Ecological quality assessment in transitional systems

Estuaries are poles of attraction for human settlement which is a source of pressures to surface water bodies. The implementation of the European Water Framework Directive (WDF, 2000/60/EC) has increased the investigation in order to develop methodologies to assess the Ecological Quality Status (EQS) of aquatic ecosystems. Transitional systems are naturally stressed and characterized by highly dynamic physical, chemical and hydro-morphologic conditions and by species with a higher level of tolerance to change, being more difficult to develop suitable quality indicators for these systems. The general purpose of this study is to test the ability of synthesis descriptors, including primary (S, taxa richness) and derived biological variable (H’, Shannon-Wiener diversity), biotic indices (AMBI and M-AMBI), body size properties (abundance distribution by body size classes, length, weight and length-weight relationships) and non-taxonomic indices (ISS), as well as functional indicators related to the decomposition rates of various experimental substrates, a macrophyte (Phragmites australis) and an alga (Fucus vesiculosus), to evaluate the environmental quality in transitional systems. This study was carried out in one of the most pristine channels of the Ria the Aveiro, Mira Channel, along a full salinity gradient and in a metals and metalloid sediment contamination area, the Estarreja Channel, and two reference channels (Canelas and Salreu). In this study were used different sampling techniques, the leaf-bag technique and a hand-held corer. In Mira Channel, the alga and the macrophyte presented an opposite trend in the decomposition rate along the salinity gradient, with the decomposition rates of the alga always higher than those of the macrophyte. The decomposition rates of the macrophyte and the alga were higher in the mid estuary and in higher salinity areas, respectively, corresponding to the preferencial distribution areas of each species. The macrobenthic fauna associated with the decaying and an artificial substrate (control) showed equally well the benthic succession from the marine to the freshwater areas and, despite the strong differences in the decay rates, no significant differences were found between the benthic communities associated with the alga and the macrophyte. The body size properties of the macrobenthic fauna associated with the P. australis leaf-bag (1mm and 5mm) and corer samples were studied along the full salinity gradient. The dominant species of the sub-set of measured specimens were not the same of the original macrobenthic fauna sampled but, despite that, the sub-set of measured specimens was also able to show the benthic succession from the marine to the freshwater areas. The body size abundance distribution of the benthic macroinvertebrates according to the ISS size classes did not show a particular trend in any sampler along the salinity gradient. Significant differences were found in the length, weight and length-weight relationships of Annelids, , Molluscs and even some species along the salinity gradient. No significant differences were found in the AMBI, M-AMBI and ISS values along the salinity gradient for all the samplers. The EQS of the corer samples obtained using the M-AMBI was lower than that of the leaf-bags. The EQS obtained with the ISS was higher than that obtained with the M-AMBI in the leaf-bags but not in the corer samples. The ecological effects of contaminated sediments associated with the industrial chemical effluents discharged in the Estarreja Channel were studied a decade after ceasing the emissions, using the Sediment Quality Triad approach and two reference channels. The results showed that despite the emissions ceased in 2004, the sediment remains polluted with high levels of metals and metalloid, available to bioaccumulation and with severe consequences at the community level. The sediment contamination problem was also studied using the leaf-bag technique with a macrophyte, an alga and a control substrate. The results showed that the decay rates, the associated macrofauna and the application of the AMBI, M-AMBI and ISS indices to the mesh-bag samples were not able to identify the sediment contamination. Contrarily to the AMBI, the M-AMBI and the ISS showed significant differences between the contaminated and the reference channels for the corer samples. Although such statistical significance, the interest of using these complex biotic indices could be questioned, when much simple ones, like the S and H’ allow to reach the same conclusions.

Spatial attention enhances object coding in local and distributed representations of the lateral occipital complex

The modulation of neural activity in visual cortex is thought to be a key mechanism of visual attention. The investigation of attentional modulation in high-level visual areas, however, is hampered by the lack of clear tuning or contrast response functions. In the present functional magnetic resonance imaging study we therefore systematically assessed how small voxel-wise biases in object preference across hundreds of voxels in the lateral occipital complex were affected when attention was directed to objects. We found that the strength of attentional modulation depended on a voxel's object preference in the absence of attention, a pattern indicative of an amplificatory mechanism. Our results show that such attentional modulation effectively increased the mutual information between voxel responses and object identity. Further, these local modulatory effects led to improved information-based object readout at the level of multi-voxel activation patterns and to an increased reproducibility of these patterns across repeated presentations. We conclude that attentional modulation enhances object coding in local and distributed object representations of the lateral occipital complex.

Observed bodies generate object-based spatial codes

Contemporary studies of spatial and social cognition frequently use human figures as stimuli. The interpretation of such studies may be complicated by spatial compatibility effects that emerge when researchers employ spatial responses, and participants spontaneously code spatial relationships about an observed body. Yet, the nature of these spatial codes – whether they are location- or object-based, and coded from the perspective of the observer or the figure – has not been determined. Here, we investigated this issue by exploring spatial compatibility effects arising for objects held by a visually presented whole-bodied schematic human figure. In three experiments, participants responded to the colour of the object held in the figure’s left or right hand, using left or right key presses. Left-right compatibility effects were found relative to the participant’s egocentric perspective, rather than the figure’s. These effects occurred even when the figure was rotated by 90 degrees to the left or to the right, and the coloured objects were aligned with the participant’s midline. These findings are consistent with spontaneous spatial coding from the participant’s perspective and relative to the normal upright orientation of the body. This evidence for object-based spatial coding implies that the domain general cognitive mechanisms that result in spatial compatibility effects may contribute to certain spatial perspective-taking and social cognition phenomena.

Object categorisations using templates constructed from multi-scale line and edge representations

Object categorisation is linked to detection, segregation and recognition. In the visual system, these processes are achieved in the ventral \what"and dorsal \where"pathways [3], with bottom-up feature extractions in areas V1, V2, V4 and IT (what) in parallel with top-down attention from PP via MT to V2 and V1 (where). The latter is steered by object templates in memory, i.e. in prefrontal cortex with a what component in PF46v and a where component in PF46d.

Multi-scale cortical keypoint representation for attention and object detection

Keypoints (junctions) provide important information for focus-of-attention (FoA) and object categorization/recognition. In this paper we analyze the multi-scale keypoint representation, obtained by applying a linear and quasi-continuous scaling to an optimized model of cortical end-stopped cells, in order to study its importance and possibilities for developing a visual, cortical architecture.We show that keypoints, especially those which are stable over larger scale intervals, can provide a hierarchically structured saliency map for FoA and object recognition. In addition, the application of non-classical receptive field inhibition to keypoint detection allows to distinguish contour keypoints from texture (surface) keypoints.

An integrated framework for combining gist vision with object segregation categorisation and recognition

There are roughly two processing systems: (1) very fast gist vision of entire scenes, completely bottom-up and data driven, and (2) Focus-of-Attention (FoA) with sequential screening of specific image regions and objects. The latter system has to be sequential because unnormalised input objects must be matched against normalised templates of canonical object views stored in memory, which involves dynamic routing of features in the visual pathways.

Cortical object segregation and categorization by multi-scale line and edge coding

In this paper we present an improved scheme for line and edge detection in cortical area V1, based on responses of simple and complex cells, truly multi-scale with no free parameters. We illustrate the multi-scale representation for visual reconstruction, and show how object segregation can be achieved with coarse-to-finescale groupings. A two-level object categorization scenario is tested in which pre-categorization is based on coarse scales only, and final categorization on coarse plus fine scales. Processing schemes are discussed in the framework of a complete cortical architecture.

Multi-scale keypoint hierarchy for Focus-of-Attention and object detection

Hypercolumns in area V1 contain frequency- and orientation-selective simple and complex cells for line (bar) and edge coding, plus end-stopped cells for key- point (vertex) detection. A single-scale (single-frequency) mathematical model of single and double end-stopped cells on the basis of Gabor filter responses was developed by Heitger et al. (1992 Vision Research 32 963-981). We developed an improved model by stabilising keypoint detection over neighbouring micro- scales.

Invariant multi-scale object categorisation and recognition

Object recognition requires that templates with canonical views are stored in memory. Such templates must somehow be normalised. In this paper we present a novel method for obtaining 2D translation, rotation and size invariance. Cortical simple, complex and end-stopped cells provide multi-scale maps of lines, edges and keypoints. These maps are combined such that objects are characterised. Dynamic routing in neighbouring neural layers allows feature maps of input objects and stored templates to converge. We illustrate the construction of group templates and the invariance method for object categorisation and recognition in the context of a cortical architecture, which can be applied in computer vision.

Multi-scale lines and edges in V1 and beyond: brightness, object categorization and recognition, and consciousness

In this paper we present an improved model for line and edge detection in cortical area V1. This model is based on responses of simple and complex cells, and it is multi-scale with no free parameters. We illustrate the use of the multi-scale line/edge representation in different processes: visual reconstruction or brightness perception, automatic scale selection and object segregation. A two-level object categorization scenario is tested in which pre-categorization is based on coarse scales only and final categorization on coarse plus fine scales. We also present a multi-scale object and face recognition model. Processing schemes are discussed in the framework of a complete cortical architecture. The fact that brightness perception and object recognition may be based on the same symbolic image representation is an indication that the entire (visual) cortex is involved in consciousness.

Repply to: Brito, A.C., Brotas, V., Caetano, M., Coutinho, T.P., Bordalo, A.A., Icely, J., Neto, J.M., Serôdio, J., Moita, T. (2012) "Defining phytoplankton class boundaries in Portuguese transitional waters: an evaluation of the ecological quality status according to the Water Framework Directive" [Ecological Indicators 19, 5-14]

We write to comment on the recently published paper “Defining phytoplankton class boundaries in Portuguese transitional waters: an evaluation of the ecological quality status according to the Water Framework Directive” (Brito et al., 2012). This paper presents an integrated methodology to analyse the ecological quality status of several Portuguese transitional waters, using phytoplanktonrelated metrics. One of the systems analysed, the Guadiana estuary in southern Portugal, is considered the most problematic estuary, with its upstream water bodies classified as Poor in terms of ecological status. We strongly disagree with this conclusion and we would like to raise awareness to some methodological constraints that, in our opinion, are the basis of such deceptive conclusions and should therefore not be neglected when using phytoplankton to assess the ecological status of natural waters.

Cortical 3D face and object recognition using 2D projections

Empirical studies concerning face recognition suggest that faces may be stored in memory by a few canonical representations. In cortical area V1 exist double-opponent colour blobs, also simple, complex and end-stopped cells which provide input for a multiscale line/edge representation, keypoints for dynamic feature routine, and saliency maps for Focus-of-Attention.

Local object gist: meaningful shapes and spatial layout at a very early stage of visual processing

In his introduction, Pinna (2010) quoted one of Wertheimer’s observations: “I stand at the window and see a house, trees, sky. Theoretically I might say there were 327 brightnesses and nuances of color. Do I have ‘327’? No. I have sky, house, and trees.” This seems quite remarkable, for Max Wertheimer, together with Kurt Koffka and Wolfgang Koehler, was a pioneer of Gestalt Theory: perceptual organisation was tackled considering grouping rules of line and edge elements in relation to figure-ground segregation, i.e., a meaningful object (the figure) as perceived against a complex background (the ground). At the lowest level – line and edge elements – Wertheimer (1923) himself formulated grouping principles on the basis of proximity, good continuation, convexity, symmetry and, often forgotten, past experience of the observer. Rubin (1921) formulated rules for figure-ground segregation using surroundedness, size and orientation, but also convexity and symmetry. Almost a century of research into Gestalt later, Pinna and Reeves (2006) introduced the notion of figurality, meant to represent the integrated set of properties of visual objects, from the principles of grouping and figure-ground to the colour and volume of objects with shading. Pinna, in 2010, went one important step further and studied perceptual meaning, i.e., the interpretation of complex figures on the basis of past experience of the observer. Re-establishing a link to Wertheimer’s rule about past experience, he formulated five propositions, three definitions and seven properties on the basis of observations made on graphically manipulated patterns. For example, he introduced the illusion of meaning by comics-like elements suggesting wind, therefore inducing a learned interpretation. His last figure shows a regular array of squares but with irregular positions on the right side. This pile of (ir)regular squares can be interpreted as the result of an earthquake which destroyed part of an apartment block. This is much more intuitive, direct and economic than describing the complexity of the array of squares.