Improvement of the GenTHREADER method for genomic fold recognition

Motivation: In order to enhance genome annotation, the fully automatic fold recognition method GenTHREADER has been improved and benchmarked. The previous version of GenTHREADER consisted of a simple neural network which was trained to combine sequence alignment score, length information and energy potentials derived from threading into a single score representing the relationship between two proteins, as designated by CATH. The improved version incorporates PSI-BLAST searches, which have been jumpstarted with structural alignment profiles from FSSP, and now also makes use of PSIPRED predicted secondary structure and bi-directional scoring in order to calculate the final alignment score. Pairwise potentials and solvation potentials are calculated from the given sequence alignment which are then used as inputs to a multi-layer, feed-forward neural network, along with the alignment score, alignment length and sequence length. The neural network has also been expanded to accommodate the secondary structure element alignment (SSEA) score as an extra input and it is now trained to learn the FSSP Z-score as a measurement of similarity between two proteins. Results: The improvements made to GenTHREADER increase the number of remote homologues that can be detected with a low error rate, implying higher reliability of score, whilst also increasing the quality of the models produced. We find that up to five times as many true positives can be detected with low error rate per query. Total MaxSub score is doubled at low false positive rates using the improved method.

Gaussian anamorphosis in the analysis step of the EnKF: a joint state-variable/observation approach

The analysis step of the (ensemble) Kalman filter is optimal when (1) the distribution of the background is Gaussian, (2) state variables and observations are related via a linear operator, and (3) the observational error is of additive nature and has Gaussian distribution. When these conditions are largely violated, a pre-processing step known as Gaussian anamorphosis (GA) can be applied. The objective of this procedure is to obtain state variables and observations that better fulfil the Gaussianity conditions in some sense. In this work we analyse GA from a joint perspective, paying attention to the effects of transformations in the joint state variable/observation space. First, we study transformations for state variables and observations that are independent from each other. Then, we introduce a targeted joint transformation with the objective to obtain joint Gaussianity in the transformed space. We focus primarily in the univariate case, and briefly comment on the multivariate one. A key point of this paper is that, when (1)-(3) are violated, using the analysis step of the EnKF will not recover the exact posterior density in spite of any transformations one may perform. These transformations, however, provide approximations of different quality to the Bayesian solution of the problem. Using an example in which the Bayesian posterior can be analytically computed, we assess the quality of the analysis distributions generated after applying the EnKF analysis step in conjunction with different GA options. The value of the targeted joint transformation is particularly clear for the case when the prior is Gaussian, the marginal density for the observations is close to Gaussian, and the likelihood is a Gaussian mixture.

Expansion quality of epidemic protocols

Epidemic protocols are a bio-inspired communication and computation paradigm for large and extreme-scale networked systems. This work investigates the expansion property of the network overlay topologies induced by epidemic protocols. An expansion quality index for overlay topologies is proposed and adopted for the design of epidemic membership protocols. A novel protocol is proposed, which explicitly aims at improving the expansion quality of the overlay topologies. The proposed protocol is tested with a global aggregation task and compared to other membership protocols. The analysis by means of simulations indicates that the expansion quality directly relates to the speed of dissemination and convergence of epidemic protocols and can be effectively used to design better protocols.

An evaluation of the theoretical potential and practical opportunity for using greywater for domestic purposes in Ghana

Assessments concerning the effects of climate change, water resource availability and water deprivation in West Africa have not frequently considered the positive contribution to be derived from collecting and reusing water for domestic purposes. Where the originating water is taken from a clean water source and has been used the first time for washing or bathing, this water is commonly called “greywater”. Greywater is a prolific resource that is generated wherever people live. Treated greywater can be used for domestic cleaning, for flushing toilets where appropriate, for washing cars, sometimes for watering kitchen gardens, and for clothes washing prior to rinsing. Therefore, a large theoretical potential exists to increase total water resource availability if greywater were to be widely reused. Locally treated greywater reduces the distribution network requirement, lower construction effort and cost and, wherever possible, minimising the associated carbon footprint. Such locally treated greywater offers significant practical opportunities for increasing the total available water resources at a local level. The reuse of treated greywater is one important action that will help to mitigate the reducing availability of clean water supplies in some areas, and the expected mitigation required in future aligns well with WHO/UNICEF (2012) aspirations. The evaluation of potential opportunities for prioritising greywater systems to support water reuse takes into account the availability of water resources, water use indicators and published estimates in order to understand typical patterns of water demand. The approach supports knowledge acquisition regarding local conditions for enabling capacity building for greywater reuse, the understanding of systems that are most likely to encourage greywater reuse, and practices and future actions to stimulate greywater infrastructure planning, design and implementation. Although reuse might be considered to increase the uncertainty of achieving a specified quality of the water supply, robust methods and technologies are available for local treatment. Resource strategies for greywater reuse have the potential to consistently improve water efficiency and availability in water impoverished and water stressed regions of Ghana and West Africa. Untreated greywater is referred to as “greywater”; treated greywater is referred to as “treated greywater” in this paper.

Internal validity of the Swedish Maternal Health Care Register

Background: The Swedish Maternal Health Care Register (MHCR) is a national quality register that has been collecting pregnancy, delivery, and postpartum data since 1999. A substantial revision of the MHCR resulted in a Web-based version of the register in 2010. Although MHCR provides data for health care services and research, the validity of the MHCR data has not been evaluated. This study investigated degree of coverage and internal validity of specific variables in the MHCR and identified possible systematic errors. Methods: This cross-sectional observational study compared pregnancy and delivery data in medical records with corresponding data in the MHCR. The medical record was considered the gold standard. The medical records from nine Swedish hospitals were selected for data extraction. This study compared data from 878 women registered in both medical records and in the MHCR. To evaluate the quality of the initial data extraction, a second data extraction of 150 medical records was performed. Statistical analyses were performed for degree of coverage, agreement and correlation of data, and sensitivity and specificity. Results: Degree of coverage of specified variables in the MHCR varied from 90.0% to 100%. Identical information in both medical records and the MHCR ranged from 71.4% to 99.7%. For more than half of the investigated variables, 95% or more of the information was identical. Sensitivity and specificity were analysed for binary variables. Probable systematic errors were identified for two variables. Conclusions: When comparing data from medical records and data registered in the MHCR, most variables in the MHCR demonstrated good to very good degree of coverage, agreement, and internal validity. Hence, data from the MHCR may be regarded as reliable for research as well as for evaluating, planning, and decision-making with respect to Swedish maternal health care services.

Newly Automated System For Integrated Assessment Of The Conditions Of Underwater Gas Pipelines

An underwater gas pipeline is the portion of the pipeline that crosses a river beneath its bottom. Underwater gas pipelines are subject to increasing dangers as time goes by. An accident at an underwater gas pipeline can lead to technological and environmental disaster on the scale of an entire region. Therefore, timely troubleshooting of all underwater gas pipelines in order to prevent any potential accidents will remain a pressing task for the industry. The most important aspect of resolving this challenge is the quality of the automated system in question. Now the industry doesn't have any automated system that fully meets the needs of the experts working in the field maintaining underwater gas pipelines. Principle Aim of this Research: This work aims to develop a new system of automated monitoring which would simplify the process of evaluating the technical condition and decision making on planning and preventive maintenance and repair work on the underwater gas pipeline. Objectives: Creation a shared model for a new, automated system via IDEF3; Development of a new database system which would store all information about underwater gas pipelines; Development a new application that works with database servers, and provides an explanation of the results obtained from the server; Calculation of the values MTBF for specified pipelines based on quantitative data obtained from tests of this system. Conclusion: The new, automated system PodvodGazExpert has been developed for timely and qualitative determination of the physical conditions of underwater gas pipeline; The basis of the mathematical analysis of this new, automated system uses principal component analysis method; The process of determining the physical condition of an underwater gas pipeline with this new, automated system increases the MTBF by a factor of 8.18 above the existing system used today in the industry.

Study of the audio coding algorithm of the MPEG-4 AAC standard and comparison among implementations of modules of the algorithm

Audio coding is used to compress digital audio signals, thereby reducing the amount of bits needed to transmit or to store an audio signal. This is useful when network bandwidth or storage capacity is very limited. Audio compression algorithms are based on an encoding and decoding process. In the encoding step, the uncompressed audio signal is transformed into a coded representation, thereby compressing the audio signal. Thereafter, the coded audio signal eventually needs to be restored (e.g. for playing back) through decoding of the coded audio signal. The decoder receives the bitstream and reconverts it into an uncompressed signal. ISO-MPEG is a standard for high-quality, low bit-rate video and audio coding. The audio part of the standard is composed by algorithms for high-quality low-bit-rate audio coding, i.e. algorithms that reduce the original bit-rate, while guaranteeing high quality of the audio signal. The audio coding algorithms consists of MPEG-1 (with three different layers), MPEG-2, MPEG-2 AAC, and MPEG-4. This work presents a study of the MPEG-4 AAC audio coding algorithm. Besides, it presents the implementation of the AAC algorithm on different platforms, and comparisons among implementations. The implementations are in C language, in Assembly of Intel Pentium, in C-language using DSP processor, and in HDL. Since each implementation has its own application niche, each one is valid as a final solution. Moreover, another purpose of this work is the comparison among these implementations, considering estimated costs, execution time, and advantages and disadvantages of each one.

Host quality of different aphid species for rearing Diaeretiella rapae (McIntosh) (Hymenoptera: Braconidae)

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Proteome of the phytopathogen Xanthomonas citri subsp citri: a global expression profile

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Observational Characterization of the Downward Atmospheric Longwave Radiation at the Surface in the City of São Paulo

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Quality of TEC Estimated with Mod Ion Using GPS and GLONASS Data

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Performance of the constructed wetland system for the treatment of water from the corumbataí river

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Suitability of DNA extracted from archival specimens of fruit-eating bats of the genus Artibeus (Chiroptera, Phyllostomidae) for polymerase chain reaction and sequencing analysis

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Global analysis of the post-SNO solar neutrino data for standard and nonstandard oscillation mechanisms

What can we learn from solar neutrino observations? Is there any solution to the solar neutrino anomaly which is favored by the present experimental panorama? After SNO results, is it possible to affirm that neutrinos have mass? In order to answer such questions we analyze the current available data from the solar neutrino experiments, including the recent SNO result, in view of many acceptable solutions to the solar neutrino problem based on different conversion mechanisms, for the first time using the same statistical procedure. This allows us to do a direct comparison of the goodness of the fit among different solutions, from which we can discuss and conclude on the current status of each proposed dynamical mechanism. These solutions are based on different assumptions: (a) neutrino mass and mixing, (b) a nonvanishing neutrino magnetic moment, (c) the existence of nonstandard flavor-changing and nonuniversal neutrino interactions, and (d) a tiny violation of the equivalence principle. We investigate the quality of the fit provided by each one of these solutions not only to the total rate measured by all the solar neutrino experiments but also to the recoil electron energy spectrum measured at different zenith angles by the Super-Kamiokande Collaboration. We conclude that several nonstandard neutrino flavor conversion mechanisms provide a very good fit to the experimental data which is comparable with (or even slightly better than) the most famous solution to the solar neutrino anomaly based on the neutrino oscillation induced by mass.

Evaluation of guava during different phases of the industrial processing

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)