Noninvasive Detection of the Skin Structure and Inversed Retrieval of Chromophore Information Based on Diffuse Reflectance Spectroscopy.

The detection of skin's structure lays the foundation for personalized laser surgery of vascular skin disease, which can be noninvasively achieved by diffuse reflectance spectroscopy (DRS). A two-step inverse Monte Carlo radiation method based on DRS under two source-detector separations was proposed to quantify the skin structure, including chromophore concentration (melanin fm and hemoglobin fb), epidermal thickness tepi, average vessel diameter Dves, depth dpws and thickness tpws of the vascular layer for diseased skin. The method fitted the simulated DRS to the measured DRS iteratively, differences between which were described by a specific objective function to amplify blood absorption at 500-600 nm, and Dves, dpws, and tpws were estimated based on fm, fb, and tpws fitted in the first step. The results showed that the two-step method dramatically improve the inversion accuracy with mean errors of fm, fb, tpws, and dpws less than 5%.

Development of a bottom-up coarse-grained model for interactions of lipids with TiO 2 nanoparticles.

Understanding interactions of inorganic nanoparticles with biomolecules is important in many biotechnology, nanomedicine, and toxicological research, however, the size of typical nanoparticles makes their direct modeling by atomistic simulations unfeasible. Here, we present a bottom-up coarse-graining approach for modeling titanium dioxide (TiO 2 ) nanomaterials in contact with phospholipids that uses the inverse Monte Carlo method to optimize the effective interactions from the structural data obtained in small-scale all-atom simulations of TiO 2 surfaces with lipids in aqueous solution. The resulting coarse-grained models are able to accurately reproduce the structural details of lipid adsorption on different titania surfaces without the use of an explicit solvent, enabling significant computational resource savings and favorable scaling. Our coarse-grained simulations show that small spherical TiO 2 nanoparticles ( r = 2 nm) can only be partially wrapped by a lipid bilayer with phosphoethanolamine headgroups, however, the lipid adsorption increases with the radius of the nanoparticle. The current approach can be used to study the effect of the size and shape of TiO 2 nanoparticles on their interactions with cell membrane lipids, which can be a determining factor in membrane wrapping as well as the recently discovered phenomenon of nanoquarantining, which involves the formation of layered nanomaterial-lipid structures.

Objective monitoring of laser tattoo removal in human volunteers using an innovative optical technique: A proof of principle.

OBJECTIVES: Assess the suitability of the technique for objective monitoring of laser tattoo removal by an extended treatment protocol. MATERIALS AND METHODS: One half of the tattoo in the first volunteer was treated with nanosecond and the other half with picosecond laser pulses at 1064 nm. In the second subject, four test areas were treated repeatedly using different radiant exposures from 1.5 to 6 J/cm2 . Measurements of diffuse reflectance spectra and photothermal radiometric transients were performed 4-20 weeks after each treatment session. Inverse Monte Carlo analysis based on a three-layer model of tattooed skin was applied to assess the tattoo characteristics and analyze their changes. RESULTS: The results clearly indicate a gradual reduction of the ink content and an increase of the subsurface depth of the tattoo layer with all treatments at a radiant exposure of 3 J/cm2 or higher. The observed dependences on laser pulse duration, radiant exposure, and a number of treatments are in excellent agreement with visual fading of the tattoo. CONCLUSIONS: The presented methodology enables noninvasive characterization of tattoos in human skin and objective monitoring of the laser removal treatment.

Bottom-Up Coarse-Grained Modeling of DNA.

Recent advances in methodology enable effective coarse-grained modeling of deoxyribonucleic acid (DNA) based on underlying atomistic force field simulations. The so-called bottom-up coarse-graining practice separates fast and slow dynamic processes in molecular systems by averaging out fast degrees of freedom represented by the underlying fine-grained model. The resulting effective potential of interaction includes the contribution from fast degrees of freedom effectively in the form of potential of mean force. The pair-wise additive potential is usually adopted to construct the coarse-grained Hamiltonian for its efficiency in a computer simulation. In this review, we present a few well-developed bottom-up coarse-graining methods, discussing their application in modeling DNA properties such as DNA flexibility (persistence length), conformation, "melting," and DNA condensation.

Noninvasive Monitoring of Dynamical Processes in Bruised Human Skin Using Diffuse Reflectance Spectroscopy and Pulsed Photothermal Radiometry.

We have augmented a recently introduced method for noninvasive analysis of skin structure and composition and applied it to monitoring of dynamical processes in traumatic bruises. The approach combines diffuse reflectance spectroscopy in visible spectral range and pulsed photothermal radiometry. Data from both techniques are analyzed simultaneously using a numerical model of light and heat transport in a four-layer model of human skin. Compared to the earlier presented approach, the newly introduced elements include two additional chromophores (ß-carotene and bilirubin), individually adjusted thickness of the papillary dermal layer, and analysis of the bruised site using baseline values assessed from intact skin in its vicinity. Analyses of traumatic bruises in three volunteers over a period of 16 days clearly indicate a gradual, yet substantial increase of the dermal blood content and reduction of its oxygenation level in the first days after injury. This is followed by the emergence of bilirubin and relaxation of all model parameters towards the values characteristic for healthy skin approximately two weeks after the injury. The assessed parameter values and time dependences are consistent with existing literature. Thus, the presented methodology offers a viable approach for objective characterization of the bruise healing process.

Three-dimensional rendering of trabecular bone microarchitecture using a probabilistic approach.

In the past, researchers have attempted to model trabecular bone using computational techniques. However, only a few of these models are visually similar, but not representative of the microstructural characteristics of real trabecular bones. In this study, we hypothesized that probabilistic modeling approaches could be used to generate representative digital models that capture the microstructural features of real trabecular bones. To test this hypothesis, we proposed a novel mathematical framework to build the digital models and compared the digital models to real bone specimens. First, an initial three-dimensional cellular structure was generated using Voronoi tessellation, with the faces and edges of the Voronoi cells considered as a pool of potential trabecular plates and rods, respectively. Then, inverse Monte Carlo simulations were performed to select, delete, or reassign plates and rods until the underlying size, orientation, and spatial distributions of the plates and rods converged to the target distributions obtained from real trabecular bone microstructures. Next, digital graphics techniques were used to define the thickness of trabecular plates and the diameter of trabecular rods, followed by writing the model into a Standard Tessellation Language file and then smoothing the model surfaces for a more natural appearance. To verify the efficacy of the digital model in capturing the microstructural features of real trabecular bones, forty-six digital models with a large variation in microstructural features were generated based on the target distributions obtained from trabecular bone specimens of twelve human cadaveric femurs. Then, the histomorphological parameters of the digital models were compared with those of the real trabecular bone specimens. The results indicate that the digital models are capable of capturing major microstructural features of the trabecular bone samples, thus proving the hypothesis that the proposed probabilistic modeling approach could render real trabecular bone microstructures.

Modified optical coefficient measurement system for bulk tissue using an optical fiber insertion with varying field of view and depth at the fiber tip.

To measure the few millimeter-scale macroscopic optical properties of biological tissue, including the scattering coefficient, while avoiding the instability that originates from sample slicing preparation processes, we performed propagated light intensity measurements through an optical fiber that punctures the bulk tissue while varying the fiber tip depth and the field of view (FOV) at the tip; the results were analyzed using the inverse Monte Carlo method. We realized FOV changes at the fiber tip in the bulk tissue using a variable aperture that was located outside the bulk tissue through a short high-numerical aperture (high-NA) multi-mode fiber with a quasi-straight shape. Using a homogeneous optical model solution, we verified the principle and operation of the constructed experimental system. A 200-µm-core-diameter silica fiber with NA of 0.5 and length of 1 m installed in a 21G needle was used. The detection fiber's shape was maintained over a radius of curvature of 30 cm. The dependences of the detected light intensity on the FOV and the depth showed better than 1.4% accuracy versus calculated dependences based on the measured optical properties of the solution. Adaptation of the method for use with complex structured biological tissue, particularly in the presence of a thick fascia, was not completely resolved. However, we believe that our specific fiber puncture-based measurement method for use in bulk tissue based on variation of the FOV with inverse Monte Carlo method-based analysis will be useful in obtaining optical coefficients while avoiding sample preparation-related instabilities.

Quantitative in vivo detection of adipose tissue browning using diffuse reflectance spectroscopy in near-infrared II window.

White adipose tissue (WAT) and brown adipose tissue (BAT) biologically function in an opposite way in energy metabolism. BAT induces energy consumption by heat production while WAT mainly stores energy in the form of triglycerides. Recent progress in the conversion of WAT cells to "beige" or "brown-like" adipocytes in animals, having functional similarity to BAT, spurred a great interest in developing the next-generation therapeutics in the field of metabolic disorders. Though magnetic resonance imaging and positron emission tomography could detect classical BAT and WAT in animals and humans, it is of a great challenge in detecting the "browning" process in vivo. Here, to the best of our knowledge, for the first time, we present a simple, cost-effective, label-free fiber optic-based diffuse reflectance spectroscopy measurement in the near infrared II window (~1050-1400 nm) for the quantitative detection of browning in a mouse model in vivo. We could successfully quantify the browning of WAT in a mouse model by estimating the lipid fraction, which serves as an endogenous marker. Lipid fraction exhibited a gradual decrease from WAT to BAT with beige exhibiting an intermediate value. in vivo browning process was also confirmed with standard molecular and biochemical assays.

Determination of optical properties of human brain tumor tissues from 350 to 1000 nm to investigate the cause of false negatives in fluorescence-guided resection with 5-aminolevulinic acid.

The optical properties of human brain tumor tissues, including glioblastoma, meningioma, oligodendroglioma, and metastasis, that were classified into "strong," "vague," and "unobservable" fluorescence by a neurosurgeon were measured and compared. The optical properties of the tissues were measured with a double integrating sphere and the inverse Monte Carlo technique from 350 to 1000 nm. Using reasons of ex-vivo measurement, the optical properties at around 420 nm were potentially affected by the hemoglobin content in tissues. Significant differences were not observed between the optical properties of the glioblastoma regions with "strong" and "unobservable" fluorescence. Sections of human brain tumor tissue with "strong" and "unobservable" fluorescence were stained with hematoxylin and eosin. The cell densities [mean ± standard deviation (S.D.)] in regions with "strong" and "unobservable" fluorescence were 31 ± 9 × 102 per mm2 and 12 ± 4 × 102 per mm2, respectively, which is a statistically significant difference. The higher fluorescence intensity is associated with higher cell density. The difference in cell density modified the scattering coefficient yet it does not lead to significant differences in the reduced scattering coefficient and thus does not affect the propagation of the diffuse fluorescent light. Hence, the false negatives, which mean a brain tumor only shows "unobservable" fluorescence and is hence classified incorrectly as nontumor, in using 5-ALA for detection of human glioblastoma do not result from the differences in optical properties of human brain glioblastoma tissues. Our results suggest that the primary cause of false negatives may be a lack of PpIX or a low accumulation of PpIX.

Evaluation of a pointwise microcirculation assessment method using liquid and multilayered tissue simulating phantoms.

A fiber-optic probe-based instrument, designed for assessment of parameters related to microcirculation, red blood cell tissue fraction (fRBC), oxygen saturation (SO2), and speed resolved perfusion, has been evaluated using state-of-the-art tissue phantoms. The probe integrates diffuse reflectance spectroscopy (DRS) at two source-detector separations and laser Doppler flowmetry, using an inverse Monte Carlo method for identifying the parameters of a multilayered tissue model. Here, we characterize the accuracy of the DRS aspect of the instrument using (1) liquid blood phantoms containing yeast and (2) epidermis-dermis mimicking solid-layered phantoms fabricated from polydimethylsiloxane, titanium oxide, hemoglobin, and coffee. The root-mean-square (RMS) deviations for fRBC for the two liquid phantoms were 11% and 5.3%, respectively, and 11% for the solid phantoms with highest hemoglobin signatures. The RMS deviation for SO2 was 5.2% and 2.9%, respectively, for the liquid phantoms, and 2.9% for the solid phantoms. RMS deviation for the reduced scattering coefficient (µs'), for the solid phantoms was 15% (475 to 850 nm). For the liquid phantoms, the RMS deviation in average vessel diameter (D) was 1 µm. In conclusion, the skin microcirculation parameters fRBC and SO2, as well as, µs' and D are estimated with reasonable accuracy.

Estimation of optical properties of neuroendocrine pancreas tumor with double-integrating-sphere system and inverse Monte Carlo model.

The investigation of laser-tissue interaction is crucial for diagnostics and therapeutics. In particular, the estimation of tissue optical properties allows developing predictive models for defining organ-specific treatment planning tool. With regard to laser ablation (LA), optical properties are among the main responsible for the therapy efficacy, as they globally affect the heating process of the tissue, due to its capability to absorb and scatter laser energy. The recent introduction of LA for pancreatic tumor treatment in clinical studies has fostered the need to assess the laser-pancreas interaction and hence to find its optical properties in the wavelength of interest. This work aims at estimating optical properties (i.e., absorption, µ a , scattering, µ s , anisotropy, g, coefficients) of neuroendocrine pancreas tumor at 1064 nm. Experiments were performed using two popular sample storage methods; the optical properties of frozen and paraffin-embedded neuroendocrine tumor of the pancreas are estimated by employing a double-integrating-sphere system and inverse Monte Carlo algorithm. Results show that paraffin-embedded tissue is characterized by absorption and scattering coefficients significantly higher than frozen samples (µ a of 56 cm(-1) vs 0.9 cm(-1), µ s of 539 cm(-1) vs 130 cm(-1), respectively). Simulations show that such different optical features strongly influence the pancreas temperature distribution during LA. This result may affect the prediction of therapeutic outcome. Therefore, the choice of the appropriate preparation technique of samples for optical property estimation is crucial for the performances of the mathematical models which predict LA thermal outcome on the tissue and lead the selection of optimal LA settings.

Robust near real-time estimation of physiological parameters from megapixel multispectral images with inverse Monte Carlo and random forest regression.

PURPOSE: Multispectral imaging can provide reflectance measurements at multiple spectral bands for each image pixel. These measurements can be used for estimation of important physiological parameters, such as oxygenation, which can provide indicators for the success of surgical treatment or the presence of abnormal tissue. The goal of this work was to develop a method to estimate physiological parameters in an accurate and rapid manner suited for modern high-resolution laparoscopic images. METHODS: While previous methods for oxygenation estimation are based on either simple linear methods or complex model-based approaches exclusively suited for off-line processing, we propose a new approach that combines the high accuracy of model-based approaches with the speed and robustness of modern machine learning methods. Our concept is based on training random forest regressors using reflectance spectra generated with Monte Carlo simulations. RESULTS: According to extensive in silico and in vivo experiments, the method features higher accuracy and robustness than state-of-the-art online methods and is orders of magnitude faster than other nonlinear regression based methods. CONCLUSION: Our current implementation allows for near real-time oxygenation estimation from megapixel multispectral images and is thus well suited for online tissue analysis.

Multiscale coarse-grained modelling of chromatin components: DNA and the nucleosome.

To model large biomolecular systems, such as cell and organelles an atomistic description is not currently achievable and is not generally practical. Therefore, simplified coarse-grained (CG) modelling becomes a necessity. One of the most important cellular components is chromatin, a large DNA-protein complex where DNA is highly compacted. Recent progress in coarse graining modelling of the major chromatin components, double helical DNA and the nucleosome core particle (NCP) is presented. First, general principles and approaches allowing rigorous bottom-to-top generation of interaction potentials in the CG models are presented. Then, recent CG models of DNA are reviewed and their adequacy is benchmarked against experimental data on the salt dependence of DNA flexibility (persistence length). Furthermore, a few recent CG models of the NCP are described and their application for studying salt-dependent NCP-NCP interaction is discussed. An example of a multiscale approach to CG modelling of chromatin is presented where interactions and self-assembly of thousands of NCPs in solution are observed.

BROMOC suite: Monte Carlo/Brownian dynamics suite for studies of ion permeation and DNA transport in biological and artificial pores with effective potentials.

The transport of ions and solutes by biological pores is central for cellular processes and has a variety of applications in modern biotechnology. The time scale involved in the polymer transport across a nanopore is beyond the accessibility of conventional MD simulations. Moreover, experimental studies lack sufficient resolution to provide details on the molecular underpinning of the transport mechanisms. BROMOC, the code presented herein, performs Brownian dynamics simulations, both serial and parallel, up to several milliseconds long. BROMOC can be used to model large biological systems. IMC-MACRO software allows for the development of effective potentials for solute-ion interactions based on radial distribution function from all-atom MD. BROMOC Suite also provides a versatile set of tools to do a wide variety of preprocessing and postsimulation analysis. We illustrate a potential application with ion and ssDNA transport in MspA nanopore.

Systematic implicit solvent coarse graining of dimyristoylphosphatidylcholine lipids.

We have used systematic structure-based coarse graining to derive effective site-site potentials for a 10-site coarse-grained dimyristoylphosphatidylcholine (DMPC) lipid model and investigated their state point dependence. The potentials provide for the coarse-grained model the same site-site radial distribution functions, bond and angle distributions as those computed in atomistic simulations carried out at four different lipid-water molar ratios. It was shown that there is a non-negligible dependence of the effective potentials on the concentration at which they were generated, which is also manifested in the properties of the lipid bilayers simulated using these potentials. Thus, effective potentials computed at low lipid concentration favor to more condensed and ordered structure of the bilayer with lower average area per lipid, while potentials obtained at higher lipid concentrations provide more fluid-like structure. The best agreement with the reference data and experiment was achieved using the set of potentials derived from atomistic simulations at 1:30 lipid:water molar ratio providing fully saturated hydration of DMPC lipids. Despite theoretical limitations of pairwise coarse-grained potentials expressed in their state point dependence, all the resulting potentials provide a stable bilayer structure with correct partitioning of different lipid groups across the bilayer as well as acceptable values of the average lipid area, compressibility and orientational ordering. In addition to bilayer simulations, the model has proven its robustness in modeling of self-aggregation of lipids from randomly dispersed solution to ordered bilayer structures, bicelles, and vesicles.