The sequence comparison index: A novel method for comparing proteins and proteomes

Historically morphological features were used as the primary means to classify organisms. However, the age of molecular genetics has allowed us to approach this field from the perspective of the organism's genetic code. Early work used highly conserved sequences, such as ribosomal RNA. The increasing number of complete genomes in the public data repositories provides the opportunity to look not only at a single gene, but at organisms' entire parts list. ^ Here the Sequence Comparison Index (SCI) and the Organism Comparison Index (OCI), algorithms and methods to compare proteins and proteomes, are presented. The complete proteomes of 104 sequenced organisms were compared. Over 280 million full Smith-Waterman alignments were performed on sequence pairs which had a reasonable expectation of being related. From these alignments a whole proteome phylogenetic tree was constructed. This method was also used to compare the small subunit (SSU) rRNA from each organism and a tree constructed from these results. The SSU rRNA tree by the SCI/OCI method looks very much like accepted SSU rRNA trees from sources such as the Ribosomal Database Project, thus validating the method. The SCI/OCI proteome tree showed a number of small but significant differences when compared to the SSU rRNA tree and proteome trees constructed by other methods. Horizontal gene transfer does not appear to affect the SCI/OCI trees until the transferred genes make up a large portion of the proteome. ^ As part of this work, the Database of Related Local Alignments (DaRLA) was created and contains over 81 million rows of sequence alignment information. DaRLA, while primarily used to build the whole proteome trees, can also be applied shared gene content analysis, gene order analysis, and creating individual protein trees. ^ Finally, the standard BLAST method for analyzing shared gene content was compared to the SCI method using 4 spirochetes. The SCI system performed flawlessly, finding all proteins from one organism against itself and finding all the ribosomal proteins between organisms. The BLAST system missed some proteins from its respective organism and failed to detect small ribosomal proteins between organisms. ^

Measurements of seawater and aerosol particles during POLARSTERN cruise ANT-XXVII/4

An analytical method for the determination of the alpha dicarbonyls glyoxal (GLY) and methylglyoxal (MGLY) from seawater and marine aerosol particles is presented. The method is based on derivatization with o-(2,3,4,5,6-Pentafluorobenzyl)-hydroxylamine (PFBHA) reagent, solvent extraction and GC-MS (SIM) analysis. The method showed good precision (RSD < 10%), sensitivity (detection limits in the low ng/l range), and accuracy (good agreement between external calibration and standard addition). The method was applied to determine GLY and MGLY in oceanic water sampled during the Polarstern cruise ANT XXVII/4 from Capetown to Bremerhaven in spring 2011. GLY and MGLY were determined in the sea surface microlayer (SML) of the ocean and corresponding bulk water (BW) with average concentrations of 228 ng/l (GLY) and 196 ng/l (MGLY). The results show a significant enrichment (factor of 4) of GLY and MGLY in the SML. Furthermore, marine aerosol particles (PM1) were sampled during the cruise and analyzed for GLY (average concentration 0.19 ng/m**3) and MGLY (average concentration 0.15 ng/m**3). On aerosol particles, both carbonyls show a very good correlation with oxalate, supporting the idea of a secondary formation of oxalic acid via GLY and MGLY. Concentrations of GLY and MGLY in seawater and on aerosol particles were correlated to environmental parameters such as global radiation, temperature, distance to the coastline and biological activity. There are slight hints for a photochemical production of GLY and MGLY in the SML (significant enrichment in the SML, higher enrichment at higher temperature). However, a clear connection of GLY and MGLY to global radiation as well as to biological activity cannot be concluded from the data. A slight correlation between GLY and MGLY in the SML and in aerosol particles could be a hint for interactions, in particular of GLY, between seawater and the atmosphere.

Major and trace element abundances at DSDP Hole 72-516F

Anomalously high values of Ir have been detected in association with the Cretaceous/Tertiary boundary in about a dozen marine or continental sections laid down about 65 Ma in many different parts of the world (Alvarez et al., 1981). One possible exception is the Cretaceous/Tertiary boundary region in DSDP Site 356, in the South Atlantic off the coast of South America. In a detailed study of that section, the maximum Ir abundance was about 0.2 ppb, much lower than the 3-90 ppb found in most of the other marine locations (authors' unpublished data on the Cretaceous/Tertiary region of Site 356, 1982). A study of Hole 516F, which is not too far from Site 356, could show whether the very low (or missing) Cretaceous/Tertiary Ir anomaly at Site 356 is characteristic of this region of the South Atlantic.

Mercury determination in urine samples by gold nanostructured screen-printed carbon electrodes after vortex-assisted ionic liquid dispersive liquid–liquid microextraction

A novel approach is presented to determine mercury in urine samples, employing vortex-assisted ionic liquid dispersive liquid–liquid microextraction and microvolume back-extraction to prepare samples, and screen-printed electrodes modified with gold nanoparticles for voltammetric analysis. Mercury was extracted directly from non-digested urine samples in a water-immiscible ionic liquid, being back-extracted into an acidic aqueous solution. Subsequently, it was determined using gold nanoparticle-modified screen-printed electrodes. Under optimized microextraction conditions, standard addition calibration was applied to urine samples containing 5, 10 and 15 μg L−1 of mercury. Standard addition calibration curves using standards between 0 and 20 μg L−1 gave a high level of linearity with correlation coefficients ranging from 0.990 to 0.999 (N = 5). The limit of detection was empirical and statistically evaluated, obtaining values that ranged from 0.5 to 1.5 μg L−1, and from 1.1 to 1.3 μg L−1, respectively, which are significantly lower than the threshold level established by the World Health Organization for normal mercury content in urine (i.e., 10–20 μg L−1). A certified reference material (REC-8848/Level II) was analyzed to assess method accuracy finding 87% and 3 μg L−1 as the recovery (trueness) and standard deviation values, respectively. Finally, the method was used to analyze spiked urine samples, obtaining good agreement between spiked and found concentrations (recovery ranged from 97 to 100%).

Precise determination of quantum critical points by the violation of the entropic area law

Finite-size scaling analysis turns out to be a powerful tool to calculate the phase diagram as well as the critical properties of two-dimensional classical statistical mechanics models and quantum Hamiltonians in one dimension. The most used method to locate quantum critical points is the so-called crossing method, where the estimates are obtained by comparing the mass gaps of two distinct lattice sizes. The success of this method is due to its simplicity and the ability to provide accurate results even considering relatively small lattice sizes. In this paper, we introduce an estimator that locates quantum critical points by exploring the known distinct behavior of the entanglement entropy in critical and noncritical systems. As a benchmark test, we use this new estimator to locate the critical point of the quantum Ising chain and the critical line of the spin-1 Blume-Capel quantum chain. The tricritical point of this last model is also obtained. Comparison with the standard crossing method is also presented. The method we propose is simple to implement in practice, particularly in density matrix renormalization group calculations, and provides us, like the crossing method, amazingly accurate results for quite small lattice sizes. Our applications show that the proposed method has several advantages, as compared with the standard crossing method, and we believe it will become popular in future numerical studies.

Enantioselective analysis of praziquantel and trans-4-hydroxypraziquantel in human plasma by chiral LC-MS/MS: Application to pharmacokinetics

A simple enantioselective method for the determination of praziquantel (PZQ) and trans-4-hydroxypraziquantel (4-OHPZQ) in human plasma was developed and validated by high-performance liquid chromatography/mass spectrometry. The plasma samples were prepared by liquid-liquid extraction using a mixture of methyl-tert-butylether/dichloromethane (2:1, v/v) as extraction solvent. The direct resolution of PZQ and 4-OHPZQ enantiomers was performed on a Chiralpak AD column using hexane-isopropanol (75:25, v/v) as the mobile phase. Diazepam was used as internal standard. The method described here is simple and reproducible. The quantitation limit of 1.25 ng/ml for each PZQ enantiomer and of 12.5 ng/ml for each 4-OHPZQ enantiomer permits the use of the method in studies investigating the kinetic disposition of a single dose of 1.5g racemic PZQ. Enantioselectivity in the kinetic disposition of PZQ and 4-OHPZQ was observed in the clinical study. with the demonstration of a higher proportion of the (+)-(S)-PZQ and (-)-(R)-4-OHPZQ enantiomers in plasma. (C) 2009 Elsevier B.V. All rights reserved.

Methemoglobin Reduction in Crocodile Blood: Are High Levels of MetHb Typical of Healthy Reptiles?

In 82 wild-caught Crocodylus porosus, levels of NADH-MetHb reductase and GSH seem adequate to maintain hemoglobin in its reduced functional state. Studies of C. porosus erythrocytes in vitro show reduction of metHb in the presence of lactate, glucose and plasma, but not pyruvate. These findings, together with recent data which show low metHb in a variety of reptiles, cast doubt on the accepted view that high levels of MetHb are typical of healthy reptiles. One explanation for the sharp contrast between earlier and more recent data could be technical. We found low metHb in Crocodylus johnstoni, Chelodina longicollis and Sphenomorphus quoyi. However, high and variable values reminiscent of many of the earlier data were obtained by omitting final centrifugation prior to spectrophotometry. Interestingly, this step is not part of the standard clinical method but is necessary in analyses of blood with nucleated red cells. These observations suggest that high metHb may not be typical of reptiles after all.

Biodiversity: bridging the gap between condition and conservation

The aim of this study is to create a two-tiered assessment combining restoration and conservation, both needed for biodiversity management. The first tier of this approach assesses the condition of a site using a standard bioassessment method, AUSRIVAS, to determine whether significant loss of biodiversity has occurred because of human activity. The second tier assesses the conservation value of sites that were determined to be unimpacted in the first step against a reference database. This ensures maximum complementarity without having to set a priori target areas. Using the reference database, we assign site-specific and comparable coefficients for both restoration (Observed/Expected taxa with > 50% probability of occurrence) and conservation values (O/E taxa with < 50%, rare taxa). In a trial on 75 sites on rivers around Sydney, NSW, Australia we were able to identify three regions: (1) an area that may need restoration; (2) an area that had a high conservation value and; (3) a region that was identified as having significant biodiversity loss but with high potential to respond to rehabilitation and become a biodiversity hotspot. These examples highlight the use of the new framework as a comprehensive system for biodiversity assessment.

Endoscopic-guided percutaneous radiofrequency cordotomy

The authors present the first clinical implementation of an endoscopic-assisted percutaneous anterolateral radiofrequency cordotomy. The aim of this article is to demonstrate the intradural endoscopic visualization of the cervical spinal cord via a percutaneous approach to refine the spinal target for anterolateral cordotomy, avoiding undesired trauma to the spinal tissue or injury to blood vessels. Initially, a lateral puncture of the spinal canal in the C1-2 interspace is performed, guided by fluoroscopy. As soon as CSF is reached by the guide cannula (17-gauge needle), the endoscope can be inserted for visualization of the spinal cord and its surrounding structures. The endoscopic visualization provided clear identification of the pial surface of the spinal cord, arachnoid membrane, dentate ligament, dorsal and ventral root entry zone, and blood vessels. The target for electrode insertion into the spinal cord was determined to be the midpoint from the dentate ligament and the ventral root entry zone. The endoscopic guidance shortened the fluoroscopy usage time and no intrathecal contrast administration was needed. Cordotomy was performed by a standard radiofrequency method after refining of the neurophysiological target. Satisfactory analgesia was provided by the procedure with no additional complications or CSF leak. The initial use of this technique suggests that a percutaneous endoscopic procedure may be useful for particular manipulation of the spinal cord, possibly adding a degree of safety to the procedure and improving its effectiveness. (DOI: 10.3171/2010.4.JNS091779)

An automated multi-unit composting facility for biodegradability evaluations

A system has been developed for studying the biodegradation of natural and synthetic polymeric material. The system is based on standard methods developed by the European Committee for Standardisation (CEN TC 261) (ISO/DIS 14855) and the American Society of Testing Materials, 'ASTM. Standard Test Method for Determining Aerobic. Biodegradation of Plastic Materials under Controlled Composting Conditions' (ASTM D 5338-92). A new low-cost compost facility has been used which satisfies the requirements of these standards. The system has been automated for data collection and has been run under the conditions specified by the standards. In the system, cellulose, newspaper and two starch-based polymers were treated with compost in a series of 3dm(3) vessels at 52 degreesC and under conditions of optimum moisture and pH. The degradation was followed over time by measuring the amount of carbon released as carbon dioxide. (C) 2001 Society of Chemical Industry.

Capacidade antioxidante de cervejas comerciais

Mestrado em Engenharia Química

Multi-elemental analysis of ready-to-eat “baby leaf” vegetables using microwave digestion and high-resolution continuum source atomic absorption spectrometry

The mineral content (phosphorous (P), potassium (K), sodium (Na), calcium (Ca), magnesium (Mg), iron (Fe), manganese (Mn), zinc (Zn) and copper (Cu)) of eight ready-to-eat baby leaf vegetables was determined. The samples were subjected to microwave-assisted digestion and the minerals were quantified by High-Resolution Continuum Source Atomic Absorption Spectrometry (HR-CS-AAS) with flame and electrothermal atomisation. The methods were optimised and validated producing low LOQs, good repeatability and linearity, and recoveries, ranging from 91% to 110% for the minerals analysed. Phosphorous was determined by a standard colorimetric method. The accuracy of the method was checked by analysing a certified reference material; results were in agreement with the quantified value. The samples had a high content of potassium and calcium, but the principal mineral was iron. The mineral content was stable during storage and baby leaf vegetables could represent a good source of minerals in a balanced diet. A linear discriminant analysis was performed to compare the mineral profile obtained and showed, as expected, that the mineral content was similar between samples from the same family. The Linear Discriminant Analysis was able to discriminate different samples based on their mineral profile.

Characterisation of noisy speech channels in 2G and 3G mobile networks

As the wireless cellular market reaches competitive levels never seen before, network operators need to focus on maintaining Quality of Service (QoS) a main priority if they wish to attract new subscribers while keeping existing customers satisfied. Speech Quality as perceived by the end user is one major example of a characteristic in constant need of maintenance and improvement. It is in this topic that this Master Thesis project fits in. Making use of an intrusive method of speech quality evaluation, as a means to further study and characterize the performance of speech codecs in second-generation (2G) and third-generation (3G) technologies. Trying to find further correlation between codecs with similar bit rates, along with the exploration of certain transmission parameters which may aid in the assessment of speech quality. Due to some limitations concerning the audio analyzer equipment that was to be employed, a different system for recording the test samples was sought out. Although the new designed system is not standard, after extensive testing and optimization of the system's parameters, final results were found reliable and satisfactory. Tests include a set of high and low bit rate codecs for both 2G and 3G, where values were compared and analysed, leading to the outcome that 3G speech codecs perform better, under the approximately same conditions, when compared with 2G. Reinforcing the idea that 3G is, with no doubt, the best choice if the costumer looks for the best possible listening speech quality. Regarding the transmission parameters chosen for the experiment, the Receiver Quality (RxQual) and Received Energy per Chip to the Power Density Ratio (Ec/N0), these were subject to speech quality correlation tests. Final results of RxQual were compared to those of prior studies from different researchers and, are considered to be of important relevance. Leading to the confirmation of RxQual as a reliable indicator of speech quality. As for Ec/N0, it is not possible to state it as a speech quality indicator however, it shows clear thresholds for which the MOS values decrease significantly. The studied transmission parameters show that they can be used not only for network management purposes but, at the same time, give an expected idea to the communications engineer (or technician) of the end-to-end speech quality consequences. With the conclusion of the work new ideas for future studies come to mind. Considering that the fourth-generation (4G) cellular technologies are now beginning to take an important place in the global market, as the first all-IP network structure, it seems of great relevance that 4G speech quality should be subject of evaluation. Comparing it to 3G, not only in narrowband but also adding wideband scenarios with the most recent standard objective method of speech quality assessment, POLQA. Also, new data found on Ec/N0 tests, justifies further research studies with the intention of validating the assumptions made in this work.

Rigid pavements distresses - pavement condition index evaluation

Pavements require maintenance in order to provide good service levels during their life period. Because of the significant costs of this operation and the importance of a proper planning, a pavement evaluation methodology, named Pavement Condition Index (PCI), was created by the U.S. Army Corps of Engineers. This methodology allows for the evaluation of the pavement condition along the life period, generally yearly, with minimum costs and, in this way, it is possible to plan the maintenance action and to adopt adequate measures, minimising the rehabilitation costs. The PCI methodology provides an evaluation based on visual inspection, namely on the distresses observed on the pavement. This condition index of the pavement is classified from 0 to 100, where 0 it is the worst possible condition and 100 the best possible condition. This methodology of pavement assessment represents a significant tool for management methods such as airport pavement management system (APMS) and life-cycle costs analysis (LCCA). Nevertheless, it has some limitations which can jeopardize the correct evaluation of the pavement behavior. Therefore the objective of this dissertation is to help reducing its limitations and make it easier and faster to use. Thus, an automated process of PCI calculation was developed, avoiding the abaci consultation, and consequently, minimizing the human error. To facilitate also the visual inspection a Tablet application was developed to replace the common inspection data sheet and thus making the survey easier to be undertaken. Following, an airport pavement condition was study accordingly with the methodology described at Standard Test Method for Airport Pavement Condition Index Surveys D5340, 2011 where its original condition level is compared with the condition level after iterate possible erroneous considered distresses as well as possible rehabilitations. Afterwards, the results obtained were analyzed and the main conclusions presented together with some future developments.

Determinação de psicofármacos em cabelo humano por técnicas cromatográficas hifenadas: um método alternativo não-invasivo

Dissertação de mestrado em Técnicas de Caracterização e Análise Química