A Multi-Faceted Binding Assessment of Aptamers Targeting the SARS-CoV-2 Spike Protein.

The COVID-19 pandemic has underscored the critical need for the advancement of diagnostic and therapeutic platforms. These platforms rely on the rapid development of molecular binders that should facilitate surveillance and swift intervention against viral infections. In this study, we have evaluated by three independent research groups the binding characteristics of various published RNA and DNA aptamers targeting the spike protein of the SARS-CoV-2 virus. For this comparative analysis, we have employed different techniques such as biolayer interferometry (BLI), enzyme-linked oligonucleotide assay (ELONA), and flow cytometry. Our data show discrepancies in the reported specificity and affinity among several of the published aptamers and underline the importance of standardized methods, the impact of biophysical techniques, and the controls used for aptamer characterization. We expect our results to contribute to the selection and application of suitable aptamers for the detection of SARS-CoV-2.

Correction for X-Ray Scatter and Detector Crosstalk in Dark-Field Radiography.

Dark-field radiography, a new X-ray imaging method, has recently been applied to human chest imaging for the first time. It employs conventional X-ray devices in combination with a Talbot-Lau interferometer with a large field of view, providing both attenuation and dark-field radiographs. It is well known that sample scatter creates artifacts in both modalities. Here, we demonstrate that also X-ray scatter generated by the interferometer as well as detector crosstalk create artifacts in the dark-field radiographs, in addition to the expected loss of spatial resolution. We propose deconvolution-based correction methods for the induced artifacts. The kernel for detector crosstalk is measured and fitted to a model, while the kernel for scatter from the analyzer grating is calculated by a Monte-Carlo simulation. To correct for scatter from the sample, we adapt an algorithm used for scatter correction in conventional radiography. We validate the obtained corrections with a water phantom. Finally, we show the impact of detector crosstalk, scatter from the analyzer grating and scatter from the sample and their successful correction on dark-field images of a human thorax.

Assessment of presumed small-molecule ligands of telomeric i-DNA by biolayer interferometry (BLI).

Biolayer interferometry (BLI) and circular dichroism (CD) spectroscopy were used to investigate the interaction between previously reported i-motif DNA (i-DNA) ligands and folded or unfolded i-DNA in acidic (pH 5.5) and near-neutral (pH 6.5) conditions. We observed that although several ligands, in particular macrocyclic bis-acridine (BisA) and pyridostatin (PDS), showed good affinities for the telomeric i-motif forming sequence, none of the ligands displayed selective interactions with the i-DNA structure nor was able to promote its formation.

Agreement between the Swept-Source Optical Coherence Tomography and the Image-Guided System for Biometry Assessment in Cataract Surgery.

PURPOSE: To assess the agreement on biometric data obtained using the Verion image-guided surgery system and the swept-source-OCT biometer IOL Master 700. MATERIALS AND METHODS: All patients underwent biometry using the SS-OCT and the Image-Guide System. The comparison between instruments was assessed using the Intraclass correlation coefficient (ICC). Level of Agreement (LoA) employing the Bland-Altman analysis. RESULTS: The image-based system produced significantly higher keratometry values, evidencing a low LoA between the SS-OCT and the image-based system, ranging from -1.30 D to 0.65 D (1.95 D), -1.04 D to 0.72 D (1.76 D), and -1.31 D to 0.65 D (1.96 D), respectively. The LoA for the Cylinder ranged from -0.46 D to 0.74 D (1.2 D) and from 0.82 to 0.94 mm for WTW. CONCLUSIONS: In our study, the SS-OCT biometer and the Image-based System evidenced statistically significant differences in measuring the main biometric parameters except for the WTW.

Critical assessment of relevant methods in the field of biosensors with direct optical detection based on fibers and waveguides using plasmonic, resonance, and interference effects.

Direct optical detection has proven to be a highly interesting tool in biomolecular interaction analysis to be used in drug discovery, ligand/receptor interactions, environmental analysis, clinical diagnostics, screening of large data volumes in immunology, cancer therapy, or personalized medicine. In this review, the fundamental optical principles and applications are reviewed. Devices are based on concepts such as refractometry, evanescent field, waveguides modes, reflectometry, resonance and/or interference. They are realized in ring resonators; prism couplers; surface plasmon resonance; resonant mirror; Bragg grating; grating couplers; photonic crystals, Mach-Zehnder, Young, Hartman interferometers; backscattering; ellipsometry; or reflectance interferometry. The physical theories of various optical principles have already been reviewed in detail elsewhere and are therefore only cited. This review provides an overall survey on the application of these methods in direct optical biosensing. The "historical" development of the main principles is given to understand the various, and sometimes only slightly modified variations published as "new" methods or the use of a new acronym and commercialization by different companies. Improvement of optics is only one way to increase the quality of biosensors. Additional essential aspects are the surface modification of transducers, immobilization strategies, selection of recognition elements, the influence of non-specific interaction, selectivity, and sensitivity. Furthermore, papers use for reporting minimal amounts of detectable analyte terms such as value of mass, moles, grams, or mol/L which are difficult to compare. Both these essential aspects (i.e., biochemistry and the presentation of LOD values) can be discussed only in brief (but references are provided) in order to prevent the paper from becoming too long. The review will concentrate on a comparison of the optical methods, their application, and the resulting bioanalytical quality.

Assessment of Antibody Self-Interaction by Bio-Layer-Interferometry as a Tool for Early Stage Formulation Development.

PURPOSE: To speed up the drug development process in the biopharmaceutical industry, high throughput methods are indispensable for assessing drug candidates and potential lead formulations, in particular during late stages of discovery and early phases of development. This study aimed to establish a bio-layer-interferometry based high throughput assay for assessing formulation dependent mAb self-interaction (SI-BLI) and to compare the results with kD values obtained by dynamic light scattering (DLS). METHODS: Self-interaction of proprietary and commercially available mAbs was analyzed by SI-BLI and dynamic light scattering (DLS). RESULTS: We found significant correlations of the SI-BLI results and kD-values obtained by DLS for both, different mAbs in one platform formulation and for mAbs formulated in several buffer compositions. In total, we assessed self-interaction propensity of different mAbs in 58 formulations and found significant Pearson correlation (p < 0.05) between kD and results of SI-BLI. CONCLUSIONS: The SI-BLI results correlate with kD and enable fast ranking of both different drug candidates and potential lead formulations. Thus, SI-BLI might decrease the risk to lose potent mAb candidates during transition from discovery to development, and help to accelerate the development of high concentration liquid formulations.

Time-of-flight resolved light field fluctuations reveal deep human tissue physiology.

Red blood cells (RBCs) transport oxygen to tissues and remove carbon dioxide. Diffuse optical flowmetry (DOF) assesses deep tissue RBC dynamics by measuring coherent fluctuations of multiply scattered near-infrared light intensity. While classical DOF measurements empirically correlate with blood flow, they remain far-removed from light scattering physics and difficult to interpret in layered media. To advance DOF measurements closer to the physics, here we introduce an interferometric technique, surmounting challenges of bulk motion to apply it in awake humans. We reveal two measurement dimensions: optical phase, and time-of-flight (TOF), the latter with 22 picosecond resolution. With this multidimensional data, we directly confirm the unordered, or Brownian, nature of optically probed RBC dynamics typically assumed in classical DOF. We illustrate how incorrect absorption assumptions, anisotropic RBC scattering, and layered tissues may confound classical DOF. By comparison, our direct method enables accurate and comprehensive assessment of blood flow dynamics in humans.

Quantitative analysis of a micro array anode structured target for hard x-ray grating interferometry.

Talbot-Lau interferometry (TLI) provides additional contrast modes for x-ray imaging that are complementary to conventional absorption radiography. TLI is particularly interesting because it is one of the few practical methods for realizing phase contrast with x-rays that is compatible with large-spot high power x-ray sources. A novel micro array anode structured target (MAAST) x-ray source offers several advantages for TLI over the conventional combination of an extended x-ray source coupled with an absorption grating including higher flux and larger field of view, and these advantages become more pronounced for x-ray energies in excess of 30 keV. A Monte Carlo simulation was performed to determine the optimal parameters for a MAAST source for use with TLI. It was found that the both spatial distribution of x-ray production and the number of x-ray produced in the MAAST have a strong dependence on the incidence angle of the electron beam.

Design optimization of a periodic microstructured array anode for hard x-ray grating interferometry.

Talbot-Lau grating interferometer (TLGI) has great advantages in x-ray imaging contrasts, especially for low-Z materials, over conventional absorption contrast. A microstructured array anode target (MAAT) source offers significantly higher imaging throughput than the combination of an extended x-ray source paired with an absorption grating (also known as source grating). The performance of the MAAT source can be optimized with respect to the areal density, dimensions, and choice of material for the microstructured metal inserts (MMI) and the substrate in which they are embedded. In this paper, we analyze the x-ray generation efficiency per incident electron, relative fraction of x-rays generated by MMI and substrate, x-ray spectrum, and angular distribution via Monte Carlo simulation. Based on the simulation results, the optimal parameters are obtained for a MAAT with incident electron energies from 30 keV to 120 keV. The corresponding temperature distribution within the MAAT is also simulated for the optimal set of the parameters via finite element analysis. As demonstrated by the thermal analysis data, the maximum allowable electron-beam power loading was derived that allows a stable operation of the transmission MAAT.

Photon detection efficiency of laboratory-based x-ray phase contrast imaging techniques for mammography: a Monte Carlo study.

An important challenge in real-world biomedical applications of x-ray phase contrast imaging (XPCI) techniques is the efficient use of the photon flux generated by an incoherent and polychromatic x-ray source. This efficiency can directly influence dose and exposure time and ideally should not affect the superior contrast and sensitivity of XPCI. In this paper, we present a quantitative evaluation of the photon detection efficiency of two laboratory-based XPCI methods, grating interferometry (GI) and coded-aperture (CA). We adopt a Monte Carlo approach to simulate existing prototypes of those systems, tailored for mammography applications. Our simulations were validated by means of a simple experiment performed on a CA XPCI system. Our results show that the fraction of detected photons in the standard energy range of mammography are about 1.4% and 10% for the GI and CA techniques, respectively. The simulations indicate that the design of the optical components plays an important role in the higher efficiency of CA compared to the GI method. It is shown that the use of lower absorbing materials as the substrates for GI gratings can improve its flux efficiency by up to four times. Along similar lines, we also show that an optimized and compact configuration of GI could lead to a 3.5 times higher fraction of detected counts compared to a standard and non-optimised GI implementation.

A low cost method for hard x-ray grating interferometry.

Grating interferometry is advantageous over conventional x-ray absorption imaging because it enables the detection of samples constituted by low atomic number elements (low-Z materials). Therefore, it has a potential application in biological science and medical diagnostics. The grating interferometry has some critical optics components such as absorption gratings which are conventionally manufactured by the lithography, electroplating, and molding (LIGA) technique and employing gold as the absorbent material in it. However, great challenge lies in its implementations for practical applications because of the cost and difficulty to achieve high aspect ratio absorbing grating devices. In this paper, we present a low-cost approach that involves using the micro-casting technique with bismuth (Bi) as the absorber in source grating and as well as filling cesium iodide thallium(CsI:Tl) in a periodically structured scintillator. No costly facilities as synchrotron radiation are required and cheap material is used in our approach. Our experiment using these components shows high quality complementary images can be obtained with contrast of absorption, phase and visibility. This alternative method conquers the limitation of costly grating devices for a long time and stands an important step towards the further practical application of grating interferometry.

Stability in computed optical interferometric tomography (Part II): in vivo stability assessment.

Stability is of utmost importance to a wide range of phase-sensitive processing techniques. In Doppler optical coherence tomography and optical coherence elastography, in addition to defocus and aberration correction techniques such as interferometric synthetic aperture microscopy and computational/digital adaptive optics, a precise understanding of the system and sample stability helps to guide the system design and choice of imaging parameters. This article focuses on methods to accurately and quantitatively measure the stability of an imaging configuration in vivo. These methods are capable of partially decoupling axial from transverse motion and are compared against the stability requirements for computed optical interferometric tomography laid out in the first part of this article.

Strategic approaches for assessment and minimization of matrix effect in ligand-binding assays.

BACKGROUND: Although substantial advances have been made in ligand-binding assays (LBA) for biotherapeutics in the past decade, there are still gaps that need to be addressed, especially in the context of understanding matrix effect and its root causes. Critical and in-depth characterization of matrix effect can provide valuable knowledge of the LBA limitations for proper results interpretation. RESULTS: This article illustrates several strategic approaches with regard to identifying the root cause of matrix effect and practical solutions, including recognizing the confounding factors associated with matrix effect, selection of proper reagents to avoid matrix effect, and a systematic approach in dealing with matrix effect in method development and validation. CONCLUSION: These strategic approaches have enhanced the management of matrix effect in LBA.

[Comparison of optical and ultrasound biometry and assessment of using both methods in practice]. / Srovnání optické a ultrazvukové biometrie a zhodnocení uzívání obou metod v praxi.

PURPOSE: The present study compares accuracy of optical biometry (OB) and ultrasound biometry (UB) based on postoperative best corrected visual acuity (BCVA) results, and assesses the extent of the usage of the measurement methods in current practice. METHODS: 335 eyes in total were operated for cataract at Beskydské ocní centrum (Beskydy Eye Centre; BOC), Frýdek-Místek hospital, in the period between 7 February 2007 and 7 April 2010. All patients were examined using both IOL-Master and Ocu-Scan prior to the surgery. All surgeries were performed using microcoaxial phacoemulsification, 2,2 mm incision, implanting IOL AcrySof SP, SPN or SPN IQ. BCVA was examined three months after the surgery. We first calculated medians of anterior-posterior axial length (AL) values measured using both methods; with both the whole set and individual subsets created according to the eye length. Difference between the two methods was calculated in mm. We calculated accurate dioptric power of the IOL, which should have been implanted in the lens bag to ensure postoperative emmetropia, using BCVA results. With each eye, we determined the size of diopter variation of the IOLs dioptric power value for emmetropia determined by an optical biometer from the accurate value of the IOLs dioptric power. Ultrasound biometry results were processed in the same way. The SRK-T formula was used for calculation with each biometry. We also calculated the number of variations above 1 D and 2 D with both biometric methods. RESULTS: The median of axial eye length measured using an optical biometer was 23,08 mm, and the median of axial eye length measured using ultrasound biometry was 22,93 mm. The difference between these values was 0,15 mm (150 microns), which equals the difference between average values of coincident measurement results. Average variation of dioptric power of an implanted IOL from retrospectively established optimum value of the IOLs optical power was 0,40 D lower with optical biometry and 0,16 D lower with ultrasound biometry. In the context of assessing the course of the curves of both methods created using a polynomial graph, this result confirms that the two methods correspond significantly, and therefore selecting any of the methods could not negatively impact determination of the implanted IOLs dioptric power. Comparing the frequency of variations above 1D and 2,0 D with OB and UB from the accurate value of the IOLs dioptric power, we discovered a substantially higher percentage of variations with UB - up to 25 % of the total set above 1,0 D. CONCLUSION: RESULTS of comparing accuracy and comfort of AL measurement with both methods justify unambiguous preference of optical biometry over ultrasound biometry in current practice. If measurement using ultrasound probe is done correctly, results of both methods correspond significantly, and so the methods are mutually replaceable. Using ultrasound biometry is therefore adequate in case optical biometry cannot be used.

In vivo assessment by Mach-Zehnder double-beam interferometry of the invasive force exerted by the Asian soybean rust fungus (Phakopsora pachyrhizi).

Asian soybean rust (Phakopsora pachyrhizi) causes a devastating disease in soybean (Glycine max). We tested the hypothesis that the fungus generates high turgor pressure in its hyaline appressoria to mechanically pierce epidermal cells. Turgor pressure was determined by a microscopic technique, called transmitted light double-beam interference Mach-Zehnder microscopy (MZM), which was developed in the 1960s as a forefront of live cell imaging. We revitalized some original microscopes and equipped them for modern image capturing. MZM data were corroborated by cytorrhysis experiments. Incipient cytorrhysis determined the turgor pressure in appressoria of P. pachyrhizi to be equivalent to 5.13 MPa. MZM data revealed that osmotically active sugar alcohols only accounted for 75% of this value. Despite having a lower turgor pressure, hyaline rust appressoria were able to penetrate non-biodegradable polytetrafluoroethylene (PTFE) membranes more efficiently than do melanized appressoria of the anthracnose fungus Colletotrichum graminicola or the rice blast fungus Magnaporthe oryzae. Our findings challenge the hypotheses that force-based penetration is a specific hallmark of fungi differentiating melanized appressoria and that this turgor-driven process is solely caused by metabolic degradation products. The appressorial turgor pressure may explain the capability of P. pachyrhizi to forcefully invade a wide range of different plants and may pave the way to novel plant protection approaches.

Cost-efficient speckle interferometry with plastic optical fiber for unobtrusive monitoring of human vital signs.

A cost-efficient plastic optical fiber (POF) system for unobtrusive monitoring of human vital signs is presented. The system is based on speckle interferometry. A laser diode is butt-coupled to the POF whose exit face projects speckle patterns onto a linear optical sensor array. Sequences of acquired speckle images are transformed into one-dimensional signals by using the phase-shifting method. The signals are analyzed by band-pass filtering and a Morlet-wavelet-based multiresolutional approach for the detection of cardiac and respiratory activities, respectively. The system is tested with 10 healthy nonhospitalized persons, lying supine on a mattress with the embedded POF. Experimental results are assessed statistically: precisions of 98.8% ± 1.5% and 97.9% ± 2.3%, sensitivities of 99.4% ± 0.6% and 95.3% ± 3%, and mean delays between interferometric detections and corresponding referential signals of 116.6 ± 55.5 and 1299.2 ± 437.3 ms for the heartbeat and respiration are obtained, respectively.

Objective assessment of stapedotomy surgery from round window motion measurement.

OBJECTIVES: As prostheses and techniques related to stapes surgery develop and improve, there is a need to assess the functional outcomes of the surgery objectively. This study provides a bench test method to assess the functional results of stapes surgery by measuring volume displacement at the round window (RW), which is closely related to pressure propagation of the travelling wave inside the cochlea and thus to hearing. DESIGN: Motion of the RW membrane in fresh temporal bones was measured using a scanning laser Doppler interferometry system for normal and reconstructed conditions, and the performance of the reconstruction with stapes surgery was quantitatively assessed by comparison of the volume displacements at the RW between the two conditions. To obtain optimal measurements, reflectivity of the laser beam of the scanning laser Doppler interferometry system was improved by retroreflective beads coated onto the surface of the RW, and orientation of the RW membrane relative to the laser beam was obtained using micro-computed tomography imaging. RESULTS: From measurements in 12 temporal bones, difference in the RW volume displacement between normal ears and ears reconstructed with stapes surgery was approximately 15 dB below 2 kHz and approximately 10 dB above 4 kHz, which was comparable with air-bone gaps in patients after stapes surgery. Two different sizes of the stapes prostheses were also tested (n = 3), and a tendency toward a better outcome with a larger diameter was found. CONCLUSION: The method developed in this study can be used to assess various prostheses and surgical conditions objectively in controlled laboratory environments. It may also have potential for providing ways to assess other middle- and inner-ear surgeries, and to study other aspects of hearing science.

Assessment of a chair-side argon-based non-thermal plasma treatment on the surface characteristics and integration of dental implants with textured surfaces.

The biomechanical effects of a non-thermal plasma (NTP) treatment, suitable for use in a dental office, on the surface character and integration of a textured dental implant surface in a beagle dog model were evaluated. The experiment compared a control treatment, which presented an alumina-blasted/acid-etched (AB/AE) surface, to two experimental treatments, in which the same AB/AE surface also received NTP treatment for a period of 20 or 60 s per implant quadrant (PLASMA 20' and PLASMA 60' groups, respectively). The surface of each specimen was characterized by electron microscopy and optical interferometry, and surface energy and surface chemistry were determined prior to and after plasma treatment. Two implants of each type were then placed at six bilateral locations in 6 dogs, and allowed to heal for 2 or 4 weeks. Following sacrifice, removal torque was evaluated as a function of animal, implant surface and time in vivo in a mixed model ANOVA. Compared to the CONTROL group, PLASMA 20' and 60' groups presented substantially higher surface energy levels, lower amounts of adsorbed C species and significantly higher torque levels (p=.001). Result indicated that the NTP treatment increased the surface energy and the biomechanical fixation of textured-surface dental implants at early times in vivo.

Noninvasive in vivo assessment of soft contact lens type on tear film surface quality.

PURPOSE: To evaluate the effect of soft contact lens type on the in vivo tear film surface quality (TFSQ) on daily disposable lenses and to establish whether two recently developed techniques for noninvasive measurement of TFSQ can distinguish between different contact lens types. METHODS: Thirteen subjects wearing four different types of daily soft contact lenses participated in the study. Dynamic area high-speed videokeratoscopy (HSV) and lateral shearing interferometry (LSI) were used to quantitatively assess TFSQ in natural blinking conditions in the morning soon after lens insertion and in the afternoon following 8 hours of lens wear. RESULTS: All considered contact lenses caused a significant reduction in TFSQ compared with bare eye measures. Significant differences (P < 0.05) in the average TFSQ were also observed between all contact lens materials in LSI measurements and in the majority of dynamic area HSV measurements. The potential relationship between the contact lens parameters and the observed decline in the prelens TFSQ was explored. CONCLUSIONS: Noninvasive techniques of tear film surface assessment have the potential to discriminate contact lens type/material on eye. LSI was found to more effectively perform this discrimination than the dynamic area HSV technique.

Simulation of optical coherence tomography images by Monte Carlo modeling based on polarization vector approach.

Monte Carlo method is applied for simulation of 2D optical coherence tomography (OCT) images of skin-like model. Layer boundaries in skin model feature curved shape which agrees with physiological structure of human skin. The effect of coherence properties of probing radiation on OCT image formation and speckles in the detected OCT signal is considered. The developed model is employed for image simulation both for conventional and polarization dependent time-domain OCT modalities. Simulation of polarized OCT signal is performed using vector approach developed previously for modeling of electromagnetic field transfer in turbid media.