Tracking Invasion Histories in the Sea: Facing Complex Scenarios Using Multilocus Data

In recent years, new analytical tools have allowed researchers to extract historical information contained in molecular data, which has fundamentally transformed our understanding of processes ruling biological invasions. However, the use of these new analytical tools has been largely restricted to studies of terrestrial organisms despite the growing recognition that the sea contains ecosystems that are amongst the most heavily affected by biological invasions, and that marine invasion histories are often remarkably complex. Here, we studied the routes of invasion and colonisation histories of an invasive marine invertebrate Microcosmus squamiger (Ascidiacea) using microsatellite loci, mitochondrial DNA sequence data and 11 worldwide populations. Discriminant analysis of principal components, clustering methods and approximate Bayesian computation (ABC) methods showed that the most likely source of the introduced populations was a single admixture event that involved populations from two genetically differentiated ancestral regions - the western and eastern coasts of Australia. The ABC analyses revealed that colonisation of the introduced range of M. squamiger consisted of a series of non-independent introductions along the coastlines of Africa, North America and Europe. Furthermore, we inferred that the sequence of colonisation across continents was in line with historical taxonomic records - first the Mediterranean Sea and South Africa from an unsampled ancestral population, followed by sequential introductions in California and, more recently, the NE Atlantic Ocean. We revealed the most likely invasion history for world populations of M. squamiger, which is broadly characterized by the presence of multiple ancestral sources and non-independent introductions within the introduced range. The results presented here illustrate the complexity of marine invasion routes and identify a cause-effect relationship between human-mediated transport and the success of widespread marine non-indigenous species, which benefit from stepping-stone invasions and admixture processes involving different sources for the spread and expansion of their range.

Integrating quantitative proteomics and metabolomics in a cellular model of diabetic retinopathy

Diabetic retinopathy is the leading cause of visual loss in individuals under the age of 55. Most investigations into the pathogenesis of diabetic retinopathy have been concentrated on the neural retina since this is where clinical lesions are manifested. Recently, however, various abnormalities in the structural and secretory functions of retinal pigment epithelium that are essential for neuroretina survival, have been found in diabetic retinopathy. In this context, here we study the effect of hyperglycemic and hypoxic conditions on the metabolism of a human retinal pigment epithelial cell line (ARPE-19) by integrating quantitative proteomics using tandem mass tagging (TMT), untargeted metabolomics using MS and NMR, and 13C-glucose isotopic labeling for metabolic tracking. We observed a remarkable metabolic diversification under our simulated in vitro hyperglycemic conditions of diabetes, characterized increased flux through polyol pathways and inhibition of the Krebs cycle and oxidative phosphorylation. Importantly, under low oxygen supply RPE cells seem to consume rapidly glycogen storages and stimulate anaerobic glycolysis. Our results therefore pave the way to future scenarios involving new therapeutic strategies addressed to modulating RPE metabolic impairment, with the aim of regulating structural and secretory alterations of RPE. Finally, this study shows the importance of tackling biomedical problems by integrating metabolomic and proteomics results.

Past climate-driven range shifts and population genetic diversity in arctic plants

AimHigh intra-specific genetic diversity is necessary for species adaptation to novel environments under climate change, but species tracking suitable conditions are losing alleles through successive founder events during range shift. Here, we investigated the relationship between range shift since the Last Glacial Maximum (LGM) and extant population genetic diversity across multiple plant species to understand variability in species responses. LocationThe circumpolar Arctic and northern temperate alpine ranges. MethodsWe estimated the climatic niches of 30 cold-adapted plant species using range maps coupled with species distribution models and hindcasted species suitable areas to reconstructions of the mid-Holocene and LGM climates. We computed the species-specific migration distances from the species glacial refugia to their current distribution and correlated distances to extant genetic diversity in 1295 populations. Differential responses among species were related to life-history traits. ResultsWe found a negative association between inferred migration distances from refugia and genetic diversities in 25 species, but only 11 had statistically significant negative slopes. The relationships between inferred distance and population genetic diversity were steeper for insect-pollinated species than wind-pollinated species, but the difference among pollination system was marginally independent from phylogenetic autocorrelation. Main conclusionThe relationships between inferred migration distances and genetic diversities in 11 species, independent from current isolation, indicate that past range shifts were associated with a genetic bottleneck effect with an average of 21% loss of genetic diversity per 1000km(-1). In contrast, the absence of relationship in many species also indicates that the response is species specific and may be modulated by plant pollination strategies or result from more complex historical contingencies than those modelled here.

Combining stable isotope analyses and geolocation to reveal kittiwake migration

Determining migratory strategies of seabirds is still a major challenge due to their relative inaccessibility. Small geolocators are improving this knowledge, but not all birds can be tracked. Stable isotope ratios in feathers can help us to understand migration, but we still have insufficient baseline knowledge for linking feather signatures to movements amongst distinct water masses. To understand the migration strategies of kittiwakes Rissa tridactyla and the link between stable isotopes in feathers and the areas in which these were grown, we tracked 6 kittiwakes from Hornøya, Norway, with light level geolocators over 1 yr. Then we analysed the stable isotopes of carbon and nitrogen in their 1st and 7th primary feathers as well as in the 1st, 3rd, 5th, 7th and 10th primaries of 12 birds found freshly dead in the same breeding colony. After breeding, all tracked birds moved east of the Svalbard Archipelago and subsequently migrated to the Labrador Sea. Thereafter, birds showed individual variation in migration strategies: 3 travelled to the NE Atlantic, whereas the others remained in the Labrador Sea until the end of the wintering period. Changes in stable isotope signatures from the 1st to the 10th primary feathers corresponded well to the sequence of movements during migration and the area in which we inferred that each feather was grown. Thus, by combining information on moult patterns and tracking data, we demonstrate that stable isotope analysis of feathers can be used to trace migratory movements of seabirds.

Trans-equatorial migration and mixing in the wintering areas of a pelagic seabird

Despite increasing interest in long-distance migration, the wintering areas, migration corridors, and population mix in winter quarters of most pelagic marine predators are unknown. Here, we present the first study tracking migration movements of shearwaters through the non-breeding period. We used geolocators (global location sensing [GLS] units based on ambient light levels) to track 22 Cory's shearwaters (Calonectris diomedea) breeding in three different areas. Most birds wintered in one or more of three relatively small areas, all clearly associated with major coastal upwelling systems of the tropical and south Atlantic. Trans-equatorial movements were dominated by prevailing trade winds and westerlies, while calm, oligotrophic areas were avoided. Breeding populations clearly differed in their preference amongst the three major wintering areas, but showed substantial mixing. This illustrates the exceptional value of GLS, not only for determining and describing the influence of oceanographic features on migration patterns, but also for assessing population mix in winter quarters. This knowledge is essential to understanding the impacts of population-level threats, such as longlining, offshore windfarms, and oil spills on multiple breeding sites, and will be critical in devising conservation policies that guarantee the sustainable exploitation of the oceans.

Metals and Selenium as bioindicators of geographic and trophic segregation in Giant Petrels Macronectes spp.

We analysed concentrations of cadmium, lead, mercury and selenium in blood from males and females of the 2 sibling species of giant petrels, the northern Macronectes halli and the southern M. giganteus, breeding sympatrically at Bird Island (South Georgia, Antarctica). Blood samples were collected in 1998 during the incubation period, from 5 November to 10 December. Between species, cadmium and lead concentrations were significantly higher for northern than for southern giant petrels, which probably resulted from northern giant petrels wintering in more polluted areas (mainly on the Patagonian Shelf and Falkland Islands) compared to southern giant petrels (wintering mainly around South Georgia and the South Sandwich Islands). Between sexes, cadmium concentrations were significantly higher for females than for males in both species, corresponding to the more pelagic habits of females compared to the more scavenging habits of males. Lead and cadmium concentrations in circulating blood decreased significantly over the incubation period, suggesting that when breeding at Bird Island, exposure to the source of pollution had ended, and these metals had been cleared from the blood and excreted, or rapidly transferred to other tissues. Association of lead and cadmium with a common source of pollution was further corroborated by a significant positive correlation between the levels of the 2 elements found. Mercury levels were similar between the species, but showed an opposite trend between sexes, with males showing higher levels than females in northern giant petrels, and the opposite was true in southern giant petrels, with no changes throughout incubation. Selenium levels were similar between sexes, but significantly greater for northern than for southern giant petrels. Moreover, there was a significant increase in the selenium levels over the incubation period in northern giant petrels. Age of adult birds did not affect metal concentrations. Coefficients of variation of metal levels were consistently lower for northern than for southern giant petrels, particularly for mercury, suggesting that the former species is more dietary specialised than the latter. Contaminant analyses, when combined with accurate information on seabird movements, obtained through geolocation or satellite tracking, help us to understand geographic variation of pollution in the marine environment.

Tracking of physical activity during adolescence: The 1993 Pelotas Birth Cohort, Brazil

Objective: To analyze physical activity during adolescence in participants of the 1993 Pelotas Birth Cohort Study, Brazil. Methods: Data on leisure time physical activity at 11, 15, and 18 years of age were analyzed. At each visit, a cut-off point of 300 min/week was used to classify adolescents as active or inactive. A total of 3,736 participants provided data on physical activity at each of the three age points. Results: A significant decline in the proportion of active adolescents was observed from 11 to 18 years of age, particularly among girls (from 32.9% to 21.7%). The proportions of girls and boys who were active at all three age points were 28.0% and 55.1%, respectively. After adjustment for sex, economic status, and skin color, participants who were active at 11 and 15 years of age were 58.0% more likely to be active at 18 years of age compared with those who were inactive at 11 and 15 years of age. Conclusions: Physical activity declined during adolescence and inactivity tended to track over time. Our findings reinforce the need to promote physical activity at early stages of life, because active behavior established early tends to be maintained over time.

The Importance of Semantics: Visual World Studies on Drawing Inferences and Resolving Anaphors

The present thesis investigated the importance of semantics in generating inferences during discourse processing. Three aspects of semantics, gender stereotypes, implicit causality information and proto-role properties, were used to investigate whether semantics is activated elaboratively during discourse comprehension and what its relative importance is in backward inferencing compared to discourse/structural cues. Visual world eye-tracking studies revealed that semantics plays an important role in both backward and forward inferencing: Gender stereotypes and implicit causality information is activated elaboratively during online discourse comprehension. Moreover, gender stereotypes, implicit causality and proto-role properties of verbs are all used in backward inferencing. Importantly, the studies demonstrated that semantic cues are weighed against discourse/structural cues. When the structural cues consist of a combination of cues that have been independently shown to be important in backward inferencing, semantic effects may be masked, whereas when the structural cues consist of a combination of fewer prominent cues, semantics can have an earlier effect than structural factors in pronoun resolution. In addition, the type of inference matters, too: During anaphoric inferencing semantics has a prominent role, while discourse/structural salience attains more prominence during non-anaphoric inferencing. Finally, semantics exhibits a strong role in inviting new inferences to revise earlier made inferences even in the case the additional inference is not needed to establish coherence in discourse. The findings are generally in line with the Mental Model approaches. Two extended model versions are presented that incorporate the current findings into the earlier literature. These models allow both forward and backward inferencing to occur at any given moment during the course of processing; they also allow semantic and discourse/structural cues to contribute to both of these processes. However, while the Mental Model 1 does not assume interactions between semantic and discourse/structural factors in forward inferencing, the Mental Model 2 does assume such a link.

Etiology and epidemiology of Pythium root rot in hydroponic crops: current knowledge and perspectives

The etiology and epidemiology of Pythium root rot in hydroponically-grown crops are reviewed with emphasis on knowledge and concepts considered important for managing the disease in commercial greenhouses. Pythium root rot continually threatens the productivity of numerous kinds of crops in hydroponic systems around the world including cucumber, tomato, sweet pepper, spinach, lettuce, nasturtium, arugula, rose, and chrysanthemum. Principal causal agents include Pythium aphanidermatum, Pythium dissotocum, members of Pythium group F, and Pythium ultimum var. ultimum. Perspectives are given of sources of initial inoculum of Pythium spp. in hydroponic systems, of infection and colonization of roots by the pathogens, symptom development and inoculum production in host roots, and inoculum dispersal in nutrient solutions. Recent findings that a specific elicitor produced by P. aphanidermatum may trigger necrosis (browning) of the roots and the transition from biotrophic to necrotrophic infection are considered. Effects on root rot epidemics of host factors (disease susceptibility, phenological growth stage, root exudates and phenolic substances), the root environment (rooting media, concentrations of dissolved oxygen and phenolic substances in the nutrient solution, microbial communities and temperature) and human interferences (cropping practices and control measures) are reviewed. Recent findings on predisposition of roots to Pythium attack by environmental stress factors are highlighted. The commonly minor impact on epidemics of measures to disinfest nutrient solution as it recirculates outside the crop is contrasted with the impact of treatments that suppress Pythium in the roots and root zone of the crop. New discoveries that infection of roots by P. aphanidermatum markedly slows the increase in leaf area and whole-plant carbon gain without significant effect on the efficiency of photosynthesis per unit area of leaf are noted. The platform of knowledge and understanding of the etiology and epidemiology of root rot, and its effects on the physiology of the whole plant, are discussed in relation to new research directions and development of better practices to manage the disease in hydroponic crops. Focus is on methods and technologies for tracking Pythium and root rot, and on developing, integrating, and optimizing treatments to suppress the pathogen in the root zone and progress of root rot.

Speaker diarization: Segmentation and clustering of speeches

Speaker diarization is the process of sorting speeches according to the speaker. Diarization helps to search and retrieve what a certain speaker uttered in a meeting. Applications of diarization systemsextend to other domains than meetings, for example, lectures, telephone, television, and radio. Besides, diarization enhances the performance of several speech technologies such as speaker recognition, automatic transcription, and speaker tracking. Methodologies previously used in developing diarization systems are discussed. Prior results and techniques are studied and compared. Methods such as Hidden Markov Models and Gaussian Mixture Models that are used in speaker recognition and other speech technologies are also used in speaker diarization. The objective of this thesis is to develop a speaker diarization system in meeting domain. Experimental part of this work indicates that zero-crossing rate can be used effectively in breaking down the audio stream into segments, and adaptive Gaussian Models fit adequately short audio segments. Results show that 35 Gaussian Models and one second as average length of each segment are optimum values to build a diarization system for the tested data. Uniting the segments which are uttered by same speaker is done in a bottom-up clustering by a newapproach of categorizing the mixture weights.

Conventional and novel cardiovascular risk factors in young Finns and their associations with structural and functional vascular changes of subclinical atherosclerosis. The Cardiovascular Risk in Young Finns Study

Background: Atherosclerosis begins in early life progressing from asymptomatic to symptomatic as we age. Although substantial progress has been made in identifying the determinants of atherosclerosis in middle to older age adults at increased cardiovascular risk, there is lack of data examining determinants and prediction of atherosclerosis in young adults. Aims: The current study was designed to investigate levels of cardiovascular risk factors in young adults, subclinical measures of atherosclerosis, and prediction of subclinical arterial changes with conventional risk factor measures and novel metabolic profiling of serum samples. Subjects and Methods: This thesis utilised data from the follow-ups performed in 2001 and 2007 in the Cardiovascular Risk in Young Finns study, a Finnish population-based prospective cohort study that examined 2,204 subjects who were aged 30-45 years in 2007. Subclinical atherosclerosis was studied using noninvasive ultrasound measurements of carotid intima-media thickness (IMT), carotid arterial distensibility (CDist) and brachial flow-mediated dilation (FMD). Measurements included conventional risk factors and metabolic profiling using highthroughput nuclear magnetic resonance (NMR) methods that provided data on 42 lipid markers and 16 circulating metabolites. Results: Trends in lipids were favourable between 2001 and 2007, whereas waist circumference, fasting glucose, and blood pressure levels increased. To study the stability of noninvasive ultrasound markers, 6-year tracking (the likelihood to maintain the original fractile over time) in 6 years was examined. IMT tracked more strongly than CDist and FMD. Cardiovascular risk scores (Framingham, SCORE, Finrisk, Reynolds and PROCAM) predicted subclinical atherosclerosis equally. Lipoprotein subclass testing did not improve the prediction of subclinical atherosclerosis over and above conventional risk factors. However, circulating metabolites improved risk stratification. Tyrosine and docosahexaenoic acid were found to be novel biomarkers of high IMT. Conclusions: Prediction of cardiovascular risk in young Finnish adults can be performed with any of the existing risk scores. The addition of metabonomics to risk stratification improves prediction of subclinical changes and enables more accurate targeting of prevention at an early stage.

Fungicide application using a trailing boom in soybean fields

The objective of this study was to determine the effects in the yield of soybean crop utilizing a trailing boom sprayer for chemical control of late season diseases. The experimental design was randomized blocks with 04 treatments, which consisted of applying fungicides with a traditional sprayer, trailing boom, the traditional sprayer plus the trailing boom simultaneously and control (without fungicide aerial application) in 05 repetitions per treatment. The variables evaluated were: final plant population, pods per plant, grains per pod, weight of one thousand grains and yield. It was concluded that the control of foliar diseases with fungicides presented weight of one thousand grains and yield significantly higher than the average of plots without fungicide application. The trailing boom did not significantly affect the yield compared to the technology currently used.

Design and characterization of large area position sensitive radiation detectors

Planar, large area, position sensitive silicon detectors are widely utilized in high energy physics research and in medical, computed tomography (CT). This thesis describes author's research work relating to development of such detector components. The key motivation and objective for the research work has been the development of novel, position sensitive detectors improving the performance of the instruments they are intended for. Silicon strip detectors are the key components of barrel-shaped tracking instruments which are typically the innermost structures of high energy physics experimental stations. Particle colliders such as the former LEP collider or present LHC produce particle collisions and the silicon strip detector based trackers locate the trajectories of particles emanating from such collisions. Medical CT has become a regular part of everyday medical care in all developed countries. CT scanning enables x-ray imaging of all parts of the human body with an outstanding structural resolution and contrast. Brain, chest and abdomen slice images with a resolution of 0.5 mm are possible and latest CT machines are able to image whole human heart between heart beats. The two application areas are presented shortly and the radiation detection properties of planar silicon detectors are discussed. Fabrication methods and preamplifier electronics of the planar detectors are presented. Designs of the developed, large area silicon detectors are presented and measurement results of the key operating parameters are discussed. Static and dynamic performance of the developed silicon strip detectors are shown to be very satisfactory for experimental physics applications. Results relating to the developed, novel CT detector chips are found to be very promising for further development and all key performance goals are met.

Paper for printed electronics and functionality

Mass-produced paper electronics (large area organic printed electronics on paper-based substrates, “throw-away electronics”) has the potential to introduce the use of flexible electronic applications in everyday life. While paper manufacturing and printing have a long history, they were not developed with electronic applications in mind. Modifications to paper substrates and printing processes are required in order to obtain working electronic devices. This should be done while maintaining the high throughput of conventional printing techniques and the low cost and recyclability of paper. An understanding of the interactions between the functional materials, the printing process and the substrate are required for successful manufacturing of advanced devices on paper. Based on the understanding, a recyclable, multilayer-coated paper-based substrate that combines adequate barrier and printability properties for printed electronics and sensor applications was developed in this work. In this multilayer structure, a thin top-coating consisting of mineral pigments is coated on top of a dispersion-coated barrier layer. The top-coating provides well-controlled sorption properties through controlled thickness and porosity, thus enabling optimizing the printability of functional materials. The penetration of ink solvents and functional materials stops at the barrier layer, which not only improves the performance of the functional material but also eliminates potential fiber swelling and de-bonding that can occur when the solvents are allowed to penetrate into the base paper. The multi-layer coated paper under consideration in the current work consists of a pre-coating and a smoothing layer on which the barrier layer is deposited. Coated fine paper may also be used directly as basepaper, ensuring a smooth base for the barrier layer. The top layer is thin and smooth consisting of mineral pigments such as kaolin, precipitated calcium carbonate, silica or blends of these. All the materials in the coating structure have been chosen in order to maintain the recyclability and sustainability of the substrate. The substrate can be coated in steps, sequentially layer by layer, which requires detailed understanding and tuning of the wetting properties and topography of the barrier layer versus the surface tension of the top-coating. A cost competitive method for industrial scale production is the curtain coating technique allowing extremely thin top-coatings to be applied simultaneously with a closed and sealed barrier layer. The understanding of the interactions between functional materials formulated and applied on paper as inks, makes it possible to create a paper-based substrate that can be used to manufacture printed electronics-based devices and sensors on paper. The multitude of functional materials and their complex interactions make it challenging to draw general conclusions in this topic area. Inevitably, the results become partially specific to the device chosen and the materials needed in its manufacturing. Based on the results, it is clear that for inks based on dissolved or small size functional materials, a barrier layer is beneficial and ensures the functionality of the printed material in a device. The required active barrier life time depends on the solvents or analytes used and their volatility. High aspect ratio mineral pigments, which create tortuous pathways and physical barriers within the barrier layer limit the penetration of solvents used in functional inks. The surface pore volume and pore size can be optimized for a given printing process and ink through a choice of pigment type and coating layer thickness. However, when manufacturing multilayer functional devices, such as transistors, which consist of several printed layers, compromises have to be made. E.g., while a thick and porous top-coating is preferable for printing of source and drain electrodes with a silver particle ink, a thinner and less absorbing surface is required to form a functional semiconducting layer. With the multilayer coating structure concept developed in this work, it was possible to make the paper substrate suitable for printed functionality. The possibility of printing functional devices, such as transistors, sensors and pixels in a roll-to-roll process on paper is demonstrated which may enable introducing paper for use in disposable “onetime use” or “throwaway” electronics and sensors, such as lab-on-strip devices for various analyses, consumer packages equipped with product quality sensors or remote tracking devices.

Experimental study applied to an industrial robot by using variable structure controllers and friction compensation

Control of an industrial robot is mainly a problem of dynamics. It includes non-linearities, uncertainties and external perturbations that should be considered in the design of control laws. In this work, two control strategies based on variable structure controllers (VSC) and a PD control algorithm are compared in relation to the tracking errors considering friction. The controller's performances are evaluated by adding an static friction model. Simulations and experimental results show it is possible to diminish tracking errors by using a model based friction compensation scheme. A SCARA robot is used to illustrate the conclusions of this paper.