Browsing by Subject "CONNECTIVITY"

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  • Cornell, Stephen J.; Suprunenko, Yevhen F.; Finkelshtein, Dmitri; Somervuo, Panu; Ovaskainen, Otso (2019)
    Individual-based models, 'IBMs', describe naturally the dynamics of interacting organisms or social or financial agents. They are considered too complex for mathematical analysis, but computer simulations of them cannot give the general insights required. Here, we resolve this problem with a general mathematical framework for IBMs containing interactions of an unlimited level of complexity, and derive equations that reliably approximate the effects of space and stochasticity. We provide software, specified in an accessible and intuitive graphical way, so any researcher can obtain analytical and simulation results for any particular IBM without algebraic manipulation. We illustrate the framework with examples from movement ecology, conservation biology, and evolutionary ecology. This framework will provide unprecedented insights into a hitherto intractable panoply of complex models across many scientific fields.
  • Becker, Daniel J.; Hall, Richard J.; Forbes, Kristian M.; Plowright, Raina K.; Altizer, Sonia (2018)
  • Szibor, Annett; Lehtimäki, Jarmo; Ylikoski, Jukka; Aarnisalo, Antti A.; Mäkitie, Antti; Hyvärinen, Petteri (2018)
    Affective processing appears to be altered in tinnitus, and the condition is to a large extent characterized by the emotional reaction to the phantom sound. Psychophysiological models of tinnitus and supporting brain imaging studies have suggested a role for the limbic system in the emergence and maintenance of tinnitus. It is not clear whether the tinnitus-related changes in these systems are specific for tinnitus only, or whether they affect emotional processing more generally. In this study, we aimed to quantify possible deviations in affective processing in tinnitus patients by behavioral and physiological measures. Tinnitus patients rated the valence and arousal of sounds from the International Affective Digitized Sounds database. Sounds were chosen based on the normative valence ratings, that is, negative, neutral, or positive. The individual autonomic response was measured simultaneously with pupillometry. We found that the subjective ratings of the sounds by tinnitus patients differed significantly from the normative ratings. The difference was most pronounced for positive sounds, where sounds were rated lower on both valence and arousal scales. Negative and neutral sounds were rated differently only for arousal. Pupil measurements paralleled the behavioral results, showing a dampened response to positive sounds. Taken together, our findings suggest that affective processing is altered in tinnitus patients. The results are in line with earlier studies in depressed patients, which have provided evidence in favor of the so-called positive attenuation hypothesis of depression. Thus, the current results highlight the close link between tinnitus and depression.
  • Salomaa, Anna; Paloniemi, Riikka; Kotiaho, Janne S.; Kettunen, Marianne; Apostolopoulou, Evangelia; Cent, Joanna (2017)
    The gradually decreasing connectivity of habitats threatens biodiversity and ecological processes valuable to humans. Green infrastructure is promoted by the European Commission as a key instrument for the conservation of ecosystems in the EU biodiversity strategy to 2020. Green infrastructure has been defined as a network of natural and semi-natural areas, designed and managed to deliver a wide range of ecosystem services. We surveyed Finnish experts' perceptions on the development of green infrastructure within the existing policy framework. Our results show that improving the implementation of existing conservation policy instruments needs to be an integral part of developing green infrastructure. Despite the potential of green infrastructure to benefit biodiversity, existing conceptual ambiguity of green infrastructure with rather complex role of ecosystem services - and the possible interpretation of this in practice - raises concerns regarding its ability to contribute to biodiversity conservation.
  • Khazaei, Mohammad; Raeisi, Khadijeh; Croce, Pierpaolo; Tamburro, Gabriella; Tokariev, Anton; Vanhatalo, Sampsa; Zappasodi, Filippo; Comani, Silvia (2021)
    Neonates spend most of their life sleeping. During sleep, their brain experiences fast changes in its functional organization. Microstate analysis permits to capture the rapid dynamical changes occurring in the functional organization of the brain by representing the changing spatio-temporal features of the electroencephalogram (EEG) as a sequence of short-lasting scalp topographies-the microstates. In this study, we modeled the ongoing neonatal EEG into sequences of a limited number of microstates and investigated whether the extracted microstate features are altered in REM and NREM sleep (usually known as active and quiet sleep states-AS and QS-in the newborn) and depend on the EEG frequency band. 19-channel EEG recordings from 60 full-term healthy infants were analyzed using a modified version of the k-means clustering algorithm. The results show that similar to 70% of the variance in the datasets can be described using 7 dominant microstate templates. The mean duration and mean occurrence of the dominant microstates were significantly different in the two sleep states. Microstate syntax analysis demonstrated that the microstate sequences characterizing AS and QS had specific non-casual structures that differed in the two sleep states. Microstate analysis of the neonatal EEG in specific frequency bands showed a clear dependence of the explained variance on frequency. Overall, our findings demonstrate that (1) the spatio-temporal dynamics of the neonatal EEG can be described by non-casual sequences of a limited number of microstate templates; (2) the brain dynamics described by these microstate templates depends on frequency; (3) the features of the microstate sequences can well differentiate the physiological conditions characterizing AS and QS.
  • Siqueira, Tadeu; Saito, Victor S.; Bini, Luis M.; Melo, Adriano S.; Petsch, Danielle K.; Landeiro, Victor L.; Tolonen, Kimmo T.; Jyrkänkallio-Mikkola, Jenny; Soininen, Janne; Heino, Jani (2020)
    Ecological drift can override the effects of deterministic niche selection on small populations and drive the assembly of some ecological communities. We tested this hypothesis with a unique data set sampled identically in 200 streams in two regions (tropical Brazil and boreal Finland) that differ in macroinvertebrate community size by fivefold. Null models allowed us to estimate the magnitude to which beta-diversity deviates from the expectation under a random assembly process while taking differences in richness and relative abundance into account, i.e., beta-deviation. We found that both abundance- and incidence-based beta-diversity was negatively related to community size only in Brazil. Also, beta-diversity of small tropical communities was closer to stochastic expectations compared with beta-diversity of large communities. We suggest that ecological drift may drive variation in some small communities by changing the expected outcome of niche selection, increasing the chances of species with low abundance and narrow distribution to occur in some communities. Habitat destruction, overexploitation, pollution, and reductions in connectivity have been reducing the size of biological communities. These environmental pressures might make smaller communities more vulnerable to novel conditions and render community dynamics more unpredictable. Incorporation of community size into ecological models should provide conceptual and applied insights into a better understanding of the processes driving biodiversity.
  • Lankinen, Kaisu; Saari, Jukka; Hlushchuk, Yevhen; Tikka, Pia; Parkkonen, Lauri; Hari, Riitta; Koskinen, Miika (2018)
    Movie viewing allows human perception and cognition to be studied in complex, real-life-like situations in a brain-imaging laboratory. Previous studies with functional magnetic resonance imaging (fMRI) and with magneto-and electroencephalography (MEG and EEG) have demonstrated consistent temporal dynamics of brain activity across movie viewers. However, little is known about the similarities and differences of fMRI and MEG or EEG dynamics during such naturalistic situations. We thus compared MEG and fMRI responses to the same 15-min black-and-white movie in the same eight subjects who watched the movie twice during both MEG and fMRI recordings. We analyzed intra-and intersubject voxel-wise correlations within each imaging modality as well as the correlation of the MEG envelopes and fMRI signals. The fMRI signals showed voxel-wise within-and between-subjects correlations up to r = 0.66 and r = 0.37, respectively, whereas these correlations were clearly weaker for the envelopes of band-pass filtered (7 frequency bands below 100 Hz) MEG signals (within-subjects correlation r <0.14 and between-subjects r <0.05). Direct MEG-fMRI voxel-wise correlations were unreliable. Notably, applying a spatial-filtering approach to the MEG data uncovered consistent canonical variates that showed considerably stronger (up to r = 0.25) between-subjects correlations than the univariate voxel-wise analysis. Furthermore, the envelopes of the time courses of these variates up to about 10 Hz showed association with fMRI signals in a general linear model. Similarities between envelopes of MEG canonical variates and fMRI voxel time-courses were seen mostly in occipital, but also in temporal and frontal brain regions, whereas intra-and intersubject correlations for MEG and fMRI separately were strongest only in the occipital areas. In contrast to the conventional univariate analysis, the spatial-filtering approach was able to uncover associations between the MEG envelopes and fMRI time courses, shedding light on the similarities of hemodynamic and electromagnetic brain activities during movie viewing.
  • Kallankari, Hanna; Saunavaara, Virva; Parkkola, Riitta; Haataja, Leena; Hallman, Mikko; Kaukola, Tuula (2021)
    Background Very preterm birth can disturb brain maturation and subject these high-risk children to neurocognitive difficulties later. Objective The aim of the study was to evaluate the impact of prematurity on microstructure of frontostriatal tracts in children with no severe neurologic impairment, and to study whether the diffusion tensor imaging metrics of frontostriatal tracts correlate to executive functioning. Materials and methods The prospective cohort study comprised 54 very preterm children (mean gestational age 28.8 weeks) and 20 age- and gender-matched term children. None of the children had severe neurologic impairment. The children underwent diffusion tensor imaging and neuropsychological assessments at a mean age of 9 years. We measured quantitative diffusion tensor imaging metrics of frontostriatal tracts using probabilistic tractography. We also administered five subtests from the Developmental Neuropsychological Assessment, Second Edition, to evaluate executive functioning. Results Very preterm children had significantly higher fractional anisotropy and axial diffusivity values (P
  • O'Toole, J. M.; Boylan, G. B.; Vanhatalo, S.; Stevenson, N. J. (2016)
    Objective: To develop an automated estimate of EEG maturational age (EMA) for preterm neonates. Methods: The EMA estimator was based on the analysis of hourly epochs of EEG from 49 neonates with gestational age (GA) ranging from 23 to 32 weeks. Neonates had appropriate EEG for GA based on visual interpretation of the EEG. The EMA estimator used a linear combination (support vector regression) of a subset of 41 features based on amplitude, temporal and spatial characteristics of EEG segments. Estimator performance was measured with the mean square error (MSE), standard deviation of the estimate (SD) and the percentage error (SE) between the known GA and estimated EMA. Results: The EMA estimator provided an unbiased estimate of EMA with a MSE of 82 days (SD = 9.1 days; SE = 4.8%) which was significantly lower than a nominal reading (the mean GA in the dataset; MSE of 267 days, SD of 16.3 days, SE = 8.4%: p <0.001). The EMA estimator with the lowest MSE used amplitude, spatial and temporal EEG characteristics. Conclusions: The proposed automated EMA estimator provides an accurate estimate of EMA in early preterm neonates. Significance: Automated analysis of the EEG provides a widely accessible, noninvasive and continuous assessment of functional brain maturity. (C) 2016 International Federation of Clinical Neurophysiology. Published by Elsevier Ireland Ltd. All rights reserved.
  • Rybicki, Joel; Abrego, Nerea; Ovaskainen, Otso (2020)
    Habitat loss is one of the key drivers of the ongoing decline of biodiversity. However, ecologists still argue about how fragmentation of habitat (independent of habitat loss) affects species richness. The recently proposed habitat amount hypothesis posits that species richness only depends on the total amount of habitat in a local landscape. In contrast, empirical studies report contrasting patterns: some find positive and others negative effects of fragmentation per se on species richness. To explain this apparent disparity, we devise a stochastic, spatially explicit model of competitive species communities in heterogeneous habitats. The model shows that habitat loss and fragmentation have complex effects on species diversity in competitive communities. When the total amount of habitat is large, fragmentation per se tends to increase species diversity, but if the total amount of habitat is small, the situation is reversed: fragmentation per se decreases species diversity.
  • de Mendoza, Guillermo; Kaivosoja, Riikka; Grönroos, Mira; Hjort, Jan; Ilmonen, Jari; Kärnä, Olli-Matti; Paasivirta, Lauri; Tokola, Laura; Heino, Jani (2018)
    1. Metacommunity theory focuses on assembly patterns in ecological communities, originally exemplified through four different, yet non-exclusive, perspectives: patch dynamics, species sorting, source-sink dynamics, and neutral theory. More recently, three exclusive components have been proposed to describe a different metacommunity framework: habitat heterogeneity, species equivalence, and dispersal. Here, we aim at evaluating the insect metacommunity of a subarctic stream network under these two different frameworks. 2. We first modelled the presence/absence of 47 stream insects in northernmost Finland, using binomial generalised linear models (GLMs). The deviance explained by pure local environmental (E), spatial (S), and climatic variables (C) was then analysed across species using beta regression. In this comparative analysis, site occupancy, as well as taxonomic and biological trait vectors obtained from principal coordinate analysis, were used as predictor variables. 3. Single-species distributions were better explained by in-stream environmental and spatial factors than by climatic forcing, but in a highly variable fashion. This variability was difficult to relate to the taxonomic relatedness among species or their biological trait similarity. Site occupancy, however, was related to model performance of the binomial GLMs based on spatial effects: as populations are likely to be better connected for common species due to their near ubiquity, spatial factors may also explain better their distributions. 4. According to the classical four-perspective framework, the observation of both environmental and spatial effects suggests a role for either mass effects or species sorting constrained by dispersal limitation, or both. Taxonomic and biological traits, including the different dispersal capability of species, were scarcely important, which undermines the patch dynamics perspective, based on differences in dispersal ability between species. The highly variable performance of models makes the reliance on an entirely neutral framework unrealistic as well. According to the three-component framework, our results suggest that the stream insect metacommunity is shaped by the effect of habitat heterogeneity (supporting both species-sorting and mass effects), rather than species equivalence or dispersal limitation. 5. While the relative importance of the source-sink dynamics perspective or the species-sorting paradigm cannot be deciphered with the data at our disposal, we can conclude that habitat heterogeneity is an important driver shaping species distributions and insect assemblages in subarctic stream metacommunities. These results exemplify that the use of the three-component metacommunity framework may be more useful than the classical four perspective paradigm in analysing metacommunities. Our findings also provide support for conservation strategies based on the preservation of heterogeneous habitats in a metacommunity context.
  • Jalkanen, Joel; Toivonen, Tuuli; Moilanen, Atte (2020)
    Context Spatial conservation prioritization (SCP) has most often been applied to the design of reserve network expansion. In addition to occurrences of species and habitats inside protected area candidate sites, one may also be interested about network-level connectivity considerations. Objectives We applied SCP to the identification of ecological networks to inform the development of a new regional plan for the region of Uusimaa (South-Finland, including the Finnish capital district). Methods Input data were 59 high-quality layers of biotope and species distribution data. We identified ecological networks based on a combination of a Zonation balanced priority ranking map and a weighted range size rarity map, to account for both relative and absolute conservation values in the process. We also identified ecological corridors between protected areas and other ecologically high-priority areas using the corridor retention method of Zonation. Furthermore, we identified candidate sites for habitat restoration. Results We found seven large ecological networks (132-1201 km(2)) which stand out from their surrounding landscape in terms of ecological value and have clear connectivity bottlenecks between them. Highest restoration needs were found between large high-priority sites that are connected via remnant habitat fragments in comparatively highly modified areas. Conclusions Land conversion should be avoided in areas of highest ecological priorities and network-level connectivity. Restoration should be considered for connectivity bottlenecks. Methods described here can be applied in any location where relevant spatial data are available. The present results are actively used by the regional council and municipalities in the region of Uusimaa.
  • Kukkala, Aija; Maiorano, Luigi; Thuiller, Wilfried; Arponen, Anni (2019)
    The concept of National responsibility species (NRS) was developed to coordinate the conservation efforts of species occurring in multiple countries. Calculated as the fraction of the global species' distribution within a country, it measures the contribution of a local population to global survival of the species. However, there may be more co-occurring species in one region than another, making the conservation of a species more cost-efficient in the first than the latter. If cost-efficient resource allocation is the goal, then identifying NRS should also be based on spatial priorities. We propose that a species is considered NRS when a large part of its distribution falls within high priority areas in a country. We identify NRS from spatial conservation prioritization outputs to (1) maximize the overall cost-efficiency of allocation of conservation resources and (2) to provide information about which species the spatial priorities are based on. We analyzed data on vertebrates in the Birds and Habitats directives in the EU28 countries and compared the traditional NRS measure to three alternative strategies. While the majority of species maintained their NRS status in most countries regardless of the approach, differences occurred, with varying numbers and identities of responsibility species in a country, or responsibilities for species shifting between countries. The differences were largest in geographically marginal countries and for species that were distributed across a few countries. Other NRS approaches may also be useful, and the choice of approach should ultimately depend on the purpose and complement information on conservation status in decision-making.
  • Lehikoinen, Petteri; Tiusanen, Maria; Santangeli, Andrea; Rajasärkkä, Ari; Jaatinen, Kim; Valkama, Jari; Virkkala, Raimo; Lehikoinen, Aleksi (2021)
    Climate change has ubiquitous impacts on ecosystems and threatens biodiversity globally. One of the most recognized impacts are redistributions of species, a process which can be hindered by habitat degradation. Protected areas (PAs) have been shown to be beneficial for preserving and reallocating species occurrences under climate change. Yet, studies investigating effects of PA networks on species' range shifts under climate change remain scarce. In theory, a well-connected network of PAs should promote population persistence under climate change and habitat degradation. To study this, we evaluated the effects of PA coverage on avian communities in Finland between two study periods of 1980-1999 and 2000-2015. Climate-driven community impacts were investigated by using community temperature index (CTI). We used linear models to study the association of PA coverage and the CTI changes in southern, central and northern Finland. In northern and central Finland, higher PA coverage was associated with lower changes in CTI and 45% PA coverage in northern and 13% in central Finland corresponded with complete mitigation of CTI increase. These results indicate that higher PA coverage strongly increases community resilience to warming climate. However a similar association between PA coverage and changes in CTI was not apparent in southern Finland. The PA coverage in southern Finland was much lower than in the two other sections and thus, may be too sparse to favour community resilience against climate change. The results provide empirical evidence for the international need to rapidly expand PA networks and halt biodiversity loss.
  • Siebenhuehner, Felix; Weiss, Shennan A.; Coppola, Richard; Weinberger, Daniel R.; Bassett, Danielle S. (2013)
  • Tokariev, Anton; Roberts, James A.; Zalesky, Andrew; Zhao, Xuelong; Vanhatalo, Sampsa; Breakspear, Michael; Cocchi, Luca (2019)
    Sleep architecture carries vital information about brain health across the lifespan. In particular, the ability to express distinct vigilance states is a key physiological marker of neurological wellbeing in the newborn infant although systems-level mechanisms remain elusive. Here, we demonstrate that the transition from quiet to active sleep in newborn infants is marked by a substantial reorganization of large-scale cortical activity and functional brain networks. This reorganization is attenuated in preterm infants and predicts visual performance at two years. We find a striking match between these empirical effects and a computational model of large-scale brain states which uncovers fundamental biophysical mechanisms not evident from inspection of the data. Active sleep is defined by reduced energy in a uniform mode of neural activity and increased energy in two more complex anteroposterior modes. Preterm-born infants show a deficit in this sleep-related reorganization of modal energy that carries novel prognostic information.
  • Boldt, Robert; Malinen, Sanna; Seppa, Mika; Tikka, Pia; Savolainen, Petri Ilmari; Hari, Riitta; Carlson, Synnöve (2013)
  • Cruz, Gabriela; Grent-'t-Jong, Tineke; Krishnadas, Rajeev; Palva, J. Matias; Palva, Satu; Uhlhaas, Peter J. (2021)
    Long-Range Temporal Correlations (LRTCs) index the capacity of the brain to optimally process information. Previous research has shown that patients with chronic schizophrenia present altered LRTCs at alpha and beta oscillations. However, it is currently unclear at which stage of schizophrenia aberrant LRTCs emerge. To address this question, we investigated LRTCs in resting-state magnetoencephalographic (MEG) recordings obtained from patients with affective disorders and substance abuse (clinically at low-risk of psychosis, CHR-N), patients at clinical high-risk of psychosis (CHR-P) (n = 115), as well as patients with a first episode (FEP) (n = 25). Matched healthy controls (n = 47) served as comparison group. LRTCs were obtained for frequencies from 4 to 40 Hz and correlated with clinical and neuropsychological data. In addition, we examined the relationship between LRTCs and transition to psychosis in CHR-P participants, and the relationship between LRTC and antipsychotic medication in FEP participants. Our results show that participants from the clinical groups have similar LRTCs to controls. In addition, LRTCs did not correlate with clinical and neurocognitive variables across participants nor did LRTCs predict transition to psychosis. Therefore, impaired LRTCs do not reflect a feature in the clinical trajectory of psychosis. Nevertheless, reduced LRTCs in the beta-band over posterior sensors of medicated FEP participants indicate that altered LRTCs may appear at the onset of the illness. Future studies are needed to elucidate the role of anti-psychotic medication in altered LRTCs.
  • Koponen, Lari M.; Nieminen, Jaakko O.; Ilmoniemi, Risto J. (2018)
    Background: Transcranial magnetic stimulation (TMS) is a non-invasive brain stimulation method: a magnetic field pulse from a TMS coil can excite neurons in a desired location of the cortex. Conventional TMS coils cause focal stimulation underneath the coil centre; to change the location of the stimulated spot, the coil must be moved over the new target. This physical movement is inherently slow, which limits, for example, feedback-controlled stimulation. Objective: To overcome the limitations of physical TMS-coil movement by introducing electronic targeting. Methods: We propose electronic stimulation targeting using a set of large overlapping coils and introduce a matrix-factorisation-based method to design such sets of coils. We built one such device and demonstrated the electronic stimulation targeting in vivo. Results: The demonstrated two-coil transducer allows translating the stimulated spot along a 30-mmlong line segment in the cortex; with five coils, a target can be selected from within a region of the cortex and stimulated in any direction. Thus, far fewer coils are required by our approach than by previously suggested ones, none of which have resulted in practical devices. Conclusion: Already with two coils, we can adjust the location of the induced electric field maximum along one dimension, which is sufficient to study, for example, the primary motor cortex. (C) 2018 The Author(s). Published by Elsevier Inc.
  • Kauttonen, Janne; Hlushchuk, Yevhen; Tikka, Pia (2015)
    One of the challenges of naturalistic neurosciences using movie-viewing experiments is how to interpret observed brain activations in relation to the multiplicity of time-locked stimulus features. As previous studies have shown less inter-subject synchronization across viewers of random video footage than story-driven films, new methods need to be developed for analysis of less story-driven contents. To optimize the linkage between our fMRI data collected during viewing of a deliberately non-narrative silent film 'At Land' by Maya Deren (1944) and its annotated content, we combined the method of elastic-net regularization with the model-driven linear regression and the well-established data-driven independent component analysis (ICA) and inter-subject correlation (ISC) methods. In the linear regression analysis, both IC and region-of-interest (ROI) time-series were fitted with time-series of a total of 36 binary-valued and one real-valued tactile annotation of film features. The elastic-net regularization and cross-validation were applied in the ordinary least-squares linear regression in order to avoid over-fitting due to the multicollinearity of regressors, the results were compared against both the partial least-squares (PLS) regression and the un-regularized full-model regression. Nonparametric permutation testing scheme was applied to evaluate the statistical significance of regression. We found statistically significant correlation between the annotation model and 9 ICs out of 40 ICs. Regression analysis was also repeated for a large set of cubic ROIs covering the grey matter. Both IC- and ROI-based regression analyses revealed activations in parietal and occipital regions, with additional smaller clusters in the frontal lobe. Furthermore, we found elastic-net based regression more sensitive than PLS and un-regularized regression since it detected a larger number of significant ICs and ROIs. Along with the ISC ranking methods, our regression analysis proved a feasible method for ordering the ICs based on their functional relevance to the annotated cinematic features. The novelty of our method is - in comparison to the hypothesis-driven manual pre-selection and observation of some individual regressors biased by choice - in applying data-driven approach to all content features simultaneously. We found especially the combination of regularized regression and ICA useful when analyzing fMRI data obtained using non-narrative movie stimulus with a large set of complex and correlated features. (C) 2015 The Authors. Published by Elsevier Inc.