On Variational Ensemble Kalman Filtering

The Extended Kalman Filter (EKF) and four dimensional assimilation variational method (4D-VAR) are both advanced data assimilation methods. The EKF is impractical in large scale problems and 4D-VAR needs much effort in building the adjoint model. In this work we have formulated a data assimilation method that will tackle the above difficulties. The method will be later called the Variational Ensemble Kalman Filter (VEnKF). The method has been tested with the Lorenz95 model. Data has been simulated from the solution of the Lorenz95 equation with normally distributed noise. Two experiments have been conducted, first with full observations and the other one with partial observations. In each experiment we assimilate data with three-hour and six-hour time windows. Different ensemble sizes have been tested to examine the method. There is no strong difference between the results shown by the two time windows in either experiment. Experiment I gave similar results for all ensemble sizes tested while in experiment II, higher ensembles produce better results. In experiment I, a small ensemble size was enough to produce nice results while in experiment II the size had to be larger. Computational speed is not as good as we would want. The use of the Limited memory BFGS method instead of the current BFGS method might improve this. The method has proven succesful. Even if, it is unable to match the quality of analyses of EKF, it attains significant skill in forecasts ensuing from the analysis it has produced. It has two advantages over EKF; VEnKF does not require an adjoint model and it can be easily parallelized.

New methods for the concentration of viruses from urban sewage using quantitative PCR.

Viruses are among the most important pathogens present in water contaminated with feces or urine and represent a serious risk to human health. Four procedures for concentrating viruses from sewage have been compared in this work, three of which were developed in the present study. Viruses were quantified using PCR techniques. According to statistical analysis and the sensitivity to detect human adenoviruses (HAdV), JC polyomaviruses (JCPyV) and noroviruses genogroup II (NoV GGII): (i) a new procedure (elution and skimmed-milk flocculation procedure (ESMP)) based on the elution of the viruses with glycine-alkaline buffer followed by organic flocculation with skimmed-milk was found to be the most efficient method when compared to (ii) ultrafiltration and glycine-alkaline elution, (iii) a lyophilization-based method and (iv) ultracentrifugation and glycine-alkaline elution. Through the analysis of replicate sewage samples, ESMP showed reproducible results with a coefficient of variation (CV) of 16% for HAdV, 12% for JCPyV and 17% for NoV GGII. Using spiked samples, the viral recoveries were estimated at 30-95% for HAdV, 55-90% for JCPyV and 45-50% for NoV GGII. ESMP was validated in a field study using twelve 24-h composite sewage samples collected in an urban sewage treatment plant in the North of Spain that reported 100% positive samples with mean values of HAdV, JCPyV and NoV GGII similar to those observed in other studies. Although all of the methods compared in this work yield consistently high values of virus detection and recovery in urban sewage, some require expensive laboratory equipment. ESMP is an effective low-cost procedure which allows a large number of samples to be processed simultaneously and is easily standardizable for its performance in a routine laboratory working in water monitoring. Moreover, in the present study, a CV was applied and proposed as a parameter to evaluate and compare the methods for detecting viruses in sewage samples.

New methods for the concentration of viruses from urban sewage using quantitative PCR.

Viruses are among the most important pathogens present in water contaminated with feces or urine and represent a serious risk to human health. Four procedures for concentrating viruses from sewage have been compared in this work, three of which were developed in the present study. Viruses were quantified using PCR techniques. According to statistical analysis and the sensitivity to detect human adenoviruses (HAdV), JC polyomaviruses (JCPyV) and noroviruses genogroup II (NoV GGII): (i) a new procedure (elution and skimmed-milk flocculation procedure (ESMP)) based on the elution of the viruses with glycine-alkaline buffer followed by organic flocculation with skimmed-milk was found to be the most efficient method when compared to (ii) ultrafiltration and glycine-alkaline elution, (iii) a lyophilization-based method and (iv) ultracentrifugation and glycine-alkaline elution. Through the analysis of replicate sewage samples, ESMP showed reproducible results with a coefficient of variation (CV) of 16% for HAdV, 12% for JCPyV and 17% for NoV GGII. Using spiked samples, the viral recoveries were estimated at 30-95% for HAdV, 55-90% for JCPyV and 45-50% for NoV GGII. ESMP was validated in a field study using twelve 24-h composite sewage samples collected in an urban sewage treatment plant in the North of Spain that reported 100% positive samples with mean values of HAdV, JCPyV and NoV GGII similar to those observed in other studies. Although all of the methods compared in this work yield consistently high values of virus detection and recovery in urban sewage, some require expensive laboratory equipment. ESMP is an effective low-cost procedure which allows a large number of samples to be processed simultaneously and is easily standardizable for its performance in a routine laboratory working in water monitoring. Moreover, in the present study, a CV was applied and proposed as a parameter to evaluate and compare the methods for detecting viruses in sewage samples.

Impedance field and noise of submicrometer n+ nn+ diodes: analytical approach

A theoretical model for the noise properties of n+nn+ diodes in the drift-diffusion framework is presented. In contrast with previous approaches, our model incorporates both the drift and diffusive parts of the current under inhomogeneous and hot-carrier conditions. Closed analytical expressions describing the transport and noise characteristics of submicrometer n+nn+ diodes, in which the diode base (n part) and the contacts (n+ parts) are coupled in a self-consistent way, are obtained

A Quantitative method for the characterization of lytic metastases of the bone from radiographic images

The aim of our study was to assess the diagnostic usefulness of the gray level parameters to distinguish osteolytic lesions using radiological images. Materials and Methods: A retrospective study was carried out. A total of 76 skeletal radiographs of osteolytic metastases and 67 radiographs of multiple myeloma were used. The cases were classified into nonflat (MM1 and OL1) and flat bones (MM2 and OL2). These radiological images were analyzed by using a computerized method. The parameters calculated were mean, standard deviation, and coefficient of variation (MGL, SDGL, and CVGL) based on gray level histogram analysis of a region-of-interest.Diagnostic utility was quantified bymeasurement of parameters on osteolyticmetastases andmultiplemyeloma, yielding quantification of area under the receiver operating characteristic (ROC) curve (AUC). Results: Flat bone groups (MM2 and OL2) showed significant differences in mean values of MGL ( = 0.048) and SDGL ( = 0.003). Their corresponding values of AUC were 0.758 for MGL and 0.883 for SDGL in flat bones. In nonflat bones these gray level parameters do not show diagnostic ability. Conclusion: The gray level parametersMGL and SDGL show a good discriminatory diagnostic ability to distinguish between multiple myeloma and lytic metastases in flat bones.

A simple and rapid method for urinary acetone analysis by headspace/gas chromatography

Urinalysis of acetone is important to monitor workers occupationally exposed to acetone and/or isopropanol, as well as in diagnosis of some diseases related to lipid metabolism impairment. This work shows a sensitive, simple and rapid static headspace-gas chromatographic procedure for quantitative determination of acetone in urine. The method was applied to measure acetone in 207 samples from general population volunteers, resulting in a mean level of 1.12 mg/L (± 0.47) and a range of 0.20 - 1.95 mg/L. The method is reproducible and reliable, making it suitable for routine analysis of acetone in urine.

Behavioral Responses in Mice Selectively Bred for High and Low Levels of Open-Field Thigmotaxis

In animal psychology, the open-field (OF) test is a traditional method for studying different aspects of rodent behavior, with thigmotaxis (i.e., wallseeking behavior) being one of the best validated OF parameters employed to measure emotionality. The main purpose of the present study was to investigate the selection response in mice selectively bred for high and low levels of OF thigmotaxis (the HOFT and LOFT lines, respectively). The mice (N = 2048) were selected for 23 generations, resulting in bidirectional phenotypic divergence between the two lines; that is, the HOFT mice were more thigmotactic (i.e., more emotional) than the LOFT mice across the different generations. The origin of the line difference in thigmotaxis was further investigated by using the crossfostering paradigm, with the results suggesting that the divergence between the two lines was primarily innate in origin and not influenced by differing maternal behavior. The stability of the selection trait was examined by testing the animals at different ages as well as in varying conditions. The results indicated that the line difference in thigmotaxis was not affected by age at the time of testing, and it also persisted in the different OF testing situations as well as during pregnancy and lactation. The examination of a possible coselection of other characteristics revealed that the more thigmotactic HOFT mice lived longer than the less thigmotactic LOFT mice. In addition, the HOFT mice tended to rear and explore less than the LOFT mice, supporting the general assumption that emotionality and exploration are inversely related. The two lines did not generally differ in ambulation and defecation, that is, in the traditional OF indexes of emotionality, conforming to the suggestion that emotionality is a multidimensional construct. The effects of sex on different OF parameters were also assessed, with the results suggesting that among the HOFT and LOFT lines, the female mice were more emotional than the male mice. The examination of the temporal changes in the HOFT and LOFT lines’ OF behavior revealed some contradictory findings that also partially conflicted with general assumptions. Although this study did not show prominent differences in maternal responsiveness between the HOFT and LOFT mothers, the results suggested that the line divergence in emotionality was more pronounced in the presence of a pup after parturition than during pregnancy. The present study clearly demonstrates that OF thigmotaxis is a strong characteristic for producing two diverging lines of mice. The difference in thigmotaxis between the selectively bred HOFT and LOFT mice seemed to be a stable and robust feature of these animals, and it appeared to stem from a genetic background.

Flow injection green method for the quantitative analysis of ketoconazole in pharmaceutical preparations

A flow injection method for the quantitative analysis of ketoconazole in tablets, based on the reaction with iron (III) ions, is presented. Ketoconazole forms a red complex with iron ions in an acid medium, with maximum absorbance at 495 nm. The detection limit was estimated to be 1×10--4 mol L-1; the quantitation limit is about 3×10--4 mol L-1 and approximately 30 determinations can be performed in an hour. The results were compared with those obtained with a reference HPLC method. Statistical comparisons were done using the Student's t procedure and the F test. Complete agreement was found at the 0.95 significance level between the proposed flow injection and the HPLC procedures. The two methods present similar precision, i.e., for HPLC the mean relative standard deviation was ca. 1.2% and for FIA ca. 1.6%.

A sensitive and robust lc-ms/ms method with monolithic column and electrospray ionization for the quantitation of efavirenz in human plasma: application to a bioequivalence study

An LC-MS/MS method has been developed for the determination of efavirenz (EFZ) in human plasma using hydrochlorothiazide as internal standard (I.S.). An ESI negative mode with multiple reaction-monitoring was used monitoring the transitions m/z 313.88→69.24 (EFZ) and 296.02→204.76 (I.S.). Samples were extracted using liquid-liquid extraction. The total run time was 2.0 min. The separation was achieved with HPLC-RP using a monolithic column. The assay was linear in the concentration range of 100 - 5000 ng mL-1. The mean recovery was 83%. Intra- and inter-day precision were < 9.5% and < 8.9%, respectively and accuracy was in the range ± 8.33%. The method was successfully applied to a bioequivalence study.

A screening method for detection of hexavalent chromium levels in soils

A rapid and low cost method to determine Cr(VI) in soils based upon alkaline metal extraction at room temperature is proposed as a semi-quantitative procedure to be performed in the field. A color comparison with standards with contents of Cr(VI) in the range of 10 to 150 mg kg-1 was used throughout. For the different types of soils studied, more than 75% of the fortified soluble Cr(VI) were recovered for all levels of spike tested for both the proposed and standard methods. Recoveries of 83 and 99% were obtained for the proposed and the standard methods, respectively, taking into account the analysis of a heavily contaminated soil sample.

Development and validation of a method for the analysis of Ochratoxin A in roasted coffee by liquid chromatography/electrospray-mass spectrometry in Tandem (LC/ESI-MS/MS)

A method using LC/ESI-MS/MS for the quantitative analysis of Ochratoxin A in roasted coffee was described. Linearity was demonstrated (r = 0.9175). The limits of detection and quantification were 1.0 and 3.0 ng g-1, respectively. Trueness, repeatability and intermediate precision values were 89.0-108.8%; 2.4-13.7%; 12.5-17.8%, respectively. To the best of our knowledge, this is the first report in which Ochratoxin A in roasted coffee is analysed by LC/ESI-MS/MS, contributing to the field of mycotoxin analysis, and it will be used for future production of Certified Reference Material.

A validated method using RP-HPLC for quantification of reserpine in the Brazilian tree Rauvolfia sellowii Müll. Arg. (Apocynaceae)

This study describes a simple, fast and reproducible method using RP-HPLC-UV, in a gradient system, for quantification of reserpine in Rauvolfia sellowii stem bark. The analysis were carried out on a C18 column; mobile phase was water and acetonitrile, and separations were carried out in 10 min, flow rate of 1.0 mL min-1, 25 ºC and 268 nm. The validation data showed that the method was specific, accurate, precise and robust. Results were linear over a range of 0.625-40.0 μg mL-1, and the mean recovery was 95.1%. The amount of reserpine found in the dried stem bark was 0.01% (m/m).

Quantification of the uranium concentration in human urine by inductively coupled plasma-sector field mass spectrometry (ICP-SFMS)

In this study, the validation of a method for analyzing the uranium (U) concentration in human urine samples by inductively coupled plasma-sector field mass spectrometry (ICP-SFMS) was conducted. PROCORAD (the Association for the Promotion of Quality Control in Radiotoxicological Analysis) provided two urine samples spiked with unknown contents of U (Sample A = 33.6 ± 1.0 µg/L and Sample B = 3.3 ± 0.1 µg/L) and one unspiked sample as a blank. The analyses were directly performed on the diluted urine samples (dilution factor = 1:20) in 5% v/v HNO3. The results obtained by ICP-SFMS corresponded well with the reference values, and the limits of detection were 235U = 0.049 × 10-3 µg/L and 238U = 7.37 × 10-3 µg/L. The ICP-SFMS technique has been shown to be successful in the analysis of the U concentration in human urine samples and for the quantification of isotopic ratios.

PREDICTING THE BOILING POINT OF PCDD/Fs BY THE QSPR METHOD BASED ON THE MOLECULAR DISTANCE-EDGE VECTOR INDEX

The quantitative structure property relationship (QSPR) for the boiling point (Tb) of polychlorinated dibenzo-p-dioxins and polychlorinated dibenzofurans (PCDD/Fs) was investigated. The molecular distance-edge vector (MDEV) index was used as the structural descriptor. The quantitative relationship between the MDEV index and Tb was modeled by using multivariate linear regression (MLR) and artificial neural network (ANN), respectively. Leave-one-out cross validation and external validation were carried out to assess the prediction performance of the models developed. For the MLR method, the prediction root mean square relative error (RMSRE) of leave-one-out cross validation and external validation was 1.77 and 1.23, respectively. For the ANN method, the prediction RMSRE of leave-one-out cross validation and external validation was 1.65 and 1.16, respectively. A quantitative relationship between the MDEV index and Tb of PCDD/Fs was demonstrated. Both MLR and ANN are practicable for modeling this relationship. The MLR model and ANN model developed can be used to predict the Tb of PCDD/Fs. Thus, the Tb of each PCDD/F was predicted by the developed models.

Electric field measurements using scanning electron microscope

The main idea of this diploma work is to study electric field distribution on the micro level. For this purpose a silicon edgeless detector was chosen as the object of investigation and scanning electron microscope as an investigation tool. Silicon edgeless detector is an important part of installation for studying proton-proton interactions in TOTEM experiment at Large Hadron Collider. For measurement of electric field distribution inside scanning electron microscope a voltage contrast method was applied.