Patricia Relue

Classification of melanoma using tree structured wavelet transforms.

This paper presents a wavelet transform based tree structure model developed and evaluated for the classification of skin lesion images into melanoma and dysplastic nevus. The tree structure model utilizes a semantic representation of the spatial-frequency information contained in the skin lesion images including textural information. Results show that the presented method is effective in discriminating melanoma from dysplastic nevus. The results are also compared with those obtained using another method of developing tree structures utilizing the maximum channel energy criteria with a fixed energy ratio threshold.

Monte Carlo simulation of light-tissue interaction: three-dimensional simulation for trans-illumination-based imaging of skin lesions

Three-dimensional, voxel-based, and wavelength-dependent skin lesion models are developed and simulated using Monte Carlo techniques. The optical geometry of the Nevoscope with trans-illumination is used in the simulations for characterizing the lesion thickness. Based on the correlation analysis between the lesion thickness and the diffuse reflectance, optical wavelengths are selected for multispectral imaging of skin lesions using the Nevoscope. Tissue optical properties reported by various researchers are compiled together to form a voxel library. Tissue models used in the simulations are developed using the voxel library which offers flexibility in updating the optical properties and adding new media types into the models independent of the Monte Carlo simulation code.

Fermentation of biomass sugars to ethanol using native industrial yeast strains

In this paper, the feasibility of a technology for fermenting sugar mixtures representative of cellulosic biomass hydrolyzates with native industrial yeast strains is demonstrated. This paper explores the isomerization of xylose to xylulose using a bi-layered enzyme pellet system capable of sustaining a micro-environmental pH gradient. This ability allows for considerable flexibility in conducting the isomerization and fermentation steps. With this method, the isomerization and fermentation could be conducted sequentially, in fed-batch, or simultaneously to maximize utilization of both C5 and C6 sugars and ethanol yield. This system takes advantage of a pH-dependent complexation of xylulose with a supplemented additive to achieve up to 86% isomerization of xylose at fermentation conditions. Commercially-proven Saccharomyces cerevisiae strains from the corn-ethanol industry were used and shown to be very effective in implementation of the technology for ethanol production.

High yield aldose–ketose transformation for isolation and facile conversion of biomass sugar to furan

Traditional approaches to producing furfural from C5 biomass sugars have several limitations which include high reaction temperatures/pressures, significant sugar loss to side-reactions, modest furfural yields, and high purification costs. We present a novel method for converting the C5 sugar xylose to furfural at facile conditions in very high yield. In this approach, we isomerize xylose to its ketose isomer in high yield via a simultaneous-isomerization-and-reactive-extraction (SIRE) scheme, concentrate and purify xylulose by back-extraction (BE) into an acid medium, and then rapidly dehydrate the xylulose sugar to furfural at relatively low temperature (∼110 °C) with no additional catalyst. To our knowledge, production of furfural from concentrated xylulose (30 g l−1) has not been reported previously; this is likely due to the difficulty of producing relatively large quantities of high-purity xylulose in a cost-effective manner. Through simple strategies, such as addition of an aprotic solvent to the aqueous medium or in situ extraction of furfural during the dehydration, furfural yields of up to 90% were achieved. The mild process conditions associated with each of the steps in the process (SIRE, BE and dehydration), along with the ability to concentrate the incoming sugar stream and recycle process streams and catalysts, results in minimal chemical and energy inputs and have a significant favorable impact on the overall process economics.

The inhibition of Escherichia coli lac operon Gene expression by antigene oligonucleotides-mathematical modeling

Gene transcription is regulated by transcription factors that can bind to specific regions on DNA. Antigene oligonucleotides (oligos) can bind to specific regions on DNA and form a triplex with the double-stranded DNA. The triplex can competitively inhibit the binding of transcription factors and, as a result, transcription can be inhibited. A genetically structured model has been developed to quantitatively describe the inhibition of the Escherichia coli lac operon gene expression by triplex-forming oligos. The model predicts that the effect of triplex-forming oligos on the lac operon gene expression depends on their target sites. Oligonucleotides targeted to the operator are much more effective than those targeted to other regulatory sites on the lac operon. In some cases, the effect of oligo binding is similar to that of a mutation in the lac operon. The model provides insight as to the specific binding site to be targeted to achieve the most effective inhibition of gene expression. The model is also capable of predicting the oligo concentration needed to inhibit gene expression, which is in general agreement with results reported by other investigators.

Simultaneous isomerization and reactive extraction of biomass sugars for high yield production of ketose sugars

A desire to achieve one-pot syntheses of value-added products from biomass sugars has led to intense research efforts to convert these sugars with high yields into their ketose forms. Aldose-to-ketose isomerization has an unfavorable equilibrium, and to date, high yield conversion to ketoses in a manner that allows for further conversion economically has yet to be demonstrated. Here, a novel strategy for simultaneous-isomerization and reactive-extraction (SIRE), where the isomerization of aldose sugars and the reactive-extraction of ketoses occur concurrently in the same vessel, is presented. In SIRE, the unfavorable aldose–ketose equilibrium is overcome by selective extraction of ketose from the reaction medium maintained at the optimal pH of the xylose–glucose isomerase (XI) enzyme; the ketose sugar is back-extracted into a low pH strip solution as a pure, concentrated sugar stream. Starting with pure xylose and using Gensweet® for isomerization, best results for xylulose concentration and purification were achieved with an extraction phase of 1-octanol containing naphthalene-2-boronic acid (N2B) and Aliquat® 336. SIRE, followed by a two-stage strip, resulted in a nearly pure xylulose stream at high concentration and yield. Sugar can be concentrated in both the extraction and stripping steps by reducing the volume ratio of the sugar-receiving phase relative to the sugar-donating phase for each step. This result is significant as the separation of isomers is regarded as one of the most challenging and high cost purification processes. When implemented with biomass hydrolyzates, this technology has the potential to provide contaminant-free, concentrated ketose sugar streams without the need for energy-intensive separation and concentration schemes.

A viable method and configuration for fermenting biomass sugars to ethanol using native Saccharomyces cerevisiae

A system that incorporates a packed bed reactor for isomerization of xylose and a hollow fiber membrane fermentor (HFMF) for sugar fermentation by yeast was developed for facile recovery of the xylose isomerase enzyme pellets and reuse of the cartridge loaded with yeast. Fermentation of pre-isomerized poplar hydrolysate produced using ionic liquid pretreatment in HFMF resulted in ethanol yields equivalent to that of model sugar mixtures of xylose and glucose. By recirculating model sugar mixtures containing partially isomerized xylose through the packed bed and the HFMF connected in series, 39 g/l ethanol was produced within 10h with 86.4% xylose utilization. The modular nature of this configuration has the potential for easy scale-up of the simultaneous isomerization and fermentation process without significant capital costs.

Fluorescence Anisotropy of Cellular NADH as a Tool to Study Different Metabolic Properties of Human Melanocytes and Melanoma Cells

In this study, we wanted to see if fluorescence anisotropy could be used to detect changes in metabolism in cells with significant light scattering and absorption properties. Fluorescence anisotropy measurements of nicotinamide adenine dinucleotide (NADH) were performed with human melanocytes and melanoma cell lines. To demonstrate the feasibility of using fluorescence anisotropy for detecting metabolic changes, the electron transport chain was blocked using rotenone, inducing an accumulation of intracellular NADH. Total fluorescence increased in all cells as a result of rotenone treatment. Fluorescence anisotropy decreased in the rotenone-treated cells relative to the controls, suggesting an increased ratio of free to protein-bound NADH in the treated cells. In general, the fluorescence anisotropy of the melanocytes was significantly higher than that of the melanoma cell lines. Reflectance spectroscopy showed that the differences in fluorescence anisotropy between the cell types were not due to differences in scattering and absorption properties. Intrinsic cellular NADH fluorescence was experimentally extracted by ratioing polarized fluorescence to polarized reflectance. NADH binding, measured as the ratio of fluorescence intensity at 430 and 465 nm, showed more protein-bound NADH in the melanocytes than in the melanoma cells, consistent with the fluorescence anisotropy measurements.

Enzymatic degradation of human skin dermis revealed by fluorescence and reflectance spectroscopy

Dermis is the major source of the fluorescence and light scattering of skin. Tumor-induced degradation of the dermis is expected to change the fluorescence and light scattering properties of skin. To investigate how these fluorescence and light scattering properties are changed, human skin dermis was degraded with enzymes to mimic tumor invasion. The enzymatic erosion process was investigated with fluorescence and reflectance spectroscopy. Dermis degradation by the enzymes resulted in a decrease in fluorescence emission and light scattering in the dermis. Fluorescence anisotropy, however, could not detect the change in the dermis induced by the enzyme treatments.

Correction: High concentration levulinic acid production from corn stover

Correction for ‘High concentration levulinic acid production from corn stover’ by Siamak Alipour et al., RSC Adv., 2016, 6, 111616–111621.