Can infants use interposition and line junction cues to infer three-dimensional (3D) structure? Previous work (Shuwairi et al., 2007) has shown that in a task that required 4-month-olds to discriminate between static 2D pictures of possible and impossible cubes, infants exhibited a spontaneous preference for displays of the impossible cube, but left open the question of whether they did so on the basis of purely local “critical regions”, or whether infants were able to employ more global clues. Here, infants were presented with possible and impossible cubes in which the strictly local cues that could have derived from exterior binding contours were deleted. Results showed that infants were still able to discriminate possible from impossible cubes, suggesting longer looking infants are sensitive to global properties and the capacity to integrate pictorial information to perceive aspects of global 3D shape may develop earlier than previously demonstrated using reaching tasks.
visual development; pictorial depth cues; cue integration; impossible objects; 3D coherence; object perception in infancy
In the possible/impossible object-decision test, priming has been consistently found for structurally possible but not impossible objects, leading Schacter, Cooper, and Delaney (1990) to suggest that priming relies on a system that represents the global three-dimensional structure of objects. Using a modified design with matching objects to control for the influence of episodic memory, Ratcliff and McKoon (1995) and Williams and Tarr (1997) found negative priming for impossible objects (i.e., lower performance for old than new items). Both argued that priming derives from two processes: episodic memory for object features and bias to respond “possible” to encoded objects or their possible parts. This study applied the matched-objects design to the original Schacter and Cooper stimuli (same possible objects and matching impossible figures) with minimal procedural variation. The data from Experiment 1 (N=96) only partially supported the bias models and suggested that priming was mediated by both local and global structural descriptions. Experiment 2 showed that negative priming for impossible objects derives from the structural properties of these objects, not the influence of episodic memory on task performance.
perceptual priming; explicit memory; bias; possible/impossible object decision; structural descriptions
When only a small number of points of light attached to the torso and limbs of a moving organism are visible, the animation correctly conveys the animal's activity. Here we report that newly hatched chicks, reared and hatched in darkness, at their first exposure to point-light animation sequences, exhibit a spontaneous preference to approach biological motion patterns. Intriguingly, this predisposition is not specific for the motion of a hen, but extends to the pattern of motion of other vertebrates, even to that of a potential predator such as a cat. The predisposition seems to reflect the existence of a mechanism in the brain aimed at orienting the young animal towards objects that move semi-rigidly (as vertebrate animals do), thus facilitating learning, i.e., through imprinting, about their more specific features of motion.
Taking advantage of the spontaneous imprinting behaviour of newly hatched chicks, Giorgio Vallortigara and colleagues study their innate ability to distinguish biological motion.
The dramatic colours of biological communication signals raise questions about how animals perceive suprathreshold colour differences, and there are long-standing questions about colour preferences and colour categorization by non-human species. This study investigates preferences of foraging poultry chicks (Gallus gallus) as they peck at coloured objects. Work on colour recognition often deals with responses to monochromatic lights and how animals divide the spectrum. We used complementary colours, where the intermediate is grey, and related the chicks' choices to three models of the factors that may affect the attractiveness. Two models assume that attractiveness is determined by a metric based on the colour discrimination threshold either (i) by chromatic contrast against the background or (ii) relative to an internal standard. An alternative third model is that categorization is important. We tested newly hatched and 9-day-old chicks with four pairs of (avian) complementary colours, which were orange, blue, red and green for humans. Chromatic contrast was more relevant to newly hatched chicks than to 9-day-old birds, but in neither case could contrast alone account for preferences; especially for orange over blue. For older chicks, there is evidence for categorization of complementary colours, with a boundary at grey.
colour; vision; behaviour; Gallus gallus; chicks
Newly hatched domestic chicks were reared with five identical objects. On days 3 or 4, chicks underwent free-choice tests in which sets of three and two of the five original objects disappeared (either simultaneously or one by one), each behind one of two opaque identical screens. Chicks spontaneously inspected the screen occluding the larger set (experiment 1). Results were confirmed under conditions controlling for continuous variables (total surface area or contour length; experiment 2). In the third experiment, after the initial disappearance of the two sets (first event, FE), some of the objects were visibly transferred, one by one, from one screen to the other (second event, SE). Thus, computation of a series of subsequent additions or subtractions of elements that appeared and disappeared, one by one, was needed in order to perform the task successfully. Chicks spontaneously chose the screen, hiding the larger number of elements at the end of the SE, irrespective of the directional cues provided by the initial (FE) and final (SE) displacements. Results suggest impressive proto-arithmetic capacities in the young and relatively inexperienced chicks of this precocial species.
number cognition; counting; number sense; arithmetic; addition; subtraction
Newly hatched domestic chicks, reared with identical objects, when presented with sets of 3 vs. 2 objects disappearing one-by-one behind separate screens, spontaneously inspected the screen occluding the larger set; even when the continuous variables (area or perimeter) were controlled for (Rugani et al., 2009). Here, using a similar paradigm, we investigated the ability of chicks to perform addition on larger sets of objects. Chicks imprinted on five identical objects, were presented at test with 6 vs. 9 objects which disappeared one-by-one (Exp. 1). In Exp. 2, the same overall number of objects (15) was used, but employing an increased ratio, i.e., 5 vs. 10. In both experiments, when continuous variables were not made equal, chicks spontaneously inspected the screen occluding the larger set. However, when the size of the objects was adjusted so as to make the total surface area or perimeter equal for the two sets, chicks did not exhibit any preference. Lack of choice in the control conditions could be due to a combination of preferences; to rejoin the larger numerousness as well as the bigger objects (Rugani et al., 2010a). In Exp. 3, chicks were familiarized, during imprinting, with objects of various dimensions, in an attempt to reduce or suppress their tendency to approach objects larger than the familiar ones. Again chicks failed to choose at test between 5 vs. 10 objects when continuous variables were made equal. Results showed that chicks, after a one-by-one presentation of a large number of objects, rejoined the larger set. In order to choose the larger set, chicks estimated the objects in the two sets and then compared the outcomes. However, differently to what has been described for small numerousness, chicks succeeded only if non-numerical cues as well as numerical cues were available. This study suggests that continuous variables are computed by chicks for sets of objects that are not present at the same time and that are no longer visible at the time of choice.
number cognition; counting; number sense; arithmetic; domestic chick; human infant; large numeracy; continuous variables
In the first of five experiments, three of four adult ducks who had been reared in visual isolation gradually developed strong approach responses towards a moving panel of colored lights. Experiment 2 provided evidence that the ducks' approach response reflected the same sort of social attachment that is typically formed to moving objects by newly hatched ducklings. Experiment 3 revealed that the fourth duck would not approach the moving stimulus even after additional exposure to it, but would approach a conspecific after group housing had been enforced for seven days. In Experiment 4, none of five adult chickens who had been reared in visual isolation developed approach responses towards the moving stimulus, even though in Experiment 5, newly hatched chicks approached the stimulus quite readily. Taken together, these findings (a) indicate that ducks retain the ability to form filial-type attachments to novel objects throughout their lives, and (b) offer preliminary evidence that chickens do not retain this ability into adulthood.
imprinting; critical period; species differences; ducks; chickens
Three-dimensional (3D) displays have become important for many applications including vision research, operation of remote devices, medical imaging, surgical training, scientific visualization, virtual prototyping, and more. In many of these applications, it is important for the graphic image to create a faithful impression of the 3D structure of the portrayed object or scene. Unfortunately, 3D displays often yield distortions in perceived 3D structure compared with the percepts of the real scenes the displays depict. A likely cause of such distortions is the fact that computer displays present images on one surface. Thus, focus cues—accommodation and blur in the retinal image—specify the depth of the display rather than the depths in the depicted scene. Additionally, the uncoupling of vergence and accommodation required by 3D displays frequently reduces one’s ability to fuse the binocular stimulus and causes discomfort and fatigue for the viewer. We have developed a novel 3D display that presents focus cues that are correct or nearly correct for the depicted scene. We used this display to evaluate the influence of focus cues on perceptual distortions, fusion failures, and fatigue. We show that when focus cues are correct or nearly correct, (1) the time required to identify a stereoscopic stimulus is reduced, (2) stereoacuity in a time-limited task is increased, (3) distortions in perceived depth are reduced, and (4) viewer fatigue and discomfort are reduced. We discuss the implications of this work for vision research and the design and use of displays.
accommodation; vergence; volumetric display; stereopsis; binocular vision; 3D display; visual fatigue; cue combination; depth perception; graphics
Most living things and many nonliving things deform as they move, requiring observers to separate object motions from object deformations. When the object is partially occluded, the task becomes more difficult because it is not possible to use two-dimensional (2-D) contour correlations (Cohen, Jain, & Zaidi, 2010). That leaves dynamic depth matching across the unoccluded views as the main possibility. We examined the role of stereo cues in extracting motion of partially occluded and deforming three-dimensional (3-D) objects, simulated by disk-shaped random-dot stereograms set at randomly assigned depths and placed uniformly around a circle. The stereo-disparities of the disks were temporally oscillated to simulate clockwise or counterclockwise rotation of the global shape. To dynamically deform the global shape, random disparity perturbation was added to each disk's depth on each stimulus frame. At low perturbation, observers reported rotation directions consistent with the global shape, even against local motion cues, but performance deteriorated at high perturbation. Using 3-D global shape correlations, we formulated an optimal Bayesian discriminator for rotation direction. Based on rotation discrimination thresholds, human observers were 75% as efficient as the optimal model, demonstrating that global shapes derived from stereo cues facilitate inferences of object motions. To complement reports of stereo and motion integration in extrastriate cortex, our results suggest the possibilities that disparity selectivity and feature tracking are linked, or that global motion selective neurons can be driven purely from disparity cues.
stereo-motion; motion from shape; computational modeling; nonrigid shapes
In our previous paper we undertook proteomic analysis of the normal developing chick retina to identify proteins that were differentially expressed during retinal development. In the present paper we use the same proteomic approach to analyze the development and onset of degeneration in the retinal dysplasia and degeneration (rdd) chick. The pathology displayed by the rdd chick resembles that observed in some of the more severe forms of human retinitis pigmentosa.
Two-dimensional gel electrophoresis (pH 4–7), gel image analysis, and mass spectrometry were used to profile the developing and degenerating retina of the rdd and wild-type (wt) chick retina.
Several proteins were identified by mass spectrometry that displayed differential expression between normal and rdd retina between embryonic day 12 (E12) and post-hatch day 1 (P1). Secernin 1 displayed the most significant variation in expression between rdd and wt retina; this may be due to differential phosphorylation in the rdd retina. Secernin 1 has dipeptidase activity and has been demonstrated to play a role in exocytosis; it has been shown to be overexpressed in certain types of cancer and has also been suggested as a potential neurotoxicologically relevant target. Its role in the retina and in particular its differential expression in the degenerate rdd retina remains unknown and will require further investigation. Other proteins that were differentially expressed in the rdd retina included valosin-containing protein, β-synuclein, stathmin 1, nucleoside diphosphate kinase, histidine triad nucleotide-binding protein, and 40S ribosomal protein S12. These proteins are reported to be involved in several cellular processes, including the ubiquitin proteasome pathway, neuroprotection, metastatic suppression, transcriptional and translational regulation, and regulation of microtubule dynamics.
This proteomic study is the first such investigation of the rdd retina and represents a unique data set that has revealed several proteins that are differentially expressed during retinal degeneration in the rdd chick. Secernin 1 showed the most significant differences in expression during this degeneration period. Further investigation of the proteins identified may provide insight into the complex events underlying retinal degeneration in this animal model.
A biologically detailed model of the binaural avian nucleus laminaris is constructed, as a two-dimensional array of multicompartment, conductance-based neurons, along tonotopic and interaural time delay (ITD) axes. The model is based primarily on data from chick nucleus laminaris. Typical chick-like parameters perform ITD discrimination up to 2 kHz, and enhancements for barn owl perform ITD discrimination up to 6 kHz. The dendritic length gradient of NL is explained concisely. The response to binaural out-of-phase input is suppressed well below the response to monaural input (without any spontaneous activity on the opposite side), implicating active potassium channels as crucial to good ITD discrimination.
Colonization of the caeca of newly hatched chicks by Salmonella typhimurium was prevented by oral administration of a mixture of cultures comprising 48 different bacterial strains originating from an adult bird known to be free from salmonellas. The treatment conferred protection to the same degree as that obtained previously with a suspension of adult caecal contents or an undefined anaerobic culture from the same source and was demonstrated in four separate laboratory trials. Examination of the caecal microflora of chicks one day after being given the protective treatment showed that the presence of high levels of lactobacilli and Bacteroides spp. which are not found usually at two days of age in chicks produced under commercial conditions was indicative of the successful establishment of an adult-type microflora. Although the usual method of administering the protective organisms was to dose the chicks directly into the crop, it was also found possible to incorporate the organisms in the drinking water given to the birds at dilutions up to one in five, the maximum tested. When chicks were given the bacterial mixture via the crop and fed on a diet containing 10 mg kg-1 nitrovin and 100 mg kg-1 monensin, the bacteroides failed to establish in the caeca and the birds were not protected against salmonella colonization. However, when the bacterial cultures were incorporated in the drinking water and the chicks given the same feed, normal protection was obtained; possible reasons for these observations are discussed.
The comparative two-dimensional graphical representation of protein-ligand complex series featuring different ligands bound to the same active site offers a quick insight in their binding mode differences. In comparison to arbitrary orientations of the residue molecules in the individual complex depictions a consistent placement improves the legibility and comparability within the series. The automatic generation of such consistent layouts offers the possibility to apply it to large data sets originating from computer-aided drug design methods.
We developed a new approach, which automatically generates a consistent layout of interacting residues for a given series of complexes. Based on the structural three-dimensional input information, a global two-dimensional layout for all residues of the complex ensemble is computed. The algorithm incorporates the three-dimensional adjacencies of the active site residues in order to find an universally valid circular arrangement of the residues around the ligand. Subsequent to a two-dimensional ligand superimposition step, a global placement for each residue is derived from the set of already placed ligands. The method generates high-quality layouts, showing mostly overlap-free solutions with molecules which are displayed as structure diagrams providing interaction information in atomic detail. Application examples document an improved legibility compared to series of diagrams whose layouts are calculated independently from each other.
The presented method extends the field of complex series visualizations. A series of molecules binding to the same protein active site is drawn in a graphically consistent way. Compared to existing approaches these drawings substantially simplify the visual analysis of large compound series.
Newly hatched chicks were vaccinated orally with a genetically defined Salmonella enteritidis aroA candidate, strain CVL30. In chickens immunized with 10(5) or 10(9) CFU and challenged by the intravenous route with 10(8) CFU of S. enteritidis 109 Nalr at 8 weeks old, there were similar reductions in colonization of the spleens, livers, and ceca of vaccinees compared with unvaccinated controls. Two groups of newly hatched female chicks were vaccinated orally with 10(9) CFU of strain CVL30, and one group was revaccinated intramuscularly with 10(9) CFU at 16 weeks old. When challenged intravenously with S. enteritidis 109 Nalr at 23 weeks old, there was a reduction in the colonization of spleens, livers, ovaries, and ceca compared with unvaccinated controls. Inclusion of the intramuscular booster gave increased protection to the ovary, although the vaccine strain was isolated on one occasion from a batch of eggs laid at 20 weeks old. In chickens immunized with 10(9) CFU of strain CVL30 and challenged orally with 10(9) CFU of S. enteritidis 109 Nalr, there was a reduction in intestinal shedding of the challenge strain from vaccines compared with unvaccinated controls. Circulating immunoglobulin G antibodies to lipopolysaccharide (LPS) were detected in unvaccinated controls within 7 to 10 days of oral challenge. In contrast, circulating immunoglobulin G antibodies to LPS in vaccinees were not altered by the oral challenge, which suggested that vaccination reduced or prevented invasion by the challenge strain from the gut or multiplication of the challenge strain in the tissues. Newly hatched chicks were vaccinated orally with ca. 10(9) CFU of strain CVL30, and 1 day later, the vaccines and unvaccinated controls were challenged orally with 10(5) or 10(9) CFU of S. enteritidis 109 Nalr. Colonization of the ceca and invasion from the gut by the S. enteritidis challenge strain was reduced in the vaccines up to 5 days postchallenge compared with controls. In a second trial, vaccinees and controls were challenged orally with 10(7) or 10(9) CFU of S. typhimurium 2391 Nalr. In contrast to the challenge with S. enteritidis, colonization of the ceca and invasion by the S. typhimurium strain were not greatly reduced.
Thirty-two different types of anaerobic bacteria isolated from chickens have been tested for anti-salmonella activity in vitro. Under the conditions of the test only Bacteroides hypermegas and a Bifidobacterium sp. were shown to inhibit the salmonellas and this was attributed to the production of volatile fatty acids (VFA's) coupled with a low pH. When these organisms were tested in newly hatched chicks no inhibition of S. typhimurium occurred. Possible explanations for this observation are considered. The pH value and concentration of VFA's in the caecal material were determined in chicks from 0-84 days. In vitro tests with S. typhimurium indicated that, whilst the organism would be able to multiply at the pH and concentration of VFA's found during the first few days after hatching, the rapid increase in VFA concentration during the first 21 days would make this increasingly difficult. The significance of the developing caecal flora in relation to VFA production and pH is discussed. Because certain feed additives are known to influence the carriage of salmonellas, the sensitivity of various caecal anaerobes to these compounds was determined in vitro, generally at 1, 10 and 100 microgram/ml. The additives tested included flavomycin, furazolidone, nitrovin, tetracyline, tylosin, sulphaquinoxaline, virginiamycin and zinc bacitracin. All the organisms tested were inhibited by 100 microgram/ml furazolidone; none were inhibited by 500 microgram/ml sulphaquinoxaline. Changes occurring in the VFA concentration, pH value and microflora of the caeca of chicks fed for 49 days or longer on a normal starter diet or the same diet containing 10 or 100 mg/kg nitrovin have been compared. When the chicks were fed on the diet containing 100 mg/kg nitrovin, the Gram-negative non-sporing anaerobes were eliminated as a significant part of the caecal flora. However, the VFA concentration combined with a low pH in chicks from 2 weeks onwards was still sufficient to inhibit salmonella multiplication. Other possibly interrelated factors which might lead to an increased salmonella carrier rate in the nitrovin-treated chickens are discussed.
Bilateral symmetry is visually salient to diverse animals including birds, but whereas experimental studies typically use bilaterally symmetrical two-dimensional patterns that are viewed approximately fronto-parallel; in nature, animals observe three-dimensional objects from all angles. Many animals and plant structures have a plane of bilateral symmetry. Here, we first (experiment I) give evidence that young poultry chicks readily generalize bilateral symmetry as a feature of two-dimensional patterns in fronto-parallel view. We then test the ability of chicks to recognize symmetry in images that would be produced by the transformed view produced by a 40° horizontal combined with a 20° vertical rotation of a pattern on a spherical surface. Experiment II gives evidence that chicks trained to distinguish symmetrical from asymmetrical patterns treat rotated views of symmetrical ‘objects’ as symmetrical. Experiment III gives evidence that chicks trained to discriminate rotated views of symmetrical ‘objects’ from asymmetrical patterns generalize to novel symmetrical objects either in fronto-parallel or rotated view. These findings emphasize the importance of bilateral symmetry for three-dimensional object recognition and raise questions about the underlying mechanisms of symmetry perception.
symmetry; vision; object recognition; domestic chick; categorization
Early Renaissance painters innovatively attempted to depict realistic three-dimensional scenes. A major problem was to produce the impression of overlap for surfaces that occlude one another in the scene but are adjoined in the picture plane. Much has been written about perspective in art but little about occlusion. Here I examine some of the strategies for depicting occlusion used by early Renaissance painters in relation to ecological considerations and perceptual research. Perceived surface overlap is often achieved by implementing the principle that an occluding surface occludes anything behind it, so that occlusion perception is enhanced by a lack of relationship of occluding contour to occluded contours. Some well-known figure-ground principles are also commonly used to stratify adjoined figures. Global factors that assist this stratification include the placement of figures on a ground plane, a high viewpoint, and figure grouping. Artists of this period seem to have differed on whether to occlude faces and heads, often carefully avoiding doing so. Halos were either eliminated selectively or placed oddly to avoid such occlusions. Finally, I argue that the marked intransitivity in occlusion by architecture in the paintings of Duccio can be related to the issue of perceptual versus cognitive influences on the visual impact of paintings.
perception of overlap; art and perception; incoherence in art; principles of occlusion
Aneurysms of the posterior inferior cerebellar artery (PICA) are rarely encountered. In particular, due to frequent anatomic complexity and the presence of nearby critical structures, PICA origin aneurysms are difficult to treat. However, recent reports of anecdotal cases using advanced endovascular instruments and skills have made the results of endovascular treatment rather outstanding. PICA preservation is the key to a successful endovascular treatment, based on the premise that a PICA origin aneurysm is well occluded. To secure PICA flow, stenting into the PICA would be the best method, however, it is nearly impossible technically via the ipsilateral vertebral artery (VA) if the PICA arose at an acute angle from the sac. In such a case, a bilateral approach for stent-assisted coiling can be a creative method for achievement of two goals of both aneurysm occlusion and PICA preservation: ipsilateral approach for coil delivery and contralateral cross-over approach for stent delivery via a retrograde smooth path into the PICA.
Posterior inferior cerebellar artery; Intracranial aneurysm; Endovascular treatment
Cell surfaces in the duodenal mucosa have been studied in maturing tissue of the chick from incubation until hatching. Changes in the distribution of mitoses in this tissue give an indication of its rate of maturation. This rate is paralleled in developmental changes in microvilli and junctional complexes. Concentration of mitotic figures towards the base of villous folds is gradual from day 9 to day 16, then rapid to day 19, after which the mature pattern is acquired. By day 11, microvilli appear in a regular pattern which does not alter through hatching. Their height remains the same to day 16 when it increases gradually to day 19, then very sharply. The angle formed between the microvilli and the cell surface increases gradually to day 16, giving evidence of advancing internal structure. Changes in cell adhesion also occur at day 16. Thereafter, following trypsin treatment cells are held together in patches by the tight junctions of the terminal bar, although the desmosomes are separated. The timing of these morphological changes is compared with that of alkaline phosphatase accumulation in this tissue as reported by Moog (13). Increase in the surface area of the microvilli parallels the increase in the activity of the enzyme.
Treatment of newly hatched chicks with silica by the intraperitoneal route delayed the onset of mortalities due to the JM strain of Marek's disease (MD' virus inoculated at 6 days of age. During the 88-day observation period fewer silica-treated chicks died of MD, but this difference was not usually statistically significant. Silica treatment had no effect on the susceptibility of 4-week-old birds. Silica treatment reduced the antibody response to MD but, in general, not significantly. The antibody response to bovine serum albumin was significantly enhanced if measured by the indirect hemagglutination test but not if measured by the agar gel diffusion test, whereas the response to Brucella abortus was enhanced significantly in N-line (MD-resistant) chicks but not significantly in P-line (MD-susceptible) chicks. Five days after infection, silica-treated chicks had significantly less fluorescing antigen in thymus and bursa than did untreated chicks; no difference was observed in the spleen. After silica treatment the glass-adherent cell population in the buffy coat was increased by up to 10-fold compared with untreated chicks. It is suggested that silica treatment induced macrophage proliferation, with subsequent restriction of MD virus spread, yet allowed an adjuvant-type effect with other antigens.
Converging evidence from different species indicates that some newborn vertebrates, including humans, have visual predispositions to attend to the head region of animate creatures. It has been claimed that newborn preferences for faces are domain-relevant and similar in different species. One of the most common criticisms of the work supporting domain-relevant face biases in human newborns is that in most studies they already have several hours of visual experience when tested. This issue can be addressed by testing newly hatched face-naïve chicks (Gallus gallus) whose preferences can be assessed prior to any other visual experience with faces.
In the present study, for the first time, we test the prediction that both newly hatched chicks and human newborns will demonstrate similar preferences for face stimuli over spatial frequency matched structured noise. Chicks and babies were tested using identical stimuli for the two species. Chicks underwent a spontaneous preference task, in which they have to approach one of two stimuli simultaneously presented at the ends of a runway. Human newborns participated in a preferential looking task.
Results and Significance
We observed a significant preference for orienting toward the face stimulus in both species. Further, human newborns spent more time looking at the face stimulus, and chicks preferentially approached and stood near the face-stimulus. These results confirm the view that widely diverging vertebrates possess similar domain-relevant biases toward faces shortly after hatching or birth and provide a behavioural basis for a comparison with neuroimaging studies using similar stimuli.
Most existing methods for phylogenetic analysis involve developing an evolutionary model and then using some type of computational algorithm to perform multiple sequence alignment. There are two problems with this approach: (1) different evolutionary models can lead to different results, and (2) the computation time required for multiple alignments makes it impossible to analyse the phylogeny of a whole genome. This motivates us to create a new approach to characterize genetic sequences.
To each DNA sequence, we associate a natural vector based on the distributions of nucleotides. This produces a one-to-one correspondence between the DNA sequence and its natural vector. We define the distance between two DNA sequences to be the distance between their associated natural vectors. This creates a genome space with a biological distance which makes global comparison of genomes with same topology possible. We use our proposed method to analyze the genomes of the new influenza A (H1N1) virus, human rhinoviruses (HRV) and mammalian mitochondrial. The result shows that a triple-reassortant swine virus circulating in North America and the Eurasian swine virus belong to the lineage of the influenza A (H1N1) virus. For the HRV and mammalian mitochondrial genomes, the results coincide with biologists' analyses.
Our approach provides a powerful new tool for analyzing and annotating genomes and their phylogenetic relationships. Whole or partial genomes can be handled more easily and more quickly than using multiple alignment methods. Once a genome space has been constructed, it can be stored in a database. There is no need to reconstruct the genome space for subsequent applications, whereas in multiple alignment methods, realignment is needed to add new sequences. Furthermore, one can make a global comparison of all genomes simultaneously, which no other existing method can achieve.
In cooperative breeding systems driven by kin selection, effective kin-recognition cues are important. Recognition could be achieved by the direct assessment of the genetic relatedness of individuals or by learning through association. In the Seychelles warbler, Acrocephalus sechellensis, female subordinates maximize indirect fitness by preferentially helping genetically related nestlings. Help seems to be based on the continued presence of the primary female who previously fed the subordinate in the nest but it has, so far, been impossible to discount the direct assessment of genetic relatedness. We used a cross-fostering experiment to separate the two possible cues. Adult birds did not discriminate between their own and cross-fostered eggs or nestlings. Cross-fostering resulted in nestlings that were unrelated to the primary female that raised them, but control nestlings were closely related to their primary females. The proportions of cross-fostered and control female offspring that stayed and became helpers on their 'natal' territory were similar. However, for both groups the chance of becoming a subordinate helper was associated with the continued presence of the primary female and not with any other factor tested. Our study provides strong evidence that helping decisions are based on associative-learning cues.
Newly hatched chicks were dosed orally with a Salmonella typhimurium wild-type strain, an S. enteritidis wild-type strain, and a genetically defined S. enteritidis aroA vaccine candidate, strain CVL30. The S. typhimurium strain, 2391 Nalr, was virulent in newly hatched chicks and caused deaths in 7 of 20 chicks after an oral dose of 10(5) organisms. The S. enteritidis wild-type strain, LA5, caused death in 1 of 25 chicks and gross pathology including pericarditis and perihepatitis in 6 of the 24 survivors after an oral dose of 10(9) organisms. S. enteritidis aroA CVL30, attenuated by ca. 6.5 log10 in BALB/c mice, was nonvirulent when administered orally to chicks and did not cause morbidity. When newly hatched chicks were dosed, the pattern of invasion and colonization of the reticuloendothelial system by strain CVL30 was similar to that of its parent strain, LA5, irrespective of the dose. Oral inoculation of newly hatched chicks with < 10 organisms of S. enteritidis LA5 or CVL30 was followed by multiplication in the cecal contents. Within 3 days of hatching, the pH of the cecal contents was reduced from ca. 7 to 5. Samples of gut contents were inoculated in vitro. The S. enteritidis strains multiplied in samples taken from the ileum and duodenum irrespective of age but multiplied in the cecal samples from newly hatched chicks only. Invasion from the gut by S. enteritidis LA5 and CVL30 was both age and dose dependent.
Humans can effortlessly segment surfaces and objects from two-dimensional (2D) images that are projections of the 3D world. The projection from 3D to 2D leads partially to occlusions of surfaces depending on their position in depth and on viewpoint. One way for the human visual system to infer monocular depth cues could be to extract and interpret occlusions. It has been suggested that the perception of contour junctions, in particular T-junctions, may be used as cue for occlusion of opaque surfaces. Furthermore, X-junctions could be used to signal occlusion of transparent surfaces.
In this contribution, we propose a neural model that suggests how surface-related cues for occlusion can be extracted from a 2D luminance image. The approach is based on feedforward and feedback mechanisms found in visual cortical areas V1 and V2. In a first step, contours are completed over time by generating groupings of like-oriented contrasts. Few iterations of feedforward and feedback processing lead to a stable representation of completed contours and at the same time to a suppression of image noise. In a second step, contour junctions are localized and read out from the distributed representation of boundary groupings. Moreover, surface-related junctions are made explicit such that they are evaluated to interact as to generate surface-segmentations in static images. In addition, we compare our extracted junction signals with a standard computer vision approach for junction detection to demonstrate that our approach outperforms simple feedforward computation-based approaches.
A model is proposed that uses feedforward and feedback mechanisms to combine contextually relevant features in order to generate consistent boundary groupings of surfaces. Perceptually important junction configurations are robustly extracted from neural representations to signal cues for occlusion and transparency. Unlike previous proposals which treat localized junction configurations as 2D image features, we link them to mechanisms of apparent surface segregation. As a consequence, we demonstrate how junctions can change their perceptual representation depending on the scene context and the spatial configuration of boundary fragments.