Improving image quality of sparse-view lung tumor CT images with U-Net.

BACKGROUND: We aimed to improve the image quality (IQ) of sparse-view computed tomography (CT) images using a U-Net for lung metastasis detection and determine the best tradeoff between number of views, IQ, and diagnostic confidence. METHODS: CT images from 41 subjects aged 62.8 ± 10.6 years (mean ± standard deviation, 23 men), 34 with lung metastasis, 7 healthy, were retrospectively selected (2016-2018) and forward projected onto 2,048-view sinograms. Six corresponding sparse-view CT data subsets at varying levels of undersampling were reconstructed from sinograms using filtered backprojection with 16, 32, 64, 128, 256, and 512 views. A dual-frame U-Net was trained and evaluated for each subsampling level on 8,658 images from 22 diseased subjects. A representative image per scan was selected from 19 subjects (12 diseased, 7 healthy) for a single-blinded multireader study. These slices, for all levels of subsampling, with and without U-Net postprocessing, were presented to three readers. IQ and diagnostic confidence were ranked using predefined scales. Subjective nodule segmentation was evaluated using sensitivity and Dice similarity coefficient (DSC); clustered Wilcoxon signed-rank test was used. RESULTS: The 64-projection sparse-view images resulted in 0.89 sensitivity and 0.81 DSC, while their counterparts, postprocessed with the U-Net, had improved metrics (0.94 sensitivity and 0.85 DSC) (p = 0.400). Fewer views led to insufficient IQ for diagnosis. For increased views, no substantial discrepancies were noted between sparse-view and postprocessed images. CONCLUSIONS: Projection views can be reduced from 2,048 to 64 while maintaining IQ and the confidence of the radiologists on a satisfactory level. RELEVANCE STATEMENT: Our reader study demonstrates the benefit of U-Net postprocessing for regular CT screenings of patients with lung metastasis to increase the IQ and diagnostic confidence while reducing the dose. KEY POINTS: • Sparse-projection-view streak artifacts reduce the quality and usability of sparse-view CT images. • U-Net-based postprocessing removes sparse-view artifacts while maintaining diagnostically accurate IQ. • Postprocessed sparse-view CTs drastically increase radiologists' confidence in diagnosing lung metastasis.

Differential recognition of lipid domains by two Gb3-binding lectins.

The two lectins LecA from Pseudomonas aeruginosa and the B-subunit of Shiga toxin from Shigella dysenteriae (StxB) share the glycosphingolipid globotriaosylceramide (Gb3) as receptor. Counterintuitively, we found that LecA and StxB segregated into different domains after recognizing Gb3 at the plasma membrane of cells. We hypothesized that the orientation of the carbohydrate head group of Gb3 embedded in the lipid bilayer differentially influences LecA and StxB binding. To test this hypothesis, we reconstituted lectin-Gb3 interaction using giant unilamellar vesicles and were indeed able to rebuild LecA and StxB segregation. Both, the Gb3 fatty acyl chain structure and the local membrane environment, modulated Gb3 recognition by LecA and StxB. Specifically, StxB preferred more ordered membranes compared to LecA. Based on our findings, we propose comparing staining patterns of LecA and StxB as an alternative method to assess membrane order in cells. To verify this approach, we re-established that the apical plasma membrane of epithelial cells is more ordered than the basolateral plasma membrane. Additionally, we found that StxB recognized Gb3 at the primary cilium and the periciliary membrane, whereas LecA only bound periciliary Gb3. This suggests that the ciliary membrane is of higher order than the surrounding periciliary membrane.

Shiga toxin binding alters lipid packing and the domain structure of Gb3-containing membranes: a solid-state NMR study.

We studied the influence of globotriaosylceramide (Gb3) lipid molecules on the properties of phospholipid membranes composed of a liquid ordered (lo)/liquid disordered (ld) phase separated 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)/N-palmitoyl-d-erythro-sphingosylphosphorylcholine (PSM)/cholesterol mixture (40/35/20, mol/mol/mol) supplemented with 5 mol% of either short acyl chain palmitoyl-Gb3 or long acyl chain lignoceryl-Gb3 using 2H solid-state NMR spectroscopy. To this end, both globotriaosylceramides were chemically synthesized featuring a perdeuterated lipid acyl chain. The solid-state 2H NMR spectra support the phase separation into a POPC-rich ld phase and a PSM/cholesterol-rich lo phase. The long chain lignoceryl-Gb3 showed a rather unusual order parameter profile of the acyl chain, which flattens out for the last ∼6 methylene segments. Such an odd chain conformation can be explained by partial chain interdigitation and/or a very fluid midplane region of the membrane. Possibly, the Gb3 molecules may thus preferentially be localized at the lo/ld phase boundary. In contrast, the short chain palmitoyl-Gb3 was well associated with the PSM/cholesterol-rich lo phase. Gb3 molecules act as membrane receptors for the Shiga toxin (STx) produced by Shigella dysenteriae and by enterohemorrhagic strains of Escherichia coli (EHEC). The B-subunits of STx (STxB) forming a pentameric structure were produced recombinantly and incubated with the membrane mixtures leading to alterations in the lipid packing properties and lateral organization of the membranes. Typically, STxB binding led to a decrease in lipid chain order in agreement with partial immersion of protein segments into the lipid-water interface of the membrane. In the presence of STxB, Gb3 preferentially partitioned into the lo membrane phase. In particular the short acyl chain palmitoyl-Gb3 showed very similar chain order parameters to PSM. In the presence of STxB, all lipid species showed isotropic contributions to the 2H NMR powder spectra; this was most pronounced for the Gb3 molecules. Such isotropic contributions are caused by highly curved membrane structures, which have previously been detected as membrane invaginations in fluorescence microscopy. Our analysis estimated that STxB induced highly curved membrane structures with a curvature radius of less than ∼10 nm likely related to the insertion of STxB segments into the lipid-water interface of the membrane.

A self-assembled, modular nucleic acid-based nanoscaffold for multivalent theranostic medicine.

Rationale: Within the field of personalized medicine there is an increasing focus on designing flexible, multifunctional drug delivery systems that combine high efficacy with minimal side effects, by tailoring treatment to the individual. Methods: We synthesized a chemically stabilized ~4 nm nucleic acid nanoscaffold, and characterized its assembly, stability and functional properties in vitro and in vivo. We tested its flexibility towards multifunctionalization by conjugating various biomolecules to the four modules of the system. The pharmacokinetics, targeting capability and bioimaging properties of the structure were investigated in mice. The role of avidity in targeted liver cell internalization was investigated by flow cytometry, confocal microscopy and in vivo by fluorescent scanning of the blood and organs of the animals. Results: We have developed a nanoscaffold that rapidly and with high efficiency can self-assemble four chemically conjugated functionalities into a stable, in vivo-applicable system with complete control of stoichiometry and site specificity. The circulation time of the nanoscaffold could be tuned by functionalization with various numbers of polyethylene glycol polymers or with albumin-binding fatty acids. Highly effective hepatocyte-specific internalization was achieved with increasing valencies of tri-antennary galactosamine (triGalNAc) in vitro and in vivo. Conclusion: With its facile functionalization, stoichiometric control, small size and high serum- and thermostability, the nanoscaffold presented here constitutes a novel and flexible platform technology for theranostics.

Synthesis and Excellent Duplex Stability of Oligonucleotides Containing 2'-Amino-LNA Functionalized with Galactose Units.

A convenient method for the preparation of oligonucleotides containing internally-attached galactose and triantennary galactose units has been developed based on click chemistry between 2'-N-alkyne 2'-amino-LNA nucleosides and azido-functionalized galactosyl building blocks. The synthesized oligonucleotides show excellent binding affinity and selectivity towards complementary DNA/RNA strands with an increase in the melting temperature of up to +23.5 °C for triply-modified variants.

Synthesis and Biophysical Investigations of Oligonucleotides Containing Galactose-Modified DNA, LNA, and 2'-Amino-LNA Monomers.

Galactose-modified thymidine, LNA-T, and 2'-amino-LNA-T nucleosides were synthesized, converted into the corresponding phosphoramidite derivatives and introduced into short oligonucleotides. Compared to the unmodified control strands, the galactose-modified oligonucleotides in general, and the N2'-functionalized 2'-amino-LNA derivatives in particular, showed improved duplex thermal stability against DNA and RNA complements and increased ability to discriminate mismatches. In addition, the 2'-amino-LNA-T derivatives induced remarkable 3'-exonuclease resistance. These results were further investigated using molecular modeling studies.

Impact of Structural Differences in Galactocerebrosides on the Behavior of 2D Monolayers.

The molecular interactions of three biologically important galactocerebrosides have been studied in monolayers formed at the soft air/water interface as 2D model membranes. Highly surface-sensitive techniques as GIXD (grazing incidence X-ray diffraction), IRRAS (infrared reflection-absorption spectroscopy), and BAM (Brewster angle microscopy) have been used. The study reveals that small differences in the chemical structure have a relevant impact on the physical-chemical properties and intermolecular interactions. The presence of a 2-d-hydroxyl group in the fatty acid favored for GalCer C24:0 (2-OH) monolayers a higher hydration state of the headgroup at low lateral pressures (<25 mN/m) and a higher condensation effect above 30 mN/m. An opposite behavior was recorded for GalCer C24:0 and GalCer C24:1, for which the intermolecular interactions are defined by the weakly hydrated but strong H-bonded interconnected head groups. Additionally, the 15-cis-double bond in the fatty acid chain (nervonic acid) of GalCer C24:1 stabilized the LE phase but did not disturb the packing parameters of the LC phase as compared with the saturated compound GalCer C24:0.

2-Hydroxy Fatty Acid Enantiomers of Gb3 Impact Shiga Toxin Binding and Membrane Organization.

Shiga toxin subunit B (STxB) binding to its cellular receptor Gb3 leads to the formation of protein-lipid clusters and bending of the membrane. A newly developed synthetic route allowed synthesizing the biologically most relevant Gb3-C24:1 2OH species with both, the natural (Gb3-R) as well as the unnatural (Gb3-S) configuration of the 2OH group. The derivatives bind STxB with identical nanomolar affinity, while the propensity to induce membrane tubules in giant unilamellar vesicles is more pronounced for Gb3-S. Fluorescence and atomic force microscopy images of phase-separated supported membranes revealed differences in the lateral organization of the protein on the membrane. Gb3-R favorably induces large and tightly packed protein clusters, while a lower protein density is found on Gb3-S doped membranes.

Influence of length and conformation of saccharide head groups on the mechanics of glycolipid membranes: Unraveled by off-specular neutron scattering.

The mechanical properties of multilayer stacks of Gb3 glycolipid that play key roles in metabolic disorders (Fabry disease) were determined quantitatively by using specular and off-specular neutron scattering. Because of the geometry of membrane stacks deposited on planar substrates, the scattered intensity profile was analyzed in a 2D reciprocal space map as a function of in-plane and out-of-plane scattering vector components. The two principal mechanical parameters of the membranes, namely, bending rigidity and compression modulus, can be quantified by full calculation of scattering functions with the aid of an effective cut-off radius that takes the finite sample size into consideration. The bulkier "bent" Gb3 trisaccharide group makes the membrane mechanics distinctly different from cylindrical disaccharide (lactose) head groups and shorter "bent" disaccharide (gentiobiose) head groups. The mechanical characterization of membranes enriched with complex glycolipids has high importance in understanding the mechanisms of diseases such as sphingolipidoses caused by the accumulation of non-degenerated glycosphingolipids in lysosomes or inhibition of protein synthesis triggered by the specific binding of Shiga toxin to Gb3.