Search bioRxiv⌕ Search

Biology subjects

Baran, T. M.

Publications and source records attributed to Baran, T. M..

2 recordsLinked to original sources

Application of Transfer Learning for Rapid Calibration of Spatially-resolved Diffuse Reflectance Probes for Extraction of Tissue Optical Properties

AbstractO_ST_ABSSignificanceC_ST_ABSTreatment planning for light-based therapies including photodynamic therapy requires tissue optical property knowledge. These are recoverable with spatially-resolved diffuse reflectance spectroscopy (DRS), but requires precise source-detector separation (SDS) determination and time-consuming simulations. AimAn artificial neural network (ANN) to map from DRS at short SDS to optical properties was created. This trained ANN was adapted to fiber-optic probes with varying SDS using transfer learning. ApproachAn ANN mapping from measurements to Monte Carlo simulation to optical properties was created with one fiber-optic probe. A second probe with different SDS was used for transfer learning algorithm creation. Data from a third were used to test this algorithm. ResultsThe initial ANN recovered absorber concentration with RMSE=0.29 {micro}M (7.5% mean error) and {micro}s at 665 nm ({micro}s,665) with RMSE=0.77 cm-1 (2.5% mean error). For probe-2, transfer learning significantly improved absorber concentration (0.38 vs. 1.67 {micro}M, p=0.0005) and {micro}s,665 (0.71 vs. 1.8 cm-1, p=0.0005) recovery. A third probe also showed improved absorber (0.7 vs. 4.1 {micro}M, p<0.0001) and {micro}s,665 (1.68 vs. 2.08 cm-1, p=0.2) recovery. ConclusionsA data-driven approach to optical property extraction can be used to rapidly calibrate new fiber-optic probes with varying SDS, with as few as three calibration spectra.

bioengineering↗

Quantification of reactive oxygen species production by the red fluorescent proteins KillerRed, SuperNova and mCherry.

Fluorescent proteins can generate reactive oxygen species (ROS) upon absorption of photons via type I and II photosensitization mechanisms. The red fluorescent proteins KillerRed and SuperNova are phototoxic proteins engineered to generate ROS and are used in a variety of biological applications. However, their relative quantum yields and rates of ROS production are unclear, which has limited the interpretation of their effects when used in biological systems. We cloned and purified KillerRed, SuperNova, and mCherry - a related red fluorescent protein not typically considered a photosensitizer - and measured the superoxide (O2 *-) and singlet oxygen (1O2) quantum yields with irradiation at 561 nm. The formation of the O2 *--specific product 2-hydroxyethidium (2-OHE+) was quantified via HPLC separation with fluorescence detection. Relative to a reference photosensitizer, Rose Bengal, the O2 *- quantum yield ({Phi}O2 *-) of SuperNova was determined to be 0.00150, KillerRed was 0.00097, and mCherry 0.00120. At an excitation fluence of 916.5 J/cm2 and matched absorption at 561 nm, SuperNova, KillerRed and mCherry made 3.81, 2.38 and 1.65 M O2 *-/min, respectively. Using the probe Singlet Oxygen Sensor Green (SOSG), we ascertained the 1O2 quantum yield ({Phi}1O2) for SuperNova to be 0.0220, KillerRed 0.0076, and mCherry 0.0057. These photosensitization characteristics of SuperNova, KillerRed and mCherry improve our understanding of fluorescent proteins and are pertinent for refining their use as tools to advance our knowledge of redox biology.\n\nGRAPHICAL ABSTRACT\n\nO_FIG O_LINKSMALLFIG WIDTH=183 HEIGHT=200 SRC=\"FIGDIR/small/777417v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (20K):\norg.highwire.dtl.DTLVardef@197ad04org.highwire.dtl.DTLVardef@dffa05org.highwire.dtl.DTLVardef@9765e4org.highwire.dtl.DTLVardef@1a26545_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗