Lossless filter for multiple repeats with bounded edit distance

Background: Identifying local similarity between two or more sequences, or identifying repeats occurring at least twice in a sequence, is an essential part in the analysis of biological sequences and of their phylogenetic relationship. Finding such fragments while allowing for a certain number of insertions, deletions, and substitutions, is however known to be a computationally expensive task, and consequently exact methods can usually not be applied in practice. Results: The filter TUIUIU that we introduce in this paper provides a possible solution to this problem. It can be used as a preprocessing step to any multiple alignment or repeats inference method, eliminating a possibly large fraction of the input that is guaranteed not to contain any approximate repeat. It consists in the verification of several strong necessary conditions that can be checked in a fast way. We implemented three versions of the filter. The first is simply a straightforward extension to the case of multiple sequences of an application of conditions already existing in the literature. The second uses a stronger condition which, as our results show, enable to filter sensibly more with negligible (if any) additional time. The third version uses an additional condition and pushes the sensibility of the filter even further with a non negligible additional time in many circumstances; our experiments show that it is particularly useful with large error rates. The latter version was applied as a preprocessing of a multiple alignment tool, obtaining an overall time (filter plus alignment) on average 63 and at best 530 times smaller than before (direct alignment), with in most cases a better quality alignment. Conclusion: To the best of our knowledge, TUIUIU is the first filter designed for multiple repeats and for dealing with error rates greater than 10% of the repeats length.

Feasibility of using solid sampling graphite furnace atomic absorption spectrometry for preparation of spiked filter papers with Cu and Zn as standards for direct solid analysis

An approach was developed for the preparation of cryogenic ground spiked filter papers with Cu and Zn for use as synthetic calibrating standards for direct solid microanalysis. Solid sampling graphite furnace atomic absorption spectrometry was used to evaluate the microhomogeneity and to check the applicability of the synthetic calibrating standards for the direct determination of Cu and Zn in vegetable certified reference materials. The found concentrations presented no statistical differences at the 95% confidence level. The homogeneity factors ranged from 2.7 to 4.2 for Cu and from 6.4 to 11.5 for Zn.

Treatment of wastewater from a cotton dyeing process with UV/H(2)O(2) using a photoreactor covered with reflective material

Wastewater containing several dyes, including sulfur black from the dyeing process in a textile mill, was treated using a UV/H(2)O(2) process. The wastewater was characterized by a low BOD/ COD ratio, intense color and high acute toxicity to the algae species Pseudokirchneriella subcaptata. The influence of the pH and H(2)O(2) concentration on the treatment process was evaluated by a full factorial design 2(2) with three replicates of the central experiment. The removal of aromatic compounds and color was improved by an increase in the H(2)O(2) concentration and a decrease in pH. The best results were obtained at pH 5.0 and 6 g L(-1). With these conditions and 120 min of UV irradiation, the removal of the color, aromatic compounds and COD were 74.1, 55.1 and 44.8%, respectively. Under the same conditions, but using a photoreactor covered with aluminum foil, the removal of the color, aromatic compounds and COD were 92.0, 77.6 and 59.4%, respectively. Moreover, the use of aluminum foil reduced the cost of the treatment by 40.8%. These results suggest the potential application of reflective materials as a photoreactor accessory to reduce electric energy consumption during the UV/H(2)O(2) process.

An algorithm for computerized automatic tuning of power system stabilizers

The main objective of this paper is to relieve the power system engineers from the burden of the complex and time-consuming process of power system stabilizer (PSS) tuning. To achieve this goal, the paper proposes an automatic process for computerized tuning of PSSs, which is based on an iterative process that uses a linear matrix inequality (LMI) solver to find the PSS parameters. It is shown in the paper that PSS tuning can be written as a search problem over a non-convex feasible set. The proposed algorithm solves this feasibility problem using an iterative LMI approach and a suitable initial condition, corresponding to a PSS designed for nominal operating conditions only (which is a quite simple task, since the required phase compensation is uniquely defined). Some knowledge about the PSS tuning is also incorporated in the algorithm through the specification of bounds defining the allowable PSS parameters. The application of the proposed algorithm to a benchmark test system and the nonlinear simulation of the resulting closed-loop models demonstrate the efficiency of this algorithm. (C) 2009 Elsevier Ltd. All rights reserved.

A novel subwavelength plasmon-polariton optical filter based on tilted coupled structures

This work proposes a completely new approach for the design of resonant structures aiming at wavelength-filtering applications. The structure consists of a subwavelength metal-insulator-metal (MIM) waveguide presenting tilted coupled structures transversely arranged in the midpoint between the input and output ports. The cavity-like response of this device has shown that this concept can be particularly attractive for optical filter design for telecom applications. The extra degree of freedom provided by the tilting of the cavity has proved to be not only very effective on improving the quality factor of these structures, but also to be an elegant way of extending the range of applications for tuning multiple wavelengths, if necessary.

A novel aerobic-anoxic biological filter for nitrogen removal from UASB effluent using biogas compounds as electron donors for denitrification

The performance of a new trickling filter (TF) configuration composed of an upper compartment for nitrification and a lower compartment for denitrification of effluent from a UASB reactor treating domestic sewage was evaluated. The TF was packed with new plastic material characterized by its durability and high percentage of void spaces. The feasibility of using the reduced compounds present in the biogas produced by a UASB reactor as electron donor for denitrification was also evaluated. Efficient nitrification and denitrification was achieved for the mean hydraulic (5.6 m(3) m(-2) d(-1)) organic (0.26 kg COD m(-3) d(-1)) and ammonia-N (0.08 kg m(-3) d(-1)) loading rates applied, resulting in ammonia-N removal ranging from 60 to 74%. The final effluent presented ammonia-N lower than 13 mg L(-1). Despite the presence of dissolved oxygen (DO) in the denitrification compartment, its performance was considered quite satisfactory and final nitrate concentrations were lower than 10 mg L(-1). The results indicate that methane was the main electron donor used for denitrification. Additionally, denitrification can probably be improved by avoiding high DO concentration in the denitrification compartment and by enhancing biogas transfer in the anoxic zone.

Advanced process of microbiological control of wastewater in combined system of disinfection with UV radiation

The purpose of this study was to present a methodology with superior efficiency for inactivating pathogenic indicators commonly found in domestic sewage. The adopted method was based on synergistic effect resulting from the introduction of a UV radiation pre-disinfection stage of sewage followed by secondary treatment. A pilot unit was installed in the sewage treatment plant of the University of Sao Paulo to simulate the combined system in full-scale operational conditions. Its performance was evaluated through microbiological examinations for determining Escherichia coli, total coliforms and coliphages. The application of UV radiation at 5.1mW/cm(2) for 10 s of exposure in the first disinfection stage was enough to reduce the surviving number of E. coli around 100 times, in comparison to the conventional method. Therefore, based on experimental data, it is possible to conclude that combining treatment and pre-disinfection stage is an effective potential technique to produce effluents with lower degree of contamination by pathogenic organisms.

Combination of an anaerobic process with O(3), UV and O(3)/UV for cellulose pulp bleaching effluent treatment

Recent studies have shown that partial oxidation by advanced oxidation processes (AOP) is able to transform hard-to-degrade compounds and increase their biodegradability. In this work, anaerobic treatment was followed by ozonation, UV radiation and ozonation in the presence of UV radiation, to treat bleaching effluents from a cellulose kraft Pulp plant. The anaerobic reactor (horizontal anaerobic immobilized Sludge bed, HAISB) was Used as a pretreatment to reduce the efficient organic load before applying ACIP. The ozone treatments were applied in three different pH environments (3, 8 and 10) with retention times of 10, 30, 45 and 60 min. COD and adsorbable organic halogens (AOX) removal efficiencies at the HAISB were approximately 50%, while the BOD removal efficiency reached 80%. Ozonation promoted further removal of AOX and COD so that the combined efficiency reached 96% for AOX and 70% for COD. In the oxidation process, BOD was either removed in small quantities or actually increased, as intended, so that a second biological treatment would be able to complete the treatment. The maximum increase in the BOD(5)/COD ratio (biodegradability indicator) Occurred at pH 8, reaching 104% for ozonation at a dosage of 1540 mg(O3).L(-1). Applying UV radiation alone resulted in lower values: a 34% increase ill the BOD(5)/COD ratio and a 76% AOX removal efficiency. These results indicate that the combination of anaerobic treatment with ozonation or ozonation/UV radiation improves the treatability of cellulose pulp bleaching efficients and that the resulting wastewater is suitable for further biological treatment under aerobic conditions with a low level of toxic compounds from the halogenated family.

Changes in optical properties caused by UV-irradiation of aquatic humic substances from the amazon river basin: Seasonal variability evaluation

Aquatic humic substances (AHS) isolated from two characteristic seasons of the Negro river, winter and summer corresponding to floody and dry periods, were structurally characterized by (13)C nuclear magnetic ressonance. Subsequently, AHS aqueous solutions were irradiated with a polychromatic lamp (290-475 nm) and monitored by its total organic carbon (TOC) content, ultraviolet-visible (UV-vis) absorbance, fluorescence and Fourier transformed infrared spectroscopy (FTIR). As a result, a photobleaching upto 80% after irradiation of 48 h was observed. Conformational rearrangements and formation of low molecular complexity structures were formed during the irradiation, as deduced from the pH decrement and the fluorescence shifting to lower wavelengths. Additionally a significant mineralization with the formation Of CO(2), CO, and inorganic carbon compounds was registered, as assumed by TOC losses of up to 70%. The differences in photodegradation between samples expressed by photobleaching efficiency were enhanced in the summer sample and related to its elevated aromatic content. Aromatic structures are assumed to have high autosensitization capacity effects mediated by the free radical generation from quinone and phenolic moieties.

Feasibility of Electronic Tap-Changing Stabilizers for Medium Voltage Lines-Precedents and New Configurations

Thyristor-based onload tap-changing ac voltage stabilizers are cheap and robust. They have replaced most mechanical tap-changers in low voltage applications from 300 VA to 300 M. Nevertheless, this replacement hardily applies to tap-changers associated to transformers feeding medium-voltage lines (typically 69 kV primary, 34.5 kV line, 10 MVA) which need periodical maintenance of contacts and oil. The Electric Power Research Institute (EPRI) has studied the feasibility of this replacement. It detected economical problems derived from the need for series association of thyristors to manage the high voltages involved, and from the current overload developed under line fault. The paper reviews the configurations used in that field and proposes new solutions, using a compensating transformer in the main circuit and multi-winding coils in the commutating circuit, with reduced overload effect and no series association of thyristors, drastically decreasing their number and rating. The stabilizer can be installed at any point of the line and the electronic circuit can be fixed to ground. Subsequent works study and synthesize several commutating circuits in detail.

Effect of UV Radiation and Pro-Oxidant on PP Biodegradability

The effect of ultraviolet exposure on the biodegration of poly(propylene) without (PP) and with 0.3 (wt/wt) (PPOx) pro-oxidant additives, produced by extrusion was studied. After UV exposure the samples were submitted to biodegradation (weight loss) in prepared soils. The samples before and after UV exposure were analyzed using differential scanning calorimetry, Fourier transform infrared spectroscopy, size exclusion chromatography, and optical microscopy. The exposure to UV radiation lead to more intense degradation of PPOx than of PP; the amount of carbonyl groups was larger for the PPOx samples than for PP, as well as the decrease in the T(m) and in the molecular weight. The samples exposed to UV radiation showed some level of fragmentation after 56 days when placed in the prepared soil; the samples which were exposed to UV for 480 h presented just a small weight loss. POLYM. ENG. SCI., 49:123-128, 2009. (C) 2008 Society of Plastics Engineers

Degradation of Poly(ethylene glycol) in Aqueous Solution by Photo-Fenton and H(2)O(2)/UV Processes

This article reports experimental results obtained in a laboratory-scale photochemical reactor on the photodegradation of poly(ethylene glycol) (PEG) in aqueous solutions by means of the photo-Fenton and H(2)O(2)/UV processes. Dilute water solutions of PEG were fed to a batch reactor, mixed with pertinent reactants, and allowed to react under different conditions. Reaction progress was evaluated by sampling and analyzing the concentration of the total organic carbon (TOC) in solution as a function of the reaction time. Organic acids formed during oxidation were determined by HPLC analyses. The main acids detected in both processes were acetic and formic. Glycolic acid was detected only in the photo-Fenton process, and malonic acid was detected only in the H(2)O(2)/UV treatment, indicating that different reaction paths occur in these processes. The characteristics of both processes are discussed, based on the evolution of the TOC-time curves and the concentration profiles of the monitored organic acids. The experimental results constitute a contribution to the design of industrial processes for the treatment of wastewaters containing soluble polymers with similar properties.

Treatment of Aqueous Effluents Containing Phenol by the O(3), O(3)-UV, and O(3)-H(2)O(2) Processes: Experimental Study and Neural Network Modeling

In this work, the oxidation of the model pollutant phenol has been studied by means of the O(3), O(3)-UV, and O(3)-H(2)O(2) processes. Experiments were carried out in a fed-batch system to investigate the effects of initial dissolved organic carbon concentration, initial, ozone concentration in the gas phase, the presence or absence of UVC radiation, and initial hydrogen peroxide concentration. Experimental results were used in the modeling of the degradation processes by neural networks in order to simulate DOC-time profiles and evaluate the relative importance of process variables.

Three filter beds for arsenite and chromate removal

Arsenic (As) and chromium (Cr) are two of the most toxic pollutants introduced into natural waters from a variety of sources, and they cause various adverse effects on living bodies when their concentrations exceed permissible limits. Laboratory experiments have been conducted to investigate the sorption of As and Cr on carbon steel and removal of trace elements from drinking water with a household filtration process. The affinity of As and Cr species for iron/iron carbide (Fe/Fe3C) sites is the key factor in controlling the removal of the elements. The method is based on the use of powder carbon steel, powdered block carbon, and ball ceramic in the ion-sorption columns as a cleaning process. The presence of carbon steel in a system that contains As3+ and Cr6+ might have a potential effect.

Analysis of a Reconfigurable Bandpass Circular Patch Filter

This paper presents an analysis of a reconfigurable patch filter based on a triple-mode circular patch resonator with four radial slots. The analysis has been carried out thanks to the development of a new theoretical approach of the tunable patch filter based on the coupling matrix. The coefficients of the coupling matrix related to the tunable behavior have been identified and some rules for their evolution have been derived. For a proof-of-concept, a bandpass filter has been designed with a continuous tunability obtained with varactors connected across the slots. State-of-the-art results have been obtained, with a frequency tuning range of 27% from 1.95 to 2.43 GHz and a change in fractional bandwidth from 8.5% to 31.5% for the respective frequencies. In the entire tuning range, the return loss is better than 10 dB and the maximum insertion loss is 2 dB. Due to the newly developed coupling matrix, measurements, simulations, and theory showed great agreement.