Robust power allocation algorithms for MIMO OFDM systems with imperfect CSI

This paper presents a Bayesian approach to the design of transmit prefiltering matrices in closed-loop schemes robust to channel estimation errors. The algorithms are derived for a multiple-input multiple-output (MIMO) orthogonal frequency division multiplexing (OFDM) system. Two different optimizationcriteria are analyzed: the minimization of the mean square error and the minimization of the bit error rate. In both cases, the transmitter design is based on the singular value decomposition (SVD) of the conditional mean of the channel response, given the channel estimate. The performance of the proposed algorithms is analyzed,and their relationship with existing algorithms is indicated. As withother previously proposed solutions, the minimum bit error rate algorithmconverges to the open-loop transmission scheme for very poor CSI estimates.

A frequency distribution approach to hotspot identification

We present a new global method for the identification of hotspots in conservation and ecology. The method is based on the identification of spatial structure properties through cumulative relative frequency distributions curves, and is tested with two case studies, the identification of fish density hotspots and terrestrial vertebrate species diversity hotspots. Results from the frequency distribution method are compared with those from standard techniques among local, partially local and global methods. Our approach offers the main advantage to be independent from the selection of any threshold, neighborhood, or other parameter that affect most of the currently available methods for hotspot analysis. The two case studies show how such elements of arbitrariness of the traditional methods influence both size and location of the identified hotspots, and how this new global method can be used for a more objective selection of hotspots.

A survey of transposable element classification systems--a call for a fundamental update to meet the challenge of their diversity and complexity.

The increase of publicly available sequencing data has allowed for rapid progress in our understanding of genome composition. As new information becomes available we should constantly be updating and reanalyzing existing and newly acquired data. In this report we focus on transposable elements (TEs) which make up a significant portion of nearly all sequenced genomes. Our ability to accurately identify and classify these sequences is critical to understanding their impact on host genomes. At the same time, as we demonstrate in this report, problems with existing classification schemes have led to significant misunderstandings of the evolution of both TE sequences and their host genomes. In a pioneering publication Finnegan (1989) proposed classifying all TE sequences into two classes based on transposition mechanisms and structural features: the retrotransposons (class I) and the DNA transposons (class II). We have retraced how ideas regarding TE classification and annotation in both prokaryotic and eukaryotic scientific communities have changed over time. This has led us to observe that: (1) a number of TEs have convergent structural features and/or transposition mechanisms that have led to misleading conclusions regarding their classification, (2) the evolution of TEs is similar to that of viruses by having several unrelated origins, (3) there might be at least 8 classes and 12 orders of TEs including 10 novel orders. In an effort to address these classification issues we propose: (1) the outline of a universal TE classification, (2) a set of methods and classification rules that could be used by all scientific communities involved in the study of TEs, and (3) a 5-year schedule for the establishment of an International Committee for Taxonomy of Transposable Elements (ICTTE).

Networks of noisy oscillators with correlated degree and frequency dispersion

We investigate how correlations between the diversity of the connectivity of networks and the dynamics at their nodes affect the macroscopic behavior. In particular, we study the synchronization transition of coupled stochastic phase oscillators that represent the node dynamics. Crucially in our work, the variability in the number of connections of the nodes is correlated with the width of the frequency distribution of the oscillators. By numerical simulations on Erdös-Rényi networks, where the frequencies of the oscillators are Gaussian distributed, we make the counterintuitive observation that an increase in the strength of the correlation is accompanied by an increase in the critical coupling strength for the onset of synchronization. We further observe that the critical coupling can solely depend on the average number of connections or even completely lose its dependence on the network connectivity. Only beyond this state, a weighted mean-field approximation breaks down. If noise is present, the correlations have to be stronger to yield similar observations.

Distributed ControlArchitecture of Power Electronics Building-Block-Based Frequency Converters

The increasing power demand and emerging applications drive the design of electrical power converters into modularization. Despite the wide use of modularized power stage structures, the control schemes that are used are often traditional, in other words, centralized. The flexibility and re-usability of these controllers are typically poor. With a dedicated distributed control scheme, the flexibility and re-usability of the system parts, building blocks, can be increased. Only a few distributed control schemes have been introduced for this purpose, but their breakthrough has not yet taken place. A demand for the further development offlexible control schemes for building-block-based applications clearly exists. The control topology, communication, synchronization, and functionality allocationaspects of building-block-based converters are studied in this doctoral thesis. A distributed control scheme that can be easily adapted to building-block-based power converter designs is developed. The example applications are a parallel and series connection of building blocks. The building block that is used in the implementations of both the applications is a commercial off-the-shelf two-level three-phase frequency converter with a custom-designed controller card. The major challenge with the parallel connection of power stages is the synchronization of the building blocks. The effect of synchronization accuracy on the system performance is studied. The functionality allocation and control scheme design are challenging in the seriesconnected multilevel converters, mainly because of the large number of modules. Various multilevel modulation schemes are analyzed with respect to the implementation, and this information is used to develop a flexible control scheme for modular multilevel inverters.

Methods of genetic diversity creation and functional display for directed evolution experiments

Protein engineering aims to improve the properties of enzymes and affinity reagents by genetic changes. Typical engineered properties are affinity, specificity, stability, expression, and solubility. Because proteins are complex biomolecules, the effects of specific genetic changes are seldom predictable. Consequently, a popular strategy in protein engineering is to create a library of genetic variants of the target molecule, and render the population in a selection process to sort the variants by the desired property. This technique, called directed evolution, is a central tool for trimming protein-based products used in a wide range of applications from laundry detergents to anti-cancer drugs. New methods are continuously needed to generate larger gene repertoires and compatible selection platforms to shorten the development timeline for new biochemicals. In the first study of this thesis, primer extension mutagenesis was revisited to establish higher quality gene variant libraries in Escherichia coli cells. In the second study, recombination was explored as a method to expand the number of screenable enzyme variants. A selection platform was developed to improve antigen binding fragment (Fab) display on filamentous phages in the third article and, in the fourth study, novel design concepts were tested by two differentially randomized recombinant antibody libraries. Finally, in the last study, the performance of the same antibody repertoire was compared in phage display selections as a genetic fusion to different phage capsid proteins and in different antibody formats, Fab vs. single chain variable fragment (ScFv), in order to find out the most suitable display platform for the library at hand. As a result of the studies, a novel gene library construction method, termed selective rolling circle amplification (sRCA), was developed. The method increases mutagenesis frequency close to 100% in the final library and the number of transformants over 100-fold compared to traditional primer extension mutagenesis. In the second study, Cre/loxP recombination was found to be an appropriate tool to resolve the DNA concatemer resulting from error-prone RCA (epRCA) mutagenesis into monomeric circular DNA units for higher efficiency transformation into E. coli. Library selections against antigens of various size in the fourth study demonstrated that diversity placed closer to the antigen binding site of antibodies supports generation of antibodies against haptens and peptides, whereas diversity at more peripheral locations is better suited for targeting proteins. The conclusion from a comparison of the display formats was that truncated capsid protein three (p3Δ) of filamentous phage was superior to the full-length p3 and protein nine (p9) in obtaining a high number of uniquely specific clones. Especially for digoxigenin, a difficult hapten target, the antibody repertoire as ScFv-p3Δ provided the clones with the highest affinity for binding. This thesis on the construction, design, and selection of gene variant libraries contributes to the practical know-how in directed evolution and contains useful information for scientists in the field to support their undertakings.

The identification and characterization of inter- and intra-species genetic diversity derived from retrotransposons in humans

Retrotransposons, which used to be considered as “junk DNA”, have begun to reveal their immense value to genome evolution and human biology due to recent studies. They consist of at least ~45% of the human genome and are more or less the same in other mammalian genomes. Retrotransposon elements (REs) are known to affect the human genome through many different mechanisms, such as generating insertion mutations, genomic instability, and alteration in gene expression. Previous studies have suggested several RE subfamilies, such as Alu, L1, SVA and LTR, are currently active in the human genome, and they are an important source of genetic diversity between human and other primates, as well as among humans. Although several groups had used Retrotransposon Insertion Polymorphisms (RIPs) as markers in studying primate evolutionary history, no study specifically focused on identifying Human-Specific Retrotransposon Element (HS-RE) and their roles in human genome evolution. In this study, by computationally comparing the human genome to 4 primate genomes, we identified a total of 18,860 HS-REs, among which are 11,664 Alus, 4,887 L1s, 1,526 SVAs and 783 LTRs (222 full length entries), representing the largest and most comprehensive list of HS-REs generated to date. Together, these HS-REs contributed a total of 14.2Mb sequence increase from the inserted REs and Target Site Duplications (TSDs), 71.6Kb increase from transductions, and 268.2 Kb sequence deletion of from insertion-mediated deletion, leading to a net increase of ~14 Mb sequences to the human genome. Furthermore, we observed for the first time that Y chromosome might be a hot target for new retrotransposon insertions in general and particularly for LTRs. The data also allowed for the first time the survey of frequency of TE insertions inside other TEs in comparison with TE insertion into none-TE regions. In summary, our data suggest that retrotransposon elements have played a significant role in the evolution of Homo sapiens.

DEVELOPMENT AND ANALYSIS OF DUAL FREQUENCY MICROSTRIP ANTENNAS

Department of Elecctronics, Cochin University of Science and Technology

Efficient Watermarking Schemes for Speaker Verification Guaranteeing Non-repudiation

Presently different audio watermarking methods are available; most of them inclined towards copyright protection and copy protection. This is the key motive for the notion to develop a speaker verification scheme that guar- antees non-repudiation services and the thesis is its outcome. The research presented in this thesis scrutinizes the field of audio water- marking and the outcome is a speaker verification scheme that is proficient in addressing issues allied to non-repudiation to a great extent. This work aimed in developing novel audio watermarking schemes utilizing the fun- damental ideas of Fast-Fourier Transform (FFT) or Fast Walsh-Hadamard Transform (FWHT). The Mel-Frequency Cepstral Coefficients (MFCC) the best parametric representation of the acoustic signals along with few other key acoustic characteristics is employed in crafting of new schemes. The au- dio watermark created is entirely dependent to the acoustic features, hence named as FeatureMark and is crucial in this work. In any watermarking scheme, the quality of the extracted watermark de- pends exclusively on the pre-processing action and in this work framing and windowing techniques are involved. The theme non-repudiation provides immense significance in the audio watermarking schemes proposed in this work. Modification of the signal spectrum is achieved in a variety of ways by selecting appropriate FFT/FWHT coefficients and the watermarking schemes were evaluated for imperceptibility, robustness and capacity char- acteristics. The proposed schemes are unequivocally effective in terms of maintaining the sound quality, retrieving the embedded FeatureMark and in terms of the capacity to hold the mark bits. Robust nature of these marking schemes is achieved with the help of syn- chronization codes such as Barker Code with FFT based FeatureMarking scheme and Walsh Code with FWHT based FeatureMarking scheme. An- other important feature associated with this scheme is the employment of an encryption scheme towards the preparation of its FeatureMark that scrambles the signal features that helps to keep the signal features unreve- laed. A comparative study with the existing watermarking schemes and the ex- periments to evaluate imperceptibility, robustness and capacity tests guar- antee that the proposed schemes can be baselined as efficient audio water- marking schemes. The four new digital audio watermarking algorithms in terms of their performance are remarkable thereby opening more opportu- nities for further research.

The effect of Ponzi schemes on crime: Evidence from the colombian case

This paper estimates the impact of a massive negative income shock led by the simultaneous crash down of several Ponzi schemes (also known as financial ``pyramids"") in Colombia on crime rates at the municipal level. Using novel data on the spatial incidence of the latest wave of Colombian pyramids and their crash down date, I estimate difference-in-differences models with both monthly and yearly frequency. I find that the negative income shock of the pyramids" crash down differentially exacerbates crime in affected municipalities compared to those with no presence of Ponzi schemes. This is true for minor offenses like commercial theft or residential burglary, but not for major crimes as murder or terrorism.

Enhancing pollinator biodiversity in intensive grasslands

Increased agricultural intensification has led to well-documented declines in the fauna and flora associated with intensive grasslands in the UK. We aimed to quantify the effectiveness of different field margin management strategies for putting bumblebee and butterfly biodiversity back into intensive grasslands. Using four intensive livestock farms in south-west England, we manipulated conventional management practices (addition of inorganic fertilizer, cutting frequency and height, and aftermath grazing) to generate seven grass-based treatments along a gradient of decreasing management intensity. We also tested two more interventionist treatments which introduced sown components into the sward: (i) a cereal, grass and legume mix, and (ii) a diverse conservation mix with kale, mixed cereals, linseed and legumes. These crop mixtures were intended to provide forage and structural resources for pollinators but were not intended to have agronomic value as livestock feed. Using a replicated block design, we monitored bumblebee and butterfly responses in 27 plots (10 x 50 m) in each farm from 2003 to 2006. Bumblebees were most abundant, species-rich and diverse in the sown treatments and virtually absent from the grass-based treatments. The diverse conservation mix treatment supported larger and more diverse bumblebee assemblages than the cereal, grass and legume mix treatment. The sown treatments, and the most extensively managed grass-based treatments, had the highest abundance, species richness and diversity of adult butterflies, whereas butterfly larvae were only found in the grass-based treatments. Bumblebee and butterfly assemblage structure was driven by floral abundance, floral richness, the availability of nectar resources, and sward structure. Only vegetation cover was correlated with butterfly larval abundance. Synthesis and applications. This study has identified management options in the margins of intensive grasslands which can enhance bumblebee and butterfly biodiversity. Extensification of conventional grass management by stopping fertilization, reducing cutting frequency and not grazing, benefits butterflies. However, to enhance bumblebees requires a more interventionist approach in the form of sowing flower-rich habitat. Both approaches are potentially suitable for adoption in agri-environment schemes in the UK and Europe.

Measuring bee diversity in different European habitats and biogeographical regions

Bee pollinators are currently recorded with many different sampling methods. However, the relative performances of these methods have not been systematically evaluated and compared. In response to the strong need to record ongoing shifts in pollinator diversity and abundance, global and regional pollinator initiatives must adopt standardized sampling protocols when developing large-scale and long-term monitoring schemes. We systematically evaluated the performance of six sampling methods (observation plots, pan traps, standardized and variable transect walks, trap nests with reed internodes or paper tubes) that are commonly used across a wide range of geographical regions in Europe and in two habitat types (agricultural and seminatural). We focused on bees since they represent the most important pollinator group worldwide. Several characteristics of the methods were considered in order to evaluate their performance in assessing bee diversity: sample coverage, observed species richness, species richness estimators, collector biases (identified by subunit-based rarefaction curves), species composition of the samples, and the indication of overall bee species richness (estimated from combined total samples). The most efficient method in all geographical regions, in both the agricultural and seminatural habitats, was the pan trap method. It had the highest sample coverage, collected the highest number of species, showed negligible collector bias, detected similar species as the transect methods, and was the best indicator of overall bee species richness. The transect methods were also relatively efficient, but they had a significant collector bias. The observation plots showed poor performance. As trap nests are restricted to cavity-nesting bee species, they had a naturally low sample coverage. However, both trap nest types detected additional species that were not recorded by any of the other methods. For large-scale and long-term monitoring schemes with surveyors with different experience levels, we recommend pan traps as the most efficient, unbiased, and cost-effective method for sampling bee diversity. Trap nests with reed internodes could be used as a complementary sampling method to maximize the numbers of collected species. Transect walks are the principal method for detailed studies focusing on plant-pollinator associations. Moreover, they can be used in monitoring schemes after training the surveyors to standardize their collection skills.

The potential of grass field margin management for enhancing beetle diversity in intensive livestock farms

1. Declining populations of UK grassland flora and fauna have been attributed to intensification of agricultural management practices, including changes in cutting, fertilizer, grazing and drainage regimes. We aimed to develop field margin management practices that could reverse declines in intensively managed grassland biodiversity that would have application in the UK and Europe. Here we focus on one aspect of grassland biodiversity, the beetles. 2. In four intensively managed livestock farms in south-west England, 10-m wide field margins in existing grasslands were managed to create seven treatments of increasing sward architectural complexity. This was achieved through combinations of inorganic (NPK) fertilizer, cattle grazing, and timing and height of cutting. To examine the potential influence of complexity on faunal diversity, beetles were identified to species level from suction samples taken between 2003 and 2005, and their assemblage structure was related to margin management, floral assemblages and sward architecture. 3. Beetle abundance, and species richness and evenness were influenced by margin management treatment and its interaction with year. Correlations with sward architecture and the percentage cover of dominant forbs and grasses were also found. Functional groups of the beetles showed different responses to the management treatments. In particular, higher proportional abundances of seed/flower-feeding guilds were found in treatments not receiving NPK fertilizer. 4. The assemblage structure was shown to respond to margin management treatments, sward architecture and the percentage cover of dominant forbs and grasses. The most extensively managed treatments were characterized by distinct successional trajectories from the control treatment. 5. Synthesis and applications. This study provides management options suitable for use within agri-environment schemes intended to improve faunal diversity associated with intensively managed lowland grasslands. Field margins receiving either no management or a single July silage cut were shown to support greater abundances and species richness of beetles, although subtler modifications of conventional management may also be beneficial, for example the absence of NPK fertilizer while maintaining grazing and silage cutting systems.

Stocking may increase mitochondrial DNA diversity but fails to halt the decline of endangered Atlantic salmon populations

Over the last 50 years, Spanish Atlantic salmon (Salmo salar) populations have been in decline. In order to bolster these populations, rivers were stocked with fish of northern European origin during the period 1974-1996, probably also introducing the furunculosis-inducing pathogen, Aeromonas salmonicida. Here we assess the relative importance of processes influencing mitochondrial (mt)DNA variability in these populations from 1948 to 2002. Genetic material collected over this period from four rivers in northern Spain (Cantabria) was used to detect variability at the mtDNA ND1 gene. Before stocking, a single haplotype was found at high frequency (0.980). Following stocking, haplotype diversity (h) increased in all rivers (mean h before stocking was 0.041, and 0.245 afterwards). These increases were due principally to the dramatic increase in frequency of a previously very low frequency haplotype, reported at higher frequencies in northern European populations proximate to those used to stock Cantabrian rivers. Genetic structuring increased after stocking: among-river differentiation was low before stocking (1950s/1960s Phi(ST) = -0.00296-0.00284), increasing considerably at the height of stocking (1980s Phi(ST) = 0.18932) and decreasing post-stocking (1990s/2002 Phi(ST) = 0.04934-0.03852). Gene flow from stocked fish therefore seems to have had a substantial role in increasing mtDNA variability. Additionally, we found significant differentiation between individuals that had probably died from infectious disease and apparently healthy, angled fish, suggesting a possible role for pathogen-driven selection of mtDNA variation. Our results suggest that stocking with non-native fish may increase genetic diversity in the short term, but may not reverse population declines.

High signal to noise ratio THz spectroscopy with ASOPS and signal processing schemes for mapping and controlling molecular and bulk relaxation processes

Asynchronous Optical Sampling has the potential to improve signal to noise ratio in THz transient sperctrometry. The design of an inexpensive control scheme for synchronising two femtosecond pulse frequency comb generators at an offset frequency of 20 kHz is discussed. The suitability of a range of signal processing schemes adopted from the Systems Identification and Control Theory community for further processing recorded THz transients in the time and frequency domain are outlined. Finally, possibilities for femtosecond pulse shaping using genetic algorithms are mentioned.