Endoscopist biopsy rate as a quality indicator for outpatient gastroscopy: a multicenter cohort study with validation.

BACKGROUND AND AIMS: The diagnosis of gastric premalignant conditions (GPCs) relies on endoscopy with mucosal sampling. We hypothesized that the endoscopist biopsy rate (EBR) might constitute a quality indicator for EGD, and we have analyzed its association with GPC detection and the rate of missed gastric cancers (GCs). METHODS: We analyzed EGD databases from 2 high-volume outpatient units. EBR values, defined as the proportion of EGDs with ≥1 biopsy to all examinations were calculated for each endoscopist in Unit A (derivation cohort) and divided by the quartile values into 4 groups. Detection of GPC was calculated for each group and compared using multivariate clustered logistic regression models. Unit B database was used for validation. All patients were followed in the Cancer Registry for missed GCs diagnosed between 1 month and 3 years after EGDs with negative results. RESULTS: Sixteen endoscopists in Unit A performed 17,490 EGDs of which 15,340 (87.7%) were analyzed. EBR quartile values were 22.4% to 36.7% (low EBR), 36.8% to 43.7% (moderate), 43.8% to 51.6% (high), and 51.7% and 65.8% (very-high); median value 43.8%. The odds ratios for the moderate, high, and very-high EBR groups of detecting GPC were 1.6 (95% confidence interval [CI], 1.3-1.9), 2.0 (95% CI, 1.7-2.4), and 2.5 (95% CI, 2.1-2.9), respectively, compared with the low EBR group (P < .001). This association was confirmed with the same thresholds in the validation cohort. Endoscopists with higher EBR (≥43.8%) had a lower risk of missed cancer compared with those in the lower EBR group (odds ratio, 0.44; 95% CI, 0.20-1.00; P = .049). CONCLUSIONS: The EBR parameter is highly variable among endoscopists and is associated with efficacy in GPC detection and the rate of missed GCs

The polymeric glyco-linker controls the signal outputs for plasmonic gold nanorod biosensors due to biocorona formation

Gold nanorods (GNRs) are a promising platform for nanoplasmonic biosensing. The localised surface plasmon resonance (LSPR) peak of GNRs is located in the near-infrared optical window and is sensitive to local binding events, enabling label-free detection of biomarkers in complex biological fluids. A key challenge in the development of such sensors is achieving target affinity and selectivity, while both minimizing non-specific binding and maintaining colloidal stability. Herein, we reveal how GNRs decorated with galactosamine-terminated polymer ligands display significantly different binding responses in buffer compared to serum, due to biocorona formation, and how biocorona displacement due to lectin binding plays a key role in their optical responses. GNRs were coated with either poly(N-(2-hydroxypropyl)methacrylamide) (PHPMA) or poly(N-hydroxyethyl acrylamide) (PHEA) prepared via reversible addition–fragmentation chain-transfer (RAFT) polymerisation and end-functionalised with galactosamine (Gal) as the lectin-targeting unit. In buffer Gal-PHEA-coated GNRs aggregated upon soybean agglutinin (SBA) addition, whereas Gal-PHPMA-coated GNRs exhibited a red-shift of the LSPR spectrum without aggregation. In contrast, when incubated in serum Gal-PHPMA-coated nanorods showed no binding response, while Gal-PHEA GNRs exhibited a dose-dependent blue-shift of the LSPR peak, which is the opposite direction (red-shift) to what was observed in buffer. This differential behaviour was attributed to biocorona formation onto both polymer-coated GNRs, shown by differential centrifugal sedimentation and nanoparticle tracking analysis. Upon addition of SBA to the Gal-PHEA coated nanorods, signal was generated due to displacement of weakly-bound biocorona components by lectin binding. However, in the case of Gal-PHPMA which had a thicker corona, attributed to lower polymer grafting densities, addition of SBA did not lead to biocorona displacement and there was no signal output. These results show that plasmonic optical responses in complex biological media can be significantly affected by biocorona formation, and that biocorona formation itself does not prevent sensing so long as its exact nature (e.g. ‘hard versus soft’) is tuned

Tuning the translational freedom of DNA for high speed AFM

Direct observation is arguably the preferred way to investigate the interactions between two molecular complexes. With the development of high speed atomic force microscopy it is becoming possible to observe directly DNA protein interactions with relevant spatial and temporal resolutions. These interactions are of central importance to biology, bio-nanotechnology but also functional biologically inspired materials. Critically, sample preparation plays a central role in all microscopy studies and minimal perturbation of the sample is desired. Here, we demonstrate the ability to tune the interactions of DNA molecules with the surface such that an association strong enough to enable high resolution AFM imaging while providing sufficient translational freedom to allow the relevant protein DNA interactions to take place, can be maintained. Furthermore, we describe a quantitative method for measuring the DNA mobility, which also allows the dissection of the different contributions to the overall movement of the DNA molecules. We find that for weak surface association, a significant contribution to the movement arises from the interaction of the AFM tip with the DNA. In combination, these methods enable the tuning of the surface translational freedom of DNA molecules to allow the direct study of a wide range of nucleo-protein interactions by high speed atomic force microscopy

Fabrication of molecular devices based on DNA self-assembly

Advances in molecular engineering have enabled the formation of increasingly sophisticated molecular systems. Use of DNA and other biomolecules has proven a particularly powerful tool for nanotechnology, with their unique chemistry allowing the synthesis of self-assembling nanoscale devices with complex structures and functionalities. The ability to integrate such constructs with solid state electronic devices would be of great value for the development of these technologies into practical devices. In this project, a method was developed allowing the specific targeted alignment and binding of single molecules to sites on nano-patterned metal electrodes, relying on the highly specific molecular recognition capabilities of DNA. The patterning method utilised self-assembled monolayers of I-mercapto11- undecanol as a molecular resist, which could be removed via reductive electrochemical desorption of the gold-thiol bond. This allowed the patterning of thiolated DNA probes on selected electrodes in an array. A DNA strand with sticky ends complementary to the surface probes can then specifically bind to the surface, bridging between sites where this enables the simultaneous hybridisation of both its single stranded regions. The surface binding and hybridisation of thiolated DNA oligonucleotides was tested using a colorimetric surface staining technique and the quality of monolayers was investigated using several methods. These trials informed the development of DNA-coated surfaces resistant to non-specific binding. The electrochemical desorption of SAMs was then investigated as a means for the high-resolution patterning of surfaces. Employing these techniques, the specific bridging of gold electrodes separated. by 70nm with 330 basepair DNA strands was demonstrated. Additionally, the selective thermal melt ing of different DNA probes and the ligation of surface-bound DNA constructs were examined as further methods of controlling the specificity of the assembly reaction.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Enhancing the Performance of DNA Surface-Hybridization Biosensors through Target Depletion

DNA surface-hybridization biosensors utilize the selective hybridization of target sequences in solution to surface-immobilized probes. In this process, the target is usually assumed to be in excess, so that its concentration does not significantly vary while hybridizing to the surface-bound probes. If the target is initially at low concentrations and/or if the number of probes is very large, and they have high affinity for the target, the DNA in solution may become depleted. In this paper we analyze the equilibrium and kinetics of hybridization of DNA biosensors in the case of strong target depletion, by extending the Langmuir adsorption model. We focus, in particular, on the detection of a small amount of a single-nucleotide "mutant" sequence (concentration c2) in a solution, which differs by one or more nucleotides from an abundant "wild-type" sequence (concentration c1 ≫ c2). We show that depletion can give rise to a strongly enhanced sensitivity of the biosensors. Using representative values of rate constants and hybridization free energies, we find that in the depletion regime one could detect relative concentrations c2/c1 that are up to 3 orders of magnitude smaller than in the conventional approach. The kinetics is surprisingly rich and exhibits a nonmonotonic adsorption with no counterpart in the no-depletion case. Finally, we show that, alongside enhanced detection sensitivity, this approach offers the possibility of sample enrichment, by substantially increasing the relative amount of the mutant over the wild-type sequence.status: publishe