Dynamics of contour, object and face processing in the human visual cortex

The neural basis of visual perception can be understood only when the sequence of cortical activity underlying successful recognition is known. The early steps in this processing chain, from retina to the primary visual cortex, are highly local, and the perception of more complex shapes requires integration of the local information. In Study I of this thesis, the progression from local to global visual analysis was assessed by recording cortical magnetoencephalographic (MEG) responses to arrays of elements that either did or did not form global contours. The results demonstrated two spatially and temporally distinct stages of processing: The first, emerging 70 ms after stimulus onset around the calcarine sulcus, was sensitive to local features only, whereas the second, starting at 130 ms across the occipital and posterior parietal cortices, reflected the global configuration. To explore the links between cortical activity and visual recognition, Studies II III presented subjects with recognition tasks of varying levels of difficulty. The occipito-temporal responses from 150 ms onwards were closely linked to recognition performance, in contrast to the 100-ms mid-occipital responses. The averaged responses increased gradually as a function of recognition performance, and further analysis (Study III) showed the single response strengths to be graded as well. Study IV addressed the attention dependence of the different processing stages: Occipito-temporal responses peaking around 150 ms depended on the content of the visual field (faces vs. houses), whereas the later and more sustained activity was strongly modulated by the observers attention. Hemodynamic responses paralleled the pattern of the more sustained electrophysiological responses. Study V assessed the temporal processing capacity of the human object recognition system. Above sufficient luminance, contrast and size of the object, the processing speed was not limited by such low-level factors. Taken together, these studies demonstrate several distinct stages in the cortical activation sequence underlying the object recognition chain, reflecting the level of feature integration, difficulty of recognition, and direction of attention.

Nitrogen dynamics and nitrogen use efficiency of spring cereals under Finnish growing conditions

Nitrogen (N) is one of the main inputs in cereal cultivation and as more than half of the arable land in Finland is used for cereal production, N has contributed substantially to agricultural pollution through fertilizer leaching and runoff. Based on this global phenomenon, the European Community has launched several directives to reduce agricultural emissions to the environment. Trough such measures, and by using economic incentives, it is expected that northern European agricultural practices will, in the future, include reduced N fertilizer application rates. Reduced use of N fertilizer is likely to decrease both production costs and pollution, but could also result in reduced yields and quality if crops experience temporary N deficiency. Therefore, more efficient N use in cereal production, to minimize pollution risks and maximize farmer income, represents a current challenge for agronomic research in the northern growing areas. The main objective of this study was to determine the differences in nitrogen use efficiency (NUE) among spring cereals grown in Finland. Additional aims were to characterize the multiple roles of NUE by analysing the extent of variation in NUE and its component traits among different cultivars, and to understand how other physiological traits, especially radiation use efficiency (RUE) and light interception, affect and interact with the main components of NUE and contribute to differences among cultivars. This study included cultivars of barley (Hordeum vulgare L.), oat (Avena sativa L.) and wheat (Triticum aestivum L.). Field experiments were conducted between 2001 and 2004 at Jokioinen, in Finland. To determine differences in NUE among cultivars and gauge the achievements of plant breeding in NUE, 17-18 cultivars of each of the three cereal species released between 1909 and 2002 were studied. Responses to nitrogen of landraces, old cultivars and modern cultivars of each cereal species were evaluated under two N regimes (0 and 90 kg N ha-1). Results of the study revealed that modern wheat, oat and barley cultivars had similar NUE values under Finnish growing conditions and only results from a wider range of cultivars indicated that wheat cultivars could have lower NUE than the other species. There was a clear relationship between nitrogen uptake efficiency (UPE) and NUE in all species whereas nitrogen utilization efficiency (UTE) had a strong positive relationship with NUE only for oat. UTE was clearly lower in wheat than in other species. Other traits related to N translocation indicated that wheat also had a lower harvest index, nitrogen harvest index and nitrogen remobilisation efficiency and therefore its N translocation efficiency was confirmed to be very low. On the basis of these results there appears to be potential and also a need for improvement in NUE. These results may help understand the underlying physiological differences in NUE and could help to identify alternative production options, such as the different roles that species can play in crop rotations designed to meet the demands of modern agricultural practices.

Ecological communities in variable environments : dynamics and diversity under coloured environmental stochasticity

While environmental variation is an ubiquitous phenomenon in the natural world which has for long been appreciated by the scientific community recent changes in global climatic conditions have begun to raise consciousness about the economical, political and sociological ramifications of global climate change. Climate warming has already resulted in documented changes in ecosystem functioning, with direct repercussions on ecosystem services. While predicting the influence of ecosystem changes on vital ecosystem services can be extremely difficult, knowledge of the organisation of ecological interactions within natural communities can help us better understand climate driven changes in ecosystems. The role of environmental variation as an agent mediating population extinctions is likely to become increasingly important in the future. In previous studies population extinction risk in stochastic environmental conditions has been tied to an interaction between population density dependence and the temporal autocorrelation of environmental fluctuations. When populations interact with each other, forming ecological communities, the response of such species assemblages to environmental stochasticity can depend, e.g., on trophic structure in the food web and the similarity in species-specific responses to environmental conditions. The results presented in this thesis indicate that variation in the correlation structure between species-specific environmental responses (environmental correlation) can have important qualitative and quantitative effects on community persistence and biomass stability in autocorrelated (coloured) environments. In addition, reddened environmental stochasticity and ecological drift processes (such as demographic stochasticity and dispersal limitation) have important implications for patterns in species relative abundances and community dynamics over time and space. Our understanding of patterns in biodiversity at local and global scale can be enhanced by considering the relevance of different drift processes for community organisation and dynamics. Although the results laid out in this thesis are based on mathematical simulation models, they can be valuable in planning effective empirical studies as well as in interpreting existing empirical results. Most of the metrics considered here are directly applicable to empirical data.

Ligand dependent intra and inter subunit communication in human tryptophanyl tRNA synthetase as deduced from the dynamics of structure networks

Homodimeric protein tryptophanyl tRNA synthetase (TrpRS) has a Rossmann fold domain and belongs to the 1c subclass of aminoacyl tRNA synthetases. This enzyme performs the function of acylating the cognate tRNA. This process involves a number of molecules (2 protein subunits, 2 tRNAs and 2 activated Trps) and thus it is difficult to follow the complex steps in this process. Structures of human TrpRS complexed with certain ligands are available. Based on structural and biochemical data, mechanism of activation of Trp has been speculated. However, no structure has yet been solved in the presence of both the tRNA(Trp) and the activated Trp (TrpAMP). In this study, we have modeled the structure of human TrpRS bound to the activated ligand and the cognate tRNA. In addition, we have performed molecular dynamics (MD) simulations on these models as well as other complexes to capture the dynamical process of ligand induced conformational changes. We have analyzed both the local and global changes in the protein conformation from the protein structure network (PSN) of MD snapshots, by a method which was recently developed in our laboratory in the context of the functionally monomeric protein, methionyl tRNA synthetase. From these investigations, we obtain important information such as the ligand induced correlation between different residues of this protein, asymmetric binding of the ligands to the two subunits of the protein as seen in the crystal structure analysis, and the path of communication between the anticodon region and the aminoacylation site. Here we are able to elucidate the role of dimer interface at a level of detail, which has not been captured so far.

The effect of horizontal resolution on simulation of very extreme US precipitation events in a global atmosphere model

We investigate the ability of a global atmospheric general circulation model (AGCM) to reproduce observed 20 year return values of the annual maximum daily precipitation totals over the continental United States as a function of horizontal resolution. We find that at the high resolutions enabled by contemporary supercomputers, the AGCM can produce values of comparable magnitude to high quality observations. However, at the resolutions typical of the coupled general circulation models used in the Fourth Assessment Report of the Intergovernmental Panel on Climate Change, the precipitation return values are severely underestimated.

Knowledge unlatched : A global library consortium model for funding Open Access scholarly books

Specialist scholarly books, including monographs, allow researchers to present their work, pose questions and to test and extend areas of theory through long-form writing. In spite of the fact that research communities all over the world value monographs and depend heavily on them as a requirement of tenure and promotion in many disciplines, sales of this kind of book are in free fall, with some estimates suggesting declines of as much as 90% over twenty years (Willinsky 2006). Cashstrapped monograph publishers have found themselves caught in a negative cycle of increasing prices and falling sales, with few resources left to support experimentation, business model innovation or engagement with digital technology and Open Access (OA). This chapter considers an important attempt to tackle failing markets for scholarly monographs, and to enable the wider adoption of OA licenses for book-length works: the 2012 – 2014 Knowledge Unlatched pilot. Knowledge Unlatched is a bold attempt to reconfigure the market for specialist scholarly books: moving it beyond the sale of ‘content’ towards a model that supports the services valued by scholarly and wider communities in the context of digital possibility. Its success has powerful implications for the way we understand copyright’s role in the creative industries, and the potential for established institutions and infrastructure to support the open and networked dynamics of a digital age.

Quasi-periodic, global oscillations in sea level pressure on intraseasonal timescales

The sea level pressure (SLP) variability in 30-60 day intraseasonal timescales is investigated using 25 years of reanalysis data addressing two issues. The first concerns the non-zero zonal mean component of SLP near the equator and its meridional connections, and the second concerns the fast eastward propagation (EP) speed of SLP compared to that of zonal wind. It is shown that the entire globe resonates with high amplitude wave activity during some periods which may last for few to several months, followed by lull periods of varying duration. SLP variations in the tropical belt are highly coherent from 25A degrees S to 25A degrees N, uncorrelated with variations in mid latitudes and again significantly correlated but with opposite phase around 60A degrees S and 65A degrees N. Near the equator (8A degrees S-8A degrees N), the zonal mean contributes significantly to the total variance in SLP, and after its removal, SLP shows a dominant zonal wavenumber one structure having a periodicity of 40 days and EP speeds comparable to that of zonal winds in the Indian Ocean. SLP from many of the atmospheric and coupled general circulation models show similar behaviour in the meridional direction although their propagation characteristics in the tropical belt differ widely.

Insight into the early stages of thermal unfolding of peanut agglutinin by molecular dynamics simulations

Peanut agglutinin is a homotetrameric nonglycosylated protein. The protein has a unique open quaternary structure. Molecular dynamics simulations have been employed follow the atomistic details of its unfolding at different temperatures. The early events of the deoligomerization of the protein have been elucidated in the present study. Simulation trajectories of the monomer as well as those of the tetramer have been compared and the tetramer is found to be substantially more stable than its monomeric counterpart. The tetramer shows retention of most of its.. secondary structure but considerable loss of the tertiary structure at high temperature. e generation of a This observation impies the molten globule-like intermediate in the later stages of deoligomerization. The quaternary structure of the protein has weakened to a large extent, but none of the subunits are separated. In addition, the importance of the metal-binding to the stability of the protein structure has also been investigated. Binding of the metal ions not only enhances the local stability of the metal-ion binding loop, but also imparts a global stability to the overall structure. The dynamics of different interfaces vary significantly as probed through interface clusters. The differences are substantially enhanced at higher temperatures. The dynamics and the stability of the interfaces have been captured mainly by cluster analysis, which has provided detailed information on the thermal deoligomerization of the protein.

Studies of Earth Dynamics with the Superconducting Gravimeter

The superconducting (or cryogenic) gravimeter (SG) is based on the levitation of a super­conducting sphere in a stable magnetic field created by current in superconducting coils. Depending on frequency, it is capable of detecting gravity variations as small as 10-11ms-2. For a single event, the detection threshold is higher, conservatively about 10-9 ms-2. Due to its high sensitivity and low drift rate, the SG is eminently suitable for the study of geodynamical phenomena through their gravity signatures. I present investigations of Earth dynamics with the superconducting gravimeter GWR T020 at Metsähovi from 1994 to 2005. The history and key technical details of the installation are given. The data processing methods and the development of the local tidal model at Metsähovi are presented. The T020 is a part of the worldwide GGP (Global Geodynamics Project) network, which consist of 20 working station. The data of the T020 and of other participating SGs are available to the scientific community. The SG T020 have used as a long-period seismometer to study microseismicity and the Earth s free oscillation. The annual variation, spectral distribution, amplitude and the sources of microseism at Metsähovi were presented. Free oscillations excited by three large earthquakes were analyzed: the spectra, attenuation and rotational splitting of the modes. The lowest modes of all different oscillation types are studied, i.e. the radial mode 0S0, the "football mode" 0S2, and the toroidal mode 0T2. The very low level (0.01 nms-1) incessant excitation of the Earth s free oscillation was detected with the T020. The recovery of global and regional variations in gravity with the SG requires the modelling of local gravity effects. The most important of them is hydrology. The variation in the groundwater level at Metsähovi as measured in a borehole in the fractured bedrock correlates significantly (0.79) with gravity. The influence of local precipitation, soil moisture and snow cover are detectable in the gravity record. The gravity effect of the variation in atmospheric mass and that of the non-tidal loading by the Baltic Sea were investigated together, as sea level and air pressure are correlated. Using Green s functions it was calculated that a 1 metre uniform layer of water in the Baltic Sea increases the gravity at Metsähovi by 31 nms-2 and the vertical deformation is -11 mm. The regression coefficient for sea level is 27 nms-2m-1, which is 87% of the uniform model. These studies are associated with temporal height variations using the GPS data of Metsähovi permanent station. Results of long time series at Metsähovi demonstrated high quality of data and correctly carried out offsets and drift corrections. The superconducting gravimeter T020 has been proved to be an eminent and versatile tool in studies of the Earth dynamics.

The 5-Methyl Group in Thymine Dynamically Influences the Structure of A-Tracts in DNA at the Local and Global Level

DNA sequences containing a stretch of several A:T basepairs without a 5'-TA-3' step are known as A-tracts and have been the subject of extensive investigation because of their unique structural features such as a narrow minor groove and their crucial role in several biological processes. One of the aspects under investigation has been the influence of the 5-methyl group of thymine on the properties of A-tracts. Detailed molecular dynamics simulation studies of the sequences d(CGCAAAUUUGCG) and d(CGCAAATTTGCG) indicate that the presence of the 5-methyl group in thymine increases the frequency of a narrow minor groove conformation, which could facilitate its specific recognition by proteins, and reduce its susceptibility to cleavage by DNase I. The bias toward a wider minor groove in the absence of the thymine 5-methyl group is a static structural feature. Our results also indicate that the presence of the thymine 5-methyl group is necessary for calibrating the backbone conformation and the basepair and dinucleotide step geometry of the core A-tract as well as the flanking CA/TG and the neighboring GC/GC steps, as observed in free and protein-bound DNA. As a consequence, it also fine-tunes the curvature of the longer DNA fragment in which the A-tract is embedded.

Fast versus slow response in climate change: implications for the global hydrological cycle

Recent studies have shown that changes in global mean precipitation are larger for solar forcing than for CO2 forcing of similar magnitude.In this paper, we use an atmospheric general circulation model to show that the differences originate from differing fast responses of the climate system. We estimate the adjusted radiative forcing and fast response using Hansen's ``fixed-SST forcing'' method.Total climate system response is calculated using mixed layer simulations using the same model. Our analysis shows that the fast response is almost 40% of the total response for few key variables like precipitation and evaporation. We further demonstrate that the hydrologic sensitivity, defined as the change in global mean precipitation per unit warming, is the same for the two forcings when the fast responses are excluded from the definition of hydrologic sensitivity, suggesting that the slow response (feedback) of the hydrological cycle is independent of the forcing mechanism. Based on our results, we recommend that the fast and slow response be compared separately in multi-model intercomparisons to discover and understand robust responses in hydrologic cycle. The significance of this study to geoengineering is discussed.

Topological phases, Majorana modes and quench dynamics in a spin ladder system

We explore the salient features of the `Kitaev ladder', a two-legged ladder version of the spin-1/2 Kitaev model on a honeycomb lattice, by mapping it to a one-dimensional fermionic p-wave superconducting system. We examine the connections between spin phases and topologically non-trivial phases of non-interacting fermionic systems, demonstrating the equivalence between the spontaneous breaking of global Z(2) symmetry in spin systems and the existence of isolated Majorana modes. In the Kitaev ladder, we investigate topological properties of the system in different sectors characterized by the presence or absence of a vortex in each plaquette of the ladder. We show that vortex patterns can yield a rich parameter space for tuning into topologically non-trivial phases. We introduce and employ a new topological invariant for explicitly determining the presence of zero energy Majorana modes at the boundaries of such phases. Finally, we discuss dynamic quenching between topologically non-trivial phases in the Kitaev ladder and, in particular, the post-quench dynamics governed by tuning through a quantum critical point.

Albedo enhancement of marine clouds to counteract global warming: impacts on the hydrological cycle

Recent studies have shown that changes in solar radiation affect the hydrological cycle more strongly than equivalent CO(2) changes for the same change in global mean surface temperature. Thus, solar radiation management ``geoengineering'' proposals to completely offset global mean temperature increases by reducing the amount of absorbed sunlight might be expected to slow the global water cycle and reduce runoff over land. However, proposed countering of global warming by increasing the albedo of marine clouds would reduce surface solar radiation only over the oceans. Here, for an idealized scenario, we analyze the response of temperature and the hydrological cycle to increased reflection by clouds over the ocean using an atmospheric general circulation model coupled to a mixed layer ocean model. When cloud droplets are reduced in size over all oceans uniformly to offset the temperature increase from a doubling of atmospheric CO(2), the global-mean precipitation and evaporation decreases by about 1.3% but runoff over land increases by 7.5% primarily due to increases over tropical land. In the model, more reflective marine clouds cool the atmospheric column over ocean. The result is a sinking motion over oceans and upward motion over land. We attribute the increased runoff over land to this increased upward motion over land when marine clouds are made more reflective. Our results suggest that, in contrast to other proposals to increase planetary albedo, offsetting mean global warming by reducing marine cloud droplet size does not necessarily lead to a drying, on average, of the continents. However, we note that the changes in precipitation, evaporation and P-E are dominated by small but significant areas, and given the highly idealized nature of this study, a more thorough and broader assessment would be required for proposals of altering marine cloud properties on a large scale.

Characterisation of Landscape with Forest Fragmentation Dynamics

Land cover (LC) and land use (LU) dynamics induced by human and natural processes play a major role in global as well as regional patterns of landscapes influencing biodiversity, hydrology, ecology and climate. Changes in LC features resulting in forest fragmentations have posed direct threats to biodiversity, endangering the sustainability of ecological goods and services. Habitat fragmentation is of added concern as the residual spatial patterns mitigate or exacerbate edge effects. LU dynamics are obtained by classifying temporal remotely sensed satellite imagery of different spatial and spectral resolutions. This paper reviews five different image classification algorithms using spatio-temporal data of a temperate watershed in Himachal Pradesh, India. Gaussian Maximum Likelihood classifier was found to be apt for analysing spatial pattern at regional scale based on accuracy assessment through error matrix and ROC (receiver operating characteristic) curves. The LU information thus derived was then used to assess spatial changes from temporal data using principal component analysis and correspondence analysis based image differencing. The forest area dynamics was further studied by analysing the different types of fragmentation through forest fragmentation models. The computed forest fragmentation and landscape metrics show a decline of interior intact forests with a substantial increase in patch forest during 1972-2007.

The Contribution of Rare Species to Community Phylogenetic Diversity across a Global Network of Forest Plots

Niche differentiation has been proposed as an explanation for rarity in species assemblages. To test this hypothesis requires quantifying the ecological similarity of species. This similarity can potentially be estimated by using phylogenetic relatedness. In this study, we predicted that if niche differentiation does explain the co-occurrence of rare and common species, then rare species should contribute greatly to the overall community phylogenetic diversity (PD), abundance will have phylogenetic signal, and common and rare species will be phylogenetically dissimilar. We tested these predictions by developing a novel method that integrates species rank abundance distributions with phylogenetic trees and trend analyses, to examine the relative contribution of individual species to the overall community PD. We then supplement this approach with analyses of phylogenetic signal in abundances and measures of phylogenetic similarity within and between rare and common species groups. We applied this analytical approach to 15 long-term temperate and tropical forest dynamics plots from around the world. We show that the niche differentiation hypothesis is supported in six of the nine gap-dominated forests but is rejected in the six disturbance-dominated and three gap-dominated forests. We also show that the three metrics utilized in this study each provide unique but corroborating information regarding the phylogenetic distribution of rarity in communities.