Quantitative assessment of airway remodelling and response to allergen in asthma.

BACKGROUND AND OBJECTIVE: In vivo evaluation of the microstructural differences between asthmatic and non-asthmatic airways and their functional consequences is relevant to understanding and, potentially, treating asthma. In this study, we use endobronchial optical coherence tomography to investigate how allergic airways with asthma differ from allergic non-asthmatic airways in baseline microstructure and in response to allergen challenge. METHODS: A total of 45 subjects completed the study, including 20 allergic, mildly asthmatic individuals, 22 non-asthmatic allergic controls and 3 healthy controls. A 3-cm airway segment in the right middle and right upper lobe were imaged in each subject immediately before and 24 h following segmental allergen challenge to the right middle lobe. Relationships between optical airway measurements (epithelial and mucosal thicknesses, mucosal buckling and mucus) and airway obstruction (FEV1 /FVC (forced expiratory volume in 1 s/forced vital capacity) and FEV1 % (FEV1 as a percentage of predictive value)) were investigated. RESULTS: Significant increases at baseline and in response to allergen were observed for all four of our imaging metrics in the asthmatic airways compared to the non-asthmatic airways. Epithelial thickness and mucosal buckling exhibited a significant relationship to FEV1 /FVC in the asthmatic group. CONCLUSION: Simultaneous assessments of airway microstructure, buckling and mucus revealed both structural and functional differences between the mildly asthmatic and control groups, with airway buckling seeming to be the most relevant factor. The results of this study demonstrate that a comprehensive, microstructural approach to assessing the airways may be important in future asthma studies as well as in the monitoring and treatment of asthma.

Multi-distance diffuse optical spectroscopy with a single optode via hypotrochoidal scanning.

Frequency-domain diffuse optical spectroscopy (FD-DOS) is an established technique capable of determining optical properties and chromophore concentrations in biological tissue. Most FD-DOS systems use either manually positioned, handheld probes or complex arrays of source and detector fibers to acquire data from many tissue locations, allowing for the generation of 2D or 3D maps of tissue. Here, we present a new method to rapidly acquire a wide range of source-detector (SD) separations by mechanically scanning a single SD pair. The source and detector fibers are mounted on a scan head that traces a hypotrochoidal pattern over the sample that, when coupled with a high-speed FD-DOS system, enables the rapid collection of dozens of SD separations for depth-resolved imaging. We demonstrate that this system has an average error of 4±2.6% in absorption and 2±1.8% in scattering across all SD separations. Additionally, by linearly translating the device, the size and location of an absorbing inhomogeneity can be determined through the generation of B-scan images in a manner conceptually analogous to ultrasound imaging. This work demonstrates the potential of single optode diffuse optical scanning for depth resolved visualization of heterogeneous biological tissues at near real-time rates.

Laser-based three-dimensional multiscale micropatterning of biocompatible hydrogels for customized tissue engineering scaffolds.

Light-induced material phase transitions enable the formation of shapes and patterns from the nano- to the macroscale. From lithographic techniques that enable high-density silicon circuit integration, to laser cutting and welding, light-matter interactions are pervasive in everyday materials fabrication and transformation. These noncontact patterning techniques are ideally suited to reshape soft materials of biological relevance. We present here the use of relatively low-energy (< 2 nJ) ultrafast laser pulses to generate 2D and 3D multiscale patterns in soft silk protein hydrogels without exogenous or chemical cross-linkers. We find that high-resolution features can be generated within bulk hydrogels through nearly 1 cm of material, which is 1.5 orders of magnitude deeper than other biocompatible materials. Examples illustrating the materials, results, and the performance of the machined geometries in vitro and in vivo are presented to demonstrate the versatility of the approach.

Photo-induced structural modification of silk gels containing azobenzene side groups.

Azobenzene modification of Bombyx mori silkworm silk creates a photo-responsive 'azosilk' biomaterial, allowing for 3D laser patterning. Written regions fluoresce, and become fluid-filled raised 'micro-blisters' with a 10-fold photo-softening effect of the modulus. Patterning is facile and versatile, with potential applications as soft tunable materials for dynamic cell guidance and microfluidics.

Highly tunable elastomeric silk biomaterials.

Elastomeric, fully degradable and biocompatible biomaterials are rare, with current options presenting significant limitations in terms of ease of functionalization and tunable mechanical and degradation properties. We report a new method for covalently crosslinking tyrosine residues in silk proteins, via horseradish peroxidase and hydrogen peroxide, to generate highly elastic hydrogels with tunable properties. The tunable mechanical properties, gelation kinetics and swelling properties of these new protein polymers, in addition to their ability to withstand shear strains on the order of 100%, compressive strains greater than 70% and display stiffness between 200 - 10,000 Pa, covering a significant portion of the properties of native soft tissues. Molecular weight and solvent composition allowed control of material mechanical properties over several orders of magnitude while maintaining high resilience and resistance to fatigue. Encapsulation of human bone marrow derived mesenchymal stem cells (hMSC) showed long term survival and exhibited cell-matrix interactions reflective of both silk concentration and gelation conditions. Further biocompatibility of these materials were demonstrated with in vivo evaluation. These new protein-based elastomeric and degradable hydrogels represent an exciting new biomaterials option, with a unique combination of properties, for tissue engineering and regenerative medicine.

Determination of multiphoton absorption of silk fibroin using the Z-scan technique.

The multiphoton absorption of silk fibroin at 810 nm was determined by open-aperture Z-scan. Three-photon absorption was confirmed at this wavelength and the three-photon cross section of silk fibroin was measured. Silk fibroin of varying molecular weight was tested and the cross section was found to increase exponentially with increasing molecular weight. The confirmation of a relatively large three-photon absorption cross section in silk will help lay the groundwork for future investigation of direct laser writing of three-dimensional structures within a silk matrix.

Self-supervised denoising of Nyquist-sampled volumetric images via deep learning.

Purpose: Deep learning has demonstrated excellent performance enhancing noisy or degraded biomedical images. However, many of these models require access to a noise-free version of the images to provide supervision during training, which limits their utility. Here, we develop an algorithm (noise2Nyquist) that leverages the fact that Nyquist sampling provides guarantees about the maximum difference between adjacent slices in a volumetric image, which allows denoising to be performed without access to clean images. We aim to show that our method is more broadly applicable and more effective than other self-supervised denoising algorithms on real biomedical images, and provides comparable performance to algorithms that need clean images during training. Approach: We first provide a theoretical analysis of noise2Nyquist and an upper bound for denoising error based on sampling rate. We go on to demonstrate its effectiveness in denoising in a simulated example as well as real fluorescence confocal microscopy, computed tomography, and optical coherence tomography images. Results: We find that our method has better denoising performance than existing self-supervised methods and is applicable to datasets where clean versions are not available. Our method resulted in peak signal to noise ratio (PSNR) within 1 dB and structural similarity (SSIM) index within 0.02 of supervised methods. On medical images, it outperforms existing self-supervised methods by an average of 3 dB in PSNR and 0.1 in SSIM. Conclusion: noise2Nyquist can be used to denoise any volumetric dataset sampled at at least the Nyquist rate making it useful for a wide variety of existing datasets.

Dual-DMD hyperspectral spatial frequency domain imaging (SFDI) using dispersed broadband illumination with a demonstration of blood stain spectral monitoring.

Spatial frequency domain imaging (SFDI) is a widefield diffuse optical measurement technique capable of generating 2D maps of sub-surface absorption and scattering in biological tissue. We developed a new hyperspectral SFDI instrument capable of collecting images at wavelengths from the visible to the near infrared. The system utilizes a custom-built monochromator with a digital micromirror device (DMD) that can dynamically select illumination wavelength bands from a broadband quartz tungsten halogen lamp, and a second DMD to provide spatially modulated sample illumination. The system is capable of imaging 10 wavelength bands in approximately 25 seconds. The spectral resolution can be varied from 12 to 30 nm by tuning the input slit width and the output DMD column width. We compared the optical property extraction accuracy between the new device and a commercial SFDI system and found an average error of 23% in absorption and 6% in scattering. The system was highly stable, with less than 5% variation in absorption and less than 0.2% variation in scattering across all wavelengths over two hours. The system was used to monitor hyperspectral changes in the optical absorption and reduced scattering spectra of blood exposed to air over 24 hours. This served as a general demonstration of the utility of this system, and points to a potential application for blood stain age estimation. We noted significant changes in both absorption and reduced scattering spectra over multiple discrete stages of aging. To our knowledge, these are the first measurement of changes in scattering of blood stains. This hyperspectral SFDI system holds promise for a multitude of applications in quantitative tissue and diffuse sample imaging.

Real-Time Handheld Probe Tracking and Image Formation Using Digital Frequency-Domain Diffuse Optical Spectroscopy.

OBJECTIVE: Frequency-domain diffuse optical spectroscopic imaging (FD-DOS) is a non-invasive method for measuring absolute concentrations of tissue chromophores such as oxy- and deoxy-hemoglobin in vivo. The utility of FD-DOS for clinical applications such as monitoring chemotherapy response in breast cancer has previously been demonstrated, but challenges for further clinical translation, such as slow acquisition speed and lack of user feedback, remain. Here, we propose a new high speed FD-DOS instrument that allows users to freely acquire measurements over the tissue surface, and is capable of rapidly imaging large volumes of tissue. METHODS: We utilize 3D monocular probe tracking combined with custom digital FD-DOS hardware and a high-speed data processing pipeline for the instrument. Results are displayed during scanning over the surface of the sample using a probabilistic Monte Carlo light propagation model. RESULTS: We show this instrument can measure absorption and scattering coefficients with an error of 7% and 1% respectively, with 0.7 mm positional accuracy. We demonstrate the equivalence of our visualization methodology with a standard interpolation approach, and demonstrate two proof-of-concept in vivo results showing superficial vasculature in the human forearm and surface contrast in a healthy human breast. CONCLUSION: Our new FD-DOS system is able to compute chromophore concentrations in real-time (1.5 Hz) in vivo. SIGNIFICANCE: This method has the potential to improve the quality of FD-DOS image scans while reducing measurement times for a variety of clinical applications.

Distinguishing Tumor from Associated Fibrosis to Increase Diagnostic Biopsy Yield with Polarization-Sensitive Optical Coherence Tomography.

PURPOSE: With recent advancements in personalized medicine, biopsies must contain sufficient tumor for histologic diagnosis and molecular testing. However, inadvertent biopsy of tumor-associated fibrosis compromises tumor yield, resulting in delayed diagnoses and/or repeat procedures when additional tumor is needed. The ability to differentiate tumor from fibrosis intraprocedurally during biopsy could significantly increase tumor yield. Polarization-sensitive optical coherence tomography (PS-OCT) is an imaging modality that is endoscope- and/or needle-compatible, and provides large volumetric views of tissue microstructure with high resolution (∼10 µm) while simultaneously measuring birefringence of organized tissues such as collagen. We aim to determine whether PS-OCT can accurately detect and distinguish tumor-associated fibrosis from tumor. EXPERIMENTAL DESIGN: PS-OCT was obtained ex vivo in 64 lung nodule samples. PS-OCT birefringence was measured and correlated to collagen content in precisely matched histology, quantified on picrosirius red (PSR) staining. RESULTS: There was a strong positive correlation between PS-OCT measurement of birefringent fibrosis and total collagen content by PSR (r = 0.793; P < 0.001). In addition, PS-OCT was able to accurately classify tumor regions with >20% fibrosis from those with low fibrosis (≤20%) that would likely yield higher tumor content (P < 0.0001). CONCLUSIONS: PS-OCT enables accurate fibrosis detection and can distinguish tumor regions with low fibrosis. PS-OCT has significant potential for clinical impact, as the ability to differentiate tumor from fibrosis could be used to guide intraprocedural tissue sampling in vivo, or for rapid biopsy adequacy assessment ex vivo, to increase diagnostic tumor yield essential for patient care and research.

High-speed spatial frequency domain imaging with temporally modulated light.

Spatial frequency domain imaging (SFDI) is a wide-field diffuse optical technique used to obtain optical properties and chromophore concentrations in highly scattering media, such as biological tissue. Here, we present a method for rapidly acquiring multispectral SFDI data by modulating each illumination wavelength at a different temporal frequency. In the remitted signal, each wavelength is temporally demodulated and processed using conventional SFDI techniques. We demonstrate a proof-of-concept system capable of acquiring wide-field maps (2048×1536 pixels, 8.5×6.4 cm) of optical properties at three wavelengths in under 2.5 s. Data acquired by this method show a good agreement with a commercial SFDI imaging system (with an average error of 13% in absorption and 8% in scattering). Additionally, we show that this strategy is insensitive to ambient lighting conditions, making it more practical for clinical translation. In the future, this technique could be expanded to tens or hundreds of wavelengths without increasing acquisition time.

Evaluation of Silk Inverse Opals for "Smart" Tissue Culture.

Visually tracking the subtle aspects of biological systems in real time during tissue culture remains challenging. Herein, we demonstrate the use of bioactive, cytocompatible, and biodegradable inverse opals from silk as a multifunctional substrate to transduce both the optical information and cells during tissue culture. We show that these substrates can visually track substrate degradation in various proteases during tissue digestion and protein deposition during the growth of mesenchymal stem cells. Uniquely, these substrates can be integrated in multiple steps of tissue culture for simple-to-use, visual, and quantitative detectors of bioactivity. These substrates can also be doped, demonstrated here with gold nanoparticles, to allow additional control of cell functions.

Directed assembly of bio-inspired hierarchical materials with controlled nanofibrillar architectures.

In natural systems, directed self-assembly of structural proteins produces complex, hierarchical materials that exhibit a unique combination of mechanical, chemical and transport properties. This controlled process covers dimensions ranging from the nano- to the macroscale. Such materials are desirable to synthesize integrated and adaptive materials and systems. We describe a bio-inspired process to generate hierarchically defined structures with multiscale morphology by using regenerated silk fibroin. The combination of protein self-assembly and microscale mechanical constraints is used to form oriented, porous nanofibrillar networks within predesigned macroscopic structures. This approach allows us to predefine the mechanical and physical properties of these materials, achieved by the definition of gradients in nano- to macroscale order. We fabricate centimetre-scale material geometries including anchors, cables, lattices and webs, as well as functional materials with structure-dependent strength and anisotropic thermal transport. Finally, multiple three-dimensional geometries and doped nanofibrillar constructs are presented to illustrate the facile integration of synthetic and natural additives to form functional, interactive, hierarchical networks.

Dityrosine Cross-Linking in Designing Biomaterials.

The development of functional biomaterials for tissue engineering and medical applications has received increasing attention. While it has been known for decades that dityrosine bonds are a key component to many biopolymer materials in native tissues, only recently have these motifs been exploited in the development of new biomaterials. Here, we first review the importance of tyrosine-tyrosine chemical bonds in the assembly and mechanical properties of natural materials. Next, we discuss the chemistries available for cross-linking via tyrosine bonds and how these interactions have been applied to biomaterials. The goal of this Review is to highlight dityrosine bonding in biomaterial development, the reactions used to form them, and their utility in cross-linking native and chemically substituted phenolic side chains, as an underutilized tool in the de novo development of biomaterials.

Bio-functionalized silk hydrogel microfluidic systems.

Bio-functionalized microfluidic systems were developed based on a silk protein hydrogel elastomeric materials. A facile multilayer fabrication method using gelatin sacrificial molding and layer-by-layer assembly was implemented to construct interconnected, three dimensional (3D) microchannel networks in silk hydrogels at 100 µm minimum feature resolution. Mechanically activated valves were implemented to demonstrate pneumatic control of microflow. The silk hydrogel microfluidics exhibit controllable mechanical properties, long-term stability in various environmental conditions, tunable in vitro and in vivo degradability in addition to optical transparency, providing unique features for cell/tissue-related applications than conventional polydimethylsiloxane (PDMS) and existing hydrogel-based microfluidic options. As demonstrated in the work here, the all aqueous-based fabrication process at ambient conditions enabled the incorporation of active biological substances in the bulk phase of these new silk microfluidic systems during device fabrication, including enzymes and living cells, which are able to interact with the fluid flow in the microchannels. These silk hydrogel-based microfluidic systems offer new opportunities in engineering active diagnostic devices, tissues and organs that could be integrated in vivo, and for on-chip cell sensing systems.

Photocrosslinking of Silk Fibroin Using Riboflavin for Ocular Prostheses.

A novel method to photocrosslink silk fibroin protein is reported, using riboflavin (vitamin B2) as a photoinitiator and the mechanism of crosslinking is determined. Exposure of riboflavin-doped liquid silk solution to light results in the formation of a transparent, elastic hydrogel. Several applications for this new material are investigated including corneal reshaping to restore visual acuity and photolithography.

Biocompatible silk step-index optical waveguides.

Biocompatible optical waveguides were constructed entirely of silk fibroin. A silk film (n=1.54) was encapsulated within a silk hydrogel (n=1.34) to form a robust and biocompatible waveguide. Such waveguides were made using only biologically and environmentally friendly materials without the use of harsh solvents. Light was coupled into the silk waveguides by direct incorporation of a glass optical fiber. These waveguides are extremely flexible, and strong enough to survive handling and manipulation. Cutback measurements showed propagation losses of approximately 2 dB/cm. The silk waveguides were found to be capable of guiding light through biological tissue.

Transparent, Nanostructured Silk Fibroin Hydrogels with Tunable Mechanical Properties.

Silk fibroin from the Bombyx mori caterpillar has been processed into many material forms, with potential applications in areas ranging from optoelectronics to tissue engineering. As a hydrogel, silk fibroin has been engineered as a substrate for the regeneration of soft tissues where hydration and mechanical compatibility are necessary. Current fabrication of silk fibroin hydrogels produces microstructured materials that lack transparency and limits the ability to fully exploit the hydrogel form. Transparency is the main characteristic of some human tissues (e.g., cornea) where silk fibroin in the film format has shown potential as scaffolding material, however, lacking the necessary hydration and successful attachment of cells without biochemical functionalization. Additionally, detection using light is an important method to translate information for instruction, sensing, and visualization of biological entities and light sensitive molecules. Here, we introduce a method for the fabrication of transparent silk hydrogels by driving the formation of nanostructures in the silk fibroin material. These nanostructures are formed by exposing silk solution (concentration below 15 mg/mL) to organic solvents that induce the amorphous to crystalline transition of the protein and indeed the sol-gel transition of the material. We have also explored a process to modulate the mechanical properties of silk fibroin hydrogel within the physiological range by controlling the amount of metal ions present in the protein structure. Nanostructured silk fibroin hydrogels are biocompatible and allow for attachment and proliferation of human dermal fibroblasts without any biochemical functionalization. In addition, seeding of human cornea epithelial cells (HCECs) on the hydrogel surface results in the formation of an epithelium, which does not alter the gels' transparency and shows biological properties that challenge the performances of HCECs seeded in collagen hydrogels, the current standard material for the engineering of corneal tissue.

Optical frequency domain imaging of ex vivo pulmonary resection specimens: obtaining one to one image to histopathology correlation.

Lung cancer is the leading cause of cancer-related deaths. Squamous cell and small cell cancers typically arise in association with the conducting airways, whereas adenocarcinomas are typically more peripheral in location. Lung malignancy detection early in the disease process may be difficult due to several limitations: radiological resolution, bronchoscopic limitations in evaluating tissue underlying the airway mucosa and identifying early pathologic changes, and small sample size and/or incomplete sampling in histology biopsies. High resolution imaging modalities, such as optical frequency domain imaging (OFDI), provide non-destructive, large area 3-dimensional views of tissue microstructure to depths approaching 2 mm in real time (Figure 1). OFDI has been utilized in a variety of applications, including evaluation of coronary artery atherosclerosis and esophageal intestinal metaplasia and dysplasia. Bronchoscopic OCT/OFDI has been demonstrated as a safe in vivo imaging tool for evaluating the pulmonary airways (Animation). OCT has been assessed in pulmonary airways and parenchyma of animal models and in vivo human airway. OCT imaging of normal airway has demonstrated visualization of airway layering and alveolar attachments, and evaluation of dysplastic lesions has been found useful in distinguishing grades of dysplasia in the bronchial mucosa. OFDI imaging of bronchial mucosa has been demonstrated in a short bronchial segment (0.8 cm). Additionally, volumetric OFDI spanning multiple airway generations in swine and human pulmonary airways in vivo has been described. Endobronchial OCT/OFDI is typically performed using thin, flexible catheters, which are compatible with standard bronchoscopic access ports. Additionally, OCT and OFDI needle-based probes have recently been developed, which may be used to image regions of the lung beyond the airway wall or pleural surface. While OCT/OFDI has been utilized and demonstrated as feasible for in vivo pulmonary imaging, no studies with precisely matched one-to-one OFDI:histology have been performed. Therefore, specific imaging criteria for various pulmonary pathologies have yet to be developed. Histopathological counterparts obtained in vivo consist of only small biopsy fragments, which are difficult to correlate with large OFDI datasets. Additionally, they do not provide the comprehensive histology needed for registration with large volume OFDI. As a result, specific imaging features of pulmonary pathology cannot be developed in the in vivo setting. Precisely matched, one-to-one OFDI and histology correlation is vital to accurately evaluate features seen in OFDI against histology as a gold standard in order to derive specific image interpretation criteria for pulmonary neoplasms and other pulmonary pathologies. Once specific imaging criteria have been developed and validated ex vivo with matched one-to-one histology, the criteria may then be applied to in vivo imaging studies. Here, we present a method for precise, one to one correlation between high resolution optical imaging and histology in ex vivo lung resection specimens. Throughout this manuscript, we describe the techniques used to match OFDI images to histology. However, this method is not specific to OFDI and can be used to obtain histology-registered images for any optical imaging technique. We performed airway centered OFDI with a specialized custom built bronchoscopic 2.4 French (0.8 mm diameter) catheter. Tissue samples were marked with tissue dye, visible in both OFDI and histology. Careful orientation procedures were used to precisely correlate imaging and histological sampling locations. The techniques outlined in this manuscript were used to conduct the first demonstration of volumetric OFDI with precise correlation to tissue-based diagnosis for evaluating pulmonary pathology. This straightforward, effective technique may be extended to other tissue types to provide precise imaging to histology correlation needed to determine fine imaging features of both normal and diseased tissues.