Update of the Cancer Potency Database (CPDB) to enable derivations of Thresholds of Toxicological Concern (TTC) for cancer potency.

The purpose of this study was to update the existing Cancer Potency Database (CPDB) in order to support the development of a dataset of compounds, with associated points of departure (PoDs), to enable a review and update of currently applied values for the Threshold of Toxicological Concern (TTC) for cancer endpoints. This update of the current CPDB, last reviewed in 2012, includes the addition of new data (44 compounds and 158 studies leading to additional 359 dose-response curves). Strict inclusion criteria were established and applied to select compounds and studies with relevant cancer potency data. PoDs were calculated from dose-response modeling, including the benchmark dose (BMD) and the lower 90% confidence limits (BMDL) at a specified benchmark response (BMR) of 10%. The updated full CPDB database resulted in a total of 421 chemicals which had dose-response data that could be used to calculate PoDs. This candidate dataset for cancer TTC is provided in a transparent and adaptable format for further analysis of TTC to derive cancer potency thresholds.

High Throughput Read-Across for Screening a Large Inventory of Related Structures by Balancing Artificial Intelligence/Machine Learning and Human Knowledge.

Read-across is an in silico method applied in chemical risk assessment for data-poor chemicals. The read-across outcomes for repeated-dose toxicity end points include the no-observed-adverse-effect level (NOAEL) and estimated uncertainty for a particular category of effects. We have previously developed a new paradigm for estimating NOAELs based on chemoinformatics analysis and experimental study qualities from selected analogues, not relying on quantitative structure-activity relationships (QSARs) or rule-based SAR systems, which are not well-suited to end points for which the underpinning data are weakly grounded in specific chemical-biological interactions. The central hypothesis of this approach is that similar compounds have similar toxicity profiles and, hence, similar NOAEL values. Analogue quality (AQ) quantifies the suitability of an analogue candidate for reading across to the target by considering similarity from structure, physicochemical, ADME (absorption, distribution, metabolism, excretion), and biological perspectives. Biological similarity is based on experimental data; assay vectors derived from aggregations of ToxCast/Tox21 data are used to derive machine learning (ML) hybrid rules that serve as biological fingerprints to capture target-analogue similarity relevant to specific effects of interest, for example, hormone receptors (ER/AR/THR). Once one or more analogues have been qualified for read-across, a decision theory approach is used to estimate confidence bounds for the NOAEL of the target. The confidence interval is dramatically narrowed when analogues are constrained to biologically related profiles. Although this read-across process works well for a single target with several analogues, it can become unmanageable when, for example, screening multiple targets (e.g., virtual screening library) or handling a parent compound having numerous metabolites. To this end, we have established a digitalized framework to enable the assessment of a large number of substances, while still allowing for human decisions for filtering and prioritization. This workflow was developed and validated through a use case of a large set of bisphenols and their metabolites.

Development of a New Threshold of Toxicological Concern Database of Non-cancer Toxicity Endpoints for Industrial Chemicals.

In cases where chemical-specific toxicity data are absent or limited, the threshold of toxicological concern (TTC) offers an alternative to assess human exposure below which "there would be no appreciable risk to human health." The application of TTC to non-cancer systemic endpoints has been pursued for decades using a chemical classification and Point of Departure (POD). This study presents a new POD dataset of oral subacute/subchronic toxicity studies in rats for 656 industrial chemicals retrieved from the Hazard Evaluation Support System (HESS) Integrated Platform, which contains hundreds of reliable repeated-dose toxicity test data of industrial chemicals under the Chemical Substances of Control Law in Japan. The HESS TTC dataset was found to have less duplication with substances in other reported TTC datasets. Each chemical was classified into a Cramer Class, with 68, 3, and 29% of these 656 chemicals distributed in Classes III, II, and I, respectively. For each Cramer Class, a provisional Tolerable Daily Intake (TDI) was derived from the 5th percentile of the lognormal distribution of PODs. The TDIs were 1.9 and 30 µg/kg bw/day for Classes III and I, respectively. The TDI for Cramer Class II could not be determined due to insufficient sample size. This work complements previous studies of the TTC approach and increases the confidence of the thresholds for non-cancer endpoints by including unique chemical structures. This new TTC dataset is publicly available and can be merged with existing databases to improve the TTC approach.

Threshold of Toxicological Concern-An Update for Non-Genotoxic Carcinogens.

The Threshold of Toxicological Concern (TTC) concept can be applied to organic compounds with the known chemical structure to derive a threshold for exposure, below which a toxic effect on human health by the compound is not expected. The TTC concept distinguishes between carcinogens that may act as genotoxic and non-genotoxic compounds. A positive prediction of a genotoxic mode of action, either by structural alerts or experimental data, leads to the application of the threshold value for genotoxic compounds. Non-genotoxic substances are assigned to the TTC value of their respective Cramer class, even though it is recognized that they could test positive in a rodent cancer bioassay. This study investigated the applicability of the Cramer classes specifically to provide adequate protection for non-genotoxic carcinogens. For this purpose, benchmark dose levels based on tumor incidence were compared with no observed effect levels (NOELs) derived from non-, pre- or neoplastic lesions. One key aspect was the categorization of compounds as non-genotoxic carcinogens. The recently finished CEFIC LRI project B18 classified the carcinogens of the Carcinogenicity Potency DataBase (CPDB) as either non-genotoxic or genotoxic compounds based on experimental or in silico data. A detailed consistency check resulted in a dataset of 137 non-genotoxic organic compounds. For these 137 compounds, NOEL values were derived from high quality animal studies with oral exposure and chronic duration using well-known repositories, such as RepDose, ToxRef, and COSMOS DB. Further, an effective tumor dose (ETD10) was calculated and compared with the lower confidence limit on benchmark dose levels (BMDL10) derived by model averaging. Comparative analysis of NOEL/EDT10/BMDL10 values showed that potentially bioaccumulative compounds in humans, as well as steroids, which both belong to the exclusion categories, occur predominantly in the region of the fifth percentiles of the distributions. Excluding these 25 compounds resulted in significantly higher but comparable fifth percentile chronic NOEL and BMDL10 values, while the fifth percentile EDT10 value was slightly higher but not statistically significant. The comparison of the obtained distributions of NOELs with the existing Cramer classes and their derived TTC values supports the application of Cramer class thresholds to all non-genotoxic compounds, such as non-genotoxic carcinogens.

Do Similar Structures Have Similar No Observed Adverse Effect Level (NOAEL) Values? Exploring Chemoinformatics Approaches for Estimating NOAEL Bounds and Uncertainties.

Determination of the no observed adverse effect level (NOAEL) of a substance is an important step in safety and regulatory assessments. Application of conventional in silico strategies, for example, quantitative structure-activity relationship (QSAR) models, to predict NOAEL values is inherently problematic. Whereas QSAR models for well-defined toxicity endpoints such as Ames mutagenicity or skin sensitization can be developed from mechanistic knowledge of molecular initiating events and adverse outcome pathways, QSAR is not appropriate for predicting a NOAEL value, a concentration at which "no effect" is observed. This paper presents a chemoinformatics approach and explores how it can be further refined through the incorporation of toxicity endpoint-specific information to estimate confidence bounds for the NOAEL of a target substance, given experimentally determined NOAEL values for one or more suitable analogues. With a sufficiently large NOAEL database, we analyze how a difference in NOAEL values for pairs of structures depends on their pairwise similarity, where similarity takes both structural features and physicochemical properties into account. The width of the estimate NOAEL confidence interval is proportional to the uncertainty. Using the new threshold of toxicological concern (TTC) database enriched with antimicrobials, examples are presented to illustrate how uncertainty decreases with increasing analogue quality and also how NOAEL bounds estimation can be significantly improved by filtering the full database to include only substances that are in structure categories relevant to the target and analogue.

A Robust, Mechanistically Based In Silico Structural Profiler for Hepatic Cholestasis.

Owing to the primary role which it holds within metabolism of xenobiotics, the liver stands at heightened risk of exposure to, and injury from, potentially hazardous substances. A principal manifestation of liver dysfunction is cholestasis-the impairment of physiological bile circulation from its point of origin within the organ to the site of action in the small intestine. The capacity for early identification of compounds liable to exert cholestatic effects is of particular utility within the field of pharmaceutical development, where contribution toward candidate attrition is great. Shortcomings associated with the present in vitro methodologies forecasting cholestasis render their predictivity questionable, permitting scope for the adoption of computational toxicology techniques. As such, the intention of this study has been to construct an in silico profiler, founded upon clinical data, highlighting structural motifs most reliably associated with the end point. Drawing upon a list of >1500 small molecular drugs, compiled and annotated by Kotsampasakou, E. and Ecker, G. F. (J. Chem. Inf. Model. 2017, 57, 608-615), we have formulated a series of 15 structural alerts. These describe fragments intrinsic within distinct pharmaceutical classes including psychoactive tricyclics, ß-lactam antimicrobials, and estrogenic/androgenic steroids. Description of the coverage and selectivity of each are provided, alongside consideration of the underlying reactive mechanisms and relevant structure-activity concerns. Provision of mechanistic anchoring ensures that potential exists for framing within the adverse outcome pathway paradigm-the chemistry conveyed through the alert, in particular enabling rationalization at the level of the molecular initiating event.

The Tox21 10K Compound Library: Collaborative Chemistry Advancing Toxicology.

Since 2009, the Tox21 project has screened ∼8500 chemicals in more than 70 high-throughput assays, generating upward of 100 million data points, with all data publicly available through partner websites at the United States Environmental Protection Agency (EPA), National Center for Advancing Translational Sciences (NCATS), and National Toxicology Program (NTP). Underpinning this public effort is the largest compound library ever constructed specifically for improving understanding of the chemical basis of toxicity across research and regulatory domains. Each Tox21 federal partner brought specialized resources and capabilities to the partnership, including three approximately equal-sized compound libraries. All Tox21 data generated to date have resulted from a confluence of ideas, technologies, and expertise used to design, screen, and analyze the Tox21 10K library. The different programmatic objectives of the partners led to three distinct, overlapping compound libraries that, when combined, not only covered a diversity of chemical structures, use-categories, and properties but also incorporated many types of compound replicates. The history of development of the Tox21 "10K" chemical library and data workflows implemented to ensure quality chemical annotations and allow for various reproducibility assessments are described. Cheminformatics profiling demonstrates how the three partner libraries complement one another to expand the reach of each individual library, as reflected in coverage of regulatory lists, predicted toxicity end points, and physicochemical properties. ToxPrint chemotypes (CTs) and enrichment approaches further demonstrate how the combined partner libraries amplify structure-activity patterns that would otherwise not be detected. Finally, CT enrichments are used to probe global patterns of activity in combined ToxCast and Tox21 activity data sets relative to test-set size and chemical versus biological end point diversity, illustrating the power of CT approaches to discern patterns in chemical-activity data sets. These results support a central premise of the Tox21 program: A collaborative merging of programmatically distinct compound libraries would yield greater rewards than could be achieved separately.

Novel technologies and an overall strategy to allow hazard assessment and risk prediction of chemicals, cosmetics, and drugs with animal-free methods.

Several alternative methods to replace animal experiments have been accepted by legal bodies. An even larger number of tests are under development or already in use for non-regulatory applications or for the generation of information stored in proprietary knowledge bases. The next step for the use of the different in vitro methods is their combination into integrated testing strategies (ITS) to get closer to the overall goal of predictive "in vitro-based risk evaluation processes." We introduce here a conceptual framework as the basis for future ITS and their use for risk evaluation without animal experiments. The framework allows incorporation of both individual tests and already integrated approaches. Illustrative examples for elements to be incorporated are drawn from the session "Innovative technologies" at the 8th World Congress on Alternatives and Animal Use in the Life Sciences, held in Montreal, 2011. For instance, LUHMES cells (conditionally immortalized human neurons) were presented as an example for a 2D cell system. The novel 3D platform developed by InSphero was chosen as an example for the design and use of scaffold-free, organotypic microtissues. The identification of critical pathways of toxicity (PoT) may be facilitated by approaches exemplified by the MatTek 3D model for human epithelial tissues with engineered toxicological reporter functions. The important role of in silico methods and of modeling based on various pre-existing data is demonstrated by Altamira's comprehensive approach to predicting a molecule's potential for skin irritancy. A final example demonstrates how natural variation in human genetics may be overcome using data analytic (pattern recognition) techniques borrowed from computer science and statistics. The overall hazard and risk assessment strategy integrating these different examples has been compiled in a graphical work flow.

Effect of ultrasound frequency on pulsed sonolytic degradation of octylbenzene sulfonic acid.

It has been shown that pulsed ultrasound can influence the amount of surfactant that can adsorb to and decompose at the surface of cavitation bubbles. However, the effect of ultrasound frequency on this process has not been considered. The current study investigates the effect of ultrasound frequency on the pulsed sonolytic degradation of octyl benzenesulfonate (OBS). Furthermore, the effect of pulsing and ultrasound frequency on the rate of *OH radical formation was determined. OBS degradation rates were compared to the rates of *OH radical formation. In this way, conclusions were made regarding the relative importance of accumulation of OBS at cavitation bubble surfaces versus sonochemical activity to the sonochemical decomposition of OBS under different conditions of sonolysis. Comparisons of the data in this way indicate that sonolytic degradation of OBS depends on both the sonochemical activity (i.e., *OH yield) and the accumulation of OBS on cavitation bubble surfaces. However, under a certain set of pulsing and ultrasound frequency exposure conditions, enhanced accumulation of OBS at the gas/solution interface of cavitation bubbles is the sole mechanism of enhanced degradation due to pulsing. On the basis of this finding, conclusions on how pulsing at various ultrasound frequencies affects cavitation bubbles were made.

Anomalous behavior of amine oxide surfactants at the air/water interface.

A commonly stated requirement for the preparation of stable Langmuir monolayers of amphiphilic molecules at an air/water interface is that the surfactant must be insoluble in the subphase solution; however, a few prior studies have reported that some soluble surfactants can, under certain conditions, be compressed. The anomalous compression of soluble amphiphiles is extremely interesting and important, as it presents the possibility of greatly increasing the number of candidate compounds suitable for Langmuir monolayer studies and Langmuir-Blodgett deposition. The aim of this work was to obtain a better understanding of the factors that determine whether monolayers of a given water-soluble surfactant can be compressed. A series of amine oxide surfactants, including a novel gemini surfactant, were studied to explore the relationship between molecular structure and behavior at the air/water interface. Amine oxides are an especially interesting class of surfactants because their self-assembly in solution and at interfaces is pH-sensitive. Surface pressure-area isotherms show that the solubility of a surfactant in the subphase solution is not, in and of itself, a useful parameter in predicting whether the monolayer is compressible. Molecular modeling calculations suggest that the tendency of molecules to self-assemble plays a much more important role than solubility in this regard. The effect of pH was also investigated. We present a hypothesis that formation of dimers or small clusters of molecules at the interface inhibits the dissolution of these species into the subphase, and as a consequence the monolayer can be compressed.

Effects of pulsed ultrasound on the adsorption of n-alkyl anionic surfactants at the gas/solution interface of cavitation bubbles.

Sonolysis of argon-saturated aqueous solutions of the nonvolatile surfactants sodium dodecyl sulfate (SDS) and sodium 1-pentanesulfonate (SPSo) was investigated at three ultrasonic frequencies under both continuous wave (CW) and pulsed ultrasound. Secondary carbon-centered radicals were detected by spin trapping using 3,5-dibromo-4-nitrosobenzenesulfonic acid (DBNBS) and electron paramagnetic resonance (EPR) spectroscopy. Following sonolysis, -*CH- radicals were observed for both surfactants under both sonication modes. Under CW at 354 kHz, the maximum plateau -*CH- radical yield was higher for SPSo than for SDS, indicating that SDS, which is more surface active under equilibrium conditions, accumulates at the gas/solution interface of cavitation bubbles to a lesser degree, compared with the less surface active surfactant, SPSo. However, after sonolysis (354 kHz) under pulsed ultrasound with a pulse length of 100 ms and an interval of 500 ms, the -*CH- radical yield at the plateau concentrations was higher for SDS than for SPSo due to increased amounts of SDS accumulation on the bubble surfaces. In contrast to the findings following sonolysis at 354 kHz, sonolysis of aqueous surfactant solutions at 620 kHz and 803 kHz showed a higher -*CH- radical yield for SDS compared with SPSo under CW but lower -*CH- radical yield with increasing pulsing interval, indicating a frequency dependence on accumulation. Results indicate that pulsing the ultrasonic wave has a significant effect on the relative adsorption ability of n-alkyl surfactants at the gas/solution surface of cavitation bubbles.

Sonochemical degradation of alkylbenzene sulfonate surfactants in aqueous mixtures.

The degradation of nonvolatile surfactants sodium 4-octylbenzene sulfonate (OBS) and dodecylbenzenesulfonate (DBS) and a nonvolatile nonsurfactant 4-ethylbenzene sulfonic acid (EBS), as single components and binary mixtures, were studied under 354 kHz ultrasound. In addition, the effects of pulsed ultrasound on degradation were also examined. Results show that in mixtures of the surfactant OBS and nonsurfactant EBS, the surfactant is selectively degraded. The reduced degradation of EBS was dependent on the mixed molar ratio of EBS/OBS. The degradation of OBS was unaffected by the presence of EBS at a molar ratio of OBS/EBS > or = 1. Furthermore, OBS degradation was significantly enhanced under pulsed ultrasound. In OBS and DBS surfactant mixtures sonicated under pulsed ultrasound, surfactants strongly affected each other's degradation rates due to competition for the reaction sites on the cavitation bubble surfaces. OBS exhibits a faster degradation rate than DBS at shorter pulse intervals due to its faster rate of transfer to the cavitation bubble interfaces. At longer pulse intervals, DBS, which is more surface active, degrades faster than OBS due to the increased amounts of DBS accumulation on the bubble surfaces.

Ultrasonic destruction of surfactants: application to industrial wastewaters.

This research focused on the use of sonication to destroy surfactants and surface tension properties in industrial wastewaters that affect traditional water treatment processes. We have investigated the sonochemical destruction of surfactants and a chelating agent to understand the release of metals from surfactants during sonication. In addition, the effects of physical properties of surfactants and the effect of ultrasonic frequency were investigated to gain an understanding of the factors affecting degradation. Sonochemical degradation of surfactants was observed to be more effective than nonsurfactant compounds. In addition, as the concentration is increased, the degradation rate constant does not decrease as significantly as with nonsurfactant compounds in the near-field acoustical processor reactor. The degradation of metal complexes is not as effective as in the absence of the metal. However, this is likely an artifact of the model complexing agent used. Surfactant metal complexes are expected to be faster, as they will accumulate at the hot bubble interface, significantly increasing ligand exchange kinetics and thus degradation of the complex.

A comparative Langmuir-Blodgett study on a set of covalently linked porphyrin-based amphiphiles: a detailed atomic force microscopic study.

A set of covalently linked phenyl-amidophenyl-substituted porphyrin amphiphiles with n-C15H31 tails have been synthesized and completely characterized. These amphiphiles form good Langmuir-Blodgett (LB) films at the air/water interface. Mean molecular areas for the series were measured from the isotherms and found to increase as the number of aliphatic chains increased from one to four. No influence of the subphase pH was observed on the isotherms. LB films can be transferred successfully onto different solid surfaces. The LB films were characterized using tapping mode atomic force microscopy (AFM). Bis-, tris-, and tetra-substituted porphyrins were found to be fairly good film-forming amphiphiles, whereas irregular aggregates were seen in the case of the monosubstituted porphyrin amphiphile. Multilayers were also formed with tetra-substituted amphiphiles on mica. Detailed AFM studies of tetra-substituted amphiphiles have been carried out to investigate the effect of preparation procedure and solid substrates on film formation and transfer. The absorption and fluorescence spectra for the amphiphiles in solution and LB films deposited onto mica and glass were recorded, which demonstrated the successful transfer of LB films onto the substrates and provided more information about the arrangement of porphyrin molecules within the LB films. For comparison, self-assembled monolayers (SAMs) and the cast thin films of the amphiphiles were prepared and characterized.

Biocomposite films synthesized at a fluid/fluid interface.

In the synthesis of mesostructured particles and films, the cooperative self-organization of amphiphilic molecules in the presence of reactive species is a key factor in the reaction mechanism. This paper presents a method for preparing structured collagen films synthesized at fluid/fluid interfaces. This work is an extension of previous efforts in our group to synthesize structured silica films in a reaction system confined at the interface between two immiscible fluid phases, providing an additional level of control over the structural evolution that occurs during reaction. Synthesis at a liquid/liquid interface was shown to provide excellent control over the mesostructure of the final product, avoiding a major problem encountered in many film synthesis techniques in which the reaction occurs at a liquid/solid interface: namely, the undesired effect of the solid surface on the film structure. The focus of this paper is the synthesis of structured composite films containing amphiphilic phospholipids and collagen. These films provide a way to pattern cell growth on biocompatible surfaces and a model system for studying the self-assembly mechanism of lipids and collagen. Self-assembled monolayers and bilayers composed of phosphatidylethanolamine (PE) lipids and collagen were investigated to determine how regularly patterned films can be prepared in a manner that preserves the bioactive properties of the collagen. Mixtures of PEs and acid-soluble collagen were spread on an aqueous subphase in a Langmuir trough. Surface pressure-area compression isotherms for the composite lipid/collagen monolayers provide information about interactions between these components. Langmuir-Blodgett (LB) techniques were utilized to transfer the composite films onto freshly cleaved mica. The mica-supported films were characterized by atomic force microscopy. The lipid/collagen ratio in the composite films was found to be the most important factor in determining how the collagen is assembled and distributed. The temperature and pH of the aqueous subphase, the process for spreading collagen on the subphase, the deposition speed, and the deposition pressure are factors that can be used to selectively control the film patterning. For most of these experimental factors, the range over which a highly structured uniform film can be fabricated over significant length scales is generally very narrow. Based on the experimental results and understanding of the fundamental interactions involved, a mechanism for the co-self-assembly of phospholipids and collagen is suggested. The adhesion and growth of Chinese hamster ovary (CHO) cells on the patterned film surfaces demonstrates the biocompatibility of these composite films.

Degradation of alkylbenzene sulfonate surfactants by pulsed ultrasound.

The application of pulsed ultrasound for the degradation of the nonvolatile surfactants sodium 4-octylbenzene sulfonate (OBS) and sodium dodecylbenzenesulfonate (DBS) was investigated at a frequency of 354 kHz. By comparing the degradation rate constants with those of continuous wave (CW) ultrasound, observed pulse enhancements were found to be dependent on the pulse length, pulse ratio, initial concentration, and surface activity of the surfactants. For a pulse length of 100 ms and a pulse ratio of 1:1 (equal on/off times), the degradation rate constant of 1 mM OBS was nearly twice the value for CW. Furthermore, the degradation rate constant for 1 mM DBS increased significantly when sonicated under a pulse length of 100 ms and a pulse on/off ratio of 1:50. However, the degradation rate of 0.1 mM OBS increased by only 30% with a 100 ms pulse length and pulse ratio of 1:1 as compared to CW, indicating concentration dependence. The enhanced degradation of surfactants by pulsed ultrasound was attributed to the accumulation of surfactants on cavitation bubble surfaces. In addition, as compared to shorter pulse intervals, longer pulse intervals enhanced DBS degradation, indicating that DBS, a more surface active compound, accumulated and equilibrated with the bubble interface more slowly.

Building predictive models for protein tyrosine phosphatase 1B inhibitors based on discriminating structural features by reassembling medicinal chemistry building blocks.

A new approach to predicting the biological activity of small molecule pharmaceutics is demonstrated. Structural features of medicinal chemistry building blocks are used as 2-D molecular descriptors. These descriptors include predefined structural features and macrostructures obtained from a supervised process in which features in the core library are reassembled to provide larger features that strongly differentiate the desired biological response variable. Chemical features derived in this manner can serve as predictor variables for diverse modeling algorithms, and application using partial least squares techniques is demonstrated here. Models are presented for inhibition by benzofuran and benzothiophene biphenyl analogues of protein tyrosine phosphatase 1B (PTP1B), a target for insulin-resistant disease states. Results are compared to models for PTP1B inhibitors available in the literature based on CoMFA-related techniques and 3-D molecular descriptors.

Sonochemical destruction of free and metal-binding ethylenediaminetetraacetic acid.

This study focused on the sonochemical degradation of ethylenediaminetetraacetic acid (EDTA) and chromium-EDTA complexes. Degradation of the copper(II)-EDTA complex was also investigated as a comparison metal complex. A 90% degradation of a 150-microM EDTA solution with continuous O2-bubbling was shown for the 20-kHz system in approximately 3 h (kpseudo-first order = 1.22 x 10(-2) min-1) and less than 1 h for the 354-kHz system (kpseudo-first order = 5.42 x 10(-2) min-1). These results are consistent with the higher concentrations of hydrogen peroxide found in the higher frequency system and an expected oxidation of EDTA in bulk solution. The presence of a chelated metal decreased the rate of degradation at both frequencies. Cr(III)-EDTA degraded the slowest, supporting the theory that the extremely slow ligand exchange rate of chromium is the determining factor in how fast degradation by hydroxyl radical can occur. The 354-kHz system showed a 17% decrease in the original 150-microM Cr(III)-EDTA complex after 3 h of sonication. All of the chromium from the degraded EDTA complex existed as a combination of oxidized Cr(VI) and possibly small amounts of a new Cr(III)-organic complex (Cr(III)-Y). The 20-kHz system showed a similar extent of degradation (16%) after 3 h of sonication, despite lower hydroxyl radical production. Fifty percent of the chromium from the degraded EDTA complex was found as free Cr3+ ion, with the remaining 50% existing as both Cr(III)-Y and Cr(VI). Varying degrees of bulk oxidation, near-bubble thermolysis, and perhaps different degradation pathways at the two frequencies are responsible for these differences.

Multiscale and Bayesian approaches to data analysis in genomics high-throughput screening.

Tremendous amounts of data are produced by high-throughput screening methods currently employed in drug discovery and product development. A typical cDNA microarray or oligonucleotide-based gene chip experiment easily generates over 10,000 data points for each array or chip. The challenge of inferring meaningful information is formidable given the size and number of these datasets. This paper reviews the current status of statistical tools available for gene expression analysis, with emphasis on Bayesian approaches and multiscale wavelet filtering. Fundamental concepts of Bayesian and multiscale modeling are discussed from the perspective of their potential to address important issues related to the analysis of gene expression data, such as the fact that genomic data often have non-Gaussian distributions and feature localization and multiple scales in both frequency and measurement dimension. Recent publications in these areas are reviewed. Wavelet filtering and the advantages of multiscale methods are demonstrated by application to publicly available gene expression data from the National Cancer Institute (NCI). Multiscale methods, including multiscale principal component analysis (MSPCA), are applied to extract gene subsets and to visualize data in multidimensions for comparisons. Similarity in cell lines and gene selection are effectively visualized and quantitatively compared.