Showing papers by "Tallinn University of Technology published in 2010"

Bottom-up effects of plant diversity on multitrophic interactions in a biodiversity experiment

Abstract: Biodiversity is rapidly declining, and this may negatively affect ecosystem processes, including economically important ecosystem services Previous studies have shown that biodiversity has positive effects on organisms and processes across trophic levels However, only a few studies have so far incorporated an explicit food-web perspective In an eight-year biodiversity experiment, we studied an unprecedented range of above- and below-ground organisms and multitrophic interactions A multitrophic data set originating from a single long-term experiment allows mechanistic insights that would not be gained from meta-analysis of different experiments Here we show that plant diversity effects dampen with increasing trophic level and degree of omnivory This was true both for abundance and species richness of organisms Furthermore, we present comprehensive above-ground/below-ground biodiversity food webs Both above ground and below ground, herbivores responded more strongly to changes in plant diversity than did carnivores or omnivores Density and richness of carnivorous taxa was independent of vegetation structure Below-ground responses to plant diversity were consistently weaker than above-ground responses Responses to increasing plant diversity were generally positive, but were negative for biological invasion, pathogen infestation and hyperparasitism Our results suggest that plant diversity has strong bottom-up effects on multitrophic interaction networks, with particularly strong effects on lower trophic levels Effects on higher trophic levels are indirectly mediated through bottom-up trophic cascades

Technological revolutions and techno-economic paradigms

Abstract: This paper locates the notion of technological revolutions in the neo-Schumpeterian effort to understand innovation and to identify the regularities, continuities and discontinuities in the process of innovation. It looks at the micro- and meso-foundations of the patterns observed in the evolution of technical change and at the interrelations with the context that shape the rhythm and direction of innovation. On this basis it defines technological revolutions, examines their structure and the role that they play in rejuvenating the whole economy through the application of the accompanying techno-economic paradigm. This over-arching meta-paradigm or shared best practice 'common sense' is in turn defined and analysed in its components and its impact, including its influence on institutional and social change.

A review of methods for leakage management in pipe networks

Abstract: Leakage in water distribution systems is an important issue which is affecting water companies and their customers worldwide. It is therefore no surprise that it has attracted a lot of attention by both practitioners and researchers over the past years. Most of the leakage management related methods developed so far can be broadly classified as follows: (1) leakage assessment methods which are focusing on quantifying the amount of water lost; (2) leakage detection methods which are primarily concerned with the detection of leakage hotspots and (3) leakage control models which are focused on the effective control of current and future leakage levels. This paper provides a comprehensive review of the above methods with the objective to identify the current state-of-the-art in the field and to then make recommendations for future work. The review ends with the main conclusion that despite all the advancements made in the past, there is still a lot of scope and need for further work, especially in area of rea...

Affinity gradients drive copper to cellular destinations

Abstract: Copper is an essential trace element for eukaryotes and most prokaryotes. However, intracellular free copper must be strictly limited because of its toxic side effects. Complex systems for copper trafficking evolved to satisfy cellular requirements while minimizing toxicity. The factors driving the copper transfer between protein partners along cellular copper routes are, however, not fully rationalized. Until now, inconsistent, scattered and incomparable data on the copper-binding affinities of copper proteins have been reported. Here we determine, through a unified electrospray ionization mass spectrometry (ESI-MS)-based strategy, in an environment that mimics the cellular redox milieu, the apparent Cu(I)-binding affinities for a representative set of intracellular copper proteins involved in enzymatic redox catalysis, in copper trafficking to and within various cellular compartments, and in copper storage. The resulting thermodynamic data show that copper is drawn to the enzymes that require it by passing from one copper protein site to another, exploiting gradients of increasing copper-binding affinity. This result complements the finding that fast copper-transfer pathways require metal-mediated protein-protein interactions and therefore protein-protein specific recognition. Together with Cu,Zn-SOD1, metallothioneins have the highest affinity for copper(I), and may play special roles in the regulation of cellular copper distribution; however, for kinetic reasons they cannot demetallate copper enzymes. Our study provides the thermodynamic basis for the kinetic processes that lead to the distribution of cellular copper.

Fine Mapping the Spatial Distribution and Concentration of Unlabeled Drugs within Tissue Micro-Compartments Using Imaging Mass Spectrometry

Abstract: Readouts that define the physiological distributions of drugs in tissues are an unmet challenge and at best imprecise, but are needed in order to understand both the pharmacokinetic and pharmacodynamic properties associated with efficacy. Here we demonstrate that it is feasible to follow the in vivo transport of unlabeled drugs within specific organ and tissue compartments on a platform that applies MALDI imaging mass spectrometry to tissue sections characterized with high definition histology. We have tracked and quantified the distribution of an inhaled reference compound, tiotropium, within the lungs of dosed rats, using systematic point by point MS and MS/MS sampling at 200 µm intervals. By comparing drug ion distribution patterns in adjacent tissue sections, we observed that within 15 min following exposure, tiotropium parent MS ions (mass-to-charge; m/z 392.1) and fragmented daughter MS/MS ions (m/z 170.1 and 152.1) were dispersed in a concentration gradient (80 fmol-5 pmol) away from the central airways into the lung parenchyma and pleura. These drug levels agreed well with amounts detected in lung compartments by chemical extraction. Moreover, the simultaneous global definition of molecular ion signatures localized within 2-D tissue space provides accurate assignment of ion identities within histological landmarks, providing context to dynamic biological processes occurring at sites of drug presence. Our results highlight an important emerging technology allowing specific high resolution identification of unlabeled drugs at sites of in vivo uptake and retention.

Systems biology approach reveals that overflow metabolism of acetate in Escherichia coli is triggered by carbon catabolite repression of acetyl-CoA synthetase

Abstract: Background The biotechnology industry has extensively exploited Escherichia coli for producing recombinant proteins, biofuels etc. However, high growth rate aerobic E. coli cultivations are accompanied by acetate excretion i.e. overflow metabolism which is harmful as it inhibits growth, diverts valuable carbon from biomass formation and is detrimental for target product synthesis. Although overflow metabolism has been studied for decades, its regulation mechanisms still remain unclear.

Seriation and matrix reordering methods: An historical overview

Abstract: Seriation is an exploratory combinatorial data analysis technique to reorder objects into a sequence along a one-dimensional continuum so that it best reveals regularity and patterning among the whole series. Unsupervised learning, using seriation and matrix reordering, allows pattern discovery simultaneously at three information levels: local fragments of relationships, sets of organized local fragments of relationships, and an overall structural pattern. This paper presents an historical overview of seriation and matrix reordering methods, several applications from the following disciplines are included in the retrospective review: archaeology and anthropology; cartography, graphics, and information visualization; sociology and sociometry; psychology and psychometry; ecology; biology and bioinformatics; cellular manufacturing; and operations research. Copyright © 2010 Wiley Periodicals, Inc. Statistical Analysis and Data Mining 3: 70-91, 2010

Internal solitary waves: propagation, deformation and disintegration

Abstract: . In coastal seas and straits, the interaction of barotropic tidal currents with the continental shelf, seamounts or sills is often observed to generate large-amplitude, horizontally propagating internal solitary waves. Typically these waves occur in regions of variable bottom topography, with the consequence that they are often modeled by nonlinear evolution equations of the Korteweg-de Vries type with variable coefficients. We shall review how these models are used to describe the propagation, deformation and disintegration of internal solitary waves as they propagate over the continental shelf and slope.

Human TrkB gene: novel alternative transcripts, protein isoforms and expression pattern in the prefrontal cerebral cortex during postnatal development

Abstract: Brain-derived neurotrophic factor and neurotrophin-4 high-affinity receptor tropomyosine related kinase (Trk) B is required for the differentiation and maintenance of specific neuron populations. Misregulation of TrkB has been reported in many human diseases, including cancer, obesity and neurological and psychiatric disorders. Alternative splicing that generates receptor isoforms with different functional properties also regulates TrkB function. Here, we describe numerous novel isoforms of TrkB proteins, including isoforms generated by alternative splicing of cassette exons in the regions encoding both the extracellular and intracellular domain and also N-terminally truncated isoforms encoded by novel 5' exon-containing transcripts. We also characterize the intracellular localization and phosphorylation potential of novel TrkB isoforms and find that these proteins have unique properties. In addition, we describe the expression profiles of all the known human TrkB transcripts in adult tissues and also during postnatal development in the human prefrontal cortex. We show that transcripts encoding the full-length TrkB receptor and the C-terminally truncated TrkB-T1 have different expression profiles as compared to the proteins they encode. Identification of 36 potential TrkB protein isoforms suggests high complexity in the synthesis, regulation and function of this important neurotrophin receptor emphasizing the need for further study of these novel TrkB variants.

Polar front shift and atmospheric CO2 during the glacial maximum of the Early Paleozoic Icehouse

Abstract: Our new data address the paradox of Late Ordovician glaciation under supposedly high pCO2 (8 to 22× PAL: preindustrial atmospheric level). The paleobiogeographical distribution of chitinozoan (“mixed layer”) marine zooplankton biotopes for the Hirnantian glacial maximum (440 Ma) are reconstructed and compared to those from the Sandbian (460 Ma): They demonstrate a steeper latitudinal temperature gradient and an equatorwards shift of the Polar Front through time from 55°–70° S to ∼40° S. These changes are comparable to those during Pleistocene interglacial-glacial cycles. In comparison with the Pleistocene, we hypothesize a significant decline in mean global temperature from the Sandbian to Hirnantian, proportional with a fall in pCO2 from a modeled Sandbian level of ∼8× PAL to ∼5× PAL during the Hirnantian. Our data suggest that a compression of midlatitudinal biotopes and ecospace in response to the developing glaciation was a likely cause of the end-Ordovician mass extinction.

Public procurement as an industrial policy tool: an option for developing countries?

Abstract: This article sets out to answer two interrelated questions: is it advisable for developing countries to use public procurement efforts for development, and should more developing countries join the World Trade Organization (WTO) Government Procurement Agreement (GPA)? We survey key arguments for and against joining the GPA, and argue that government procurement should not be seen only as an indirect support measure for development, but also as a direct vehicle for promoting innovation and industries and, thus, growth and development. We also show that using public procurement for development assumes high levels of policy capacity, which most developing countries lack. In addition, we show how the GPA as well as other WTO agreements make it complicated for the developing countries to benefit from public procurement for innovation. The article suggests that the developing countries could apply a mix of direct and indirect (so-called soft) public-procurement-for-innovation measures. In order to do this, developing countries need to develop the policy capacity to take advantage of the complex and multi-layered industrial policy space still available under WTO rules.

Enantioselective Henry Reaction Catalyzed by CuII Salt and Bipiperidine

Abstract: A complex derived from the enantiomeric bipiperidine and copper(II) acetate hydrate is an efficient catalyst for the enantioselective Henry reaction. The easy availability of both catalyst components, mild reaction conditions, high yield, and good to excellent enantioselectivity make the catalyst useful for everyday practice.

Diversity promotes temporal stability across levels of ecosystem organization in experimental grasslands.

Abstract: The diversity–stability hypothesis states that current losses of biodiversity can impair the ability of an ecosystem to dampen the effect of environmental perturbations on its functioning. Using data from a long-term and comprehensive biodiversity experiment, we quantified the temporal stability of 42 variables characterizing twelve ecological functions in managed grassland plots varying in plant species richness. We demonstrate that diversity increases stability i) across trophic levels (producer, consumer), ii) at both the system (community, ecosystem) and the component levels (population, functional group, phylogenetic clade), and iii) primarily for aboveground rather than belowground processes. Temporal synchronization across studied variables was mostly unaffected with increasing species richness. This study provides the strongest empirical support so far that diversity promotes stability across different ecological functions and levels of ecosystem organization in grasslands.

Presence of fluoroquinolones and sulfonamides in urban sewage sludge and their degradation as a result of composting

Abstract: The concentrations of some widely used pharmaceuticals, namely fluoroquinolones (ciprofloxacin C17 H18FN3O3, norfloxacin C17 H18FN3O3 and ofloxacin C18 H20FN3O4 and sulfonamides (sulfadimethoxine C12 H14N4O4s and sulfamethoxazole C10 H11N3O3S were determined in urban sewage sludge utilized for making compost. The levels of degradation of these pharmaceuticals resulting from sludge treatment were assessed. The concentrations of the studied pharmaceuticals sufficiently varied both in sewage sludge and in compost and due to this phenomenon the possible danger resulting from the presence of pharmaceuticals in sewage sludge, used for composting, can not be ignored. The concentrations of the studied pharmaceuticals were lower in compost, if compared to the relevant concentrations in sewage sludge. The highest pharmaceutical concentration in sewage sludge — 426 μg/kg — was detected in the case of ciprofloxacin. The highest concentrations present in compost were 22 μg/kg of norfloxacin and 20 μg/kg of ciprofloxacin. Results show that before using the sewage sludge for making compost or before using the compost a fertilizer for food plants, they should be carefully tested against the content of commonly used pharmaceuticals.

Rogue waves - towards a unifying concept?: Discussions and debates

Abstract: This paper contains the discussion inputs by the contributors of the special issue on the subject of rogue waves.

The gentle art of levitation

Abstract: We present a closed dependent type theory whose inductive types are given not by a scheme for generative declarations, but by encoding in a universe. Each inductive datatype arises by interpreting its description - a first-class value in a datatype of descriptions. Moreover, the latter itself has a description. Datatype-generic programming thus becomes ordinary programming. We show some of the resulting generic operations and deploy them in particular, useful ways on the datatype of datatype descriptions itself. Simulations in existing systems suggest that this apparently self-supporting setup is achievable without paradox or infinite regress.

Development and application of a lexicon to describe the flavor of pomegranate juice

Abstract: A lexicon for describing the sensory flavor characteristics of pomegranate juices was developed. Thirty-three pomegranate juices, including concentrated products, products from concentrate, and freshly squeezed and pasteurized products, were studied. More than 30 sensory attributes were identified, defined, and referenced by a highly trained descriptive sensory panel. The lexicon that was established includes attributes to describe a range of flavors associated with pomegranates, such as brown spice, fermented, molasses, vinegar, wine-like, woody, apple, berry, cranberry, cherry and grape. Generally, pomegranate juice can be described by the flavor characteristics of sour, sweet, musty/earthy, fruity aromatics and an astringent mouthfeel. The flavor characteristics of pomegranate juices are reminiscent of a combination of concord grapes, cranberries, blackberries, cherries, currants and raspberries, but there also are vegetable notes such as beets and carrots. The lexicon provides attribute descriptors, definitions and references that were previously lacking in literature on pomegranates.

Monads need not be endofunctors

Abstract: We introduce a generalisation of monads, called relative monads, allowing for underlying functors between different categories. Examples include finite-dimensional vector spaces, untyped and typed λ-calculus syntax and indexed containers. We show that the Kleisli and Eilenberg-Moore constructions carry over to relative monads and are related to relative adjunctions. Under reasonable assumptions, relative monads are monoids in the functor category concerned and extend to monads, giving rise to a coreflection between monads and relative monads. Arrows are also an instance of relative monads.

Unprecedented low twentieth century winter sea ice extent in the Western Nordic Seas since A.D. 1200

Abstract: We reconstructed decadal to centennial variability of maximum sea ice extent in the Western Nordic Seas for A.D. 1200–1997 using a combination of a regional tree-ring chronology from the timberline area in Fennoscandia and δ18O from the Lomonosovfonna ice core in Svalbard. The reconstruction successfully explained 59% of the variance in sea ice extent based on the calibration period 1864–1997. The significance of the reconstruction statistics (reduction of error, coefficient of efficiency) is computed for the first time against a realistic noise background. The twentieth century sustained the lowest sea ice extent values since A.D. 1200: low sea ice extent also occurred before (mid-seventeenth and mid-eighteenth centuries, early fifteenth and late thirteenth centuries), but these periods were in no case as persistent as in the twentieth century. Largest sea ice extent values occurred from the seventeenth to the nineteenth centuries, during the Little Ice Age (LIA), with relatively smaller sea ice-covered area during the sixteenth century. Moderate sea ice extent occurred during thirteenth–fifteenth centuries. Reconstructed sea ice extent variability is dominated by decadal oscillations, frequently associated with decadal components of the North Atlantic Oscillation/Arctic Oscillation (NAO/AO), and multi-decadal lower frequency oscillations operating at ~50–120 year. Sea ice extent and NAO showed a non-stationary relationship during the observational period. The present low sea ice extent is unique over the last 800 years, and results from a decline started in late-nineteenth century after the LIA.

Unreported Employment and Envelope Wages in Mid-Transition: Comparing Developments and Causes in the Baltic Countries

Abstract: This paper compares the prevalence and determinants of unreported employment in the three Baltic countries in 1998 and 2002 using a hitherto little used data set. The prevalence of unreported employment varies substantially across the three countries and across the two sampling years. Microeconometric estimations show that firm-related characteristics, such as sectoral activity, firm size and employment changes, are important determinants of unreported employment in all three countries. The impact of socio-demographic factors, such as gender, age and education, is generally less important and varies across countries and time. Only a small part of the changes in unreported employment between 1998 and 2002 can be accounted for by changes in firm-specific factors and socio-demographic characteristics. Exploratory calculations suggest that the gain for individuals undertaking unreported employment is modest or non-existent, in particular among individuals who engage regularly in such activities. This suggests that the many of the recipients of envelope wages may have few alternatives to accepting unreported employment.