterns, that is, mannan structures present in the cell wall of Candida. The molecular recognition mechanism is however poorly understood. We postulated that small differences in mannan-branching may result in considerable differences in the binding affinity. Here, we exploit atomic force microscope-based dynamic force spectroscopy with single Candida cells to gain better insight in the carbohydrate recognition capacity of DC-SIGN. We demonstrate that slight differences in the N-mannan structure of Candida, that is, the absence or presence of a phosphomannan side chain, results in differences in the recognition by DC-SIGN as follows: (i) it contributes to the compliance of the outer cell wall of Candida, and (ii) its presence results in a higher binding energy of 1.6 kB T. The single-bond affinity of tetrameric DC-SIGN for wild-type C. albicans is ~10.7 kB T and a dissociation constant kD of 23 μM, which is relatively strong compared with other carbohydrate-protein interactions described in the literature. In conclusion, this study shows that DC-SIGN specifically recognizes mannan patterns on C. albicans with high affinity. Knowledge on the binding pocket of DC-SIGN and its pathogenic ligands will lead to a better understanding of how fungal-associated carbohydrate structures are recognized by receptors of the immune system and can ultimately contribute to the development of new anti-fungal drugs.
MeSH term(s)	Binding Sites/physiology ; Candida albicans/metabolism ; Carbohydrates ; Cell Adhesion/physiology ; Cell Adhesion Molecules/metabolism ; Cell Wall/metabolism ; Lectins, C-Type/metabolism ; Ligands ; Mannans/metabolism ; Microscopy, Atomic Force/methods ; Protein Binding/physiology ; Receptors, Cell Surface/metabolism ; Spectrum Analysis/methods
Chemical Substances	Carbohydrates ; Cell Adhesion Molecules ; DC-specific ICAM-3 grabbing nonintegrin ; Lectins, C-Type ; Ligands ; Mannans ; Receptors, Cell Surface ; phosphomannan (9044-08-0)
Language	English
Publishing date	2015-11
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1015084-5
ISSN	1099-1352 ; 0952-3499
ISSN (online)	1099-1352
ISSN	0952-3499
DOI	10.1002/jmr.2481
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