LATENT RANK CHANGE DETECTION FOR ANALYSIS OF SPLICE-JUNCTION MICROARRAYS WITH NONLINEAR EFFECTS

Alternative splicing of gene transcripts greatly expands the functional capacity of the genome, and certain splice isoforms may indicate specific disease states such as cancer. Splice junction microarrays interrogate thousands of splice junctions, but data analysis is difficult and error prone because of the increased complexity compared to differential gene expression analysis. We present Rank Change Detection (RCD) as a method to identify differential splicing events based upon a straightforward probabilistic model comparing the over-or underrepresentation of two or more competing isoforms. RCD has advantages over commonly used methods because it is robust to false positive errors due to nonlinear trends in microarray measurements. Further, RCD does not depend on prior knowledge of splice isoforms, yet it takes advantage of the inherent structure of mutually exclusive junctions, and it is conceptually generalizable to other types of splicing arrays or RNA-Seq. RCD specifically identifies the biologically important cases when a splice junction becomes more or less prevalent compared to other mutually exclusive junctions. The example data is from different cell lines of glioblastoma tumors assayed with Agilent microarrays.

Advanced functionality for radio analysis in the Offline software framework of the Pierre Auger Observatory

The advent of the Auger Engineering Radio Array (AERA) necessitates the development of a powerful framework for the analysis of radio measurements of cosmic ray air showers. As AERA performs ""radio-hybrid"" measurements of air shower radio emission in coincidence with the surface particle detectors and fluorescence telescopes of the Pierre Auger Observatory, the radio analysis functionality had to be incorporated in the existing hybrid analysis solutions for fluorescence and surface detector data. This goal has been achieved in a natural way by extending the existing Auger Offline software framework with radio functionality. In this article, we lay out the design, highlights and features of the radio extension implemented in the Auger Offline framework. Its functionality has achieved a high degree of sophistication and offers advanced features such as vectorial reconstruction of the electric field, advanced signal processing algorithms, a transparent and efficient handling of FFTs, a very detailed simulation of detector effects, and the read-in of multiple data formats including data from various radio simulation codes. The source code of this radio functionality can be made available to interested parties on request. (C) 2011 Elsevier B.V. All rights reserved.

Matrix effects observed during pesticides residue analysis in fruits by GC

The influence of the sample matrix in the CC-electron-capture detection analysis of the pesticides dimethoate, diazinon, chlorothalonil.. parathion methyl and fenitrothion in fruits samples has been studied. Experiments have been carried out where the pesticide responses in standard solutions prepared in selected solvent were compared with their response when present in apple, mango, papaya, banana, pineapple and melon extracts. The presence of matrix effects (MEs) and their extent were shown to be simultaneously influenced by several factors (matrix concentration, matrix type, pesticide concentration, analytical range). Pronounced MEs were observed particularly for dimethoate and diazinon in all matrices tested; in lower concentrations, all pesticides presented significant ME. The other pesticides presented variable ME. Higher ME enhancement was detected at lower pesticide concentration levels of and/or at higher matrix concentration solutions. The ME detected for fenitrothion, in the analytical range evaluated, were dependent on matrix type. For each pesticide, solvent and matrix-matched calibrations were compared for all fruit samples, and it could be concluded that quantitation based on standard solutions prepared in blank matrix extract (matrix-matched calibration) should be used to compensate the MEs and to obtain more accurate results for the pesticides studied.

Depression: a predictor of smoking relapse in a 6-month follow-up after hospitalization for acute coronary syndrome

Objective The objective of the study was to investigate whether depression is a predictor of postdischarge smoking relapse among patients hospitalized for myocardial infarction (MI) or unstable angina (ILIA), in a smoke-free hospital. Methods Current smokers with MI or UA were interviewed while hospitalized; patients classified with major depression (MD) or no humor disorder were reinterviewed 6 months post discharge to ascertain smoking status. Potential predictors of relapse (depression; stress; anxiety; heart disease risk perception; coffee and alcohol consumption; sociodemographic, clinical, and smoking habit characteristics) were compared between those with MD (n = 268) and no humor disorder (n = 135). Results Relapsers (40.4%) were more frequently and more severely depressed, had higher anxiety and lower self-efficacy scale scores, diagnosis of UA, shorter hospitalizations, started smoking younger, made fewer attempts to quit, had a consort less often, and were more frequently at the `precontemplation` stage of change. Multivariate analysis showed relapse-positive predictors to be MD [odds ratio (OR): 2.549; 95% confidence interval (CI): 1.519-4.275] (P<0.001); `precontemplation` stage of change (OR: 7.798; 95% CI: 2.442-24.898) (P<0.001); previous coronary bypass graft surgery (OR: 4.062; 95% CI: 1.356-12.169) (P=0.012); and previous anxiolytic use (OR: 2.365; 95% CI: 1.095-5.107) (P=0.028). Negative predictors were diagnosis of MI (OR: 0.575; 95% CI: 0.361-0.916) (P=0.019); duration of hospitalization (OR: 0.935; 95% CI: 0.898-0.973) (P=0.001); smoking onset age (OR: 0.952; 95% CI: 0.910-0.994) (P=0.028); number of attempts to quit smoking (OR: 0.808; 95% CI: 0.678-0.964) (P=0.018); and `action` stage of change (OR: 0.065; 95% CI: 0.008-0.532) (P= 0.010). Conclusion Depression, no motivation, shorter hospitalization, and severity of illness contributed to postdischarge resumption of smoking by patients with acute coronary syndrome, who underwent hospital-initiated smoking cessation.

Dynamic Solid Phase DNA Extraction and PCR Amplification in Polyester-Toner Based Microchip

A variety of substrates have been used for fabrication of microchips for DNA extraction, PCR amplification, and DNA fragment separation, including the more conventional glass and silicon as well as alternative polymer-based materials. Polyester represents one such polymer, and the laser-printing of toner onto polyester films has been shown to be effective for generating polyester-toner (PeT) microfluidic devices with channel depths on the order of tens of micrometers. Here, we describe a novel and simple process that allows for the production of multilayer, high aspect-ratio PeT microdevices with substantially larger channel depths. This innovative process utilizes a CO(2) laser to create the microchannel in polyester sheets containing a uniform layer of printed toner, and multilayer devices can easily be constructed by sandwiching the channel layer between uncoated cover sheets of polyester containing precut access holes. The process allows the fabrication of deep channels, with similar to 270 mu m, and we demonstrate the effectiveness of multilayer PeT microchips for dynamic solid phase extraction (dSPE) and PCR amplification. With the former, we found that (i) more than 65% of DNA from 0.6 mu L of blood was recovered, (ii) the resultant DNA was concentrated to greater than 3 ng/mu L., (which was better than other chip-based extraction methods), and (iii) the DNA recovered was compatible with downstream microchip-based PCR amplification. Illustrative of the compatibility of PeT microchips with the PCR process, the successful amplification of a 520 bp fragment of lambda-phage DNA in a conventional thermocycler is shown. The ability to handle the diverse chemistries associated with DNA purification and extraction is a testimony to the potential utility of PeT microchips beyond separations and presents a promising new disposable platform for genetic analysis that is low cost and easy to fabricate.

Wavelet analysis of MODIS time series to detect expansion and intensification of row-crop agriculture in Brazil

Since 2000, the southwestern Brazilian Amazon has undergone a rapid transformation from natural vegetation and pastures to row-crop agricultural with the potential to affect regional biogeochemistry. The goals of this research are to assess wavelet algorithms applied to MODIS time series to determine expansion of row-crops and intensification of the number of crops grown. MODIS provides data from February 2000 to present, a period of agricultural expansion and intensification in the southwestern Brazilian Amazon. We have selected a study area near Comodoro, Mato Grosso because of the rapid growth of row-crop agriculture and availability of ground truth data of agricultural land-use history. We used a 90% power wavelet transform to create a wavelet-smoothed time series for five years of MODIS EVI data. From this wavelet-smoothed time series we determine characteristic phenology of single and double crops. We estimate that over 3200 km(2) were converted from native vegetation and pasture to row-crop agriculture from 2000 to 2005 in our study area encompassing 40,000 km(2). We observe an increase of 2000 km(2) of agricultural intensification, where areas of single crops were converted to double crops during the study period. (C) 2007 Elsevier Inc. All rights reserved.

Runoff sources and land cover change in the Amazon: an end-member mixing analysis from small watersheds

The flowpaths by which water moves from watersheds to streams has important consequences for the runoff dynamics and biogeochemistry of surface waters in the Amazon Basin. The clearing of Amazon forest to cattle pasture has the potential to change runoff sources to streams by shifting runoff to more surficial flow pathways. We applied end-member mixing analysis (EMMA) to 10 small watersheds throughout the Amazon in which solute composition of streamwater and groundwater, overland flow, soil solution, throughfall and rainwater were measured, largely as part of the Large-Scale Biosphere-Atmosphere Experiment in Amazonia. We found a range in the extent to which streamwater samples fell within the mixing space determined by potential flowpath end-members, suggesting that some water sources to streams were not sampled. The contribution of overland flow as a source of stream flow was greater in pasture watersheds than in forest watersheds of comparable size. Increases in overland flow contribution to pasture streams ranged in some cases from 0% in forest to 27-28% in pasture and were broadly consistent with results from hydrometric sampling of Amazon forest and pasture watersheds that indicate 17- to 18-fold increase in the overland flow contribution to stream flow in pastures. In forest, overland flow was an important contribution to stream flow (45-57%) in ephemeral streams where flows were dominated by stormflow. Overland flow contribution to stream flow decreased in importance with increasing watershed area, from 21 to 57% in forest and 60-89% in pasture watersheds of less than 10 ha to 0% in forest and 27-28% in pastures in watersheds greater than 100 ha. Soil solution contributions to stream flow were similar across watershed area and groundwater inputs generally increased in proportion to decreases in overland flow. Application of EMMA across multiple watersheds indicated patterns across gradients of stream size and land cover that were consistent with patterns determined by detailed hydrometric sampling.

Experimental Analysis of Structural Change and Rheological Behavior of Macromolecular Solutions with Guar and Xanthan Gums in Crossflow Microfiltration Processing

The present paper reports on the structural change and rheological behavior of mixtures of macromolecular suspensions (guar and xanthan gums) in crossflow microfiltration processing. Mixtures in suspension of guar and xanthan gums at low concentrations (1,000 ppm) and different proportions were processed by microfiltration with membrane of nominal pore size of 0.4 mu m. The rheological behavior of the mixtures was investigated in rotational viscometers at two different temperatures, 25 and 40 C, at the beginning and at the end of each experiment. The shear stress (t) in function of the shear rate (gamma) was fitted and analyzed with the power-law model. All the mixtures showed flow behavior index values (n) lower than 1, characterizing non-Newtonian fluids (pseudoplastic). The samples of both mixtures and permeates were also analyzed by absorbency spectroscopy in infrared radiation. The absorbency analysis showed that there is good synergism between xanthan and guar gums without structure modifications or gel formation in the concentration process by microfiltration.

Leak detection by inverse transient analysis in an experimental PVC pipe system

Leakage reduction in water supply systems and distribution networks has been an increasingly important issue in the water industry since leaks and ruptures result in major physical and economic losses. Hydraulic transient solvers can be used in the system operational diagnosis, namely for leak detection purposes, due to their capability to describe the dynamic behaviour of the systems and to provide substantial amounts of data. In this research work, the association of hydraulic transient analysis with an optimisation model, through inverse transient analysis (ITA), has been used for leak detection and its location in an experimental facility containing PVC pipes. Observed transient pressure data have been used for testing ITA. A key factor for the success of the leak detection technique used is the accurate calibration of the transient solver, namely adequate boundary conditions and the description of energy dissipation effects since PVC pipes are characterised by a viscoelastic mechanical response. Results have shown that leaks were located with an accuracy between 4-15% of the total length of the pipeline, depending on the discretisation of the system model.

Solid-phase microextraction using poly(pyrrole) film and liquid chromatography with UV detection for analysis of antidepressants in plasma samples

Poly(pyrrole) (PPY) coating was prepared on a stainless-steel (SS) wire for solid-phase microextraction (SPME) by electrochemical deposition (cyclic voltammetric). The PPY was evaluated by analyzing new-generation antidepressants (mirtazapine, citalopram, paroxetine, duloxetine, fluoxetine, and sertraline) in plasma sample by SPME and liquid chromatography with UV detection (LC-UV). The effect of electrolyte Solution (lithium perchlorate or tetrabutylammonium perchlorate) and the number of cycles (50, 100 or 200) applied during the polymerization process on the SPME performance was evaluated. Important factors in the optimization of SPME efficiency such as extraction time, temperature, pH, influence of plasma proteins on sorption mechanisms, and desorption conditions are discussed. The SPME-PPY/LC method showed to be linear in concentrations ranging from the limit of quantification (LOQ) to 1200 ng mL(-1). The LOQ values range from 16 to 25 ng mL-1. The inter-day precision of the SPME-PPY/LC method presented coefficient of variation (CV) lower than 15%. Based on analytical validation results, the SPME-PPY/LC methodology showed to be adequate for antidepressant analysis, from therapeutic to toxic levels. In order to evaluate the proposed method for clinical use, the SPME-PPY/LC method was applied to the analysis of plasma samples from elderly depressed patients. (c) 2009 Elsevier B.V. All rights reserved,

Microextraction in packed sorbent for analysis of antidepressants in human plasma by liquid chromatography and spectrophotometric detection

A sensitive and reproducible method by microextraction packed sorbent and liquid chromatography with UV detection (MEPS/LC-UV) is described for the determination of new generation antidepressants (sertraline, mirtazapine, fluoxetine, citalopram and paroxetine) in human plasma samples. The MEPS variables, such as sample volume, pH, number of extraction cycles (draw-eject), and desorption conditions (solvent and solvent volume of elution) influenced the MEPS/LC efficiency significantly. Important factors in the optimization of MEPS efficiency, as well as washing steps and carryover effect are discussed. The analyses were carried out using small sample volumes (400 mu L.), and in a short time period (3 min for the entire sample preparation step). The MEPS/LC-UV method was shown to be linear at concentrations ranging from the limit of quantification (LOQ) to 1000 ng mL(-1). The LOQ values ranged from 10 to 25 ng mL(-1). The inter-day precision of the method presented coefficient of the variation ranging from 1.3% to 8.7%. On the basis of analytical validation, it is shown that the MEPS/LC-UV methodology is adequate for antidepressant analysis, from therapeutic to toxic levels. In order to evaluate the proposed method for clinical use, the MEPS/LC-UV method was applied to analysis of plasma samples from elderly depressed patients. (C) 2010 Elsevier B.V. All rights reserved.

Analysis of Different Staining Techniques for C4d Detection in Renal Allograft Biopsies

Capillary C4d deposition has been recognized as a marker of antibody-mediated rejection (AMR). Although the detection of capillary C4d by means of immunofluorescence (IF) in cryostat sections is well established, frozen tissue is not always available, thus limiting the diagnosis of AMR. The aim of the present study was to analyze different techniques for C4d staining and the prevalence of C4d in renal allograft biopsies. Detection of C4d was carried out using IF or immunohistochemistry (IHC) on frozen and paraffin sections of renal allograft biopsies available from the same patients. Biopsies obtained from 20 patients were classified into 3 groups: no rejection, acute rejection, and chronic allograft nephropathy (CAN). The capillary C4d deposition prevalence in frozen-IF, considered the gold standard technique for C4d detection, was 45% (9/20 cases). Compared with frozen-IF, the frozen-IHC technique presented an 85% concordance rate (17/20 cases; r =.70; P <.001; sensitivity = 77.8%; specificity = 90.9%). The paraffin-IF technique showed similar results, with an 80% concordance rate (16/20 cases; r =.64; P <.005; sensitivity = 55.6%; specificity = 100%), whereas C4d detection occurred in only 65% of paraffin-IHC cases (13/20; r =.30; not significant; sensitivity = 66.7%; specificity = 63.6%). No capillary C4d deposition was detected in cases without evidence of rejection. However, 4/7 cases (57%) of acute rejection were C4d positive. In the CAN group, 5111 cases (45%) were C4d positive. In conclusion, these results demonstrated that frozen-IHC and paraffin-IF can be considered alternative techniques to frozen-IF for C4d detection. The paraffin-IHC technique displayed the lowest concordance rate for C4d detection.

Agreement for Detecting Glaucoma Progression with the GDx Guided Progression Analysis, Automated Perimetry, and Optic Disc Photography

Purpose: To evaluate the ability of the GDx Variable Corneal Compensation (VCC) Guided Progression Analysis (GPA) software for detecting glaucomatous progression. Design: Observational cohort study. Participants: The study included 453 eyes from 252 individuals followed for an average of 46 +/- 14 months as part of the Diagnostic Innovations in Glaucoma Study. At baseline, 29% of the eyes were classified as glaucomatous, 67% of the eyes were classified as suspects, and 5% of the eyes were classified as healthy. Methods: Images were obtained annually with the GDx VCC and analyzed for progression using the Fast Mode of the GDx GPA software. Progression using conventional methods was determined by the GPA software for standard automated achromatic perimetry (SAP) and by masked assessment of optic disc stereophotographs by expert graders. Main Outcome Measures: Sensitivity, specificity, and likelihood ratios (LRs) for detection of glaucoma progression using the GDx GPA were calculated with SAP and optic disc stereophotographs used as reference standards. Agreement among the different methods was reported using the AC(1) coefficient. Results: Thirty-four of the 431 glaucoma and glaucoma suspect eyes (8%) showed progression by SAP or optic disc stereophotographs. The GDx GPA detected 17 of these eyes for a sensitivity of 50%. Fourteen eyes showed progression only by the GDx GPA with a specificity of 96%. Positive and negative LRs were 12.5 and 0.5, respectively. None of the healthy eyes showed progression by the GDx GPA, with a specificity of 100% in this group. Inter-method agreement (AC1 coefficient and 95% confidence intervals) for non-progressing and progressing eyes was 0.96 (0.94-0.97) and 0.44 (0.28-0.61), respectively. Conclusions: The GDx GPA detected glaucoma progression in a significant number of cases showing progression by conventional methods, with high specificity and high positive LRs. Estimates of the accuracy for detecting progression suggest that the GDx GPA could be used to complement clinical evaluation in the detection of longitudinal change in glaucoma. Financial Disclosure(s): Proprietary or commercial disclosure may be found after the references. Ophthalmology 2010; 117: 462-470 (C) 2010 by the American Academy of Ophthalmology.

Transcriptional Response of Peripheral Lymphocytes to Early Fibrosarcoma: A Model System for Cancer Detection Based on Hybridization Signatures

Since circulating leukocytes, mainly B and T cells, continuously maintain vigilant and comprehensive immune surveillance, these cells could be used as reporters for signs of infection or other pathologies, including cancer. Activated lymphocyte clones trigger a sensitive transcriptional response, which could be identified by gene expression profiling. To assess this hypothesis, we conducted microarray analysis of the gene expression profile of lymphocytes isolated from immunocompetent BALB/c mice subcutaneously injected with different numbers of tumorigenic B61 fibrosarcoma cells. Flow cytometry demonstrated that the number of circulating T (CD3(+)CD4(+) or CD3(+)CD8(+)) or B (CD19(+)) cells did not change. However, the lymphocytes isolated from tumor cell-injected animals expressed a unique transcriptional profile that was identifiable before the development of a palpable tumor mass. This finding demonstrates that the transcriptional response appears before alterations in the main lymphocyte subsets and that the gene expression profile of peripheral lymphocytes can serve as a sensitive and accurate method for the early detection of cancer. Exp Biol Med 234:802-812, 2009