On the estimation of metabolic profiles in metagenomics

Metagenomics enables the characterization of the specific metabolic potential of a microbial community. The common approach towards a quantitative representation of this potential is to count the number of metagenomic sequence fragments that can be assigned to metabolic pathways by means of predicted gene functions. The resulting pathway abundances make up the metabolic profile of the metagenome and several different schemes for computing these profiles have been used. So far, none of the existing approaches actually estimates the proportion of sequences that can be assigned to a particular pathway. In most publications of metagenomic studies, the utilized abundance scores lack a clear statistical meaning and usually cannot be compared across different studies. Here, we introduce a mixture model-based approach to the estimation of pathway abundances that provides a basis for statistical interpretation and fast computation of metabolic profiles. Using the KEGG database our results on a large-scale analysis of data from the Human Microbiome Project show a good representation of metabolic differences between different body sites. Further, the results indicate that our mixture model even provides a better representation than the dedicated HUMAnN tool which has been developed for metabolic analysis of human microbiome data

Probabilistic Action System Trace Semantics

Action systems are a construct for reasoning about concurrent, reactive systems, in which concurrent behaviour is described by interleaving atomic actions. Sere and Troubitsyna have proposed an extension to action systems in which actions may be expressed and composed using discrete probabilistic choice as well as demonic nondeterministic choice. In this paper we develop a trace-based semantics for probabilistic action systems. This semantics provides a simple theoretical base on which practical refinement rules for probabilistic action systems may be justified

UFO: a web server for ultra-fast functional profiling of whole genome protein sequences

<p>Abstract</p> <p>Background</p> <p>Functional profiling is a key technique to characterize and compare the functional potential of entire genomes. The estimation of profiles according to an assignment of sequences to functional categories is a computationally expensive task because it requires the comparison of all protein sequences from a genome with a usually large database of annotated sequences or sequence families.</p> <p>Description</p> <p>Based on machine learning techniques for Pfam domain detection, the UFO web server for ultra-fast functional profiling allows researchers to process large protein sequence collections instantaneously. Besides the frequencies of Pfam and GO categories, the user also obtains the sequence specific assignments to Pfam domain families. In addition, a comparison with existing genomes provides dissimilarity scores with respect to 821 reference proteomes. Considering the underlying UFO domain detection, the results on 206 test genomes indicate a high sensitivity of the approach. In comparison with current state-of-the-art HMMs, the runtime measurements show a considerable speed up in the range of four orders of magnitude. For an average size prokaryotic genome, the computation of a functional profile together with its comparison typically requires about 10 seconds of processing time.</p> <p>Conclusion</p> <p>For the first time the UFO web server makes it possible to get a quick overview on the functional inventory of newly sequenced organisms. The genome scale comparison with a large number of precomputed profiles allows a first guess about functionally related organisms. The service is freely available and does not require user registration or specification of a valid email address.</p

Expansion of citrus crops in Botucatu - SP, obtained by aerial photography

A expansão da citricultura no Estado de São Paulo e particularmente no Município de Botucatu, associada ao avanço das técnicas de monitoramento ambiental, como o sensoriamento remoto foram os fatores determinantes para o desenvolvimento da presente pesquisa. O objetivo deste trabalho foi avaliar as alterações espaço-temporal da citricultura no Município de Botucatu-SP, no período de 1962 a 2005, utilizando-se de geotecnologias, como: fotografias aéreas pancromáticas de 1962, 1972 e 1977 e coloridas de 2000 e 2005, associadas às técnicas de Sensoriamento Remoto e Sistema de Informações Geográficas - SIG. Os resultados obtidos permitiram concluir que a expansão citrícola do Município de Botucatu-SP teve um incremento de 3,41% e uma expansão de 65,27% no período de cinco anos (2000 a 2005); ou seja, um aumento de 12722,56 ha. As fotografias aéreas associadas ao SIG foram eficientes na determinação da expansão citrícola no Município de Botucatu-SP.La expansión de la citricultura en lo Estado de São Paulo y en particular en lo municipio deBotucatu, asociado con el avance de las técnicas de monitoreo ambiental, tales como el sensoreamiento remoto, son los factores determinantes para el desarrollo de esta investigación. El objetivo de este estudio fue evaluar los cambios espaciales y temporales de los cítricos en Botucatu-SP, en el periodo 1962 a 2005, utilizando geo tecnologías, tales como fotografías aéreas pancromáticas de 1962, 1972 y 1977 y en color 2000 y 2005 asociados a las técnicas de sensoreamiento remoto y Sistemas de Información Geográfica - GIS. Los resultados obtenidos posibilitaran la conclusión de que la expansión de los cítricos en Botucatu-SP tuvo un incremento del 3,41% y una expansión de 65,27% en lo período de cinco años (2000 a 2005), es decir, un aumento de 12.722, 56 ha. Las fotografías aéreas asociadas con el SIG fueron efectivas en la determinación de la expansión del cultivo de cítricos en Botucatu-SP.The expansion of the citrus crops in the State of São Paulo and particularly in Botucatu, associated to the progress of the techniques of environmental monitoring, as the remote sensing, were the decisive factors for the development of the present researches. The objective of this work was to evaluate the space-temporary alterations of the citrus crops in Botucatu-SP, in the period from 1962 to 2005, using geotechnology, such as: panchromatic aerial photographs of 1962, 1972 and 1977 and colored of 2000 and 2005, associated to the techniques of Remote Sensing and Geographic Information System - GIS. The obtained results allowed to conclude that the expansion of the citrus crops of Botucatu-SP had an increment of 3,41% and an expansion of 65,27% in the period of five years (2000 to 2005); that means an increase of 12722,56 ha. The aerial photography associated to SIG was efficient in the determination of the expansion citrus crops in Botucatu-SP

A synchronous program algebra: a basis for reasoning about shared-memory and event-based concurrency

This research started with an algebra for reasoning about rely/guarantee concurrency for a shared memory model. The approach taken led to a more abstract algebra of atomic steps, in which atomic steps synchronise (rather than interleave) when composed in parallel. The algebra of rely/guarantee concurrency then becomes an instantiation of the more abstract algebra. Many of the core properties needed for rely/guarantee reasoning can be shown to hold in the abstract algebra where their proofs are simpler and hence allow a higher degree of automation. The algebra has been encoded in Isabelle/HOL to provide a basis for tool support for program verification. In rely/guarantee concurrency, programs are specified to guarantee certain behaviours until assumptions about the behaviour of their environment are violated. When assumptions are violated, program behaviour is unconstrained (aborting), and guarantees need no longer hold. To support these guarantees a second synchronous operator, weak conjunction, was introduced: both processes in a weak conjunction must agree to take each atomic step, unless one aborts in which case the whole aborts. In developing the laws for parallel and weak conjunction we found many properties were shared by the operators and that the proofs of many laws were essentially the same. This insight led to the idea of generalising synchronisation to an abstract operator with only the axioms that are shared by the parallel and weak conjunction operator, so that those two operators can be viewed as instantiations of the abstract synchronisation operator. The main differences between parallel and weak conjunction are how they combine individual atomic steps; that is left open in the axioms for the abstract operator.Comment: Extended version of a Formal Methods 2016 paper, "An algebra of synchronous atomic steps

A Study of the Drop-outs from the Watertown High School, Grades IX Through XII, During the Five School Years 1946 to 1951

The problem of encouraging pupils to remain in high school until graduation is of major importance not only to the schools but the community as well. It has been said that the public schools, and especially the secondary schools, have continued to be highly selective institutions. Adjustments within the school have not, in many cases, kept pace with changing school enrollments. Today we find a widely divergent student body necessitating wider ranges of experience to meet the needs of these individuals if we are to keep them in school until graduation. The schools, charged with the responsibility of preparing youth for citizenship and effective living in this democracy, cannot afford to allow these boys and girls to leave school before they have had the essential minimum of training provided in the twelve years of formal education. During the several years of teaching in the Watertown Public Schools, the writer has observed the departure of a number of pupils prior to graduation. As an adviser to many of these pupils, the writer gave serious thought to the problem of keeping these pupils in school. Realizing the need for a more thorough knowledge of this problem, the writer conferred with D.W. Tieszen, the high-school principal, concerning the scope and procedures for the study. It was decided that a study of all accountable pupils withdrawing from school, yet remaining in the community for a- period of at least six months, during the last five years period, September 1946 to.June 1951, would give sufficient data for the study. The study includes all pupils dropping school during the ninth, tenth, eleventh, and twelfth grades as well as those pupils remaining to the end of the school year but failing to register at the beginning of the next school term. The study does not include any pupils dropping prior to registration at the ninth-grade level nor those pupils withdrawing from the parochial school within the city

Probabilistic Demonic Refinement Algebra

We propose an abstract algebra for reasoning about probabilistic programs in a total-correctness framework. In contrast to probablisitic Kleene algebra it allows genuine reasoning about total correctness and in addition to Kleene star also has a strong iteration operator. We define operators that determine whether a program is enabled, has certain failure or does not have certain failure, respectively. The algebra is applied to the derivation of refinement rules for probabilistic action systems

Algebraic Reasoning for Probabilistic Action Systems and While-Loops

Back and von Wright have developed algebraic laws for reasoning about loops in the refinement calculus. We extend their work to reasoning about probabilistic loops in the probabilistic refinement calculus. We apply our algebraic reasoning to derive transformation rules for probabilistic action systems and probabilistic while-loops. In particular we focus on developing data refinement rules for these two constructs. Our extension is interesting since some well known transformation rules that are applicable to standard programs are not applicable to probabilistic ones: we identify some of these important differences and we develop alternative rules where possible. In particular, our probabilistic action system and while-loop data refinement rules are new: they differ from the non-probabilistic rules