Shannon, rényie and tsallis entropy analysis of DNA using phase plane

This paper analyzes DNA information using entropy and phase plane concepts. First, the DNA code is converted into a numerical format by means of histograms that capture DNA sequence length ranging from one up to ten bases. This strategy measures dynamical evolutions from 4 up to 410 signal states. The resulting histograms are analyzed using three distinct entropy formulations namely the Shannon, Rényie and Tsallis definitions. Charts of entropy versus sequence length are applied to a set of twenty four species, characterizing 486 chromosomes. The information is synthesized and visualized by adapting phase plane concepts leading to a categorical representation of chromosomes and species.

Efficiency of sampling methods and effort to assess arthropod diversity in Azorean native forests

The BALA project (Biodiversity of Arthropods of Laurisilva of the Azores) is a research initiative to quantify the spatial distribution of arthropod biodiversity in native forests of the Azores archipelago. Arthropods were collected using a combination of two techniques, targeting epigean (ground dwelling) and canopy (arboreal) arthropods: pitfall traps (with Turquin and Ethylene solutions) and beating samples (using the three most dominant plant species). A total of 109 transects distributed amongst 18 forest fragments in seven of the nine Azorean islands were used in this study. The performance of alternative sampling methods and effort were tested. No significant differences were found in the accumulated number of species captured whether an alternative method was used or whether another transect with similar effort was established in another location within the same fragment. A combination of Ethylene and Turquin traps captured more species per individual, Turquin and beating captured more species per sample, and Turquin captured more species per unit time. An optimization exercise was performed and we found that the protocol applied during recent years is very close to optimal, allowing its future replication with confidence. The minimum combinations of sampling effort and methods, in order to monitor or to inventory diversity, taking into account different proportions of sample completeness are discussed.

Long-term monitoring across elevational gradients to assess ecological hypothesis : a description of standardized sampling methods in oceanic islands and first results

We are launching a long-term study to characterize the biodiversity at different elevations in several Azorean Islands. Our aim is to use the Azores as a model archipelago to answer the fundamental question of what generates and maintains the global spatial heterogeneity of diversity in islands and to be able to understand the dynamics of change across time. An extensive, standardized sampling protocol was applied in most of the remnant forest fragments of five Azorean Islands. Fieldwork followed BRYOLAT methodology for the collection of bryophytes, ferns and other vascular plant species. A modified version of the BALA protocol was used for arthropods. A total of 70 plots (10 m x 10 m) are already established in five islands (Flores, Pico, São Jorge, Terceira and São Miguel), all respecting an elevation step of 200 m, resulting in 24 stations examined in Pico, 12 in Terceira, 10 in Flores, 12 in São Miguel and 12 in São Jorge. The first results regarding the vascular plants inventory include 138 vascular species including taxa from Lycopodiophyta (N=2), Pteridophyta (N=27), Pinophyta (N=2) and Magnoliophyta (N=107). In this contribution we also present the main research question for the next six years within the 2020 Horizon.

Shannon information and power law analysis of the chromosome code

This paper studies the information content of the chromosomes of twenty-three species. Several statistics considering different number of bases for alphabet character encoding are derived. Based on the resulting histograms, word delimiters and character relative frequencies are identified. The knowledge of this data allows moving along each chromosome while evaluating the flow of characters and words. The resulting flux of information is captured by means of Shannon entropy. The results are explored in the perspective of power law relationships allowing a quantitative evaluation of the DNA of the species.

Shannon entropy analysis of the genome code

This paper studies the chromosome information of twenty five species, namely, mammals, fishes, birds, insects, nematodes, fungus, and one plant. A quantifying scheme inspired in the state space representation of dynamical systems is formulated. Based on this algorithm, the information of each chromosome is converted into a bidimensional distribution. The plots are then analyzed and characterized by means of Shannon entropy. The large volume of information is integrated by averaging the lengths and entropy quantities of each species. The results can be easily visualized revealing quantitative global genomic information.

On lattices from combinatorial game theory modularity and a representation theorem: finite case

We show that a self-generated set of combinatorial games, S. may not be hereditarily closed but, strong self-generation and hereditary closure are equivalent in the universe of short games. In [13], the question "Is there a set which will give a non-distributive but modular lattice?" appears. A useful necessary condition for the existence of a finite non-distributive modular L(S) is proved. We show the existence of S such that L(S) is modular and not distributive, exhibiting the first known example. More, we prove a Representation Theorem with Games that allows the generation of all finite lattices in game context. Finally, a computational tool for drawing lattices of games is presented. (C) 2014 Elsevier B.V. All rights reserved.

The comb signal and its Fourier transform

SignalProcessing, Vol. 81, nº 3

On sampling collection procedure effectiveness for forest soil characterization

One of the most important measures to prevent wild forest fires is the use of prescribed and controlled burning actions as it reduce the fuel mass availability. The impact of these management activities on soil physical and chemical properties varies according to the type of both soil and vegetation. Decisions in forest management plans are often based on the results obtained from soil-monitoring campaigns. Those campaigns are often man-labor intensive and expensive. In this paper we have successfully used the multivariate statistical technique Robust Principal Analysis Compounds (ROBPCA) to investigate on the sampling procedure effectiveness for two different methodologies, in order to reflect on the possibility of simplifying and reduce the sampling collection process and its auxiliary laboratory analysis work towards a cost-effective and competent forest soil characterization.

Soil sampling design and sampling techniques for soil properties monitoring – common difficulties related to forest soils

Mathematical models and statistical analysis are key instruments in soil science scientific research as they can describe and/or predict the current state of a soil system. These tools allow us to explore the behavior of soil related processes and properties as well as to generate new hypotheses for future experimentation. A good model and analysis of soil properties variations, that permit us to extract suitable conclusions and estimating spatially correlated variables at unsampled locations, is clearly dependent on the amount and quality of data and of the robustness techniques and estimators. On the other hand, the quality of data is obviously dependent from a competent data collection procedure and from a capable laboratory analytical work. Following the standard soil sampling protocols available, soil samples should be collected according to key points such as a convenient spatial scale, landscape homogeneity (or non-homogeneity), land color, soil texture, land slope, land solar exposition. Obtaining good quality data from forest soils is predictably expensive as it is labor intensive and demands many manpower and equipment both in field work and in laboratory analysis. Also, the sampling collection scheme that should be used on a data collection procedure in forest field is not simple to design as the sampling strategies chosen are strongly dependent on soil taxonomy. In fact, a sampling grid will not be able to be followed if rocks at the predicted collecting depth are found, or no soil at all is found, or large trees bar the soil collection. Considering this, a proficient design of a soil data sampling campaign in forest field is not always a simple process and sometimes represents a truly huge challenge. In this work, we present some difficulties that have occurred during two experiments on forest soil that were conducted in order to study the spatial variation of some soil physical-chemical properties. Two different sampling protocols were considered for monitoring two types of forest soils located in NW Portugal: umbric regosol and lithosol. Two different equipments for sampling collection were also used: a manual auger and a shovel. Both scenarios were analyzed and the results achieved have allowed us to consider that monitoring forest soil in order to do some mathematical and statistical investigations needs a sampling procedure to data collection compatible to established protocols but a pre-defined grid assumption often fail when the variability of the soil property is not uniform in space. In this case, sampling grid should be conveniently adapted from one part of the landscape to another and this fact should be taken into consideration of a mathematical procedure.

Reinforcement Learning Based on the Bayesian Theorem for Electricity Markets Decision Support

This paper presents the applicability of a reinforcement learning algorithm based on the application of the Bayesian theorem of probability. The proposed reinforcement learning algorithm is an advantageous and indispensable tool for ALBidS (Adaptive Learning strategic Bidding System), a multi-agent system that has the purpose of providing decision support to electricity market negotiating players. ALBidS uses a set of different strategies for providing decision support to market players. These strategies are used accordingly to their probability of success for each different context. The approach proposed in this paper uses a Bayesian network for deciding the most probably successful action at each time, depending on past events. The performance of the proposed methodology is tested using electricity market simulations in MASCEM (Multi-Agent Simulator of Competitive Electricity Markets). MASCEM provides the means for simulating a real electricity market environment, based on real data from real electricity market operators.

Computational design with flexible backbone sampling for protein remodeling and scaffolding of complex binding sites

Dissertation presented to obtain the Doutoramento (Ph.D.) degree in Biochemistry at the Instituto de Tecnologia Qu mica e Biol ogica da Universidade Nova de Lisboa

Studies on entomological monitoring: mosquito species frequency in riverine habitats of the Igarapava Dam, Southern Region, Brazil

Diversity of mosquito species was evaluated in different habitats before and after the Igarapava reservoir flooding in the Grande River, Southern Cerrado of Brazil. We aimed at verifying changes in these mosquito populations in consequence of the lake formation. Four habitats were selected as sampling stations: peridomiciliary habitat, pasture, "veredas" and gallery forest patch. Bimonthly collections were made with the Shannon trap and human bait, including diurnal, crepuscular and nocturnal period of mosquito activity. The Shannon Index results from the potential vectors were compared using Student t-test. Aedes scapularis, Anopheles darlingi and An. albitarsis senso latu seasonal abundance were described with moving average and compared using chi2 test. There were changes in the mosquito frequency in the habitats, except for the "veredas" that was 13 km away from the catchment area. The altering in mosquito species seasonal abundance suggests breeding places expansion. Diversity indexes can be used to monitor changes in mosquito vector population in environments where abrupt disturbance can alter disease transmission cycles.

Confined Placental Mosaicism in Chorionic Vilus Sampling - Case Report

Objectives: Chorionic Vilus Sampling (CVS) has several advantages over amniocentesis: it may be performed at an earlier gestational age, the results are quicker to obtain and there’s a lower miscarriage risk – 1%. However, the higher prevalence of discrepant fetal and vilus sampling material’s karyotype findings is a disadvantage of this technique – 0.5%. This is caused, amongst other causes, by placental mosaicism which consists of two genetically different cell lines. There are three types of placental mosaicism according to the abnormal cell line location: Type I – in the cytotrophoblast; Type II – in the vilus’ stroma; Type III – in both the above locations. Material and Methods: We present a case report about a 36-year-old pregnant woman going through our Department’s 1st trimester combined screening program; a CVS was performed, which showed Confined Placental Mosaicism (CPM). Results and Conclusion: Although the pregnant woman was in the low-risk group for aneuploidy, the patient wanted the cytogenetic study to be performed in order to reduce maternal anxiety. CVS was performed at the gestational age of 12 weeks + 5 days and the karyotype was 47XY+2/46XY. For the correct interpretation of this data an amniocentesis was performed at the gestational age of 15 weeks + 6 days, which showed a 46XY karyotype. We therefore conclude that the cytogenetic analysis of the CVS was the result of a CPM. A careful follow-up including fetal echocardiogram and seriated ultrasonographic monitoring was used to safely exclude malformations and fetal growth restriction. We verified no occurences throughout pregnancy, delivery and perinatal period. CVS practice was recently implemented in our country and has many advantages over amniocentesis. Besides the fact that an earlier gestational age usually means less affective bonding to the fetus and therefore makes medical termination of pregnancy somewhat less difficult, one should consider specific situations like the one reported in which CPM may be diagnosed. This condition is associated with increased risk of fetal growth restriction, so the clinician should be aware of the need for a more careful follow-up, since perinatal complications, which should be anticipated and treated, can be expected in 16-21% of these cases.

Brazilian mosquito (Diptera: Culicidae) fauna: I. Anopheles species from Porto Velho, Rondônia state, western Amazon, Brazil

This study contributes to knowledge of Anopheles species, including vectors of Plasmodium from the western Brazilian Amazon in Porto Velho, Rondônia State. The sampling area has undergone substantial environmental changes as a consequence of agricultural and hydroelectric projects, which have caused intensive deforestation and favored habitats for some mosquito species. The purpose of this study was to diagnose the occurrence of anopheline species from collections in three locations along an electric-power transmission line. Each locality was sampled three times from 2010 to 2011. The principal adult mosquitoes captured in Shannon trap were Anopheles darlingi, An. triannulatus, An. nuneztovari l.s., An.gilesi and An. costai. In addition, larvae were collected in ground breeding sites for Anopheles braziliensis, An. triannulatus, An. darlingi, An. deaneorum, An. marajoara, An. peryassui, An. nuneztovari l.s. and An. oswaldoi-konderi. Anopheles darlingi was the most common mosquito in the region. We discuss Culicidae systematics, fauna distribution, and aspects of malaria in altered habitats of the western Amazon.

INVENTORY OF MOSQUITOES (DIPTERA: CULICIDAE) IN CONSERVATION UNITS IN BRAZILIAN TROPICAL DRY FORESTS

In Brazil, most studies of the Culicidae family are concentrated in rainforest regions. As such, there is a lack of knowledge regarding the diversity of Culicidae in regions with different climatic and vegetational characteristics. The aim of this study was to compile an inventory of Culicidae in protected areas of the semi-arid region of the state of Minas Gerais, Brazil, in order to better understand the diversity of the family within this region. The study was conducted across four protected areas in the northern region of the state, in tropical dry forest (TDF) fragments. Sampling methods included Shannon trap and CDC light trap, as well as active collection. A total of 11,219 mosquito specimens were collected between August 2008 and July 2012, belonging to 11 genera and 45 species; 15 new records for the state of Minas Gerais were registered, as well as 26 new records for semi-arid regions within the state. The high number of new Culicidae records in this region demonstrates the importance of inventory studies for increasing the knowledge of culicid biodiversity in Minas Gerais, and in particular within semi-arid regions of the state.