Effect of agitation on the performance of an anaerobic sequencing batch biofilm reactor in the treatment of dairy effluents

Agitation rate is an important parameter in the operation of Anaerobic Sequencing Biofilm Batch Reactors (ASBBRs), and a proper agitation rate guarantees good mixing, improves mass transfer, and enhances the solubility of the particulate organic matter. Dairy effluents have a high amount of particulate organic matter, and their anaerobic digestion presents inhibitory intermediates (e. g., long-chain fatty acids). The importance of studying agitation in such batch systems is clear. The present study aimed to evaluate how agitation frequency influences the anaerobic treatment of dairy effluents. The ASBBR was fed with wastewater from milk pasteurisation process and cheese manufacture with no whey segregation. The organic matter concentration, measured as chemical oxygen demand (COD), was maintained at approximately 8,000 mg/L. The reactor was operated with four agitation frequencies: 500 rpm, 350 rpm, 200 rpm, and no agitation. In terms of COD removal efficiency, similar results were observed for 500 rpm and 350 rpm (around 90%) and for 200 rpm and no agitation (around 80%). Increasing the system`s agitation thus not only improved the global efficiency of organic matter removal but also influenced volatile acid production and consumption and clearly modified this balance in each experimental condition.

Comparing detection and location performance of perpendicular and parallel broadside GPR antenna orientations

GPR (Ground Penetrating Radar) results are shown for perpendicular broadside and parallel broadside antenna orientations. Performance in detection and localization of concrete tubes and steel tanks is compared as a function of acquisition configuration. The comparison is done using 100 MHz and 200 MHz center frequency antennas. All tubes and tanks are buried at the geophysical test site of IAG/USP in Sao Paulo city, Brazil. The results show that the long steel pipe with a 38-mm diameter was well detected with the perpendicular broadside configuration. The concrete tubes were better detected with the parallel broadside configuration, clearly showing hyperbolic diffraction events from all targets up to 2-m depth. Steel tanks were detected with the two configurations. However, the parallel broadside configuration was generated to a much lesser extent an apparent hyperbolic reflection corresponding to constructive interference of diffraction hyperbolas of adjacent targets placed at the same depth. Vertical concrete tubes and steel tanks were better contained with parallel broadside antennas, where the apexes of the diffraction hyperbolas better corresponded to the horizontal location of the buried target disposition. The two configurations provide details about buried targets emphasizing how GPR multi-component configurations have the potential to improve the subsurface image quality as well as to discriminate different buried targets. It is judged that they hold some applicability in geotechnical and geoscientific studies. (C) 2009 Elsevier B.V. All rights reserved.

Next Generation Sequencing of Pooled Samples Reveals New SNRNP200 Mutations Associated with Retinitis Pigmentosa

The gene SNRNP200 is composed of 45 exons and encodes a protein essential for pre-mRNA splicing, the 200 kDa helicase hBrr2. Two mutations in SNRNP200 have recently been associated with autosomal dominant retinitis pigmentosa (adRP), a retinal degenerative disease, in two families from China. In this work we analyzed the entire 35-Kb SNRNP200 genomic region in a cohort of 96 unrelated North American patients with adRP. To complete this large-scale sequencing project, we performed ultra high-throughput sequencing of pooled, untagged PCR products. We then validated the detected DNA changes by Sanger sequencing of individual samples from this cohort and from an additional one of 95 patients. One of the two previously known mutations (p.S1087L) was identified in 3 patients, while 4 new missense changes (p.R681C, p.R681H, p.V683L, p.Y689C) affecting highly conserved codons were identified in 6 unrelated individuals, indicating that the prevalence of SNRNP200-associated adRP is relatively high. We also took advantage of this research to evaluate the pool-and-sequence method, especially with respect to the generation of false positive and negative results. We conclude that, although this strategy can be adopted for rapid discovery of new disease-associated variants, it still requires extensive validation to be used in routine DNA screenings. (C) 2011 Wiley-Liss, Inc.

Exploring Bacterial Diversity of Endodontic Microbiota by Cloning and Sequencing 16S rRNA

Introduction: The characterization of microbial communities infecting the endodontic system in each clinical condition may help on the establishment of a correct prognosis and distinct strategies of treatment. The purpose of this study was to determine the bacterial diversity in primary endodontic infections by 16S ribosomal-RNA (rRNA) sequence analysis. Methods: Samples from root canals of untreated asymptomatic teeth (n = 12) exhibiting periapical lesions were obtained, 165 rRNA bacterial genomic libraries were constructed and sequenced, and bacterial diversity was estimated. Results: A total of 489 clones were analyzed (mean, 40.7 +/- 8.0 clones per sample). Seventy phylotypes were identified of which six were novel phylotypes belonging to the family Ruminococcaceae. The mean number of taxa per canal was 10.0, ranging from 3 to 21 per sample; 65.7% of the cloned sequences represented phylotypes for which no cultivated isolates have been reported. The most prevalent taxa were Atopobium rimae (50.0%), Dialister invisus, Pre-votella oris, Pseudoramibacter alactolyticus, and Tannerella forsythia (33.3%). Conclusions: Although several key species predominate in endodontic samples of asymptomatic cases with periapical lesions, the primary endodontic infection is characterized by a wide bacterial diversity, which is mostly represented by members of the phylum Firmicutes belonging to the class Clostridia followed by the phylum Bacteroidetes. (J Ended 2011;37:922-926)

Sequence-specific reconstruction from fragmentary databases using seed sequences: implementation and validation on SAGE, proteome and generic sequencing data

Motivation: DNA assembly programs classically perform an all-against-all comparison of reads to identify overlaps, followed by a multiple sequence alignment and generation of a consensus sequence. If the aim is to assemble a particular segment, instead of a whole genome or transcriptome, a target-specific assembly is a more sensible approach. GenSeed is a Perl program that implements a seed-driven recursive assembly consisting of cycles comprising a similarity search, read selection and assembly. The iterative process results in a progressive extension of the original seed sequence. GenSeed was tested and validated on many applications, including the reconstruction of nuclear genes or segments, full-length transcripts, and extrachromosomal genomes. The robustness of the method was confirmed through the use of a variety of DNA and protein seeds, including short sequences derived from SAGE and proteome projects.

Intraspecific variation in 16S rRNA gene of Mycoplasma synoviae determined by DNA sequencing

Mycoplasma synoviae (MS) is an important avian pathogen may cause both respiratory disease and joint inflammation synovitis in poultry, causing economic losses to the Brazilian poultry industry. The genotypic variation in 16S rRNA gene is unknown. Partial sequences of 16S rRNA gene of 19 strains of M. synoviae were sequenced and analyzed in order to obtain molecular characterization and evaluation of the genetic variability of strains from distinct Brazilian areas of poultry production. Different polymorphic patterns were observed. The number of polymorphic alterations in the studied strains ranged from 0 to 6. The nucleotide variations, including deletion, insertion and substitutions, ranged from 3 to 5. The genotypic diversity observed in this study may be explained by spontaneous mutations that may occur when a lineage remains in the same flock for long periods. The culling and reposition in poultry flocks may be responsible for the entry of new strains in different areas. (C) 2008 Elsevier Ltd. All rights reserved.

A Parallel Hardware Architecture for Scale and Rotation Invariant Feature Detection

This paper proposes a parallel hardware architecture for image feature detection based on the Scale Invariant Feature Transform algorithm and applied to the Simultaneous Localization And Mapping problem. The work also proposes specific hardware optimizations considered fundamental to embed such a robotic control system on-a-chip. The proposed architecture is completely stand-alone; it reads the input data directly from a CMOS image sensor and provides the results via a field-programmable gate array coupled to an embedded processor. The results may either be used directly in an on-chip application or accessed through an Ethernet connection. The system is able to detect features up to 30 frames per second (320 x 240 pixels) and has accuracy similar to a PC-based implementation. The achieved system performance is at least one order of magnitude better than a PC-based solution, a result achieved by investigating the impact of several hardware-orientated optimizations oil performance, area and accuracy.

Thermal wave scattering by two overlapping and parallel cylinders

In this paper an analytical solution of the temperature of an opaque material containing two overlapping and parallel subsurface cylinders, illuminated by a modulated light beam, is presented. The method is based on the expansion of plane and cylindrical thermal waves in series of Bessel and Hankel functions. This model is addressed to the study of heat propagation in composite materials with interconnection between inclusions, as is the case of inverse opals and fiber reinforced composites. Measurements on calibrated samples using lock-in infrared thermography confirm the validity of the model.

FAST, PARALLEL AND SECURE CRYPTOGRAPHY ALGORITHM USING LORENZ`S ATTRACTOR

A novel cryptography method based on the Lorenz`s attractor chaotic system is presented. The proposed algorithm is secure and fast, making it practical for general use. We introduce the chaotic operation mode, which provides an interaction among the password, message and a chaotic system. It ensures that the algorithm yields a secure codification, even if the nature of the chaotic system is known. The algorithm has been implemented in two versions: one sequential and slow and the other, parallel and fast. Our algorithm assures the integrity of the ciphertext (we know if it has been altered, which is not assured by traditional algorithms) and consequently its authenticity. Numerical experiments are presented, discussed and show the behavior of the method in terms of security and performance. The fast version of the algorithm has a performance comparable to AES, a popular cryptography program used commercially nowadays, but it is more secure, which makes it immediately suitable for general purpose cryptography applications. An internet page has been set up, which enables the readers to test the algorithm and also to try to break into the cipher.

PARALLEL ALGORITHMS FOR MAXIMAL CLIQUES IN CIRCLE GRAPHS AND UNRESTRICTED DEPTH SEARCH

We present parallel algorithms on the BSP/CGM model, with p processors, to count and generate all the maximal cliques of a circle graph with n vertices and m edges. To count the number of all the maximal cliques, without actually generating them, our algorithm requires O(log p) communication rounds with O(nm/p) local computation time. We also present an algorithm to generate the first maximal clique in O(log p) communication rounds with O(nm/p) local computation, and to generate each one of the subsequent maximal cliques this algorithm requires O(log p) communication rounds with O(m/p) local computation. The maximal cliques generation algorithm is based on generating all maximal paths in a directed acyclic graph, and we present an algorithm for this problem that uses O(log p) communication rounds with O(m/p) local computation for each maximal path. We also show that the presented algorithms can be extended to the CREW PRAM model.

Performance results of running parallel applications on the InteGrade

The InteGrade middleware intends to exploit the idle time of computing resources in computer laboratories. In this work we investigate the performance of running parallel applications with communication among processors on the InteGrade grid. As costly communication on a grid can be prohibitive, we explore the so-called systolic or wavefront paradigm to design the parallel algorithms in which no global communication is used. To evaluate the InteGrade middleware we considered three parallel algorithms that solve the matrix chain product problem, the 0-1 Knapsack Problem, and the local sequence alignment problem, respectively. We show that these three applications running under the InteGrade middleware and MPI take slightly more time than the same applications running on a cluster with only LAM-MPI support. The results can be considered promising and the time difference between the two is not substantial. The overhead of the InteGrade middleware is acceptable, in view of the benefits obtained to facilitate the use of grid computing by the user. These benefits include job submission, checkpointing, security, job migration, etc. Copyright (C) 2009 John Wiley & Sons, Ltd.

Reliability Nonparametric Bayesian Estimation in Parallel Systems

Relevant results for (sub-)distribution functions related to parallel systems are discussed. The reverse hazard rate is defined using the product integral. Consequently, the restriction of absolute continuity for the involved distributions can be relaxed. The only restriction is that the sets of discontinuity points of the parallel distributions have to be disjointed. Nonparametric Bayesian estimators of all survival (sub-)distribution functions are derived. Dual to the series systems that use minimum life times as observations, the parallel systems record the maximum life times. Dirichlet multivariate processes forming a class of prior distributions are considered for the nonparametric Bayesian estimation of the component distribution functions, and the system reliability. For illustration, two striking numerical examples are presented.

A FREE BOUNDARY ISOPERIMETRIC PROBLEM IN HYPERBOLIC 3-SPACE BETWEEN PARALLEL HOROSPHERES

We investigate the isoperimetric problem of finding the regions of prescribed volume with minimal boundary area between two parallel horospheres in hyperbolic 3-space (the part of the boundary contained in the horospheres is not included). We reduce the problem to the study of rotationally invariant regions and obtain the possible isoperimetric solutions by studying the behavior of the profile curves of the rotational surfaces with constant mean curvature in hyperbolic 3-space. We also classify all the connected compact rotational surfaces M of constant mean curvature that are contained in the region between two horospheres, have boundary partial derivative M either empty or lying on the horospheres, and meet the horospheres perpendicularly along their boundary.

Purification, characterization and sequencing of the major beta-1,3-glucanase from the midgut of Tenebrio molitor larvae

The major beta-1,3-glucanase from Tenebrio molitor (TLam) was purified to homogeneity (yield, 6%; enrichment, 113 fold; specific activity, 4.4 U/mg). TLam has a molecular weight of 50 kDa and a pH optimum of 6. It is an encloglucanase that hydrolyzes beta-1,3-glucans as laminarin and yeast beta-1,3-1,6-glucan, but is inactive toward other polysaccharides (as unbranched beta-1,3-glucans or mixed beta-1,3-1,4-glucan from cereals) or disaccharides. The enzyme is not inhibited by high substrate concentrations and has low processivity (0.6). TLam has two ionizable groups involved in catalysis, and His, Tyr and Arg residues plus a divalent ion at the active site. A Cys residue important for TLam activity is exposed after laminarin binding. The cDNA coding for this enzyme was cloned and sequenced. It belongs to glycoside hydrolase family 16, and is related to other insect glucanases and glucan-binding proteins. Sequence analysis and homology modeling allowed the identification of some residues (E174, E179, H204, Y304, R127 and R181) at the active site of the enzyme, which may be important for TLam activity. TLam efficiently lyses fungal cells, suggesting a role in making available walls and cell contents to digestion and in protecting the midgut from pathogen infections. (C) 2009 Elsevier Ltd. All rights reserved.

Sequencing of Spodoptera frugiperda midgut trehalases and demonstration of secretion of soluble trehalase by midgut columnar cells

Both soluble (SfTre1) and membrane-bound (SfTre2) trehalases occur along the midgut of Spodoptera frugiperda larvae. Released SfTre2 was purified as a 67 kDa protein. Its K(m) (1.6 mM) and thermal stability (half life 10 min at 62 degrees C) are different from the previously isolated soluble trehalase (K(m) = 0.47 mM; 100% stable at 62 degrees C). Two cDNAs coding for S. frugiperda trehalases have been cloned using primers based on consensus sequences of trehalases and having as templates a cDNA library prepared from total polyA-containing RNA extracted from midguts. One cDNA codes for a trehalase that has a predicted transmembrane sequence and was defined as SfTre2. The other, after being cloned and expressed, results in a recombinant trehalase with a K(m) value and thermal stability like those of native soluble trehalase. This enzyme was defined as SfTre1 and, after it was used to generate antibodies, it was immunolocalized at the secretory vesicles and at the glycocalyx of columnar cells. Escherichia coli trehalase 3D structure and sequence alignment with SfTre1 support a proposal regarding the residue modulating the pKa value of the proton donor.