A group model for stable multi-subject ICA on fMRI datasets

Spatial Independent Component Analysis (ICA) is an increasingly used data-driven method to analyze functional Magnetic Resonance Imaging (fMRI) data. To date, it has been used to extract sets of mutually correlated brain regions without prior information on the time course of these regions. Some of these sets of regions, interpreted as functional networks, have recently been used to provide markers of brain diseases and open the road to paradigm-free population comparisons. Such group studies raise the question of modeling subject variability within ICA: how can the patterns representative of a group be modeled and estimated via ICA for reliable inter-group comparisons? In this paper, we propose a hierarchical model for patterns in multi-subject fMRI datasets, akin to mixed-effect group models used in linear-model-based analysis. We introduce an estimation procedure, CanICA (Canonical ICA), based on i) probabilistic dimension reduction of the individual data, ii) canonical correlation analysis to identify a data subspace common to the group iii) ICA-based pattern extraction. In addition, we introduce a procedure based on cross-validation to quantify the stability of ICA patterns at the level of the group. We compare our method with state-of-the-art multi-subject fMRI ICA methods and show that the features extracted using our procedure are more reproducible at the group level on two datasets of 12 healthy controls: a resting-state and a functional localizer study

Suivi à moyen terme des impacts écologiques des feux et des coupes forestières sur la communauté zooplanctonique des lacs de l'écozone boréale

Cet article vise à évaluer les effets à moyen terme des feux et des coupes de forêt sur la biomasse, la richesse spécifique et la composition du zooplancton des lacs de la forêt boréale au Québec. L'étude a été réalisée durant trois ans (1996-1998) après les perturbations sur 3 sous-ensembles de lacs similaires au niveau de leur morphométrie, incluant 7 lacs naturels non perturbés sur leur bassin versant, 7 lacs affectés par des coupes sur plus de 43% de la surface du bassin versant et 7 lacs affectés par des feux sur plus de 50% de la surface du bassin versant. Notre étude indique que le zooplancton a une forte résilience aux perturbations des lacs de la forêt boréale par les feux et les coupes. Les assemblages d'espèces sont très stables et varient peu entre les lacs naturels et les lacs perturbés. Les Rotifères sont le seul groupe affecté par les perturbations; leur richesse spécifique et leur biomasse sont plus fortes dans les lacs perturbés que dans les lacs naturels. Les feux ont un effet d'eutrophisation plus marqué que les coupes. Dans les lacs affectés par les feux, les apports accrus de nutriments favorisent la croissance du phytoplancton puis des rotifères. Toutefois, dans les lacs affectés par les coupes, la forte couleur de l'eau due aux apports accrus en carbone organique dissous est un facteur limitant, et la hausse du phytoplancton et des rotifères est moins accentuée. La richesse spécifique et la biomasse des Crustacés (Cladocères, Copépodes Calanoïdes et Cyclopoïdes) ne varient pas avec les perturbations. Sur l'ensemble du suivi, le niveau de perturbation n'est pas fortement relié aux changements dans la biomasse des groupes taxinomiques qui s'expliquent plutôt par les variations annuelles de la température de l'eau et des concentrations en chlorophylle a.This paper aims to evaluate mid-term impacts of forest wildfires and harvesting on the biomass, species richness and assemblages of zooplankton communities in boreal lakes in Québec. The research was carried out during a post-perturbation 3-year survey (1996-1998) on three subsets of lakes (natural, cut, burnt lakes). It complements previous short-term studies conducted 1 year after perturbations in the same region by PATOINE et al. (2000, 2002a) on different subsets of lakes, which failed to detect significant effects. This comparative study attempts to minimize the spatial variability among natural and perturbed lakes by selecting lakes with similar morphometric conditions. For this selection, we applied a multivariate approach developed by DUHAIME and PINEL-ALLOUL (2005). Making sure that natural and perturbed lakes have similar morphometric features allows minimization of the confounding effects of lake and watershed conditions on organic carbon and nutrient exports from perturbed watersheds, and subsequently on lake water quality and biota.The initial 3-year survey was conducted on 31 lakes including 15 natural lakes without any perturbation in their watershed over the past 70 years, and 9 burnt lakes with more than 50% of their watershed intensively burnt, and 7 logged lakes with more than 43% of their watershed clear-cut. Lakes were visited three times per summer (May-June, July, August-September) between 6:00 to 15:00h, during the 3 years (1996-98) following the fires and harvesting of 1995. Watershed and lake morphometry, and water quality, and algal communities were monitored and studied by CARIGNAN et al. (2000) and PLANAS et al. (2000). Fish communities were sampled and studied by SAINT-ONGE and MAGNAN (2000). Zooplankton was sampled using a cantilever net (53 µm mesh size) on vertical hauls from 1 m above the sediments to the lake surface. Sampling methods and analysis of zooplankton were previously described by PATOINE et al. (2000, 2002a). We estimated species richness and assemblages, as well as the biomass of each zooplankton group (Rotifera, Cladocera, Copepoda Cyclopoida and Calanoida) and of the total community in each year and each lake. Simple ANOVA were used to evaluate global changes over the mid-term survey in zooplankton attributes among the three subsets of lakes (natural, cut, burnt). RMANOVA (analysis of variance with repeated measures) were used to test the effects of watershed conditions related to perturbations (natural, cut, burnt lakes), the effects of annual variations during the survey and their interaction. Redundancy analysis (RDA) served to evaluate the relationships between changes in the biomass of zooplankton groups during the survey in the three subsets of lakes and the changes in environmental factors and perturbation intensity. Environmental factors retained for the analysis were the drainage ratio (ratio of watershed area to lake area), lake water transparency, concentrations of total phosphorus, total nitrogen and dissolved organic carbon, water temperature in the euphotic zone, chlorophyll a concentrations, and biomass classes of dominant fish (yellow perch, white sucker). The perturbation intensity, expressed as the percentage of watershed area clear-cut or burnt, was also included in the model.Based on their similarity in morphometric variables (drainage ratio, lake volume, area and maximum depth, percentage of wetlands in the watershed), we retained for the study 7 cut lakes (C2, C9, C12, C23, C24, C29, C48), 7 burnt lakes (FBP9, FBP10, FP2, FP24, FP30, FP31, FP32), and 7 natural lakes (N5, N16, N56, N70, N82, N88, N109). Variations in morphometric characteristics were found within each subset of lakes (reference, burnt, logged), and we did not detect significant variation among groups. However, we did find significant differences in water quality variables among subsets of lakes. Thus, in our study, we have minimized the effects of variable morphometry among watersheds and lakes that could confound the responses of lakes to perturbations, while maintaining the same effects of fires and harvesting on water quality, as previously observed (CARIGNAN et al. 2000). This allowed us to test scaling-up effects of these changes on zooplankton communities.Our study shows that zooplankton communities in boreal lakes have strong resilience to environmental perturbations by wildfires and clear-cut logging. Species assemblages were very stable and varied little between natural and perturbed lakes. Some rotifer species such as Keratella taurocephala, known as a species adapted to acidic and humic lakes, had higher abundance in the cut lakes most enriched in dissolved organic carbon. Another rotifer species, Polyarthra vulgaris, adapted to eutrophic lake and reservoir ecosystems, was more abundant in the burnt lakes that were the most enriched in nutrients. Only short life-span and r-strategic species such as rotifers showed increases in species richness in the perturbed lakes compared to natural lakes. Compared to previous studies, our study showed that this increase in the number of rotifer species lasted for the 3-year survey. Rotifers also showed higher biomass in perturbed lakes (especially burnt lakes), but only during the first two years of the survey. In general, fires had greater eutrophication effects than did clear-cut harvest. In lakes impacted by fires, increases in nutrient inputs (total phosphorus, total nitrogen) favoured phytoplankton and rotifer growth, while in lakes impacted by logging, increases in dissolved organic carbon and water color limited the increase of phytoplankton and rotifers. For the crustaceans (Cladocera, Calanoida, Cyclopoida), neither species richness nor biomass was related to watershed perturbations. In general, our study indicates that natural sources of temporal variation between years had greater effects on the biomass of some zooplankton groups than did the perturbations. Overall, increases in Rotifera biomass were primarily related to higher mean summer water temperature whereas increases in Cyclopoida biomass were related to higher chlorophyll a concentrations. Perturbation intensity, nutrient concentrations, and drainage ratio also tended to increase the responses of these zooplankton groups, but their influence over the mid-term survey was not significant. A higher biomass of Calanoida was observed in lakes (mainly natural ones) with high water transparency and low nutrients. Variation in Cladocera biomass was not related to lake enrichment, higher temperature or perturbation intensity. Our mid-term study generally confirms the effects of wildfires and logging, as previously suggested, but not significantly detected by other studies (PATOINE et al. 2000, 2002a) conducted only during the first year after the perturbations. It shows the usefulness of mid-term monitoring to better assess the ecological impacts of natural and anthropogenic perturbations on aquatic ecosystems

Configurable unitary transformations and linear logic gates using quantum memories

We show that a set of optical memories can act as a configurable linear optical network operating on frequency-multiplexed optical states. Our protocol is applicable to any quantum memories that employ off-resonant Raman transitions to store optical information in atomic spins. In addition to the configurability, the protocol also offers favourable scaling with an increasing number of modes where N memories can be configured to implement an arbitrary N-mode unitary operations during storage and readout. We demonstrate the versatility of this protocol by showing an example where cascaded memories are used to implement a conditional CZ gate.Comment: 5 pages, 2 figure

Les réseaux trophiques lacustres: structure, fonctionnement, interactions et variations spatio-temporelles

L'analyse comparative des réseaux trophiques lacustres est d'un grand intérêt pour le développement de la limnologie contemporaine et l'aménagement des lacs. L'analyse des mécanismes écologiques déterminant la structure et le fonctionnement des réseaux trophiques dans les lacs tempérés a permis l'émergence de plusieurs modèles, souvent contradictoires, et suscité d'intenses débats sur le rôle respectif des ressources et des prédateurs. Par contre, dans les lacs tropicaux, les études sont en majorité descriptives et la recherche de principes généraux et de concepts unificateurs y est rare. Cette synthèse présente l'état des connaissances, les approches méthodologiques, les modèles de régulation concernant la structure et le fonctionnement des réseaux trophiques lacustres. Les réseaux trophiques semblent varier selon un gradient de situations intermédiaires entre deux modèles extrêmes : (a) les milieux à cascades trophiques intenses et à effet atténué des ressources (lacs tempérés oligo-mésotrophes) caractérisés par la présence de poissons piscivores et de zooplancton herbivore de grande taille (tels Daphnia spp.) et (b) les milieux à régulation intermédiaire (lacs tempérés méso-eutrophes et la plupart des lacs tropicaux), caractérisés par la présence de poissons filtreurs microphages omnivores et de zooplancton herbivore de petite taille. Notre synthèse souligne aussi l'importance d'allier les approches expérimentales en enceintes ou par biomanipulation à des suivis à long terme et des modélisations pour avoir une bonne compréhension et des prédictions précises du fonctionnement des écosystèmes lacustres à différentes échelles spatiales et temporelles et pour différentes conditions climatiques, géographiques ou trophiques.Comparative analysis of lake food webs is a focal point of research in contemporary limnology and lake management. The study of ecological processes determining foodweb structure and function lead to the emergence of constrasting hypotheses and intense debates on the relative role of nutrients and food web structure in regulating temperate lake ecosystems. In contrast, studies in tropical lakes are in general descriptive and the search for integrate concepts and models is yet in development. This review paper presents an overview and a critical analysis of actual knowledge, methodological approaches, regulation models and controversies on foodweb structure and function in temperate and tropical lakes. Our synthesis suggests that the apparent diversity in models of lake foodwebs could reflect a gradient (or contiuum) of intermediate foodweb situations, regulated by various environmental factors. The differences among lakes could be related to three main biotic factors, independently of the climatic, geographical and trophic conditions: 1. the important cascading effect of strictly piscivorous fish in temperate lakes compared to the weak cascades induced by opportunistic omnivorous fish in tropical lakes, 2. the primacy of omnivory and opportunistic feeding behaviour of tropical fish, 3. the key role of herbivorous macrozooplankton (cladocerans, mostly Daphnia spp.) in temperate lakes where they are both selective preys of planktivorous fish and efficient grazers of nanophytoplankton, and 4. the synchronous reproduction of fish with seasonal plankton succession in temperate lakes, compared to continuous reproduction of fish and lack of seasonal coupling in tropical lakes. Consequently, food webs regulation ranges along a gradient of situations with two extreme models: 1. a model with intense cascading (top-down) regulation and attenuation of bottom-up effects typical of oligo-mesotrophic temperate lakes, characterized by the dominance of piscivorous fish and large herbivorous zooplankton (Daphnia spp.), and 2. a model with intermediate regulation encountered in eutrophic temperate lakes and most of tropical lakes, characterized par the dominance of filter omnivorous fish and small size zooplankton. Our synthesis also emphasizes the importance of coupling experimental approches in mesocosms or whole-lake biomanipulation with long-term monitoring and modelisation to fully understand and predict the functionning of lake ecosystems over different spatial and temporal scale

First insights into serum metabolomics of trenbolone/estradiol implanted bovines; screening model to predict hormone-treated and control animals’ status

International audienceThe use of anabolic agents in livestock production is a subject of much concern. Although prohibited for more than 20&nbsp;years within the EU, growth promoting practices are still widely suspected. To meet the current challenges for detecting illicit practices, ‘omics’ strategies have recently been demonstrated as important new investigative tools. These investigations, based on the observation of physiological disturbances, mainly in urine, demonstrated the possibility to monitor biomarkers enabling high throughput determination of animal status in terms of hormonal treatment. In this context, serum was investigated for the first time as an alternative and potential complementary sample type. A metabolomic approach based on liquid chromatography coupled to high resolution mass spectrometry, was exploited in order to, highlight metabolic perturbations in serum of Revalor-XS® (trenbolone acetate/estradiol) implanted bovines. Univariate and multivariate statistical analyses were carried out to establish descriptive and predictive models. These models enabled the discrimination of anabolised from control animals, and highlighted a number of metabolites which contributed the most in the observed discrimination. Further, a screening model combining a set of selected markers intensities was generated and it successfuly classified animals according to their status, up to 4&nbsp;weeks post Revalor-XS® implant. This research indicates, for the first time, that serum metabolomics has an important role in screening to detect for anabolic misuse in bovines.</p

Gradient echo quantum memory in warm atomic vapor

Video Article - http://www.jove.com/video/50552Gradient echo memory (GEM) is a protocol for storing optical quantum states of light in atomic ensembles. The primary motivation for such a technology is that quantum key distribution (QKD), which uses Heisenberg uncertainty to guarantee security of cryptographic keys, is limited in transmission distance. The development of a quantum repeater is a possible path to extend QKD range, but a repeater will need a quantum memory. In our experiments we use a gas of rubidium 87 vapor that is contained in a warm gas cell. This makes the scheme particularly simple. It is also a highly versatile scheme that enables in-memory refinement of the stored state, such as frequency shifting and bandwidth manipulation. The basis of the GEM protocol is to absorb the light into an ensemble of atoms that has been prepared in a magnetic field gradient. The reversal of this gradient leads to rephasing of the atomic polarization and thus recall of the stored optical state. We will outline how we prepare the atoms and this gradient and also describe some of the pitfalls that need to be avoided, in particular four-wave mixing, which can give rise to optical gain.Olivier Pinel, Mahdi Hosseini, Ben M. Sparkes, Jesse L. Everett, Daniel Higginbottom, Geoff T. Campbell, Ping Koy Lam, Ben C. Buchle

Variations à court terme des compartiments planctoniques d'un lac humique du Bouclier canadien

Les variations spatio-temporelles à court terme des compartiments planctoniques ont été étudiées simultanément du 30 juillet au 5 août 1986 dans un lac humique du Bouclier canadien. L'abondance du bactérioplancton fluctue de 1,4 à 1,7.106 cell. ml.-1 (coloration DAPI) ou de 2,7 à 7,7.106 cell. ml-1; (coloration Acridine Orange). La production du bactérioplancton estimée par incorporation de 3H méthyl thimidine, varie de 4 à 24.106 cell. l-1 h-1. Les valeurs d'activité hétérotrophe potentielle bactérienne estimée par assimilation de 14C glucose, s'échelonnent de 0,007 à 0,065 µg C.l-1. h-1. La biomasse pigmentaire (chlore. a et pheopigments) varie de 6,8 à 21,7 mg.m-3 . La production primaire est très faible (max. : 10 mg C. m-3 .h-1; 20 mg C.m-2 .h-1 ) et décroît très rapidement avec la profondeur (25 % à 82 % dans le premier mètre). Le microzooplancton (Rotifères, Bosmina, nauplies) représente plus de 90 % du peuplement zooplanctonique et les taux de broutage global du macrozooplancton sont faibles (25 % j-1). Les compartiments hétérotrophes prédominent dans le métabolisme du lac par rapport au compartiment autotrophe. Les patrons de variation spatiale reflètent la stratification verticale des compartiments et des processus autotrophes et hétérotrophes. Les maxima de photosynthèse, d'ATP et de production bactérienne se situent dans les eaux épilimnétiques tandis que les maxima d'abondance du bactérioptancton et des pigments se rencontrent dans l'hypolimnion. Le zooplancton est plus dense et broute d'avantage dans la strate 1-3 m. Ces variations spatiales semblent influencer l'activité hétérotrophe potentielle du bactérioptancton. Nos résultats montrent aussi des variations temporelles à court terme de la production primaire, de l'assimilation hétérotrophe et du broutage du macrozooplancton. Cette étude préliminaire met en lumière la nécessité de tenir compte des variations à court terme lors des études des relations trophodynamiques dans les écosystèmes planctoniques.Short term spatial and temporal variations in planktonic compartments were studied simultaneously, from July 30th to August 5th, 1986, in a humic lake on the Canadian Shield. Abundance of bacterioplankton ranged from 1,4 to 1,7 106 cell. ml-1 (DAP1) or from 2,7 to 7,7 106 cell. ml-1 (Acridine Orange). Bacterial production, as measured by incorporation of 3H methyl-thimidine, was estimated at 4-24 106 cells. l-1. h-1 and potential heterotrophic bacterial activity ranged from 0,007 to 0,065 µg C.l-1. h-1, as estimated by 14C glucose incorporation. Pigments biomass (chloro. a and phaeopigments) varied from 6,8 to 21,7 mg m-3. Primary production was low (max. : 10 mg C.m-3. h-1; 20 mg C.m-2. h-1) and decreased rapidly with depth (25-82 % in 1 m depth). Microzooplankton (rotifera, Bosmina, nauplii) accounted for more than 90 % of total numbers and macrozooplankton global grazing rates were low (25 % d-1). The heterotrophic compartments play a greater rate in the lake metabolism than the autotrophic compartment. Spatial variations reflect the stratification of the heterotrophic and autotrophic organisms and processes with depth. Maximum levels in primary production, ATP and bacterial production occur in epilimnetic waters, while maxima in bacterial numbers and algal pigments occur in the hypolimnion. Zooplancton density and macrozooplankton grazing rates were higher in the 1-3 m strata. These spatial patterns seem to influence the vertical profiles of the bacterial potential heterotrophic activity. Our results also show short term temporal variations in primary production, potential heterotrophic activity of bacterioplankton and macrozooplankton grazing rates. This preliminary study stresses the importance of short term variations in the assessment of the trophodynamics of the planktonic food wed

Effective connectivity reveals strategy differences in an expert calculator

Mathematical reasoning is a core component of cognition and the study of experts defines the upper limits of human cognitive abilities, which is why we are fascinated by peak performers, such as chess masters and mental calculators. Here, we investigated the neural bases of calendrical skills, i.e. the ability to rapidly identify the weekday of a particular date, in a gifted mental calculator who does not fall in the autistic spectrum, using functional MRI. Graph-based mapping of effective connectivity, but not univariate analysis, revealed distinct anatomical location of “cortical hubs” supporting the processing of well-practiced close dates and less-practiced remote dates: the former engaged predominantly occipital and medial temporal areas, whereas the latter were associated mainly with prefrontal, orbitofrontal and anterior cingulate connectivity. These results point to the effect of extensive practice on the development of expertise and long term working memory, and demonstrate the role of frontal networks in supporting performance on less practiced calculations, which incur additional processing demands. Through the example of calendrical skills, our results demonstrate that the ability to perform complex calculations is initially supported by extensive attentional and strategic resources, which, as expertise develops, are gradually replaced by access to long term working memory for familiar material

Cohort-level brain mapping: learning cognitive atoms to single out specialized regions

International audienceFunctional Magnetic Resonance Imaging (fMRI) studies map the human brain by testing the response of groups of individuals to carefully-crafted and contrasted tasks in order to delineate specialized brain regions and networks. The number of functional networks extracted is limited by the number of subject-level contrasts and does not grow with the cohort. Here, we introduce a new group-level brain mapping strategy to differentiate many regions reflecting the variety of brain network configurations observed in the population. Based on the principle of functional segregation, our approach singles out functionally-specialized brain regions by learning group-level functional profiles on which the response of brain regions can be represented sparsely. We use a dictionary-learning formulation that can be solved efficiently with on-line algorithms, scaling to arbitrary large datasets. Importantly, we model inter-subject correspondence as structure imposed in the estimated functional profiles, integrating a structure-inducing regularization with no additional computational cost. On a large multi-subject study, our approach extracts a large number of brain networks with meaningful functional profiles