Comparative genomic approaches for investigating evolution in the microbial and viral populations of the rumen

The rumen is home to a diverse population of microorganisms encompassing all three domains of life: Bacteria, Archaea, and Eukarya. Viruses have also been documented to be present in large numbers; however, little is currently known about their role in the dynamics of the rumen ecosystem. This research aimed to use a comparative genomics approach in order to assess the potential evolutionary mechanisms at work in the rumen environment. We proposed to do this by first assessing the diversity and potential for horizontal gene transfer (HGT) of multiple strains of the cellulolytic rumen bacterium, Ruminococcus flavefaciens, and then by conducting a survey of rumen viral metagenome (virome) and subsequent comparison of the virome and microbiome sequences to ascertain if there was genetic information shared between these populations. We hypothesize that the bacteriophages play an integral role in the community dynamics of the rumen, as well as driving the evolution of the rumen microbiome through HGT. In our analysis of the Ruminococcus flavefaciens genomes, there were several mobile elements and clustered regularly interspaced short palindromic repeat (CRISPR) sequences detected, both of which indicate interactions with bacteriophages. The rumen virome sequences revealed a great deal of diversity in the viral populations. Additionally, the microbial and viral populations appeared to be closely associated; the dominant viral types were those that infect the dominant microbial phyla. The correlation between the distribution of taxa in the microbiome and virome sequences as well as the presence of CRISPR loci in the R. flavefaciens genomes, suggested that there is a “kill-the-winner” community dynamic between the viral and microbial populations in the rumen. Additionally, upon comparison of the rumen microbiome and rumen virome sequences, we found that there are many sequence similarities between these populations indicating a potential for phage-mediated HGT. These results suggest that the phages represent a gene pool in the rumen that could potentially contain genes that are important for adaptation and survival in the rumen environment, as well as serving as a molecular ‘fingerprint’ of the rumen ecosystem.

Liquid film dynamics in horizontal and tilted tubes: dry spots and sliding drops

Using a model derived from lubrication theory, we consider the evolution of a thin viscous film coating the interior or exterior of a cylindrical tube. The flow is driven by surface tension and gravity and the liquid is assumed to wet the cylinder perfectly. When the tube is horizontal, we use large-time simulations to describe the bifurcation structure of the capillary equilibria appearing at low Bond number. We identify a new film configuration in which an isolated dry patch appears at the top of the tube and demonstrate hysteresis in the transition between rivulets and annular collars as the tube length is varied. For a tube tilted to the vertical, we show how a long initially uniform rivulet can break up first into isolated drops and then annular collars, which subsequently merge. We also show that the speed at which a localized drop moves down the base of a tilted tube is non-monotonic in tilt angle.

Business model evolution and firm performance of entrepreneurial companies

This research explores the business model (BM) evolution process of entrepreneurial companies and investigates the relationship between BM evolution and firm performance. Recently, it has been increasingly recognised that the innovative design (and re-design) of BMs is crucial to the performance of entrepreneurial firms, as BM can be associated with superior value creation and competitive advantage. However, there has been limited theoretical and empirical evidence in relation to the micro-mechanisms behind the BM evolution process and the entrepreneurial outcomes of BM evolution. This research seeks to fill this gap by opening up the ‘black box’ of the BM evolution process, exploring the micro-patterns that facilitate the continuous shaping, changing, and renewing of BMs and examining how BM evolutions create and capture value in a dynamic manner. Drawing together the BM and strategic entrepreneurship literature, this research seeks to understand: (1) how and why companies introduce BM innovations and imitations; (2) how BM innovations and imitations interplay as patterns in the BM evolution process; and (3) how BM evolution patterns affect firm performances. This research adopts a longitudinal multiple case study design that focuses on the emerging phenomenon of BM evolution. Twelve entrepreneurial firms in the Chinese Online Group Buying (OGB) industry were selected for their continuous and intensive developments of BMs and their varying success rates in this highly competitive market. Two rounds of data collection were carried out between 2013 and 2014, which generates 31 interviews with founders/co-founders and in total 5,034 pages of data. Following a three-stage research framework, the data analysis begins by mapping the BM evolution process of the twelve companies and classifying the changes in the BMs into innovations and imitations. The second stage focuses down to the BM level, which addresses the BM evolution as a dynamic process by exploring how BM innovations and imitations unfold and interplay over time. The final stage focuses on the firm level, providing theoretical explanations as to the effects of BM evolution patterns on firm performance. This research provides new insights into the nature of BM evolution by elaborating on the missing link between BM dynamics and firm performance. The findings identify four patterns of BM evolution that have different effects on a firm’s short- and long-term performance. This research contributes to the BM literature by presenting what the BM evolution process actually looks like. Moreover, it takes a step towards the process theory of the interplay between BM innovations and imitations, which addresses the role of companies’ actions, and more importantly, reactions to the competitors. Insights are also given into how entrepreneurial companies achieve and sustain value creation and capture by successfully combining the BM evolution patterns. Finally, the findings on BM evolution contributes to the strategic entrepreneurship literature by increasing the understanding of how companies compete in a more dynamic and complex environment. It reveals that, the achievement of superior firm performance is more than a simple question of whether to innovate or imitate, but rather an integration of innovation and imitation strategies over time. This study concludes with a discussion of the findings and their implications for theory and practice.

Secular and tidal evolution of circumbinary systems

We investigate the secular dynamics of three-body circumbinary systems under the effect of tides. We use the octupolar non-restricted approximation for the orbital interactions, general relativity corrections, the quadrupolar approximation for the spins, and the viscous linear model for tides. We derive the averaged equations of motion in a simplified vectorial formalism, which is suitable to model the long-term evolution of a wide variety of circumbinary systems in very eccentric and inclined orbits. In particular, this vectorial approach can be used to derive constraints for tidal migration, capture in Cassini states, and stellar spin–orbit misalignment. We show that circumbinary planets with initial arbitrary orbital inclination can become coplanar through a secular resonance between the precession of the orbit and the precession of the spin of one of the stars. We also show that circumbinary systems for which the pericenter of the inner orbit is initially in libration present chaotic motion for the spins and for the eccentricity of the outer orbit. Because our model is valid for the non-restricted problem, it can also be applied to any three-body hierarchical system such as star–planet–satellite systems and triple stellar systems.

Impacts of high-nitrate freshwater inputs on macrotidal ecosystems. I. Seasonal evolution of nutrient limitation for the diatom-dominated phytoplankton of the Bay of Brest (France)

The chemical factors (inorganic nitrogen, phosphate, silicic acid) that potentially or actually control primary production were determined for the Bay of Brest, France, a macrotidal ecosystem submitted to high-nitrate-loaded freshwater inputs (winter nitrate freshwater concentrations >700 mu M, Si:N molar ratio as low as 0.2, i.e. among the lowest ever published). Intensive data collection and observations were carried out from February 1993 to March 1994 to determine the variations of physical [salinity, temperature, photosynthetically active radiation (PAR), freshwater discharges] and chemical (oxygen and nutrients) parameters and their impacts on the phytoplankton cycle (fluorescence, pigments, primary production). With insufficient PAR the winter stocks of nutrients were almost nonutilized and the nitrate excess was exported to the adjacent ocean, due to rapid tidal exchange. By early April, a diatom-dominated spring bloom developed (chlorophyll a maximum = 7.7 mu g l(-1); primary production maximum = 2.34 g C m(-2) d(-1)) under high initial nutrient concentrations. Silicic acid was rapidly exhausted over the whole water column; it is inferred to be the primary limiting factor responsible for the collapse of the spring bloom by mid-May. Successive phytoplankton developments characterized the period of secondary blooms during summer and fall (successive surface chlorophyll a maxima = 3.5, 1.6, 1.8 and 1.0 mu g l(-1); primary production = 1.24, 1.18 and 0.35 g C m(-2) d(-1)). Those secondary blooms developed under lower nutrient concentrations, mostly originating from nutrient recycling. Until August, Si and P most likely limited primary production, whereas the last stage of the productive period in September seemed to be N limited instead, this being a period of total nitrate depletion in almost the whole water column. Si limitation of spring blooms has become a common feature in coastal ecosystems that receive freshwater inputs with Si:N molar ratios <1. The peculiarity of Si Limitation in the Bay of Brest is its extension through the summer period.

Urban dynamics evaluation of Envigado city

This article presents the methodological conceptualization and the main results of a System Dynamics model, which main objective is to support the housing policies in the city of Envigado -- The used methodology developed a scenario-based model to emulate the approximate evolution of the housing demand and supply for the city, using a scenario of the Gross Domestic Product (GDP) and a housing authorization strategy as input -- Diverse results were obtained, for instance it was found that due to the soil availability, the housing supply reaches the saturation point between 2040 and 2046 -- Finally this article could be considered as an example of how academic tools such as System Dynamics can be used by decisions makers in the government

Co-evolution of friendships and antipathies: A longitudinal study of preschool peer groups

Material suplementar está disponível em: http://journal.frontiersin.org/article/10.3389/fpsyg. 2016.01509

Nonlinear evolution of harmonically forced perturbations on a wingtip vortex

Wingtip vortices are created by flying airplanes due to lift generation. The vortex interaction with the trailing aircraft has sparked researchers’ interest to develop an efficient technique to destroy these vortices. Different models have been used to describe the vortex dynamics and they all show that, under real flight conditions, the most unstable modes produce a very weak amplification. Another linear instability mechanism that can produce high energy gains in short times is due to the non-normality of the system. Recently, it has been shown that these non-normal perturbations also produce this energy growth when they are excited with harmonic forcing functions. In this study, we analyze numerically the nonlinear evolution of a spatially, pointwise and temporally forced perturbation, generated by a synthetic jet at a given radial distance from the vortex core. This type of perturbation is able to produce high energy gains in the perturbed base flow (10^3), and is also a suitable candidate for use in engineering applications. The flow field is solved for using fully nonlinear three-dimensional direct numerical simulation with a spectral multidomain penalty method model. Our novel results show that the nonlinear effects are able to produce locally small bursts of instability that reduce the intensity of the primary vortex.

Vortex Shedding Dynamics in Long Aspect-Ratio Aerodynamics Bodies

The focus of the current dissertation is to study qualitatively the underlying physics of vortex-shedding and wake dynamics in long aspect-ratio aerodynamics in incompressible viscous flow through the use of the KLE method. We carried out a long series of numerical experiments in the cases of flow around the cylinder at low Reynolds numbers. The study of flow at low Reynolds numbers provides an insight in the fluid physics and also plays a critical role when applying to stalled turbine rotors. Many of the conclusions about the qualitative nature of the physical mechanisms characterizing vortex formation, shedding and further interaction analyzed here at low Re could be extended to other Re regimes and help to understand the separation of the boundary layers in airfoils and other aerodynamic surfaces. In the long run, it aims to provide a better understanding of the complex multi-physics problems involving fluid-structure-control interaction through improved mathematical computational models of the multi-physics process. Besides the scientific conclusions produced, the research work on streamlined and bluff-body condition will also serve as a valuable guide for the future design of blade aerodynamics and the placement of wind turbines and hydrakinetic turbines, increasing the efficiency in the use of expensive workforce, supplies, and infrastructure. After the introductory section describing the main fields of application of wind power and hydrokinetic turbines, we describe the main features and theoretical background of the numerical method used here. Then, we present the analysis of the numerical experimentation results for the oscillatory regime right before the onset of vortex shedding for circular cylinders. We verified the wake length of the closed near-wake behind the cylinder and analysed the decay of the wake at the wake formation region, and then studied the St-Re relationship at the Reynolds numbers before the wake sheds compared to the experimental data. We found a theoretical model that describes the time evolution of the amplitude of fluctuations in the vorticity field on the twin vortex wake, which accurately matches the numerical results in terms of the frequency of the oscillation and rate of decay. We also proposed a model based on an analog circuit that is able to interpret the concerning flow by reducing the number of degrees of freedom. It follows the idea of the non-linear oscillator and resembles the dynamics mechanism of the closed near-wake with a common configured sine wave oscillator. This low-dimensional circuital model may also help to understand the underlying physical mechanisms, related to vorticity transport, that give origin to those oscillations.

Enterococcus faecalis prophage dynamics and contributions to pathogenic traits

Polylysogeny is frequently considered to be the result of an adaptive evolutionary process in which prophages confer fitness and/or virulence factors, thus making them important for evolution of both bacterial populations and infectious diseases. The Enterococcus faecalis V583 isolate belongs to the high-risk clonal complex 2 that is particularly well adapted to the hospital environment. Its genome carries 7 prophage-like elements (V583-pp1 to -pp7), one of which is ubiquitous in the species. In this study, we investigated the activity of the V583 prophages and their contribution to E. faecalis biological traits. We systematically analyzed the ability of each prophage to excise from the bacterial chromosome, to replicate and to package its DNA. We also created a set of E. faecalis isogenic strains that lack from one to all six non-ubiquitous prophages by mimicking natural excision. Our work reveals that prophages of E. faecalis V583 excise from the bacterial chromosome in the presence of a fluoroquinolone, and are able to produce active phage progeny. Intricate interactions between V583 prophages were also unveiled: i) pp7, coined EfCIV583 for E. faecalis chromosomal island of V583, hijacks capsids from helper phage 1, leading to the formation of distinct virions, and ii) pp1, pp3 and pp5 inhibit excision of pp4 and pp6. The hijacking exerted by EfCIV583 on helper phage 1 capsids is the first example of molecular piracy in Gram positive bacteria other than staphylococci. Furthermore, prophages encoding platelet-binding-like proteins were found to be involved in adhesion to human platelets, considered as a first step towards the development of infective endocarditis. Our findings reveal not only a role of E. faecalis V583 prophages in pathogenicity, but also provide an explanation for the correlation between antibiotic usage and E. faecalis success as a nosocomial pathogen, as fluoriquinolone may provoke release of prophages and promote gene dissemination among isolates.

Vortex evolution in the wake of accelerating low-aspect-ratio plates and three-dimensional bodies of revolution

To find examples of effecient locomotion and manoeuvrability, one need only turn to the elegant solutions natural flyers and swimmers have converged upon. This dissertation is specifically motivated by processes of evolutionary convergence, which have led to the propulsors and body shapes in nature that exhibit strong geometric collapse over diverse scales. These body features are abstracted in the studies presented herein using low-aspect-ratio at plates and a three-dimensional body of revolution (a sphere). The highly-separated vortical wakes that develop during accelerations are systematically characterized as a function of planform shape, aspect ratio, Reynolds number, and initial boundary conditions. To this end, force measurements and time-resolved (planar) particle image velocimetry have been used throughout to quantify the instantaneous forces and vortex evolution in the wake of the bluff bodies. During rectilinear motions, the wake development for the flat plates is primarily dependent on plate aspect ratio, with edge discontinuities and curvature playing only a secondary role. Furthermore, the axisymmetric case, i.e. the circular plate, shows strong sensitivity to Reynolds number, while this sensitivity quickly diminishes with increasing aspect ratio. For rotational motions, global insensitivity to plate aspect ratio has been observed. For the sphere, it has been shown that accelerations play an important role in the mitigation of flow separation. These results - expounded upon in this dissertation - have begun to shed light on the specific vortex dynamics that may be coopted by flying and swimming species of all shapes and sizes towards efficient locomotion.

Measure-valued mass evolution problems with flux boundary conditions and solution-dependent velocities

In this paper we prove well-posedness for a measure-valued continuity equation with solution-dependent velocity and flux boundary conditions, posed on a bounded one-dimensional domain. We generalize the results of an earlier paper [J. Differential Equations, 259 (2015), pp. 10681097] to settings where the dynamics are driven by interactions. In a forward-Euler-like approach, we construct a time-discretized version of the original problem and employ those results as a building block within each subinterval. A limit solution is obtained as the mesh size of the time discretization goes to zero. Moreover, the limit is independent of the specific way of partitioning the time interval [0, T]. This paper is partially based on results presented in Chapter 5 of [Evolution Equations for Systems Governed by Social Interactions, Ph.D. thesis, Eindhoven University of Technology, 2015], while a number of issues that were still open there are now resolved.

Federative dynamics in the EU under the influence of EU citizenship rights in times of crisis

The federative debate has been tied to the history of the EU integration from the start. Even though the EU is a polity in formation, the comparison with the state model has limited usefulness in assessing the evolution of federative dynamics in the EU. In the context of the EU, federalism should not be regarded as a static arrangement, but rather as a process that has been unfolding despite or because of EU integration setbacks. By the same token, EU citizenship is necessarily distinct from national citizenship. Our purpose in this article is to understand the federative dynamics of the EU in relation to the emergence of a “community of rights”. We also aim to establish if, and how, the on-going crisis has triggered a change in the EU federative process as a result of the weakening/strengthening of citizenship rights.

Advanced representation of the ocean/sea ice dynamics at high latitudes

Sea ice is a fundamental element of global climate system, with numerous impacts on the polar environment. The ongoing drastic changes in the Earth’s sea ice cover highlight the necessity of monitoring the polar regions and systematically evaluating the quality of different numerical products. The main objective of this thesis is to improve our knowledge of the representation of Arctic and Antarctic sea ice using comprehensive global ocean reanalyses and coupled climate models. The dissertation will explore (i) the Antarctic marginal ice zone (MIZ) and pack ice area in the ensemble mean of four global ocean reanalyses called GREP; (ii) historical representation of the Arctic and Antarctic sea ice state in HighResMIP models; (iii) the future evolution of Arctic sea ice in HighResMIP models. Global ocean reanalyses and GREP are found to adequately capture interannual and seasonal variability in both pack ice and MIZ areas at hemispheric and regional scales. The advantage of the ensemble-mean approach is proved as GREP smooths the strengths and weaknesses of single systems and provides the most consistent and reliable estimates. This work is intended to encourage the use of GREP in a wide range of applications. The analysis of sea ice representation in the coupled climate models shows no systematic impact of the increased horizontal resolution. We argue that a few minor improvements in sea ice representation with the enhanced horizontal resolution are presumably not worth the major effort of costly computations. The thesis highlights the critical importance to distinguish the MIZ from consolidated pack ice both for investigating changes in sea ice distribution and evaluating the product’s performance. Considering that the MIZ is predicted to dominate the Arctic sea ice cover, the model physics parameterizations and sea ice rheology might require modifications. The results of the work can be useful for modelling community.

Characterization of Mars rotational dynamics from Doppler tracking of the InSight lander

In the last decades the evolution of radio science has made it possible to infer the atmosphere composition, the surface and the internal structure of the planets. Since the arrival of the first landers on Mars it was possible to make accurate measurements of the dynamics of this planet; in this thesis we will focus on InSight, considering the data disclosed by the JPL relative to the period from November 26th, 2018 to August 15th, 2021. In particular, the Doppler and Range measurements conducted by the RISE (Rotation and Interior Structure Experiment) will be analyzed. Since the accuracy of these measurements was improved significantly the effects due to the atmosphere of Mars might be measured so it should thus be possible to obtain a better estimate of the parameters characterizing the rotational dynamic of Mars. A large part of this study will therefore be dedicated to the study, modeling, implementation and analysis of the atmosphere of Mars, in both its components: troposphere and ionosphere. Once the complete model of Mars had been built, i.e. including the atmosphere, it was then possible to analyze the residuals, obtained between the data of the measurements carried out and the values predicted by the developed model, in order to obtain an estimate of the rotational dynamic of Mars.