Exploration of the parameter space in an agent-based model of tuberculosis spread: emergence of drug resistance in developing vs developed countries

In this work we present an agent-based model for the spread of tuberculosis where the individuals can be infected with either drug-susceptible or drug-resistant strains and can also receive a treatment. The dynamics of the model and the role of each one of the parameters are explained. The whole set of parameters is explored to check their importance in the numerical simulation results. The model captures the beneficial impact of the adequate treatment on the prevalence of tuberculosis. Nevertheless, depending on the treatment parameters range, it also captures the emergence of drug resistance. Drug resistance emergence is particularly likely to occur for parameter values corresponding to less efficacious treatment, as usually found in developing countries.

Sedimentary processes on the NW Iberian Continental Shelf since the Little Ice Age

The OMEX core CD110 W90, retrieved from the Douro Mud Patch (DMP) off the River Douro in the north of Portugal, records the period since the beginning of Little Ice Age (LIA). The core chronology is based upon the data attributes for Pb-210, Cs-137 and a C-14 dating from a level near the core base. Geochemical, granulometric, microfaunal (benthic foraminifera) and compositional data suggest the occurrence of precipitation changes which may have been, at least partially, influenced by the North Atlantic Oscillation (NAO), that contributes to the regulation of the ocean-atmosphere dynamics in the North Atlantic. Southwesterly Atlantic storm track is associated with the negative phases of the NAO, when the Azores High is anomalously weak, higher oceanographic hydrodynamism, downwelling events and increased rainfall generally occurs. Prevalence of these characteristics during the LIA left a record that corresponds to phases of major floods. During these phases the DMP received a higher contribution of relatively coarse-grained terrigenous sediments, enriched in quartz particles, which diluted the contribution of other minerals, as indicated by reduced concentrations of several lithogenic chemical elements such as: Al, As, Ba, Ce, Co, Cu, Fe, K, La, Li, Mg, Mn, Mo, Na, Ni, P, Rb, Sc, Sn, Th, V and Y. The presence of biogenic carbonate particles also underwent dilution, as revealed by the smaller abundance of foraminifera and correlative lower concentrations of Ca and Sr. During this period, the DMP also received an increased contribution of organic matter, indicated by higher values of lignin remains and a benthic foraminifera high productivity index, or BFHP, which gave rise to early diagenetic changes with pyrite formation. Since the beginning of the 20th century this contribution diminished, probably due to several drier periods and the impact of human activities in the river basins, e.g. construction of dams, or, on the littoral areas, construction of hard-engineering structures and sand extraction activities. During the first half of the 20th century mainly positive phases of the NAO prevailed, caused by the above normal strengthening of the subtropical high pressure centre of the Azores and the deepening of the low pressure centre in Iceland. These phases may have contributed to the reduction in the supply of both terrigenous sediments and organic matter from shallow water to the DMP. During the positive phases of the NAO, sedimentation became finer. The development of mining and industrial activities during the 20th century is marked, in this core, by higher concentrations of Pb. Furthermore, the erosion of heaps resulting from wolfram exploitation leaves its signature as a peak of W concentrations recorded in the sediments of the DMP deposited between the 1960s and the 1990s. Wolfram exploitation was an important activity in the middle part of the 20th century, particularly during the period of the Second World War. (C) 2012 Elsevier Ltd. All rights reserved.

Interpolation estimate for a finite-element space with embedded discontinuities

We consider a recently proposed finite-element space that consists of piecewise affine functions with discontinuities across a smooth given interface Γ (a curve in two dimensions, a surface in three dimensions). Contrary to existing extended finite element methodologies, the space is a variant of the standard conforming Formula space that can be implemented element by element. Further, it neither introduces new unknowns nor deteriorates the sparsity structure. It is proved that, for u arbitrary in Formula, the interpolant Formula defined by this new space satisfies Graphic where h is the mesh size, Formula is the domain, Formula, Formula, Formula and standard notation has been adopted for the function spaces. This result proves the good approximation properties of the finite-element space as compared to any space consisting of functions that are continuous across Γ, which would yield an error in the Formula-norm of order Graphic. These properties make this space especially attractive for approximating the pressure in problems with surface tension or other immersed interfaces that lead to discontinuities in the pressure field. Furthermore, the result still holds for interfaces that end within the domain, as happens for example in cracked domains.

Space and Motion Perception and Discomfort in Air Travel

RAMOS RT, MATTOS DA, REBOUCAS ITS, RANVAUD RD. Space and motion perception and discomfort in air travel. Aviat Space Environ Med 2012; 83:1162-6. Introduction: The perception of comfort during air trips is determined by several factors. External factors like cabin design and environmental parameters (temperature, humidity, air pressure, noise, and vibration) interact with individual characteristics (anxiety traits, fear of flying, and personality) from arrival at the airport to landing at the destination. In this study, we investigated the influence of space and motion discomfort (SMD), fear of heights, and anxiety on comfort perception during all phases of air travel. Methods: We evaluated 51 frequent air travelers through a modified version of the Flight Anxiety Situations Questionnaire (FAS), in which new items were added and where the subjects were asked to report their level of discomfort or anxiety (not fear) for each phase of air travel (Chronbach's alpha = 0.974). Correlations were investigated among these scales: State-Trait Anxiety Inventory (STAB, Cohen's Acrophobia Questionnaire, and the Situational Characteristics Questionnaire (SitQ, designed to estimate SMD levels). Results: Scores of SitQ correlated with discomfort in situations involving space and movement perception (Pearson's rho = 0.311), while discomfort was associated with cognitive mechanisms related to scores in the anxiety scales (Pearson's rho = 0.375). Anxiety traits were important determinants of comfort perception before and after flight, while the influence of SMD was more significant during the time spent in the aircraft cabin. Discussion: SMD seems to be an important modulator of comfort perception in air travel. Its influence on physical well being and probably on cognitive performance, with possible effects on flight safety, deserves further investigation.

Transiting exoplanets from the CoRoT space mission XX. CoRoT-20b: A very high density, high eccentricity transiting giant planet

We report the discovery by the CoRoT space mission of a new giant planet, CoRoT-20b. The planet has a mass of 4.24 +/- 0.23 M-Jup and a radius of 0.84 +/- 0.04 R-Jup. With a mean density of 8.87 +/- 1.10 g cm(-3), it is among the most compact planets known so far. Evolutionary models for the planet suggest a mass of heavy elements of the order of 800 M-circle plus if embedded in a central core, requiring a revision either of the planet formation models or both planet evolution and structure models. We note however that smaller amounts of heavy elements are expected by more realistic models in which they are mixed throughout the envelope. The planet orbits a G-type star with an orbital period of 9.24 days and an eccentricity of 0.56. The star's projected rotational velocity is v sin i = 4.5 +/- 1.0 km s(-1), corresponding to a spin period of 11.5 +/- 3.1 days if its axis of rotation is perpendicular to the orbital plane. In the framework of Darwinian theories and neglecting stellar magnetic breaking, we calculate the tidal evolution of the system and show that CoRoT-20b is presently one of the very few Darwin-stable planets that is evolving toward a triple synchronous state with equality of the orbital, planetary and stellar spin periods.

A new enrichment space for the treatment of discontinuous pressures in multi-fluid flows

In this work, a new enrichment space to accommodate jumps in the pressure field at immersed interfaces in finite element formulations, is proposed. The new enrichment adds two degrees of freedom per element that can be eliminated by means of static condensation. The new space is tested and compared with the classical P1 space and to the space proposed by Ausas et al (Comp. Meth. Appl. Mech. Eng., Vol. 199, 10191031, 2010) in several problems involving jumps in the viscosity and/or the presence of singular forces at interfaces not conforming with the element edges. The combination of this enrichment space with another enrichment that accommodates discontinuities in the pressure gradient has also been explored, exhibiting excellent results in problems involving jumps in the density or the volume forces. Copyright (c) 2011 John Wiley & Sons, Ltd.

Records of sedimentary dynamics in the continental shelf and upper slope between Aveiro-Espinho (N Portugal)

The sedimentary unconsolidated cover of the Aveiro-Espinho continental shelf and upper slope (NW Portugal) records a complex interplay of processes including wave energy and currents, fluvial input, sediment transport alongshore and cross-shelf, geological and oceanographic processes and sediment sources and sinks. In order to study this record, a set of surface sediment samples was studied. Sediment grain size and composition, as well as the mineralogical composition (by XRD) of the fine (<63 mu m) and clay (<2 mu m) fractions and benthic microfaunal (foraminifera) data were analysed. Cluster analysis applied to the sedimentological data (grain size, sediment composition and mineralogy) allowed the establishment of three main zones corresponding to the: inner-, mid- and outer-shelf/upper slope. On the inner-shelf, the sedimentary coverture is composed of siliciclastic fine to very fine sand, essentially comprising modern (immature) terrigenous particles. The sediment grain size, as well as mineralogical and microfaunal composition, denote the high energetic conditions of this sector in which the alongshore transport of sand is predominantly southward and occurs mostly during the spring-summer oceanographic regime, when the main river providing sediments to this area, the River Douro, undergoes periods of drought. This effect may emphasize the erosive character of this coastal sector at present, since the Ria de Aveiro provides the shelf with few sediments. On the mid-shelf, an alongshore siliciclastic band of coarse sand and gravel can be found between the 40 m and 60 m isobaths. This gravelly deposit includes relic sediments deposited during lower sea-level stands. This structure stays on the surface due to the high bottom energy, which promotes the remobilization of the fine-grained sediments, and/or events of sediments bypassing. Benthic foraminifera density and "Benthic Foraminifera High Productivity" (BFHP) proxy values are in general low, which is consistent with the overall small supply of organic matter to the oceanic bottom in the inner- and mid-shelf. However, the Ria de Aveiro outflow, which delivers organic matter to the shelf, leaves its imprint mainly on the mid-shelf, identifiable by the increase in foraminifera density and BFHP values in front of the lagoon mouth. The higher values of BFHP along the 100 m isobath trace the present position of an oceanic thermal front whose situation may have changed in the last 3/5 ka BP. This zone marks a clear difference in the density, diversity and composition of benthic foraminifera assemblages. Here, in addition, sediment composition changes significantly, giving rise to carbonate-rich fine to medium sand in the deeper sector. The low bottom energy and the small sedimentation rate of the outer-shelf contributed to the preservation of a discontinuous carbonate-rich gravel band, between the 100 m and 140 m isobaths, also related to paleo-littorals, following the transgression that has occurred since the Last Glacial Maximum. The winter oceanographic regime favours the transport of fine grained sediments to the outer-shelf and upper slope. The inner- and mid-shelf, however, have low amounts of this kind of sediment and the Cretacic carbonated complexes Pontal da Galega and Pontal da Cartola, rocky outcrops located at the mid- and outer-shelf, act as morphological barriers to the cross-shelf transport of sediments. Thus a reduced sedimentation rate occurs in these deeper sectors, as indicated by the lower abundance of detrital minerals, which is compensated for the high sedimentary content of biogenic carbonates. The relatively high BFHP and Shannon Index values indicate water column stratification, high supply of organic matter and environmental stability, which provide favourable conditions for a diversified benthic fauna to flourish. These conditions also encourage authigenic chemical changes, favourable to glauconite formation, as well as illite and kaolinite degradation. Benthic foraminifera and clay mineral assemblages also reveal the effect of the internal waves pushing upward, and downslope losses of the sediments on the outer-shelf and upper slope.

Simcluster: clustering enumeration gene expression data on the simplex space

Abstract Background Transcript enumeration methods such as SAGE, MPSS, and sequencing-by-synthesis EST "digital northern", are important high-throughput techniques for digital gene expression measurement. As other counting or voting processes, these measurements constitute compositional data exhibiting properties particular to the simplex space where the summation of the components is constrained. These properties are not present on regular Euclidean spaces, on which hybridization-based microarray data is often modeled. Therefore, pattern recognition methods commonly used for microarray data analysis may be non-informative for the data generated by transcript enumeration techniques since they ignore certain fundamental properties of this space. Results Here we present a software tool, Simcluster, designed to perform clustering analysis for data on the simplex space. We present Simcluster as a stand-alone command-line C package and as a user-friendly on-line tool. Both versions are available at: http://xerad.systemsbiology.net/simcluster. Conclusion Simcluster is designed in accordance with a well-established mathematical framework for compositional data analysis, which provides principled procedures for dealing with the simplex space, and is thus applicable in a number of contexts, including enumeration-based gene expression data.

Relationship between space distribution of the benthic macroinvertebrates community and trophic state in a Neotropical reservoir (Itupararanga, Brazil)

The purpose of this work was to verify the benthic macroinvertebrates community responses through environmental factors along a headwater tropical reservoir. Samplings were taken with a Van-Veen grab along the reservoir in littoral and profundal regions and in the headwater, next to the dam and the middle of the reservoir. Samples were taken during both wet and dry seasons. Dissolved oxygen concentrations, electric conductivity, temperature and pH near the sediment have been performed in situ, at every sampling station by using a multiprobe and Secchi disc. Total water phosphorus and chlorophyll a concentrations were analyzed to determine the trophic state index. Sediment's organic matter, total phosphorus, nitrogen concentrations and granulometric composition were measured. In order to verify which environmental variables would have more influence over the benthic macroinvertebrates community, a canonical correspondence analysis (CCA) was performed. The total number of recorded taxa was 28. Among them, the family Chironomidae (Diptera) was the richest group (19 taxa). It can be proposed that the benthic macroinvertebrates community may be influenced by environmental conditions such as nutrient and organic matter availability, as well as dissolved oxygen concentration. Macroinvertebrates are adequate bioindicators of water quality due to their sensibility to environmental changes mentioned before. Chironomus sp, Limnodrilus hoffmeisteri and Branchiura sowerbyi comprises a group that can be considered bio-indicators of eutrophic conditions. A second group can be considered as indicator of mesotrophic conditions. The presence of two or more members from that group which comprises Tanytarsini spp, Fissimentum sp, Pelomus sp and Goeldichironomus sp, like predominant taxa, may indicates mesotrophic conditions.

On some Banach space constants arising in nonlinear fixed point and eigenvalue theory

[EN] As is well known, in any infinite-dimensional Banach space one may find fixed point free self-maps of the unit ball, retractions of the unit ball onto its boundary, contractions of the unit sphere, and nonzero maps without positive eigenvalues and normalized eigenvectors. In this paper, we give upper and lower estimates, or even explicit formulas, for the minimal Lipschitz constant and measure of noncompactness of such maps.

The structure of planktonic communities under variable coastal upwelling conditions off Cape Ghir (31ºN), in the Canary Current System (NW Africa)

Universidad de Las Palmas de Gran Canaria. Facultad de Ciencias del Mar. Programa de doctorado en Oceanografía. Diploma de Estudios Avanzados

A tuple space implementation for large-scale infrastructures

Coordinating activities in a distributed system is an open research topic. Several models have been proposed to achieve this purpose such as message passing, publish/subscribe, workflows or tuple spaces. We have focused on the latter model, trying to overcome some of its disadvantages. In particular we have applied spatial database techniques to tuple spaces in order to increase their performance when handling a large number of tuples. Moreover, we have studied how structured peer to peer approaches can be applied to better distribute tuples on large networks. Using some of these result, we have developed a tuple space implementation for the Globus Toolkit that can be used by Grid applications as a coordination service. The development of such a service has been quite challenging due to the limitations imposed by XML serialization that have heavily influenced its design. Nevertheless, we were able to complete its implementation and use it to implement two different types of test applications: a completely parallelizable one and a plasma simulation that is not completely parallelizable. Using this last application we have compared the performance of our service against MPI. Finally, we have developed and tested a simple workflow in order to show the versatility of our service.

Determination of bioactive and potentially toxic compounds in food: raw material analysis and shelf life evaluation

"Bioactive compounds" are extranutritional constituents that typically occur in small quantities in food. They are being intensively studied to evaluate their effects on health. Bioactive compounds include both water soluble compounds, such as phenolics, and lipidic substances such as n-3 fatty acids, tocopherols and sterols. Phenolic compounds, tocopherols and sterols are present in all plants and have been studied extensively in cereals, nuts and oil. n-3 fatty acids are present in fish and all around the vegetable kingdom. The aim of the present work was the determination of bioactive and potentially toxic compounds in cereal based foods and nuts. The first section of this study was focused on the determination of bioactive compounds in cereals. Because of that the different forms of phytosterols were investigated in hexaploid and tetraploid wheats. Hexaploid cultivars were the best source of esterified sterols (40.7% and 37.3% of total sterols for Triticum aestivum and Triticum spelta, respectively). Significant amounts of free sterols (65.5% and 60.7% of total sterols for Triticum durum and Triticum dicoccon, respectively) were found in the tetraploid cultivars. Then, free and bound phenolic compounds were identified in barley flours. HPLCESI/ MSD analysis in negative and positive ion mode established that barley free flavan-3- ols and proanthocyanidins were four dimers and four trimers having (epi)catechin and/or (epi)gallocatechin (C and/or GC) subunits. Hydroxycinnamic acids and their derivatives were the main bound phenols in barley flours. The results obtained demonstrated that barley flours were rich in phenolic compounds that showed high antioxidant activity. The study also examined the relationships between phenolic compounds and lipid oxidation of bakery. To this purpose, the investigated barley flours were used in the bakery production. The formulated oven products presented an interesting content of phenolic compounds, but they were not able to contain the lipid oxidation. Furthermore, the influence of conventional packaging on lipid oxidation of pasta was evaluated in n-3 enriched spaghetti and egg spaghetti. The results proved that conventional packaging was not appropriated to preserve pasta from lipid oxidation; in fact, pasta that was exposed to light showed a high content of potentially toxic compounds derived from lipid oxidation (such as peroxide, oxidized fatty acids and COPs). In the second section, the content of sterols, phenolic compounds, n-3 fatty acids and tocopherols in walnuts were reported. Rapid analytical techniques were used to analyze the lipid fraction and to characterize phenolic compounds in walnuts. Total lipid chromatogram was used for the simultaneous determination of the profile of sterols and tocopherols. Linoleic and linolenic acids were the most representative n-6 and n-3 essential dietary fatty acids present in these nuts. Walnuts contained substantial amounts of γ- and δ-tocopherol, which explained their antioxidant properties. Sitosterol, Δ5-avenasterol and campesterol were the major free sterols found. Capillary electrophoresis coupled to DAD and microTOF was utilized to determine phenolic content of walnut. A new compound in walnut ((2E,4E)- 8-hydroxy-2,7-dimethyl-2,4-decadiene-1,10-dioic acid 6-O-β-D-glucopiranosyl ester, [M−H]− 403.161m/z) with a structure similar to glansreginins was also identified. Phenolic compounds corresponded to 14–28% of total polar compounds quantified. Aglycone and glycosylated ellagic acid represented the principal components and account for 64–75% of total phenols in walnuts. However, the sum of glansreginins A, B and ((2E,4E)-8-hydroxy- 2,7-dimethyl-2,4-decadiene-1,10-dioic acid 6-O-β-D-glucopiranosyl ester was in the range of 72–86% of total quantified compounds.

Substructuring approache in state space models for dynamic system parameters identification

In the recent decade, the request for structural health monitoring expertise increased exponentially in the United States. The aging issues that most of the transportation structures are experiencing can put in serious jeopardy the economic system of a region as well as of a country. At the same time, the monitoring of structures is a central topic of discussion in Europe, where the preservation of historical buildings has been addressed over the last four centuries. More recently, various concerns arose about security performance of civil structures after tragic events such the 9/11 or the 2011 Japan earthquake: engineers looks for a design able to resist exceptional loadings due to earthquakes, hurricanes and terrorist attacks. After events of such a kind, the assessment of the remaining life of the structure is at least as important as the initial performance design. Consequently, it appears very clear that the introduction of reliable and accessible damage assessment techniques is crucial for the localization of issues and for a correct and immediate rehabilitation. The System Identification is a branch of the more general Control Theory. In Civil Engineering, this field addresses the techniques needed to find mechanical characteristics as the stiffness or the mass starting from the signals captured by sensors. The objective of the Dynamic Structural Identification (DSI) is to define, starting from experimental measurements, the modal fundamental parameters of a generic structure in order to characterize, via a mathematical model, the dynamic behavior. The knowledge of these parameters is helpful in the Model Updating procedure, that permits to define corrected theoretical models through experimental validation. The main aim of this technique is to minimize the differences between the theoretical model results and in situ measurements of dynamic data. Therefore, the new model becomes a very effective control practice when it comes to rehabilitation of structures or damage assessment. The instrumentation of a whole structure is an unfeasible procedure sometimes because of the high cost involved or, sometimes, because it’s not possible to physically reach each point of the structure. Therefore, numerous scholars have been trying to address this problem. In general two are the main involved methods. Since the limited number of sensors, in a first case, it’s possible to gather time histories only for some locations, then to move the instruments to another location and replay the procedure. Otherwise, if the number of sensors is enough and the structure does not present a complicate geometry, it’s usually sufficient to detect only the principal first modes. This two problems are well presented in the works of Balsamo [1] for the application to a simple system and Jun [2] for the analysis of system with a limited number of sensors. Once the system identification has been carried, it is possible to access the actual system characteristics. A frequent practice is to create an updated FEM model and assess whether the structure fulfills or not the requested functions. Once again the objective of this work is to present a general methodology to analyze big structure using a limited number of instrumentation and at the same time, obtaining the most information about an identified structure without recalling methodologies of difficult interpretation. A general framework of the state space identification procedure via OKID/ERA algorithm is developed and implemented in Matlab. Then, some simple examples are proposed to highlight the principal characteristics and advantage of this methodology. A new algebraic manipulation for a prolific use of substructuring results is developed and implemented.

Algorithms for UAS insertion in civil air space

One of the most interesting challenge of the next years will be the Air Space Systems automation. This process will involve different aspects as the Air Traffic Management, the Aircrafts and Airport Operations and the Guidance and Navigation Systems. The use of UAS (Uninhabited Aerial System) for civil mission will be one of the most important steps in this automation process. In civil air space, Air Traffic Controllers (ATC) manage the air traffic ensuring that a minimum separation between the controlled aircrafts is always provided. For this purpose ATCs use several operative avoidance techniques like holding patterns or rerouting. The use of UAS in these context will require the definition of strategies for a common management of piloted and piloted air traffic that allow the UAS to self separate. As a first employment in civil air space we consider a UAS surveillance mission that consists in departing from a ground base, taking pictures over a set of mission targets and coming back to the same ground base. During all mission a set of piloted aircrafts fly in the same airspace and thus the UAS has to self separate using the ATC avoidance as anticipated. We consider two objective, the first consists in the minimization of the air traffic impact over the mission, the second consists in the minimization of the impact of the mission over the air traffic. A particular version of the well known Travelling Salesman Problem (TSP) called Time-Dependant-TSP has been studied to deal with traffic problems in big urban areas. Its basic idea consists in a cost of the route between two clients depending on the period of the day in which it is crossed. Our thesis supports that such idea can be applied to the air traffic too using a convenient time horizon compatible with aircrafts operations. The cost of a UAS sub-route will depend on the air traffic that it will meet starting such route in a specific moment and consequently on the avoidance maneuver that it will use to avoid that conflict. The conflict avoidance is a topic that has been hardly developed in past years using different approaches. In this thesis we purpose a new approach based on the use of ATC operative techniques that makes it possible both to model the UAS problem using a TDTSP framework both to use an Air Traffic Management perspective. Starting from this kind of mission, the problem of the UAS insertion in civil air space is formalized as the UAS Routing Problem (URP). For this reason we introduce a new structure called Conflict Graph that makes it possible to model the avoidance maneuvers and to define the arc cost function of the departing time. Two Integer Linear Programming formulations of the problem are proposed. The first is based on a TDTSP formulation that, unfortunately, is weaker then the TSP formulation. Thus a new formulation based on a TSP variation that uses specific penalty to model the holdings is proposed. Different algorithms are presented: exact algorithms, simple heuristics used as Upper Bounds on the number of time steps used, and metaheuristic algorithms as Genetic Algorithm and Simulated Annealing. Finally an air traffic scenario has been simulated using real air traffic data in order to test our algorithms. Graphic Tools have been used to represent the Milano Linate air space and its air traffic during different days. Such data have been provided by ENAV S.p.A (Italian Agency for Air Navigation Services).