Relative meaning of lines and corners in geometric figures for their recognition by humans

Neurons tuned to line-crossings (corners, crosses, Y-like and three-ray star-like figures) of different shape and orientation rather than to a single bar were found in the area 17 of the cat visual cortex. We studied the relative role of lines and corners of 2D and 3D geometrical figures for their recognition by humans. Probability of figure recognition during its tachistoscopic presentation was compared for the whole (control) and partly masked figures. Sides or corners of the figures were masked to varying degrees and probabilities of correct response were compared. The recognition probability successively decreases with increasing extent of figure masking. This decrease is significantly more pronounced for the figures without corners than for the figures without part of the lines. The relatively greater significance of the corners than sides of geometrical figures for human visual recognition and some possible neuronal mechanisms of this effect are discussed.     

Gender distinctions in recognition of partly masked geometric figures

Visual recognition of entire and partly masked geometric figure by men and women was studied. Probabilities of correct recognition of the entire (control) and partly masked figures (without some parts of their lines or corners) under conditions of their near-threshold tachistoscopic presentation were compared. A gradual decrease in recognition probability with increasing masking was observed. It was more pronounced for figures without some corners than for figures without part of their sides. Reliable gender differences were found: men better than women recognized figures, especially, with masked corners. Possible reasons for gender differences in recognition of geometrical figures are discussed, in particular, the role of striate sensitivity to a single light bar and a line crossing in the observed phenomena.     

Identification of images as a series of gradual transformations of geometrical figures

In the course of psychophysiological experiments with a tachistiscopic presentation of geometrical figures as transformations from a square into a triangle, the subjects worked out a distance scale for optical mouse movement depending on the degree of similarity between the presented figure and a square. This curve appears as a gradual decrease in the distance during the figure’s transformation from a square into a triangle. Significant variation in the shape of the curve was revealed upon exclusion of one of the images of the alphabet. The results are discussed in the context of the lateral inhibition phenomena and compared with the data of the theory of identification.     

Characteristics of the autonomic regulation in humans with different susceptibility to cold

To determine the strained adaptation to cold, the cardiovascular reactivity under local cold exposure and the characteristics of regulation of the circulatory system in persons with high individual susceptibility to cold was studied. It was shown that the subjective characteristics of high susceptibility to cold in the form of initial symptoms of Raynaud’s phenomenon correlated with the symptoms of aggravated and generalized cold-induced vasoconstriction (CIV) during the local cold test. The analysis of the heart rate variability (HRV) in persons with aggravated CIV revealed a decrease in the parameters of the time-domain characteristics of HRV (RRNN, SDNN, RMSSD, pNN₅₀, and coefficient of variation) as well as a decrease in the total power (TP) of the frequency-domain characteristics and the absolute values of the frequency bands (VLF, LF, and HF) with a relative increase of the LF component. This reflects possible changes in the autonomic regulation of the cardiovascular system, which manifest themselves in a reduced contribution of reflectory mechanisms to the heart rate regulation followed by relative predominance of baroreflex regulation. The diagnostic value of aggravated cold-induced vasoconstriction in identifying disorders of adaptation to cold or premorbid state of the cardiovascular system is discussed.     

Interhemispheric EEG interrelations in recognition of masked visual images accompanied by music

Changes in the EEG depend on the style of accompanying music. Classical music produces more patterns with increased diagonal coherences in the γ frequency band, where two foci of integration are formed at points T ₄ and T ₆. During listening to rock music, a larger proportion of all changes occurred in the θ-and α₁ frequency bands; an integration focus was formed at point T ₆ in the α₁ and γ frequency bands. An increase in diagonal coherences that was observed during the recognition was especially pronounced in the Δ-, θ-and α₁ frequency bands. In addition, there was an increase in the coherence between the potentials recorded at points O ₁-P ₄ and O ₂-F ₇, and it was observed in all the frequency bands. During the recognition of masked visual images accompanied by classical or rock music, there were more patterns with an increased diagonal coherence of the currently dominant activity. Before erroneous recognition, a widely generalized increase in coherence over the brain cortex was observed in the Δ, θ, and α₁ bands, which was an informative indicator of the subsequent erroneous recognition. In tests with recognition unaccompanied by music, as well as with music, the main change in symmetrical coherences was either a decrease in or an absence of changes in this indicator versus the background value.     

Dominant TCR-alpha requirements for a self antigen recognition in humans

TCR-alpha and -beta chains are composed of somatically rearranged V, D, and J germline-encoded gene segments that confer Ag specificity. Recent crystallographic analyses revealed that TCR-alpha has more contacts with peptide than TCR-beta, suggesting the possibility that peptide recognition predominantly relies on TCR-alpha. T cells specific for the self Ag Melan-A/MART-1 possess an exceptionally high precursor frequency in human histocompatibility leukocyte Ag-A2 individuals. This provided a unique situation for assessment of the structural relationship between TCR and peptide/MHC ligand at both the pre- and postimmune levels. Molecular and phenotypic analysis of many different Melan-A-specific T cell populations revealed that a structural constraint is imposed on the TCR for engagement with Melan-A peptides presented by HLA-A2, namely the highly preferential use of a particular TCRAV segment, AV2. Examination of CD8 single-positive thymocytes indicated that this preferential use in forming the Melan-A-specific TCR is mainly imposed by intrathymic positive selection. Our data demonstrate a dominant function of TCRAV2 segment in forming the TCR repertoire specific for the human self Ag Melan-A/MART-1 and support the view that Ag recognition is mediated predominantly by TCR-alpha.     

Visual discrimination of simple geometrical patterns: II. Atypical responses in a subject suffering difficulties with pattern recognition

We have applied the experimental methods described by Ike et al. (Spatial Vision, 1987, 2, 13-29) in the study of pattern discrimination by subjects who, during childhood, experienced severe difficulties with reading and spelling. Of the six subjects studied, one still suffers from such difficulties and we show that she performs atypically in certain of the discrimination tasks. In particular, her discrimination responses for elements such as delta are markedly different from those of all other subjects. We interpret these abnormal responses on the basis of the discrimination mechanisms for line orientation and rotation of the elements which were discussed by Ike et al. (1987).     

Reaction of laying hens to humans in the home or a novel environment

Tests assessing the fear of humans by measuring avoidance or approach reactions of the test animals towards humans can be useful tools in welfare assessment schemes. In this study, we wanted to compare tests assessing the reactions of laying hens towards humans in the home environment to a test performed in a novel environment. As well we investigated inter-test correlations in the home environment. We performed several tests to assess the hens’ approach and avoidance reactions towards an unfamiliar human inside the home environment of laying hens in 14 caged flocks and 10 free-range flocks. We measured the reactions of hens to a stationary person and a moving person approaching individual hens in both systems, as well as reactions to a stationary person trying to touch individual hens in non-cage systems and reactions of caged hens to a person passing by. Additionally, a standardised arena test was performed outside the home environment to compare the birds’ avoidance reactions towards an approaching human in a novel environment. In caged hens no significant correlations of tests performed inside the home environment with the arena test could be found, but there were moderate to high correlations (r_s > 0.6) with one parameter of the arena test in non-caged hens. The different tests applied inside the home environment correlated significantly and moderately to highly with each other, supporting the validity of these tests to measure fear of humans. The caged laying hens in our study reacted differently in the novel environment from the non-caged birds, indicating that the birds’ reactions towards humans in an unfamiliar environment depend on the housing system. In summary, a comparison of the level of fear of humans between flocks in different housing systems by using an arena test outside the home environment seems difficult and was not possible in the present study.     

Ultrafast electron transfer in the recognition of different DNA sequences by a DNA-binding protein with different dynamical conformations

Ultrafast electron transfer (ET) phenomenon in protein and protein–DNA complex is very much crucial and often leads to the regulation of various kinds of redox reactions in biological system. Although, the conformation of the protein in protein–DNA complex is concluded to play the key role in the ET process, till date very little evidences exist in the literature. λ-repressor–operator DNA interaction, particularly O_R1 and O_R2, is a key component of the λ-genetic switch and is a model system for understanding the chemical principles of the conformation-dependent ET reaction, governed by differential protein dynamics upon binding with different DNA target sequences. Here, we have explored the photoinduced electron transfer from the tryptophan moieties of the protein λ-repressor to two operators DNA of different sequences (O_R1 and O_R2) using picosecond-resolved fluorescence spectroscopy. The enhanced flexibility and different conformation of the C-terminal domain of the repressor upon complexation with O_R1 DNA compared to O_R2 DNA are found to have pronounced effect on the rate of ET. We have also observed the ET phenomenon from a dansyl chromophore, bound to the lysine residue, distal from the DNA-binding domain of the protein to the operator DNA with a specific excitation at 299?nm wavelength. The altered ET dynamics as a consequence of differential protein conformation upon specific DNA sequence recognition may have tremendous biological implications.     

Ultrafast electron transfer in the recognition of different DNA sequences by a DNA-binding protein with different dynamical conformations

Ultrafast electron transfer (ET) phenomenon in protein and protein-DNA complex is very much crucial and often leads to the regulation of various kinds of redox reactions in biological system. Although, the conformation of the protein in protein-DNA complex is concluded to play the key role in the ET process, till date very little evidences exist in the literature. λ-repressor-operator DNA interaction, particularly O(R)1 and O(R)2, is a key component of the λ-genetic switch and is a model system for understanding the chemical principles of the conformation-dependent ET reaction, governed by differential protein dynamics upon binding with different DNA target sequences. Here, we have explored the photoinduced electron transfer from the tryptophan moieties of the protein λ-repressor to two operators DNA of different sequences (O(R)1 and O(R)2) using picosecond-resolved fluorescence spectroscopy. The enhanced flexibility and different conformation of the C-terminal domain of the repressor upon complexation with O(R)1 DNA compared to O(R)2 DNA are found to have pronounced effect on the rate of ET. We have also observed the ET phenomenon from a dansyl chromophore, bound to the lysine residue, distal from the DNA-binding domain of the protein to the operator DNA with a specific excitation at 299 nm wavelength. The altered ET dynamics as a consequence of differential protein conformation upon specific DNA sequence recognition may have tremendous biological implications.     

KSHV Latency Locus Cooperates with Myc to Drive Lymphoma in Mice

Kaposi sarcoma-associated herpesvirus (KSHV) has been linked to Kaposi sarcoma and B-cell malignancies. Mechanisms of KSHV-induced oncogenesis remain elusive, however, in part due to lack of reliable in vivo models. Recently, we showed that transgenic mice expressing the KSHV latent genes, including all viral microRNAs, developed splenic B cell hyperplasia with 100% penetrance, but only a fraction converted to B cell lymphomas, suggesting that cooperative oncogenic events were missing. Myc was chosen as a possible candidate, because Myc is deregulated in many B cell lymphomas. We crossed KSHV latency locus transgenic (latency) mice to Cα Myc transgenic (Myc) mice. By itself these Myc transgenic mice develop lymphomas only rarely. In the double transgenic mice (Myc/latency) we observed plasmacytosis, severe extramedullary hematopoiesis in spleen and liver, and increased proliferation of splenocytes. Myc/latency mice developed frank lymphoma at a higher rate than single transgenic latency or Myc mice. These data indicate that the KSHV latency locus cooperates with the deregulated Myc pathways to further lymphoma progression.     

Detecting clusters of different geometrical shapes in microarray gene expression data

MOTIVATION: Clustering has been used as a popular technique for finding groups of genes that show similar expression patterns under multiple experimental conditions. Many clustering methods have been proposed for clustering gene-expression data, including the hierarchical clustering, k-means clustering and self-organizing map (SOM). However, the conventional methods are limited to identify different shapes of clusters because they use a fixed distance norm when calculating the distance between genes. The fixed distance norm imposes a fixed geometrical shape on the clusters regardless of the actual data distribution. Thus, different distance norms are required for handling the different shapes of clusters. RESULTS: We present the Gustafson-Kessel (GK) clustering method for microarray gene-expression data. To detect clusters of different shapes in a dataset, we use an adaptive distance norm that is calculated by a fuzzy covariance matrix (F) of each cluster in which the eigenstructure of F is used as an indicator of the shape of the cluster. Moreover, the GK method is less prone to falling into local minima than the k-means and SOM because it makes decisions through the use of membership degrees of a gene to clusters. The algorithmic procedure is accomplished by the alternating optimization technique, which iteratively improves a sequence of sets of clusters until no further improvement is possible. To test the performance of the GK method, we applied the GK method and well-known conventional methods to three recently published yeast datasets, and compared the performance of each method using the Saccharomyces Genome Database annotations. The clustering results of the GK method are more significantly relevant to the biological annotations than those of the other methods, demonstrating its effectiveness and potential for clustering gene-expression data. AVAILABILITY: The software was developed using Java language, and can be executed on the platforms that JVM (Java Virtual Machine) is running. It is available from the authors upon request. SUPPLEMENTARY INFORMATION: Supplementary data are available at http://dragon.kaist.ac.kr/gk.     

Plasma nitrite concentrations reflect the degree of endothelial dysfunction in humans

A reduced nitric oxide availability is a hallmark of endothelial dysfunction occurring early in atherosclerosis. Recently, we have shown that plasma nitrite mirrors acute changes in endothelial nitric oxide synthase activity in various mammals, including humans. Here, we examined the hypothesis that plasma nitrite levels are reduced in humans with endothelial dysfunction and the decrease is correlated with increasing numbers of cardiovascular risk factors (RF). Plasma nitrite concentrations were quantified by flow-injection analysis. The coefficient of variation for repeated measurements of plasma nitrite was <8%, and heart rate and blood pressure at the time of blood sampling had no significant effect on nitrite values measured (n=10). Baseline levels of plasma nitrite followed a normal distribution in each group studied and decreased progressively with increasing numbers of cardiovascular risk factors (n=351, p<0.001): 351+/-13 (0 RF), 261+/-10 (1 RF), 253+/-11 (2 RF), 222+/-18 (3 RF), and 171+/-29 nmol/L (4 RF). Intima media thickness (IMT) and flow-mediated dilation (FMD) were determined via ultrasound. Plasma nitrite and FMD levels were lower, whereas IMT was greater in individuals with endothelial dysfunction (n=12) compared to healthy volunteers (n=12). Nitrite correlated significantly with FMD (r=0.56, p<0.001) and inversely with IMT (r= -0.49, p<0.01). Plasma nitrite levels are reliably measurable in humans, indicate endothelial dysfunction, and correlate with cardiovascular risk factors. Future studies are necessary to identify the prognostic relevance of plasma nitrite determination in patients suffering from cardiovascular disease.