Spatial Smoothing for Diffusion Tensor Imaging with low Signal to Noise Ratios

Though low signal to noise ratio (SNR) experiments in DTI give key information about tracking and anisotropy, e.g. by measurements with very small voxel sizes, due to the complicated impact of thermal noise such experiments are up to now seldom analysed. In this paper Monte Carlo simulations are presented which investigate the random fields of noise for different DTI variables in low SNR situations. Based on this study a strategy for spatial smoothing, which demands essentially uniform noise, is derived. To construct a convenient filter the weights of the nonlinear Aurich chain are adapted to DTI. This edge preserving three dimensional filter is then validated in different variants via a quasi realistic model and is applied to very new data with isotropic voxels of the size 1x1x1 mm3 which correspond to a spatial mean SNR of approximately 3

DTI denoising for data with low signal to noise ratios

Low signal to noise ratio (SNR) experiments in diffusion tensor imaging (DTI) give key information about tracking and anisotropy, e. g., by measurements with small voxel sizes or with high b values. However, due to the complicated and dominating impact of thermal noise such data are still seldom analysed. In this paper Monte Carlo simulations are presented which investigate the distributions of noise for different DTI variables in low SNR situations. Based on this study a strategy for the application of spatial smoothing is derived. Optimal prerequisites for spatial filters are unbiased, bell shaped distributions with uniform variance, but, only few variables have a statistics close to that. To construct a convenient filter a chain of nonlinear Gaussian filters is adapted to peculiarities of DTI and a bias correction is introduced. This edge preserving three dimensional filter is then validated via a quasi realistic model. Further, it is shown that for small sample sizes the filter is as effective as a maximum likelihood estimator and produces reliable results down to a local SNR of approximately 1. The filter is finally applied to very recent data with isotropic voxels of the size 1×1×1mm^3 which corresponds to a spatially mean SNR of 2.5. This application demonstrates the statistical robustness of the filter method. Though the Rician noise model is only approximately realized in the data, the gain of information by spatial smoothing is considerable

Population Trends of a Mixed-Species Colony of Humboldt and Magellanic Penguins in Southern Chile after Establishing a Protected Area

Worldwide marine protected areas (MPAs) have been designated to protect marine resources, including top predators such as seabirds. There is no conclusive information on whether protected areas can improve population trends of seabirds when these are further exploited as tourist attractions, an activity that has increased in past decades. Humboldt Penguins (Spheniscus humboldti) and Magellanic Penguins (S. magellanicus) breed sympatrically on Puñihuil Islets, two small coastal islands off the west coast of Chiloé Island (41° S) in southern Chile that are subject to exploitation for tourism. Our goal was to compare the population size of the mixed colony of Humboldt and Magellanic Penguins before and after protection from unregulated tourism and freely roaming goats in 1997. For this purpose, two censuses were conducted in 2004 and 2008, and the numbers compared with those obtained in 1997 by other authors. The proportion of occupied, unoccupied, and collapsed/flooded burrows changed between years; there were 68% and 34% fewer collapsed burrows in 2004 and 2008, respectively, than in 1997. For the total number of burrows of both species, we counted 48% and 63% more burrows in 2004 and 2008, respectively, than in 1997. We counted 13% more burrows of Humboldt Penguins in 2008 than in 1997, and for Magellanic Penguins, we estimated a 64% increase in burrows in 2008. Presumably, this was as a result of habitat improvement attributable to the exclusion of tourists and the removal of goats from the islets. Although tourist visits to the islets are prohibited, tourism activities around the colonies are prevalent and need to be taken into account to promote appropriate management

Tendance d’une colonie mixte de Manchots de Humboldt et de Manchots de Magellan dans le sud du Chili à la suite de l’établissement d’une aire protégée

Worldwide marine protected areas (MPAs) have been designated to protect marine resources, including top predators such as seabirds. There is no conclusive information on whether protected areas can improve population trends of seabirds when these are further exploited as tourist attractions, an activity that has increased in past decades. Humboldt Penguins (Spheniscus humboldti) and Magellanic Penguins (S. magellanicus) breed sympatrically on Puñihuil Islets, two small coastal islands off the west coast of Chiloé Island (41° S) in southern Chile that are subject to exploitation for tourism. Our goal was to compare the population size of the mixed colony of Humboldt and Magellanic Penguins before and after protection from unregulated tourism and freely roaming goats in 1997. For this purpose, two censuses were conducted in 2004 and 2008, and the numbers compared with those obtained in 1997 by other authors. The proportion of occupied, unoccupied, and collapsed/ flooded burrows changed between years; there were 68% and 34% fewer collapsed burrows in 2004 and 2008, respectively, than in 1997. For the total number of burrows of both species, we counted 48% and 63% more burrows in 2004 and 2008, respectively, than in 1997. We counted 13% more burrows of Humboldt Penguins in 2008 than in 1997, and for Magellanic Penguins, we estimated a 64% increase in burrows in 2008. Presumably, this was as a result of habitat improvement attributable to the exclusion of tourists and the removal of goats from the islets. Although tourist visits to the islets are prohibited, tourism activities around the colonies are prevalent and need to be taken into account to promote appropriate management.Les aires marines protégées ont été établies à l’échelle mondiale pour protéger les ressources marines, dont les prédateurs au sommet de la chaîne alimentaire comme les oiseaux marins. Rien n’indique de façon concluante que la protection d’aires permet une hausse des populations d’oiseaux marins dans les cas où ces populations représentent toujours une attraction touristique, activité dont la popularité a augmenté au cours des dernières décennies. Les Manchots de Humboldt (Spheniscus humboldti) et les Manchots de Magellan (S. magellanicus) nichent de façon sympatrique sur les îlots Puñihuil, deux petites îles au large de la côte ouest de l’île de Chiloé (41° S.) qui font l’objet de visites touristiques dans le sud du Chili. L’objectif de notre étude était de comparer la taille des deux populations de manchots avant et après l’établissement d’une réglementation touchant le tourisme et les chèvres en liberté en 1997. À cette fin, deux relevés ont été effectués en 2004 et 2008, et les résultats ont été comparés à ceux obtenus en 1997 par d’autres auteurs. La proportion de terriers occupés, non occupés ou effondrés/inondés a varié selon les années; ainsi, il y a eu 68 % et 34 % moins de terriers effondrés en 2004 et 2008, respectivement, qu’en 1997. Pour ce qui est du nombre de terriers des deux espèces, nous avons compté 48 % et 63 % plus de terriers en 2004 et 2008, respectivement, qu’en 1997. Nous avons compté 13 % plus de terriers de Manchots de Humboldt en 2008 par rapport à 1997, et avons observé une hausse de 64 % pour les terriers de Manchots de Magellan en 2008. Nous pouvons présumer que ces hausses résultent de l’amélioration de l’habitat consécutive à l’exclusion des touristes et au retrait des chèvres des îlots. Même si les visites touristiques sont maintenant interdites sur les îlots, l’activité touristique aux abords des colonies a toujours cours et doit être prise en compte si on veut mettre en place une gestion adéquate.Fil: Reyes Arriagada, Ronnie. Universidad Austral de Chile; Chile;Fil: Hiriart Bertrand, Luciano. Universidad Andres Bello; Chile;Fil: Riquelme, Victoria. Universidad Austral de Chile; Chile;Fil: Simeone, Alejandro. Universidad Andres Bello; Chile;Fil: Pütz, Klemens. Antartic Research Trust; Suiza;Fil: Lüthi, Benno. Antartic Research Trust; Suiza;Fil: Raya Rey, Andrea Nélida. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Austral de Investigaciones Cientificas; Argentina

Gene Expression Profiling Following Maternal Deprivation: Involvement of the Brain Renin-Angiotensin System

The postnatal development of the mouse is characterized by a stress hypo-responsive period (SHRP), where basal corticosterone levels are low and responsiveness to mild stressors is reduced. Maternal separation is able to disrupt the SHRP and is widely used to model early trauma. In this study we aimed at identifying of brain systems involved in acute and possible long-term effects of maternal separation. We conducted a microarray-based gene expression analysis in the hypothalamic paraventricular nucleus after maternal separation, which revealed 52 differentially regulated genes compared to undisturbed controls, among them are 37 up-regulated and 15 down-regulated genes. One of the prominently up-regulated genes, angiotensinogen, was validated using in-situ hybridization. Angiotensinogen is the precursor of angiotensin II, the main effector of the brain renin-angiotensin system (RAS), which is known to be involved in stress system modulation in adult animals. Using the selective angiotensin type I receptor [AT(1)] antagonist candesartan we found strong effects on CRH and GR mRNA expression in the brain and ACTH release following maternal separation. AT(1) receptor blockade appears to enhance central effects of maternal separation in the neonate, suggesting a suppressing function of brain RAS during the SHRP. Taken together, our results illustrate the molecular adaptations that occur in the paraventricular nucleus following maternal separation and contribute to identifying signaling cascades that control stress system activity in the neonate

Deducing corticotropin-releasing hormone receptor type 1 signaling networks from gene expression data by usage of genetic algorithms and graphical Gaussian models

<p>Abstract</p> <p>Background</p> <p>Dysregulation of the hypothalamic-pituitary-adrenal (HPA) axis is a hallmark of complex and multifactorial psychiatric diseases such as anxiety and mood disorders. About 50-60% of patients with major depression show HPA axis dysfunction, i.e. hyperactivity and impaired negative feedback regulation. The neuropeptide corticotropin-releasing hormone (CRH) and its receptor type 1 (CRHR1) are key regulators of this neuroendocrine stress axis. Therefore, we analyzed CRH/CRHR1-dependent gene expression data obtained from the pituitary corticotrope cell line AtT-20, a well-established <it>in vitro </it>model for CRHR1-mediated signal transduction. To extract significantly regulated genes from a genome-wide microarray data set and to deduce underlying CRHR1-dependent signaling networks, we combined supervised and unsupervised algorithms.</p> <p>Results</p> <p>We present an efficient variable selection strategy by consecutively applying univariate as well as multivariate methods followed by graphical models. First, feature preselection was used to exclude genes not differentially regulated over time from the dataset. For multivariate variable selection a maximum likelihood (MLHD) discriminant function within GALGO, an R package based on a genetic algorithm (GA), was chosen. The topmost genes representing major nodes in the expression network were ranked to find highly separating candidate genes. By using groups of five genes (chromosome size) in the discriminant function and repeating the genetic algorithm separately four times we found eleven genes occurring at least in three of the top ranked result lists of the four repetitions. In addition, we compared the results of GA/MLHD with the alternative optimization algorithms greedy selection and simulated annealing as well as with the state-of-the-art method random forest. In every case we obtained a clear overlap of the selected genes independently confirming the results of MLHD in combination with a genetic algorithm.</p> <p>With two unsupervised algorithms, principal component analysis and graphical Gaussian models, putative interactions of the candidate genes were determined and reconstructed by literature mining. Differential regulation of six candidate genes was validated by qRT-PCR.</p> <p>Conclusions</p> <p>The combination of supervised and unsupervised algorithms in this study allowed extracting a small subset of meaningful candidate genes from the genome-wide expression data set. Thereby, variable selection using different optimization algorithms based on linear classifiers as well as the nonlinear random forest method resulted in congruent candidate genes. The calculated interacting network connecting these new target genes was bioinformatically mapped to known CRHR1-dependent signaling pathways. Additionally, the differential expression of the identified target genes was confirmed experimentally.</p

Exceptional foraging plasticity in King Penguins (Aptenodytes patagonicus) from a recently established breeding site in Tierra del Fuego, Chile

Indexación: ScopusAnimals constantly test the borders of their own ecological niche and tend to expand their range, which is now additionally challenged by global climate change. Following human exploitation throughout the Southern Ocean in the 19th and the beginning of the 20th century, numbers of King Penguin breeding pairs have increased and former breeding sites have been re-colonized. Since 2010 a breeding colony became (re-)established at Bahía Inútil, Strait of Magellan, Tierra del Fuego, Chile. The aims of this study were to study the foraging ecology of King Penguins at this new breeding site, which is characterized by a set of different environmental variables as it is located within the confined environment of the Magellan Strait, more than 300 km from the open ocean. During the course of this study, thirty-two birds were successfully equipped with external devices that recorded 206 foraging trips by breeding and non-breeding birds. With one exception, all birds foraged throughout the year exclusively in the Magellan Strait with the main foraging areas located within 100 km from the colony. The diving activities of 15 King Penguins were recorded during 59 foraging trips, the deepest dive was 160 m and the longest dive lasted 6.75 mins. Based on a representative subsample of 3000 dives, mean dive depth was 32 ± 34 m and mean dive duration 117 ± 84 s. Accordingly, foraging trip durations throughout the year were significantly shorter than those recorded for conspecifics elsewhere. In accordance with these changes in foraging behavior, stomach contents from seven birds showed a mix of fish and squid, with Falkland sprats Sprattus fuegensis as the main prey item present in all samples. The implications of these behavioral adaptations are discussed with regard to this unusual confined foraging environment and predicted changes in the performance of King Penguins breeding elsewhere following global change. © 2021 The Author

Assessing Brain Activity through Spatial Bayesian Variable Selection

Statistical parametric mapping (SPM), relying on the general linear model and classical hypothesis testing, is a benchmark tool for assessing human brain activity using data from fMRI experiments. Friston et al. (2002a) discuss some limitations of this frequentist approach and point out promising Bayesian perspectives. In particular, a Bayesian formulation allows explicit modeling and estimation of activation probabilities. In this paper, we directly address this issue and develop a new regression based approach using spatial Bayesian variable selection. Our method has several advantages. First, spatial correlation is directly modeled for activation probabilities and indirectly for activation amplitudes. As a consequence, there is no need for spatial adjustment in a post-processing step. Second, anatomical prior information, such as the distribution of grey matter or expert knowledge, can be included as part of the model. Third, the method has superior edge-preservation properties as well as being fast to compute. When applied to data from a simple visual experiment, the results demonstrate improved sensitivity for detecting activated cortical areas and for better preserving details of activated structures

MAPK Signaling Determines Anxiety in the Juvenile Mouse Brain but Depression-Like Behavior in Adults

MAP kinase signaling has been implicated in brain development, long-term memory, and the response to antidepressants. Inducible Braf knockout mice, which exhibit protein depletion in principle forebrain neurons, enabled us to unravel a new role of neuronal MAPK signaling for emotional behavior. Braf mice that were induced during adulthood showed normal anxiety but increased depression-like behavior, in accordance with pharmacological findings. In contrast, the inducible or constitutive inactivation of Braf in the juvenile brain leads to normal depression-like behavior but decreased anxiety in adults. In juvenile, constitutive mutants we found no alteration of GABAergic neurotransmission but reduced neuronal arborization in the dentate gyrus. Analysis of gene expression in the hippocampus revealed nine downregulated MAPK target genes that represent candidates to cause the mutant phenotype