Emergent patterns of social organization in captive Cercocebus torquatus: Testing the GrooFiWorld agent-based model

We empirically applied the GrooFiWorld agent-based model (Puga-González et al. 2009) in a group of captive mangabeys (Cercocebus torquatus). We analysed several measurements related to aggression and affiliative patterns. The group adopted a combination of despotic and egalitarian behaviours resulting from the behavioural flexibility observed in the Cercopithecinae subfamily. Our study also demonstrates that the GrooFiWorld agent-based model can be extended to other members of the Cercopithecinae subfamily generating parsimonious hypotheses related to the social organization.

Digital evidence, 'absence' of data and ambiguous patterns of reasoning

In this paper we discuss the use of digital data by the Swiss Federal Criminal Court in a recent case of attempted homicide. We use this case to examine drawbacks for the defense when the presentation of scientific evidence is partial, especially when the only perspective mentioned is that of the prosecution. We tackle this discussion at two distinct levels. First, we pursue an essentially non-technical presentation of the topic by drawing parallels between the court's summing up of the case and flawed patterns of reasoning commonly seen in other forensic disciplines, such as DNA and particle traces (e.g., gunshot residues). Then, we propose a formal analysis of the case, using elements of probability and graphical probability models, to justify our main claim that the partial presentation of digital evidence poses a risk to the administration of justice in that it keeps vital information from the defense. We will argue that such practice constitutes a violation of general principles of forensic interpretation as established by forensic science literature and current recommendations by forensic science interest groups (e.g., the European Network of Forensic Science Institutes). Finally, we posit that argument construction and analysis using formal methods can help replace digital evidence appropriately into context and thus support a sound evaluation of the evidence.

Travellers' profile, travel patterns and vaccine practices-a 10-year prospective study in a Swiss Travel Clinic.

BACKGROUND: The travel clinic in Lausanne serves a catchment area of 700 000 of inhabitants and provides pre- and post-travel consultations. This study describes the profile of attendees before departure, their travel patterns and the travel clinic practices in terms of vaccination over time. METHODS: We included all pre-travel first consultation data recorded between November 2002 and December 2012 by a custom-made program DIAMM/G. We analysed client profiles, travel characteristics and vaccinations prescribed over time. RESULTS: Sixty-five thousand and forty-six client-trips were recorded. Fifty-one percent clients were female. Mean age was 32 years. In total, 0.1% were aged <1 year and 0.2% ≥80 years. Forty-six percent of travellers had pre-existing medical conditions. Forty-six percent were travelling to Africa, 35% to Asia, 20% to Latin America and 1% (each) to Oceania and Europe; 19% visited more than one country. India was the most common destination (9.6% of travellers) followed by Thailand (8.6%) and Kenya (6.4%). Seventy-three percent of travellers were planning to travel for ≤ 4 weeks. The main reasons for travel were tourism (75%) and visiting friends and relatives (18%). Sixteen percent were backpackers. Pre-travel advice were sought a median of 29 days before departure. Ninety-nine percent received vaccine(s). The most frequently administered vaccines were hepatitis A (53%), tetanus-diphtheria (46%), yellow fever (39%), poliomyelitis (38%) and typhoid fever (30%). CONCLUSIONS: The profile of travel clinic attendees was younger than the general Swiss population. A significant proportion of travellers received vaccinations that are recommended in the routine national programme. These findings highlight the important role of travel clinics to (i) take care of an age group that has little contact with general practitioners and (ii) update vaccination status. The most commonly prescribed travel-related vaccines were for hepatitis A and yellow fever. The question remains to know whether clients do attend travel clinics because of compulsory vaccinations or because of real travel health concern or both.

Complex patterns of global spread in invasive insects: eco-evolutionary and management consequences

The advent of simple and affordable tools for molecular identification of novel insect invaders and assessment of population diversity has changed the face of invasion biology in recent years. The widespread application of these tools has brought with it an emerging understanding that patterns in biogeography, introduction history and subsequent movement and spread of many invasive alien insects are far more complex than previously thought. We reviewed the literature and found that for a number of invasive insects, there is strong and growing evidence that multiple introductions, complex global movement, and population admixture in the invaded range are commonplace. Additionally, historical paradigms related to species and strain identities and origins of common invaders are in many cases being challenged. This has major consequences for our understanding of basic biology and ecology of invasive insects and impacts quarantine, management and biocontrol programs. In addition, we found that founder effects rarely limit fitness in invasive insects and may benefit populations (by purging harmful alleles or increasing additive genetic variance). Also, while phenotypic plasticity appears important post-establishment, genetic diversity in invasive insects is often higher than expected and increases over time via multiple introductions. Further, connectivity among disjunct regions of global invasive ranges is generally far higher than expected and is often asymmetric, with some populations contributing disproportionately to global spread. We argue that the role of connectivity in driving the ecology and evolution of introduced species with multiple invasive ranges has been historically underestimated and that such species are often best understood in a global context.

Complete Analysis of Configuration Rules to Guarantee Reliable Network Security Policies

Peer-reviewed

Modeling the transport phenomena within arterial wall: porous media approach

The transport of macromolecules, such as low-density lipoprotein (LDL), and their accumulation in the layers of the arterial wall play a critical role in the creation and development of atherosclerosis. Atherosclerosis is a disease of large arteries e.g., the aorta, coronary, carotid, and other proximal arteries that involves a distinctive accumulation of LDL and other lipid-bearing materials in the arterial wall. Over time, plaque hardens and narrows the arteries. The flow of oxygen-rich blood to organs and other parts of the body is reduced. This can lead to serious problems, including heart attack, stroke, or even death. It has been proven that the accumulation of macromolecules in the arterial wall depends not only on the ease with which materials enter the wall, but also on the hindrance to the passage of materials out of the wall posed by underlying layers. Therefore, attention was drawn to the fact that the wall structure of large arteries is different than other vessels which are disease-resistant. Atherosclerosis tends to be localized in regions of curvature and branching in arteries where fluid shear stress (shear rate) and other fluid mechanical characteristics deviate from their normal spatial and temporal distribution patterns in straight vessels. On the other hand, the smooth muscle cells (SMCs) residing in the media layer of the arterial wall respond to mechanical stimuli, such as shear stress. Shear stress may affect SMC proliferation and migration from the media layer to intima. This occurs in atherosclerosis and intimal hyperplasia. The study of blood flow and other body fluids and of heat transport through the arterial wall is one of the advanced applications of porous media in recent years. The arterial wall may be modeled in both macroscopic (as a continuous porous medium) and microscopic scales (as a heterogeneous porous medium). In the present study, the governing equations of mass, heat and momentum transport have been solved for different species and interstitial fluid within the arterial wall by means of computational fluid dynamics (CFD). Simulation models are based on the finite element (FE) and finite volume (FV) methods. The wall structure has been modeled by assuming the wall layers as porous media with different properties. In order to study the heat transport through human tissues, the simulations have been carried out for a non-homogeneous model of porous media. The tissue is composed of blood vessels, cells, and an interstitium. The interstitium consists of interstitial fluid and extracellular fibers. Numerical simulations are performed in a two-dimensional (2D) model to realize the effect of the shape and configuration of the discrete phase on the convective and conductive features of heat transfer, e.g. the interstitium of biological tissues. On the other hand, the governing equations of momentum and mass transport have been solved in the heterogeneous porous media model of the media layer, which has a major role in the transport and accumulation of solutes across the arterial wall. The transport of Adenosine 5´-triphosphate (ATP) is simulated across the media layer as a benchmark to observe how SMCs affect on the species mass transport. In addition, the transport of interstitial fluid has been simulated while the deformation of the media layer (due to high blood pressure) and its constituents such as SMCs are also involved in the model. In this context, the effect of pressure variation on shear stress is investigated over SMCs induced by the interstitial flow both in 2D and three-dimensional (3D) geometries for the media layer. The influence of hypertension (high pressure) on the transport of lowdensity lipoprotein (LDL) through deformable arterial wall layers is also studied. This is due to the pressure-driven convective flow across the arterial wall. The intima and media layers are assumed as homogeneous porous media. The results of the present study reveal that ATP concentration over the surface of SMCs and within the bulk of the media layer is significantly dependent on the distribution of cells. Moreover, the shear stress magnitude and distribution over the SMC surface are affected by transmural pressure and the deformation of the media layer of the aorta wall. This work reflects the fact that the second or even subsequent layers of SMCs may bear shear stresses of the same order of magnitude as the first layer does if cells are arranged in an arbitrary manner. This study has brought new insights into the simulation of the arterial wall, as the previous simplifications have been ignored. The configurations of SMCs used here with elliptic cross sections of SMCs closely resemble the physiological conditions of cells. Moreover, the deformation of SMCs with high transmural pressure which follows the media layer compaction has been studied for the first time. On the other hand, results demonstrate that LDL concentration through the intima and media layers changes significantly as wall layers compress with transmural pressure. It was also noticed that the fraction of leaky junctions across the endothelial cells and the area fraction of fenestral pores over the internal elastic lamina affect the LDL distribution dramatically through the thoracic aorta wall. The simulation techniques introduced in this work can also trigger new ideas for simulating porous media involved in any biomedical, biomechanical, chemical, and environmental engineering applications.

Process intensification: From optimised flow patterns to microprocess technology

This thesis is focused on process intensification. Several significant problems and applications of this theme are covered. Process intensification is nowadays one of the most popular trends in chemical engineering and attempts have been made to develop a general, systematic methodology for intensification. This seems, however, to be very difficult, because intensified processes are often based on creativity and novel ideas. Monolith reactors and microreactors are successful examples of process intensification. They are usually multichannel devices in which a proper feed technique is important for creating even fluid distribution into the channels. Two different feed techniques were tested for monoliths. In the first technique a shower method was implemented by means of perforated plates. The second technique was a dispersion method using static mixers. Both techniques offered stable operation and uniform fluid distribution. The dispersion method enabled a wider operational range in terms of liquid superficial velocity. Using dispersion method, a volumetric gas-liquid mass transfer coefficient of 2 s-1 was reached. Flow patterns play a significant role in terms of the mixing performance of micromixers. Although the geometry of a T-mixer is simple, channel configurations and dimensions had a clear effect on mixing efficiency. The flow in the microchannel was laminar, but the formation of vortices promoted mixing in micro T-mixers. The generation of vortices was dependent on the channel dimensions, configurations and flow rate. Microreactors offer a high ratio of surface area to volume. Surface forces and interactions between fluids and surfaces are, therefore, often dominant factors. In certain cases, the interactions can be effectively utilised. Different wetting properties of solid materials (PTFE and stainless steel) were applied in the separation of immiscible liquid phases. A micro-scale plate coalescer with hydrophilic and hydrophobic surfaces was used for the continuous separation of organic and aqueous phases. Complete phase separation occurred in less than 20 seconds, whereas the separation time by settling exceeded 30 min. Fluid flows can be also intensified in suitable conditions. By adding certain additives into turbulent fluid flow, it was possible to reduce friction (drag) by 40 %. Drag reduction decreases frictional pressure drop in pipelines which leads to remarkable energy savings and decreases the size or number of pumping facilities required, e.g., in oil transport pipes. Process intensification enables operation often under more optimal conditions. The consequent cost savings from reduced use of raw materials and reduced waste lead to greater economic benefits in processing.

Identification of molecular subtypes and gene expression patterns of breast cancer analysing RNA-seq data

Breast cancer is the most common diagnosed cancer and the leading cause of cancer death among females worldwide. It is considered a highly heterogeneous disease and it must be classified into more homogeneous groups. Hence, the purpose of this study was to classify breast tumors based on variations in gene expression patterns derived from RNA sequencing by using different class discovery methods. 42 breast tumors paired-samples were sequenced by Illumine Genome Analyzer and the data was analyzed and prepared by TopHat2 and htseq-count. As reported previously, breast cancer could be grouped into five main groups known as basal epithelial-like group, HER2 group, normal breast-like group and two Luminal groups with a distinctive expression profile. Classifying breast tumor samples by using PAM50 method, the most common subtype was Luminal B and was significantly associated with ESR1 and ERBB2 high expression. Luminal A subtype had ESR1 and SLC39A6 significant high expression, whereas HER2 subtype had a high expression of ERBB2 and CNNE1 genes and low luminal epithelial gene expression. Basal-like and normal-like subtypes were associated with low expression of ESR1, PgR and HER2, and had significant high expression of cytokeratins 5 and 17. Our results were similar compared with TGCA breast cancer data results and with known studies related with breast cancer classification. Classifying breast tumors could add significant prognostic and predictive information to standard parameters, and moreover, identify marker genes for each subtype to find a better therapy for patients with breast cancer.

LSB Matching Steganalysis Based on Patterns of Pixel Differences and Random Embedding

Peer-reviewed

Determinacion de la configuracion E-Z de los acidos Fumarico y Maleico. Un experimento orientado a incentivar el desarrollo de la investigacion cientifica en alumnos de Pregrado

In this work we intend to eliminate the idea that laboratory exercises seem like cookbooks. That is, exercises shall be presented as a problematic situation. Based on observation and experimentation, the students should determine the E-Z configuration of maleic and fumaric acids. The basis of this laboratory exercise is the acid-catalyzed isomerization of maleic acid to fumaric acid. Students are given the starting material, reagents and the experimental procedure. They are told that the starting material is a dicarboxylic acid containing a C=C double bond of formula C4H4O4. Students determine melting points, solubilities, acidity and chromatographic patterns for both the starting material and the product, so that a configuration of each acid can be proposed. This type of experiment yields excellent results, because the students are left to deduce that maleic acid is less stable than fumaric acid. Additionally, they conclude that maleic acid is the "Z" isomer and fumaric acid is the "E" isomer. Finally, this laboratory exercise allows the students to develop simultaneously their critical-thinking skills with the respective laboratory techniques and not to see chemistry as recipes to be followed.

Geographic patterns of genetic variation in a broadly distributed marine vertebrate: new insights into loggerhead turtle stock structure from expanded mitochondrial DNA sequences

Previous genetic studies have demonstrated that natal homing shapes the stock structure of marine turtle nesting populations. However, widespread sharing of common haplotypes based on short segments of the mitochondrial control region often limits resolution of the demographic connectivity of populations. Recent studies employing longer control region sequences to resolve haplotype sharing have focused on regional assessments of genetic structure and phylogeography. Here we synthesize available control region sequences for loggerhead turtles from the Mediterranean Sea, Atlantic, and western Indian Ocean basins. These data represent six of the nine globally significant regional management units (RMUs) for the species and include novel sequence data from Brazil, Cape Verde, South Africa and Oman. Genetic tests of differentiation among 42 rookeries represented by short sequences (380 bp haplotypes from 3,486 samples) and 40 rookeries represented by long sequences (~800 bp haplotypes from 3,434 samples) supported the distinction of the six RMUs analyzed as well as recognition of at least 18 demographically independent management units (MUs) with respect to female natal homing. A total of 59 haplotypes were resolved. These haplotypes belonged to two highly divergent global lineages, with haplogroup I represented primarily by CC-A1, CC-A4, and CC-A11 variants and haplogroup II represented by CC-A2 and derived variants. Geographic distribution patterns of haplogroup II haplotypes and the nested position of CC-A11.6 from Oman among the Atlantic haplotypes invoke recent colonization of the Indian Ocean from the Atlantic for both global lineages. The haplotypes we confirmed for western Indian Ocean RMUs allow reinterpretation of previous mixed stock analysis and further suggest that contemporary migratory connectivity between the Indian and Atlantic Oceans occurs on a broader scale than previously hypothesized. This study represents a valuable model for conducting comprehensive international cooperative data management and research in marine ecology.

The Design of a Software Lifecycle Management Framework to a Configuration Management System

Keeping track of software assets and managing software installations in IT environments can be a hard endeavor, especially when the size and diversity of the environment grows. How to install and uninstall software efficiently and cost effectively? Are there too few or too many software licenses purchased? If installed, is the software actually in use? Software Asset Management (SAM) is a process that involves managing and optimizing the purchase, deployment, maintenance, utilization, and disposal of software applications within an organization. This master’s thesis describes a special Software Lifecycle Management Framework to provide solutions to the multitude of challenges within SAM. The main objectives when designing the framework was to provide a set of tools to control the software assets during their entire lifecycle while trying to minimize the costs related to owning and managing them.

Conservation Laws in Cellular Automata

Conservation laws in physics are numerical invariants of the dynamics of a system. In cellular automata (CA), a similar concept has already been defined and studied. To each local pattern of cell states a real value is associated, interpreted as the “energy” (or “mass”, or . . . ) of that pattern.The overall “energy” of a configuration is simply the sum of the energy of the local patterns appearing on different positions in the configuration. We have a conservation law for that energy, if the total energy of each configuration remains constant during the evolution of the CA. For a given conservation law, it is desirable to find microscopic explanations for the dynamics of the conserved energy in terms of flows of energy from one region toward another. Often, it happens that the energy values are from non-negative integers, and are interpreted as the number of “particles” distributed on a configuration. In such cases, it is conjectured that one can always provide a microscopic explanation for the conservation laws by prescribing rules for the local movement of the particles. The onedimensional case has already been solved by Fuk´s and Pivato. We extend this to two-dimensional cellular automata with radius-0,5 neighborhood on the square lattice. We then consider conservation laws in which the energy values are chosen from a commutative group or semigroup. In this case, the class of all conservation laws for a CA form a partially ordered hierarchy. We study the structure of this hierarchy and prove some basic facts about it. Although the local properties of this hierarchy (at least in the group-valued case) are tractable, its global properties turn out to be algorithmically inaccessible. In particular, we prove that it is undecidable whether this hierarchy is trivial (i.e., if the CA has any non-trivial conservation law at all) or unbounded. We point out some interconnections between the structure of this hierarchy and the dynamical properties of the CA. We show that positively expansive CA do not have non-trivial conservation laws. We also investigate a curious relationship between conservation laws and invariant Gibbs measures in reversible and surjective CA. Gibbs measures are known to coincide with the equilibrium states of a lattice system defined in terms of a Hamiltonian. For reversible cellular automata, each conserved quantity may play the role of a Hamiltonian, and provides a Gibbs measure (or a set of Gibbs measures, in case of phase multiplicity) that is invariant. Conversely, every invariant Gibbs measure provides a conservation law for the CA. For surjective CA, the former statement also follows (in a slightly different form) from the variational characterization of the Gibbs measures. For one-dimensional surjective CA, we show that each invariant Gibbs measure provides a conservation law. We also prove that surjective CA almost surely preserve the average information content per cell with respect to any probability measure.

Shaping urban traffic patterns through congestion charging : What factors drive success or failure?

Congestion costs are emerging as one of the most important challenges faced by metropolitan planners and transport authorities in first world economies. In US these costs were as high as 78 million dollars in 2005 and are growing due to fast increases in travel delays. In order to solve the current and severe levels of congestion the US department of transportation have recently started a program to initiate congestion pricing in five metropolitan areas. In this context it is important to determine those factors helping its implementation and success, but also the problems or difficulties associated with charging projects. In this article we analyze worldwide experiences with urban road charging in order to extract interesting and helpful lessons for policy makers engaged in congestion pricing projects and for those interested in the introduction of traffic management tools to regulate the entrance to big cities.

Síntese de enaminonas

The general term "enaminone" is applied to any compound bearing the conjugated system N-C=C-C=O. Enaminones are typical capto-dative ethylenes, showing particular properties due to pi-electron delocalization. Their reactivity can be predicted by structural patterns of substitution, conformation and configuration, making them versatile synthetic building blocks. In this review, a variety of methods for the synthesis of enaminones is described. The methods were divided into condensation of amines to beta-dicarbonyl compounds, addition of amines to a,b-unsaturated carbonyl compounds, condensation between carbonyl compounds and N-unsaturated functions and other methods, covering the period from 1993 to 2001.