Spontaneous discrimination of possible and impossible objects by newly hatched chicks

Four-month-old infants can integrate local cues provided by two-dimensional pictures and interpret global inconsistencies in structural information to discriminate between possible and impossible objects. This leaves unanswered the issue of the relative contribution of maturation of biologically predisposed mechanisms and of experience with real objects, to the development of this capability. Here we show that, after exposure to objects in which junctions providing cues to global structure were occluded, day-old chicks selectively approach the two-dimensional image that depicted the possible rather than the impossible version of a three-dimensional object, after restoration of the junctions. Even more impressively, completely naive newly hatched chicks showed spontaneous preferences towards approaching two-dimensional depictions of structurally possible rather than impossible objects. These findings suggest that the vertebrate brain can be biologically predisposed towards approaching a two-dimensional image representing a view of a structurally possible three-dimensional object.     

Computational object recognition: a biologically motivated approach

We propose a conceptual framework for artificial object recognition systems based on findings from neurophysiological and neuropsychological research on the visual system in primate cortex. We identify some essential questions, which have to be addressed in the course of designing object recognition systems. As answers, we review some major aspects of biological object recognition, which are then translated into the technical field of computer vision. The key suggestions are the use of incremental and view-based approaches together with the ability of online feature selection and the interconnection of object-views to form an overall object representation. The effectiveness of the computational approach is estimated by testing a possible realization in various tasks and conditions explicitly designed to allow for a direct comparison with the biological counterpart. The results exhibit excellent performance with regard to recognition accuracy, the creation of sparse models and the selection of appropriate features.     

Camouflage and visual perception

How does an animal conceal itself from visual detection by other animals? This review paper seeks to identify general principles that may apply in this broad area. It considers mechanisms of visual encoding, of grouping and object encoding, and of search. In most cases, the evidence base comes from studies of humans or species whose vision approximates to that of humans. The effort is hampered by a relatively sparse literature on visual function in natural environments and with complex foraging tasks. However, some general constraints emerge as being potentially powerful principles in understanding concealment—a ‘constraint’ here means a set of simplifying assumptions. Strategies that disrupt the unambiguous encoding of discontinuities of intensity (edges), and of other key visual attributes, such as motion, are key here. Similar strategies may also defeat grouping and object-encoding mechanisms. Finally, the paper considers how we may understand the processes of search for complex targets in complex scenes. The aim is to provide a number of pointers towards issues, which may be of assistance in understanding camouflage and concealment, particularly with reference to how visual systems can detect the shape of complex, concealed objects.     

Haptic object perception: spatial dimensionality and relation to vision

Enabled by the remarkable dexterity of the human hand, specialized haptic exploration is a hallmark of object perception by touch. Haptic exploration normally takes place in a spatial world that is three-dimensional; nevertheless, stimuli of reduced spatial dimensionality are also used to display spatial information. This paper examines the consequences of full (three-dimensional) versus reduced (two-dimensional) spatial dimensionality for object processing by touch, particularly in comparison with vision. We begin with perceptual recognition of common human-made artefacts, then extend our discussion of spatial dimensionality in touch and vision to include faces, drawing from research on haptic recognition of facial identity and emotional expressions. Faces have often been characterized as constituting a specialized input for human perception. We find that contrary to vision, haptic processing of common objects is impaired by reduced spatial dimensionality, whereas haptic face processing is not. We interpret these results in terms of fundamental differences in object perception across the modalities, particularly the special role of manual exploration in extracting a three-dimensional structure.     

Developing a multi-Kinect-system for monitoring in dairy cows: object recognition and surface analysis using wavelets

Camera-based systems in dairy cattle were intensively studied over the last years. Different from this study, single camera systems with a limited range of applications were presented, mostly using 2D cameras. This study presents current steps in the development of a camera system comprising multiple 3D cameras (six Microsoft Kinect cameras) for monitoring purposes in dairy cows. An early prototype was constructed, and alpha versions of software for recording, synchronizing, sorting and segmenting images and transforming the 3D data in a joint coordinate system have already been implemented. This study introduced the application of two-dimensional wavelet transforms as method for object recognition and surface analyses. The method was explained in detail, and four differently shaped wavelets were tested with respect to their reconstruction error concerning Kinect recorded depth maps from different camera positions. The images’ high frequency parts reconstructed from wavelet decompositions using the haar and the biorthogonal 1.5 wavelet were statistically analyzed with regard to the effects of image fore- or background and of cows’ or persons’ surface. Furthermore, binary classifiers based on the local high frequencies have been implemented to decide whether a pixel belongs to the image foreground and if it was located on a cow or a person. Classifiers distinguishing between image regions showed high (⩾0.8) values of Area Under reciever operation characteristic Curve (AUC). The classifications due to species showed maximal AUC values of 0.69.     

Visual perception of light organ patterns in deep‐sea shrimps and implications for conspecific recognition

Darkness and low biomass make it challenging for animals to find and identify one another in the deep sea. While spatiotemporal variation in bioluminescence is thought to underlie mate recognition for some species, its role in conspecific recognition remains unclear. The deep‐sea shrimp genus, Sergestes sensu lato (s.l.), is one group that is characterized by species‐specific variation in light organ arrangement, providing us the opportunity to test whether organ variation permits recognition to the species level. To test this, we analyzed the visual capabilities of three species of Sergestes s.l. in order to (a) test for sexual dimorphism in eye‐to‐body size scaling relationships, (b) model the visual ranges (i.e., sighting distances) over which these shrimps can detect intraspecific bioluminescence, and (c) assess the maximum possible spatial resolution of the eyes of these shrimps to estimate their capacity to distinguish the light organs of each species. Our results showed that relative eye size scaled negatively with body length across species and without sexual dimorphism. Though the three species appear capable of detecting one another's bioluminescence over distances ranging from < 1 to ~6 m, their limited spatial resolution suggests they cannot resolve light organ variation for the purpose of conspecific recognition. Our findings point to factors other than conspecific recognition (e.g., neutral drift, phenotypic constraint) that have led to the extensive diversification of light organs in Sergestes s.l and impart caution about interpreting ecological significance of visual characters based on the resolution of human vision. This work provides new insight into deep‐sea animal interaction, supporting the idea that—at least for these mesopelagic shrimps—nonvisual signals may be required for conspecific recognition.     

Colour choices of naive bumble bees and their implications for colour perception

The innate preferences of inexperienced bumble bees, Bombus terrestris, for floral colour stimuli were studied using artificial flowers. The artificial flowers provided a colour pattern and consisted of a star-shaped corolla and of central colour patches similar to the nectar guide of natural flowers. The innate choice behaviour was assessed in terms of the number of approach flights from some distance towards the artificial flowers and the percentage of approach flights terminating in antennal contact with the floral guide. The colours of the floral guide, the corolla and the background were varied. It was shown that the innate flower colour preference in bumble bees has two components. 1. The frequency of approaches from a distance is correlated with the colour difference between the corolla and the background against which it is presented. If the corolla colour was constant but its background colour varied, the relative attractiveness of the corolla increased with its colour difference to the background. The colour difference assessment underlying this behaviour on a perceptual basis can be attained by means of colour opponent coding, a system well-established in Hymenoptera. 2. The frequency of antennal contacts with the floral guides relative to that of approach flights cannot be accounted for by colour opponent coding alone. Whether the approach flights are interrupted, or whether they end in an antennal contact with the nectar guide is strongly dependent on the direction (sign) of the colour difference, not only its magnitude. The choice behaviour requires a unique perceptual dimension, possibly that of colour saturation or that of hue perception comparable to components of colour perception in humans.     

Crystal structure of aspartate racemase from Pyrococcus horikoshii OT3 and its implications for molecular mechanism of PLP-independent racemization

There exists a d-enantiomer of aspartic acid in lactic acid bacteria and several hyperthermophilic archaea, which is biosynthesized from the l-enantiomer by aspartate racemase. Aspartate racemase is a representative pyridoxal 5'-phosphate (PLP)-independent amino acid racemase. The "two-base" catalytic mechanism has been proposed for this type of racemase, in which a pair of cysteine residues are utilized as the conjugated catalytic acid and base. We have determined the three-dimensional structure of aspartate racemase from the hyperthermophilic archaeum Pyrococcus horikoshii OT3 at 1.9 A resolution by X-ray crystallography and refined it to a crystallographic R factor of 19.4% (R(free) of 22.2%). This is the first structure reported for aspartate racemase, indeed for any amino acid racemase from archaea. The crystal structure revealed that this enzyme forms a stable dimeric structure with a strong three-layered inter-subunit interaction, and that its subunit consists of two structurally homologous alpha/beta domains, each containing a four-stranded parallel beta-sheet flanked by six alpha-helices. Two strictly conserved cysteine residues (Cys82 and Cys194), which have been shown biochemically to act as catalytic acid and base, are located on both sides of a cleft between the two domains. The spatial arrangement of these two cysteine residues supports the "two-base" mechanism but disproves the previous hypothesis that the active site of aspartate racemase is located at the dimeric interface. The structure revealed a unique pseudo mirror-symmetry in the spatial arrangement of the residues around the active site, which may explain the molecular recognition mechanism of the mirror-symmetric aspartate enantiomers by the non-mirror-symmetric aspartate racemase.     

Size and shape dimorphism in great ape mandibles and implications for fossil species recognition

Sexual dimorphism is an important source of morphological variation, and species differences in dimorphism may be reflected in magnitude, pattern, or both. While the extant great apes are commonly used as a reference sample for distinguishing between sexual dimorphism and intertaxic variation in the fossil record, few studies have evaluated mandibular dimorphism in these taxa. In this study, percentage, degree, and pattern of mandibular dimorphism are evaluated in Pongo, Gorilla, and Pan. Mandibular dimorphism patterns are explored to determine the extent to which such patterns accurately track great ape phylogeny. Pattern stability is assessed to determine whether there are stable patterns of mandibular size and shape dimorphism that may be usefully applied to hominoid or hominid fossil species recognition studies. Finally, the established patterns of dimorphism are used to address recent debates surrounding great ape taxonomy. Results demonstrate that mandibular dimorphism is universally expressed in size, but only Pongo and Gorilla exhibit shape dimorphism. Pattern similarity tends to be greater between subspecies of the same species than between higher-order taxa, suggesting that within the great apes, there is a relationship between dimorphism pattern and phylogeny. However, this relationship is not exact, given that dimorphism patterns are weakly correlated between some closely related taxa, while great ape subspecies may be highly correlated with taxa belonging to other species or genera. Furthermore, dimorphism patterns are not significantly correlated between great ape genera, even between Gorilla and Pan. Dimorphism patterns are more stable in Gorilla and Pongo as compared to Pan, but there is little pattern stability between species or genera. Importantly, few variables differ significantly between taxa that simultaneously show consistently relatively low levels of dimorphism and low levels of variation within taxa. Combined, these findings indicate that mandibular dimorphism patterns can and do vary considerably, even among closely related species, and suggest that it would be difficult to employ great ape mandibular dimorphism patterns for purposes of distinguishing between intra- and interspecies variation in fossil samples. Finally, the degree of pattern similarity in mandibular dimorphism is lower than previously observed by others for craniofacial dimorphism. Thus, the possibility cannot be ruled out that patterns of craniofacial dimorphism in great apes may be associated with a stronger phylogenetic signal than are patterns of mandibular dimorphism.     

Structural basis for the specific recognition of IL-18 by its alpha receptor

Interleukin 18 (IL-18), a member of the IL-1 family of cytokines, is an important regulator of innate and acquired immune responses. It signals through its ligand-binding primary receptor IL-18Rα and accessory receptor IL-18Rβ. Here we report the crystal structure of IL-18 with the ectodomain of IL-18Rα, which reveals the structural basis for their specific recognition. It confirms that surface charge complementarity determines the ligand-binding specificity of primary receptors in the IL-1 receptor family. We suggest that IL-18 signaling complex adopts an architecture similar to other agonistic cytokines and propose a general ligand-receptor assembly and activation model for the IL-1 family.     

Dissociable roles for histone acetyltransferases p300 and PCAF in hippocampus and perirhinal cortex‐mediated object memory

The importance of histone acetylation for certain types of memory is now well established. However, the specific contributions of the various histone acetyltransferases to distinct memory functions remain to be determined; therefore, we employed selective histone acetyltransferase protein inhibitors and short‐interference RNAs to evaluate the roles of CREB‐binding protein (CBP), E1A‐binding protein (p300) and p300/CBP‐associated factor (PCAF) in hippocampus and perirhinal cortex (PRh)‐mediated object memory. Rats were tested for short‐ (STM) and long‐term memory (LTM) in the object‐in‐place task, which relies on the hippocampus and PRh for spatial memory and object identity processing, respectively. Selective inhibition of these histone acetyltransferases by small‐interfering RNA and pharmacological inhibitors targeting the HAT domain produced dissociable effects. In the hippocampus, CBP or p300 inhibition impaired long‐term but not short‐term object memory, while inhibition of PCAF impaired memory at both delays. In PRh, HAT inhibition did not impair STM, and only CBP and PCAF inhibition disrupted LTM; p300 inhibition had no effects. Messenger RNA analyses revealed findings consistent with the pattern of behavioral effects, as all three enzymes were upregulated in the hippocampus (dentate gyrus) following learning, whereas only CBP and PCAF were upregulated in PRh. These results demonstrate, for the first time, the necessity of histone acetyltransferase activity for PRh‐mediated object memory and indicate that the specific mnemonic roles of distinctive histone acetyltransferases can be dissociated according to specific brain regions and memory timeframe.     

Surface motifs by a computer vision technique: Searches,detection, and implications for protein–ligand recognition

We describe the application of a method geared toward structural and surface comparison of proteins. The method is based on the Geometric Hashing Paradigm adapted from Computer Vision. It allows for comparison of any two sets of 3-D coordinates, such as protein backbones, protein core or protein surface motifs, and small molecules such as drugs. Here we apply our method to 4 types of comparisons between pairs of molecules: (1) comparison of the backbones of two protein domains; (2) search for a predefined 3-D C_α motif within the full backbone of a domain; and in particular, (3) comparison of the surfaces of two receptor proteins; and (4) comparison of the surface of a receptor to the surface of a ligand. These aspects complement each other and can contribute toward a better understandingof protein structure and biomolecular recognition. Searches for 3-D surface motifs can be carried out on either receptors or on ligands. The latter may result in the detection of pharmacophoric patterns. If the surfaces of the binding sites of either the receptors or of the ligands are relatively similar, surface superpositioning may aid significantly in the docking problem. Currently, only distance invariants are used in the matching, although additional geometric surface invariants are considered. The speed of our Geometric Hashing algorithm is encouraging, with a typical surface comparison taking only seconds or minutes of CPU time on a SUN 4 SPARC workstation. The direct application of this method to the docking problem is also discussed. We demonstrate the success of this methodin its application to two members of the globin family and to two dehydrogenases. © 1993 Wiley-Liss, Inc.     

Immunohistochemical evidence of cone-based ultraviolet vision in divergent bat species and implications for its evolution

We characterized Fos-like expression patterns in the primary visual cortex (V1) by binocular flicking stimulation with UV light to investigate cone-based UV vision in four bat species representing four lineages: Hipposideros armiger and Scotophilus kuhlii, insectivores using constant frequency (CF) or frequency modulation (FM) echolocation, respectively, and Rousettus leschenaultii and Cynopterus sphinx, cave-roosting and tree-roosting fruit bats, respectively. The optic centre processing the visual image, V1, appears more distinctly immunostaining in S. kuhlii and C. sphinx after 1 h of UV light stimuli while in H. armiger and R. leschenaultii, staining was no more distinct than in corresponding controls. Our immunohistochemical evidence supports differences in the distribution of cone-based UV vision in the order Chiroptera and supports our earlier postulate that due to possible sensory tradeoffs and roosting ecology, defects in the short wavelength opsin genes have resulted in loss of UV vision in CF but not in FM bats. In addition, fruit bats roosting in caves have lost UV vision but not those roosting in trees. Our results thus confirm that bats are a further mammalian taxon that has retained cone-based UV sensitivity in some species.     

A method to search for similar protein local structures at ligand-binding sites and its application to adenine recognition

We have developed a method of searching for similar spatial arrangements of atoms around a given chemical moiety in proteins that bind a common ligand. The first step in this method is to consider a set of atoms that closely surround a given chemical moiety. Then, to compare the spatial arrangements of such surrounding atoms in different proteins, they are translated and rotated so that the chemical moieties are superposed on each other. Spatial arrangements of surrounding atoms in a pair of proteins are judged to be similar, when there are many corresponding atoms occupying similar spatial positions. Because the method focuses on the arrangements of surrounding atoms, it can detect structural similarities of binding sites in proteins that are dissimilar in their amino acid sequences or in their chain folds. We have applied this method to identify modes of nucleotide base recognition by proteins. An all-against-all comparison of the arrangements of atoms surrounding adenine moieties revealed an unexpected structural similarity between protein kinases, cAMP-dependent protein kinase (cAPK), and casein kinase-1 (CK1), and D-Ala:D-Ala ligase (DD-ligase) at their adenine-binding sites, despite a lack of similarity in their chain folds. The similar local structure consists of a four-residue segment and three sequentially separated residues. In particular the four-residue segments of these enzymes were found to have nearly identical conformations in their backbone parts, which are involved in the recognition of adenine. This common local structure was also found in substrate-free three-dimensional structures of other proteins that are similar to DD-ligase in the chain fold and of other protein kinases. As the proteins with different folds were found to share a common local structure, these proteins seem to constitute a remarkable example of convergent evolution for the same recognition mechanism. Received: 9 December 1996 / Accepted: 7 February 1997     

Specificity and multiplicity in the recognition of individuals: implications for the evolution of social behaviour

Recognition of conspecifics occurs when individuals classify sets of conspecifics based on sensory input from them and associate these sets with different responses. Classification of conspecifics can vary in specificity (the number of individuals included in a set) and multiplicity (the number of sets differentiated). In other words, the information transmitted varies in complexity. Although recognition of conspecifics has been reported in a wide variety of organisms, few reports have addressed the specificity or multiplicity of this capability. This review discusses examples of these patterns, the mechanisms that can produce them, and the evolution of these mechanisms. Individual recognition is one end of a spectrum of specificity, and binary classification of conspecifics is one end of a spectrum of multiplicity. In some cases, recognition requires no more than simple forms of learning, such as habituation, yet results in individually specific recognition. In other cases, recognition of individuals involves complex associations of multiple cues with multiple previous experiences in particular contexts. Complex mechanisms for recognition are expected to evolve only when simpler mechanisms do not provide sufficient specificity and multiplicity to obtain the available advantages. In particular, the evolution of cooperation and deception is always promoted by specificity and multiplicity in recognition. Nevertheless, there is only one demonstration that recognition of specific individuals contributes to cooperation in animals other than primates. Human capacities for individual recognition probably have a central role in the evolution of complex forms of human cooperation and deception. Although relatively little studied, this capability probably rivals cognitive abilities for language.     

城市生活垃圾蚯蚓处理的因素优化及其重金属富集研究

采用模拟试验、小区试验与生产试验等研究了垃圾成分、软化方式、培养方式、环境温度和蚯蚓杂交等因素对蚯蚓处理城市生活垃圾的影响及其重金属富集效应。结果表明,改变垃圾成分、提高垃圾碳氮比,在20℃温度左右时,采用蚯蚓粪软化和室内层床培养方式,可使蚯蚓增殖率和垃圾腐解率都有所提高,同时利用驯化的重庆赤子爱胜蚓与背暗异唇蚓进行杂交,也可以提高蚯蚓处理垃圾的效果,蚯蚓处理过程中重金属富集系数与软化方式之间没有显著相关性,而与重金属种类、培养方式之间具有较强的依存性,砷、镉在腐解物中最易富集,而汞不易富集,垄埂式培养比层床式容易富集重金属,露天培养比室内培养更易富集重金属。     

Binding of specific DNA base-pair mismatches by N-methylpurine-DNA glycosylase and its implication in initial damage recognition

Most DNA glycosylases including N-methylpurine-DNA glycosylase (MPG), which initiate DNA base excision repair, have a wide substrate range of damaged or altered bases in duplex DNA. In contrast, uracil-DNA glycosylase (UDG) is specific for uracil and excises it from both single-stranded and duplex DNAs. Here we show by DNA footprinting analysis that MPG, but not UDG, bound to base-pair mismatches especially to less stable pyrimidine-pyrimidine pairs, without catalyzing detectable base cleavage. Thermal denaturation studies of these normal and damaged (e.g. 1,N(6)-ethenoadenine, varepsilonA) base mispairs indicate that duplex instability rather than exact fit of the flipped out damaged base in the catalytic pocket is a major determinant in the initial recognition of damage by MPG. Finally, based on our determination of binding affinity and catalytic efficiency we conclude that the initial recognition of substrate base lesions by MPG is dependent on the ease of flipping of the base from unstable pairs to a flexible catalytic pocket.     

Raltegravir flexibility and its impact on recognition by the HIV‐1 IN targets

HIV‐1 IN is a pertinent target for the development of AIDS chemotherapy. The first IN‐specific inhibitor approved for the treatment of HIV/AIDS, RAL, was designed to block the ST reaction. We characterized the structural and conformational features of RAL and its recognition by putative HIV‐1 targets – the unbound IN, the vDNA, and the IN?vDNA complex – mimicking the IN states over the integration process. RAL binding to the targets was studied by performing an extensive sampling of the inhibitor conformational landscape and by using four different docking algorithms: Glide, Autodock, VINA, and SurFlex. The obtained data evidenced that: (i) a large binding pocket delineated by the active site and an extended loop in the unbound IN accommodates RAL in distinct conformational states all lacking specific interactions with the target; (ii) a well‐defined cavity formed by the active site, the vDNA, and the shortened loop in the IN?vDNA complex provide a more optimized inhibitor binding site in which RAL chelates Mg²⁺ cations; (iii) a specific recognition between RAL and the unpaired cytosine of the processed DNA is governed by a pair of strong H‐bonds similar to those observed in DNA base pair G‐C. The identified RAL pose at the cleaved vDNA shed light on a putative step of RAL inhibition mechanism. This modeling study indicates that the inhibition process may include as a first step RAL recognition by the processed vDNA bound to a transient intermediate IN state, and thus provides a potentially promising route to the design of IN inhibitors with improved affinity and selectivity. Copyright © 2013 John Wiley & Sons, Ltd.     

What is it like to be a rat? Rat sensory perception and its implications for experimental design and rat welfare

This review of rat sensory perception spans eight decades of work conducted across diverse research fields. It covers rat vision, audition, olfaction, gustation, and somatosensation, and describes how rat perception differs from and coincides with ours. As Nagel's seminal work (1974) implies, we cannot truly know what it is like to be a rat, but we can identify and acknowledge their perceptual biases. These primarily nocturnal rodents are extremely sensitive to light, with artificial lighting frequently causing retinal degeneration, and their vision extends into the ultraviolet. Their olfactory sensitivity and ultrasonic hearing means they are influenced by environmental factors and conspecific signals that we cannot perceive. Rat and human gustation are similar, being opportunistic omnivores, yet this sense becomes largely redundant in the laboratory, where rodents typically consume a single homogenous diet. Rat somatosensation differs from ours in their thigmotactic tendencies and highly sensitive, specialised vibrissae. Knowledge of species-specific perceptual abilities can enhance experimental designs, target resources, and improve animal welfare. Furthermore, the sensory environment has influences from neurone to behaviour, so it can not only affect the senses directly, but also behaviour, health, physiology, and neurophysiology. Research shows that environmental enrichment is necessary for normal visual, auditory, and somatosensory development. Laboratory rats are not quite the simple, convenient models they are sometimes taken for; although very adaptable, they are complex mammals existing in an environment they are not evolutionarily adapted for. Here, many important implications of rat perception are highlighted, and suggestions are made for refining experiments and housing.