201 research outputs found
Artificial Sequences and Complexity Measures
In this paper we exploit concepts of information theory to address the
fundamental problem of identifying and defining the most suitable tools to
extract, in a automatic and agnostic way, information from a generic string of
characters. We introduce in particular a class of methods which use in a
crucial way data compression techniques in order to define a measure of
remoteness and distance between pairs of sequences of characters (e.g. texts)
based on their relative information content. We also discuss in detail how
specific features of data compression techniques could be used to introduce the
notion of dictionary of a given sequence and of Artificial Text and we show how
these new tools can be used for information extraction purposes. We point out
the versatility and generality of our method that applies to any kind of
corpora of character strings independently of the type of coding behind them.
We consider as a case study linguistic motivated problems and we present
results for automatic language recognition, authorship attribution and self
consistent-classification.Comment: Revised version, with major changes, of previous "Data Compression
approach to Information Extraction and Classification" by A. Baronchelli and
V. Loreto. 15 pages; 5 figure
RNAi-mediated suppression of isoprene emission in poplar transiently impacts phenolic metabolism under high temperature and high light intensities: a transcriptomic and metabolomic analysis
In plants, isoprene plays a dual role: (a) as thermo-protective agent proposed to prevent degradation of enzymes/membrane structures involved in photosynthesis, and (b) as reactive molecule reducing abiotic oxidative stress. The present work addresses the question whether suppression of isoprene emission interferes with genome wide transcription rates and metabolite fluxes in grey poplar (Populusxcanescens) throughout the growing season. Gene expression and metabolite profiles of isoprene emitting wild type plants and RNAi-mediated non-isoprene emitting poplars were compared by using poplar Affymetrix microarrays and non-targeted FT-ICR-MS (Fourier transform ion cyclotron resonance mass spectrometry). We observed a transcriptional down-regulation of genes encoding enzymes of phenylpropanoid regulatory and biosynthetic pathways, as well as distinct metabolic down-regulation of condensed tannins and anthocyanins, in non-isoprene emitting genotypes during July, when high temperature and light intensities possibly caused transient drought stress, as indicated by stomatal closure. Under these conditions leaves of non-isoprene emitting plants accumulated hydrogen peroxide (H2O2), a signaling molecule in stress response and negative regulator of anthocyanin biosynthesis. The absence of isoprene emission under high temperature and light stress resulted transiently in a new chemo(pheno)type with suppressed production of phenolic compounds. This may compromise inducible defenses and may render non-isoprene emitting poplars more susceptible to environmental stress
Assessing Interaction Networks with Applications to Catastrophe Dynamics and Disaster Management
In this paper we present a versatile method for the investigation of
interaction networks and show how to use it to assess effects of indirect
interactions and feedback loops. The method allows to evaluate the impact of
optimization measures or failures on the system. Here, we will apply it to the
investigation of catastrophes, in particular to the temporal development of
disasters (catastrophe dynamics). The mathematical methods are related to the
master equation, which allows the application of well-known solution methods.
We will also indicate connections of disaster management with excitable media
and supply networks. This facilitates to study the effects of measures taken by
the emergency management or the local operation units. With a fictious, but
more or less realistic example of a spreading epidemic disease or a wave of
influenza, we illustrate how this method can, in principle, provide decision
support to the emergency management during such a disaster. Similar
considerations may help to assess measures to fight the SARS epidemics,
although immunization is presently not possible
Otro título: PRIO Loreto 2010-2015
Esta es la versión resumida del PRIO Loreto 2010-2015 aprobado por
Ordenanza Regional Nº 006-2010-GRL-CR.El Plan Regional de Igualdad de Oportunidades entre Mujeres y Varones de Loreto 2010-2015” – PRIOL dirigido a superar las desigualdades sociales entre mujeres y hombres, y mediante el cual asume su compromiso de promover y garantizar los derechos humanos de las mujeres y las niñas en la región de Loreto.Con el apoyo de la Agencia Española de Cooperación Internacional para el Desarrollo - AECID
Genome of the Avirulent Human-Infective Trypanosome—Trypanosoma rangeli
Background: Trypanosoma rangeli is a hemoflagellate protozoan parasite infecting humans and other wild and domestic mammals across Central and South America. It does not cause human disease, but it can be mistaken for the etiologic agent of Chagas disease, Trypanosoma cruzi. We have sequenced the T. rangeli genome to provide new tools for elucidating the distinct and intriguing biology of this species and the key pathways related to interaction with its arthropod and mammalian hosts. Methodology/Principal Findings: The T. rangeli haploid genome is ,24 Mb in length, and is the smallest and least repetitive trypanosomatid genome sequenced thus far. This parasite genome has shorter subtelomeric sequences compared to those of T. cruzi and T. brucei; displays intraspecific karyotype variability and lacks minichromosomes. Of the predicted 7,613 protein coding sequences, functional annotations could be determined for 2,415, while 5,043 are hypothetical proteins, some with evidence of protein expression. 7,101 genes (93%) are shared with other trypanosomatids that infect humans. An ortholog of the dcl2 gene involved in the T. brucei RNAi pathway was found in T. rangeli, but the RNAi machinery is non-functional since the other genes in this pathway are pseudogenized. T. rangeli is highly susceptible to oxidative stress, a phenotype that may be explained by a smaller number of anti-oxidant defense enzymes and heatshock proteins. Conclusions/Significance: Phylogenetic comparison of nuclear and mitochondrial genes indicates that T. rangeli and T. cruzi are equidistant from T. brucei. In addition to revealing new aspects of trypanosome co-evolution within the vertebrate and invertebrate hosts, comparative genomic analysis with pathogenic trypanosomatids provides valuable new information that can be further explored with the aim of developing better diagnostic tools and/or therapeutic targets
MIPModDB: a central resource for the superfamily of major intrinsic proteins
The channel proteins belonging to the major intrinsic proteins (MIP) superfamily are diverse and are found in all forms of life. Water-transporting aquaporin and glycerol-specific aquaglyceroporin are the prototype members of the MIP superfamily. MIPs have also been shown to transport other neutral molecules and gases across the membrane. They have internal homology and possess conserved sequence motifs. By analyzing a large number of publicly available genome sequences, we have identified more than 1000 MIPs from diverse organisms. We have developed a database MIPModDB which will be a unified resource for all MIPs. For each MIP entry, this database contains information about the source, gene structure, sequence features, substitutions in the conserved NPA motifs, structural model, the residues forming the selectivity filter and channel radius profile. For selected set of MIPs, it is possible to derive structure-based sequence alignment and evolutionary relationship. Sequences and structures of selected MIPs can be downloaded from MIPModDB database which is freely available at http://bioinfo.iitk.ac.in/MIPModDB
Shear strengthening of concrete members with TRM jackets: Effect of shear span-to-depth ratio, material and amount of external reinforcement
An experimental work on reinforced concrete (RC) rectangular beams strengthened in shear with textile reinforced mortar (TRM) jackets is presented in this paper, with focus on the following investigated parameters: (a) the amount of external TRM reinforcement ratio, ρf, by means of using different number of textile layers and different types of textile fibre materials (carbon, glass, basalt); (b) the textile geometry, and (c) the shear span-to-depth ratio, a/d. In total, 22 tests were conducted on simply supported rectangular RC beams under (three-point bending) monotonic loading. The experimental results revealed that: (1) TRM is very effective when the failure is attributed to debonding of the TRM jacket from the concrete substrate; (2) the trend of effective strains for carbon, glass and basalt TRM jackets is descending for increasing values of the TRM reinforcement ratio, ρf, when failure is associated to debonding of the jacket; (3) the effect of textile geometry is significant only for low values of ρf, resulting in variances in the capacity enhancement and the failure modes, and (4) the shear span-to-depth ratio has practically no effect to the failure mode nor to the TRM jacket contribution to the total shear resistance of the RC beams
Occupational Exposure to Endocrine-Disrupting Chemicals and Birth Weight and Length of Gestation: A European Meta-Analysis
BACKGROUND: Women of reproductive age can be exposed to
endocrine-disrupting chemicals (EDCs) at work and exposure to
EDCs in pregnancy may affect fetal growth. OBJECTIVES: We
assessed whether maternal occupational exposure to EDCs during
pregnancy as classified by application of a job exposure matrix
was associated with birth weight, term low birth weight (LBW),
length of gestation, and preterm delivery. METHODS: Using
individual participant data from 133,957 mother-child pairs in
13 European cohorts spanning births from 1994 to 2011, we linked
maternal job titles with exposure to 10 EDC groups as assessed
through a job exposure matrix. For each group, we combined the
two levels of exposure categories (possible and probable) and
compared birth outcomes with the unexposed group (exposure
unlikely). We performed meta-analyses of cohort-specific
estimates. RESULTS: Eleven percent of pregnant women were
classified as exposed to EDCs at work during pregnancy based on
job title. Classification of exposure to one or more EDC group
was associated with an increased risk of term LBW (OR 1.25,
95%CI 1.04, 1.49), as were most specific EDC groups; this
association was consistent across cohorts. Further, the risk
increased with increasing number of EDC groups (OR 2.11 95%CI
1.10, 4.06 for exposure to 4 or more EDC groups). There were few
associations (p < 0.05) with the other outcomes; women
holding job titles classified as exposed to bisphenol A or
brominated flame retardants were at higher risk for longer
length of gestation. CONCLUSION: Results from our large
population-based birth cohort design indicate that employment
during pregnancy in occupations classified as possibly or
probably exposed to EDCs was associated with an increased risk
of term LBW
Next-Generation Sequencing Reveals Recent Horizontal Transfer of a DNA Transposon between Divergent Mosquitoes
Horizontal transfer of genetic material between complex organisms often involves transposable elements (TEs). For example, a DNA transposon mariner has been shown to undergo horizontal transfer between different orders of insects and between different phyla of animals. Here we report the discovery and characterization of an ITmD37D transposon, MJ1, in Anopheles sinensis. We show that some MJ1 elements in Aedes aegypti and An. sinensis contain intact open reading frames and share nearly 99% nucleotide identity over the entire transposon, which is unexpectedly high given that these two genera had diverged 145–200 million years ago. Chromosomal hybridization and TE-display showed that MJ1 copy number is low in An. sinensis. Among 24 mosquito species surveyed, MJ1 is only found in Ae. aegypti and the hyrcanus group of anopheline mosquitoes to which An. sinensis belongs. Phylogenetic analysis is consistent with horizontal transfer and provides the basis for inference of its timing and direction. Although report of horizontal transfer of DNA transposons between higher eukaryotes is accumulating, our analysis is one of a small number of cases in which horizontal transfer of nearly identical TEs among highly divergent species has been thoroughly investigated and strongly supported. Horizontal transfer involving mosquitoes is of particular interest because there are ongoing investigations of the possibility of spreading pathogen-resistant genes into mosquito populations to control malaria and other infectious diseases. The initial indication of horizontal transfer of MJ1 came from comparisons between a 0.4x coverage An. sinensis 454 sequence database and available TEs in mosquito genomes. Therefore we have shown that it is feasible to use low coverage sequencing to systematically uncover horizontal transfer events. Expanding such efforts across a wide range of species will generate novel insights into the relative frequency of horizontal transfer of different TEs and provide the evolutionary context of these lateral transfer events
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