Integration of data systems and technology improves research and collaboration for a superfund research center

Large collaborative centers are a common model for accomplishing integrated environmental health research. These centers often include various types of scientific domains (e.g., chemistry, biology, bioinformatics) that are integrated to solve some of the nation's key economic or public health concerns. The Superfund Research Center (SRP) at Oregon State University (OSU) is one such center established in 2008 to study the emerging health risks of polycyclic aromatic hydrocarbons while using new technologies both in the field and laboratory. With outside collaboration at remote institutions, success for the center as a whole depends on the ability to effectively integrate data across all research projects and support cores. Therefore, the OSU SRP center developed a system that integrates environmental monitoring data with analytical chemistry data and downstream bioinformatics and statistics to enable complete "source-to-outcome" data modeling and information management. This article describes the development of this integrated information management system that includes commercial software for operational laboratory management and sample management in addition to open-source custom-built software for bioinformatics and experimental data management.     

Insecticidal Effects of Organotin(IV) Compounds on Plutella Xylostella (L.) Larvae. II. Inhibitory Potencies Against Acetylcholinesterase and Evidence for Synergism in Tests With Bacillus Thuringiensis(BER.) and Malathion

Features of pesticide synergism and acetylcholinesterase (AChE) inhibition (in vitro) were studied using a selected range of organotin compounds against the early 4th instar larvae of a highly resistant strain of the diamondback moth (DBM), Plutella xylostella, a major universal pest of cruciferous vegetables.Fourteen triorganotin compounds were evaluated for their ability to enhance the toxicity of the microbial insecticide, Bacillus thuringiensis (BT) and of the commercial insecticide, Malathion to Plutella xylostella larvae. Supplemental synergism was observed with triphenyl- and tricyclopentyltin hydroxides in combinations with Bacillus thuringiensis. Increased synergism was observed with an increase in the number of cyclopentyl groups on tin in the mixed series, Cyp(n) Ph(3-n) SnX, where X = OH, and 1-(1,2,4-triazolyl). The combination of (p-chlorophenyl)diphenyltin N,N-dimethyldithiocarbamate at LD(10) and LD(25) concentrations with sublethal concentrations of Malathion as well as of tricyclohexyltin methanesulphonate at the 0.01% (w/v) concentration with Malathion exerted strong synergistic effects (supplemental synergism) with toxicity index (T.I) values of 7.2, 19.8 and 10.1, respectively.Studies on the in vitro inhibition of acetylcholinesterase prepared from the DBM larvae showed that while most of the triorganotin Compounds tested were without effect on the enzyme, compounds containing the thiocarbamylacetate or the dithiocarbamylacetate moieties demonstrated appreciable levels of inhibition, being comparable in efficacy to commercial grades of Malathion and Methomyl.     

Classifying algorithms for SIFT-MS technology and medical diagnosis

Selected Ion Flow Tube-Mass Spectrometry (SIFT-MS) is an analytical technique for real-time quantification of trace gases in air or breath samples. SIFT-MS system thus offers unique potential for early, rapid detection of disease states. Identification of volatile organic compound (VOC) masses that contribute strongly towards a successful classification clearly highlights potential new biomarkers. A method utilising kernel density estimates is thus presented for classifying unknown samples. It is validated in a simple known case and a clinical setting before-after dialysis. The simple case with nitrogen in Tedlar bags returned a 100% success rate, as expected. The clinical proof-of-concept with seven tests on one patient had an ROC curve area of 0.89. These results validate the method presented and illustrate the emerging clinical potential of this technology.     

Pulse colliding in a self-mode-locked ring-cavity ti:sapphire laser

A new self-mode-locked ring-cavity Ti:sapphire laser is described that is self-mode locked in both unidirectional and bidirectional operations. We found that clockwise and counterclockwise pulses collide with each other at the Ti:sapphire rod when the laser is mode locked in a bidirectional operation. Spectrum narrowing and pulse broadening were found in bidirectional rather than unidirectional mode-locked operation. This is explained by the performance of a transient grating in the gain medium that restricts oscillation to a narrow spectral range.     

Postural instability induced by virtual reality exposure: development of a certification protocol

Exposure to virtual environments often causes users to experience symptoms of motion sickness. An accessory manifestation of motion sickness symptoms is postural disequilibrium. If the postural disequilibrium that occurs persists beyond the time an individual is within the confines of the laboratory or system site, user safety could be compromised and products liability issues could be forthcoming. In this study, a portable, automated postural assessment system is developed that can be employed before and after exposure to a virtual reality (VR) system in order to certify that a user's balance on exiting the system is at least demonstrably as good as it was on entering. It is argued that if the "coming out" balance performance is sufficiently poorer than the "going in" balance, then the user should be retained until the pretest balance performance is regained. The results from a set of normative and validation experiments on postural equilibrium identified several reliable measures of stance that could serve as a basis for certification. Furthermore, a new automated video-based measure using only head movement showed that performance over sessions is stable and reliable. The head movement changes that occur with stimuli, such as alcohol and simulator exposure, are well behaved, predictable, and significant even with small samples. The implication is that the proposed objective measure of postural stability, in conjunction with procedures for obtaining self-reports of symptoms, can afford some measure of certification that exposure to a given VR system is without harm.     

Self-absorption correction for solid-state photoluminescence quantum yields obtained from integrating sphere measurements

A new method is presented for analyzing the effects of self-absorption on photoluminescence integrating sphere quantum yield measurements. Both the observed quantum yield and luminescence spectrum are used to determine the self-absorption probability, taking into account both the initial emission and subsequent absorption and reemission processes. The analysis is experimentally validated using the model system of the laser dye perylene red dispersed in a polymer film. This approach represents an improvement over previous methods that tend to overestimate the true quantum yield, especially in cases with high sample absorbance or quantum yield values.     

The discovery of biomarkers for type 2 diabetic nephropathy by serum proteome analysis

Diabetic nephropathy (DN) is a serious kidney complication of diabetes, and constitutes the leading cause of end-stage renal disease. The earliest clinical evidence of DN is microalbuminuria, a term which refers to the appearance of small but abnormal amounts of albumin in the urine. However, screening methods for DN, such as biomarker assays, are yet to be developed for type 2 DN. In the present study, in an attempt to identify the biomarkers for initial diagnoses of type 2 DN, the protein profiles of human sera collected from 30 microalbuminuric type 2 diabetic patients were compared with those collected from 30 normoalbuminuric type 2 diabetic patients, via 2-DE. As a result, a total of 18 spots were determined to have different protein levels in the microalbuminuric patients. Twelve spots had lower protein levels of approximately 50%, and the other six had higher levels of approximately 100-300% as compared to the spots of normoalbuminuric patients. These spots were identified with ESI-Q-TOF (ESI-quadrupole-TOF) MS. Among the identified proteins, vitamin D-binding protein (DBP) and pigment epithelium-derived factor (PEDF) were verified by Western blotting. The results of this study indicate that the DBP may be employed as diagnostic and monitoring biomarkers of type 2 DN, contingent on further study into the matter.     

Precision of the CAESAR scan-extracted measurements

Three-dimensional (3D) body scanners are increasingly used to derive 1D body dimensions from 3D whole body scans for instance, as input for clothing grading systems to make made-to-measure clothing or for width and depth dimensions of a seated workstation. In this study, the precision of the scanner-derived 1D dimensions from the CAESAR survey, a multinational anthropometric survey, was investigated. Two combinations of scanning teams with 3D whole body scanners were compared, one called the US Team and the other the Dutch Team. Twenty subjects were measured three times by one scanner and one team, and three times by the other combination. The subjects were marked prior to scanning using small dots, and the linear distances between the dots were calculated after processing the scans. The mean absolute difference (MAD) of the repetitions was calculated and this was compared to reported acceptable errors in manual measurements from the US Army's ANSUR survey when similar measurements were available. In addition, the coefficient of variation (CV) was calculated for all measurements. The results indicate that the CAESAR scan-extracted measurements are highly reproducible; for most measures the MAD is less than 5mm. In addition, more than 93% of the MAD values for CAESAR are significantly smaller than the ANSUR survey acceptable errors. Therefore, it is concluded that the type of scan-extracted measures used in CAESAR are as good as or better than comparable manual measurements. Scan-extracted measurements that do not use markers or are not straight-line distances are not represented here and additional studies would be needed to verify their precision.