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PubMed1988

[The history of color theories].

The origins of color theories are closely linked to the Greeks' theories of vision. Plato explained vision as a combined action of light from within (i.e. from the eye) and light from without: this view was, in a certain sense, revived by Goethe. Aristotle, on the other hand, defined vision as the passive reception, by the eye, of an action originating in objects: thus, he was the originator of scientific optics, as propounded 2000 years later by Newton. The present author compares Newton's experimental analysis of spectral colors produced by triangular glass prisms with Goethe's more intuitive theory of the primordial phenomena (Urphänomene) of color vision. Apparently, Goethe started from the same point as Newton: experimentation with optical prisms. But he looked, as it were, in the opposite direction: he did not examine the objective image formed by a prism but described what he himself perceived when looking through a prism. It was this subjective image which he analyzed and on which he built his own color theory. The direction of his argument was fixed right from the beginning: from the very first glance through his prism he was convinced--by intuition, not by reflection--that Newton must have been wrong. No wonder this prejudice led him astray! However, Goethe's careful and skillful analysis of the subjective perception of light and colors bore other fruits. Under the heading of "physiological colors" he describes, in his "Farbenlehre", some important phenomena of visual physiology such as simultaneous and successive color contrasts.(ABSTRACT TRUNCATED AT 250 WORDS)

Color Perception↗
PubMed2006

Theoretical investigation of the dissociation dynamics of vibrationally excited vinyl bromide on an ab initio potential-energy surface obtained using modified novelty sampling and feed-forward neural networks.

The reaction dynamics of vibrationally excited vinyl bromide have been investigated using classical trajectory methods on a neural network potential surface that is fitted to an ab initio database of 12 122 configuration energies obtained from electronic structure calculations conducted at the MP4(SDQ) level of theory using a 6-31G(d,p) basis set for the carbon and hydrogen atoms and Huzinaga's (43334334) basis set augmented with split outer s and p orbitals (4332143214) and a polarization f orbital with an exponent of 0.5 for the bromine atom. The sampling of the 12-dimensional configuration hyperspace of vinyl bromide prior to execution of the electronic structure calculations is accomplished by combining novelty-sampling methods, chemical intuition, and trajectory sampling on empirical and neural network surfaces. The final potential is obtained using a two-layer feed-forward neural network comprising 38 and 1 neurons, respectively, with hyperbolic tangent sigmoid and linear transfer functions in the hidden and output layers, respectively. The fitting is accomplished using the Levenberg-Marquardt algorithm with early stopping and Bayesian regularization methods to avoid overfitting. The interpolated potentials have a standard deviation from the ab initio results of 0.0578 eV, which is within the range generally regarded as "chemical accuracy" for the purposes of electronic structure calculations. It is shown that the potential surface may be easily and conveniently transferred from one research group to another. The files required for transfer of the vinyl bromide surface can be obtained from the Electronic Physics Auxiliary Publication Service. Total dissociation rate coefficients for vinyl bromide are obtained at five different excitation energies between 4.50 and 6.44 eV. Branching ratios into each of the six open reaction channels are computed at 24 vibrational energies in the range between 4.00 and 6.44 eV. The distribution of vibrational energies in HBr formed via three-center dissociation from vinyl bromide is determined and compared with previous theoretical and experimental results. It is concluded that the combination of ab initio electronic structure calculations, novelty sampling with chemical intuition and trajectories on empirical analytic surfaces, and feed-forward neural networks provides a viable framework in which to execute purely ab initio molecular-dynamics studies on complex systems with multiple open reaction channels.

Journal Article↗
PubMed2006

On the relationship between the local tracking procedures and monotonic schemes in quantum optimal control.

Numerical simulations of (bilinear) quantum control often rely on either monotonically convergent algorithms or tracking schemes. However, despite their mathematical simplicity, very limited intuitive understanding exists at this time to explain the former type of algorithms. Departing from the usual mathematical formalization, we present in this paper an interpretation of the monotonic algorithms as finite horizon, local in time, tracking schemes. Our purpose is not to present a new class of procedures but rather to introduce the necessary rigorous framework that supports this interpretation. As a by-product we show that at each instant, estimates of the future quality of the current control field are available and used in the optimization. When the target is expressed as reaching a prescribed final state, we also present an intuitive geometrical interpretation as the minimization of the distance between two correlated trajectories: one starting from the given initial state and the other backward in time from the target state. As an illustration, a stochastic monotonic algorithm is introduced. Numerical discretizations of the two procedures are also presented.

Journal Article↗
PubMed2003

Low force decelerates L-selectin dissociation from P-selectin glycoprotein ligand-1 and endoglycan.

Selectin-ligand interactions mediate the tethering and rolling of circulating leukocytes on vascular surfaces during inflammation and immune surveillance. To support rolling, these interactions are thought to have rapid off-rates that increase slowly as wall shear stress increases. However, the increase of off-rate with force, an intuitive characteristic named slip bonds, is at odds with a shear threshold requirement for selectin-mediated cell rolling. As shear drops below the threshold, fewer cells roll and those that do roll less stably and with higher velocity. We recently demonstrated a low force regime where the off-rate of P-selectin interacting with P-selectin glycoprotein ligand-1 (PSGL-1) decreased with increasing force. This counter-intuitive characteristic, named catch bonds, might partially explain the shear threshold phenomenon. Because L-selectin-mediated cell rolling exhibits a much more pronounced shear threshold, we used atomic force microscopy and flow chamber experiments to determine off-rates of L-selectin interacting with their physiological ligands and with an antibody. Catch bonds were observed at low forces for L-selectin-PSGL-1 interactions coinciding with the shear threshold range, whereas slip bonds were observed at higher forces. These catch-slip transitional bonds were also observed for L-selectin interacting with endoglycan, a newly identified PSGL-1-like ligand. By contrast, only slip bonds were observed for L-selectin-antibody interactions. These findings suggest that catch bonds contribute to the shear threshold for rolling and are a common characteristic of selectin-ligand interactions.

Animals↗
PubMed2000

Patients or customers: ethical limits of market economy in health care.

There is a move away from a market economy in health care in the United States and a move towards such a market in Germany. This article tries to make explicit what underlies the moral intuition that there is a tension between a market economy and health care. First, health care is analyzed in terms of the economic theory of the market and incompatibilities are described. The moral problem is identified as the danger of liquefying the distinction between persons and things. The basic moral intuition seems to be the classical social contract: as a functioning market is governed by the principle of commutative justice, free riders have to be kept away, which is achieved by coercion that is not provided by the market; coercion can be justified by a social contract. The special moral problems of a social contract for health care are discussed. It is argued that public coercion in order to collect contributions for essential health care is justified.

Delivery of Health Care↗
PubMed1990

Type T personality and the Jungian classification system.

The Type T personality has been described as a personality dimension referring to individual differences in stimulation seeking, excitement seeking, thrill seeking, arousal seeking, and risk taking. This article explores its relationship to the theoretically relevant personality classification system of C.G. Jung, employing the Myers-Briggs Type Indicator as a measure of Jungian types. A sample of high-school students was administered the Myers-Briggs and a measure of Type T. Pearson correlations revealed Type T to be significantly related to the Jungian Intuitive and Perceptive types, with the Type T personality being described as intuitive and perceptive. Interpretations of these exploratory findings were offered.

Adolescent↗
PubMed1994

Preventing alcohol abuse by college women: a relational perspective 2.

In recent theoretical formulations, researchers have pointed out that relationships are integral to women's psychological development and identity. Alcohol plays a role for women in seeming to facilitate relationships and in self-medicating when relationships are not mutual or are abusive. Theories about women's psychological development can also be applied to designing prevention strategies by emphasizing relational material, affective content, and intuitive learning styles. An interactive style is strongly encouraged and is demonstrated in a prevention program that seeks to engage the audience emotionally. Components of the prevention model are outlined, including emphasizing the use of peers in design and implementation, strengthening support systems and relational ties, and valuing empathic and intuitive skills. Suggestions are also offered for applying these components to the culture of the college community.

Alcoholism↗
PubMed1978

The psychophysical relationships between color and flavor.

Psychophysics has become a well-defined discipline in science and is undergoing a period of transition from the theoretical and academic to the applied. Certainly the use of magnitude estimation in flavor evaluation is becoming more accepted, and concurrently the food research area is utilizing the colorimetric techniques which are available. However, there has been virtually no investigation carried out on the quantitative relationships which exist between color and flavor in a psychophysical sense. Intuitively, many researchers state the qualitative effect of color on flavor, but the quantification of these techniques is practically nonexistent. This paper will attempt to summarize the psychophysical techniques which are available for such studies, as well as discuss the importance of these studies. Great controversy exists concerning the need for colorants in food. If color does indeed affect flavor quantitatively, it will affect intake and, therefore, final nutritional status of the public in a quantitative manner. This controversy should be resolved in the light of fact, not intuition.

Color↗
PubMed2001

Telepresence surgery: first experiences with laparoscopic radical prostatectomy.

The concept of an intelligent steerable surgical instrument system has been described by various authors. Since 1998, telesurgical minimally invasive procedures have been performed with the da Vinci system, mainly for cardiac bypass surgery. We present our initial experience using the device for robot-assisted laparoscopic radical prostatectomy. The intuitive surgical system consists of two main components: the surgeon's viewing and control console with 3D-imaging, and the surgical arm unit that positions and manoeuvres detachable surgical instruments. These instruments are introduced via two 8 mm trocars and allow movements in all six degrees of freedom (DoF). The surgeon performs the procedure while seated at the console holding specially designed instruments. Highly specialised computer software and mechanics transmit the surgeon's hand movements exactly to the microsurgical movements of the manipulators at the operative site. The system used is a W-shaped five trocar arrangement, with the robot's arms at the lateral trocars (8 mm) and two assistant trocars medially (10 mm). A sixth trocar was used in the right suprapubic area for retraction of the gland (Foley catheter). The left assistant used different instruments, such as bipolar forceps, Ultracision, and Endoclip, wheras the right assistant mainly used the suction–irrigation device. The Intuitive System was attached after trocar placement and exposure of Retzius' space. We treated six patients (two pT2, four pT3, median Gleason score 6). The operating room time averaged 315 (range 242–480) min, including pelvic lymph-node dissection. No intra-operative complications occured, one patient required transfusions. There were no positive margins, median catheter time was 5 days. Three patients were completely continent after 1 month. Telerobotic laparoscopic radical prostatectomy is feasible. There is a learning curve with the device, mainly due to the magnification, 3D image and lack of tactile feedback. However, the experienced surgeon can become familiar with the device after a short time. There is still a need for further development of instruments for urological procedures.

Journal Article↗
PubMed2003

Cryptic forcible insemination: male snakes exploit female physiology, anatomy, and behavior to obtain coercive matings.

Whether males can inseminate uncooperative females is a central determinant of mating system evolution that profoundly affects the interpretation of phenomena such as multiple mating by females, mate choice, reproductive seasonality, and courtship tactics. Forcible insemination is usually inferred from direct physical battles between the sexes and has been dismissed on intuitive grounds for many kinds of animals. For example, snakes have elongate flexible bodies (making it difficult for a male to restrain a female physically), males are typically smaller than females, and copulation requires female cloacal gaping to enable intromission. Male garter snakes (Thamnophis sirtalis) do not display any overt aggression during courtship and simply lie over the female and exhibit rhythmic pulsating caudocephalic waves of muscular contraction; previous studies have interpreted this behavior as a mechanism for eliciting female receptivity. In contrast, we show that male garter snakes forcibly inseminate females. They do so by taking advantage of specific features of snake physiology, respiratory anatomy, and antipredator behavior. The snake lung extends along most of the body, with the large posterior section (the saccular lung) lacking any respiratory exchange surface. Rhythmic caudocephalic waves by courting male garter snakes push anoxic air from the saccular lung forward and across the respiratory surfaces such that females cannot obtain oxygen. Their stress response involves cloacal gaping, which functions in other contexts to repel predators by extruding feces and musk but in this situation permits male intromission. Thus, superficially benign courtship behaviors may involve cryptic coercion even in species for which intuition dismisses any possibility of forcible insemination.

Animals↗
PubMed2005

Anomalous anticipatory skin conductance response to acoustic stimuli: experimental results and speculation about a mechanism.

OBJECTIVES: The primary aim of this study was to conduct a replication, simplification, and extension of similar previous studies that claimed anomalous anticipatory skin conductance responses prior to various stimuli and to provide sufficient protocol and analysis details in order to foster additional replications. A secondary aim was to provide a testable model in order to understand the observed results. DESIGN: We used standard skin conductance measures and techniques to search within 50 participants for responses prior to 1-second duration, 97-dB acoustic stimuli, compared to prior to silent controls. We used an interstimulus interval randomly and uniformly distributed between 30 and 50 seconds. OUTCOME MEASURES: The dependent variable was the difference between proportions of 3.5-second prestimulus intervals prior to acoustic stimuli and prior to silent controls that contained a fully formed, nonspecific skin conductance response (ns-SCR). The null hypothesis was that the proportion difference should be zero. RESULTS: We found a significant proportion difference of 0.032 (Z = 2.08; effect size = 0.077 +/- 0.037; p(1t) = 0.0018), which is a replication of earlier similar studies. CONCLUSIONS: We examined and ruled out a number of potential artifacts that might have accounted for this finding. To understand these results, we demonstrated, by Monte Carlo techniques, that a possible explanation is that experimenters may have used their own intuition to initiate experiment runs to somehow sort otherwise random nonspecific skin conductance responses into appropriate bins in order to mimic physiological responses. We found experimental evidence to support this idea as an operational mechanism. If this speculation is confirmed in prospective studies, then this intuition-based mimicking of effects may profoundly impact the interpretation of results from complementary and alternative medical studies that use statistical inference to assess outcomes.

Acoustic Stimulation↗
PubMed2006

Evaluation of laparoscopic performance with alteration in angle of vision.

BACKGROUND AND PURPOSE: Optimal placement allows intuitive laparoscope positioning between two working trocars (0 degrees angle). However, this configuration may require the assistant to operate in an awkward position. We evaluated the effect of alteration of laparoscope position on surgeon performance and correlated this with surgical experience. SUBJECTS AND METHODS: Participants were stratified by laparoscopic experience. Group 1 (N = 10) was naïve (no surgical experience), group 2 (N = 7) had moderate laparoscopic experience (1-100 cases), and group 3 (N = 6) was laparoscopically experienced (>100 cases). Participants were timed performing a simple laparoscopic task three times in a trainer with camera angles randomized along the horizontal plane: 0 degrees , 45 degrees , 90 degrees , 135 degrees , and 180 degrees . RESULTS: All participants showed progressive deterioration in performance as the angle deviated from baseline. The mean time required to complete the tasks was significantly higher for group 1 v groups 2 and 3 at 135 degrees (158 v 77 and 73 seconds) and 180 degrees (153 v 89 and 86 seconds). Performance curves for each group revealed more pronounced deterioration of performance with alteration in the angle of vision in group 1 than in groups 2 and 3 (P < 0.01). There was no difference between groups 2 and 3 (P = 0.19). CONCLUSIONS: Even modest alteration in laparoscopic perspective results in deterioration of performance for all levels of surgical experience. Experienced laparoscopists adapt more quickly to complexities presented by alteration in camera angles. Novice surgeons should focus on trocar positioning to maintain intuitive surgical perspective and should refrain from working with alterations in camera angles until significant laparoscopic experience has been gained.

Clinical Competence↗
PubMed2006

The inconsistency of "optimal" cutpoints obtained using two criteria based on the receiver operating characteristic curve.

The use of biomarkers is of ever-increasing importance in clinical diagnosis of disease. In practice, a cutpoint is required for dichotomizing naturally continuous biomarker levels to distinguish persons at risk of disease from those who are not. Two methods commonly used for establishing the "optimal" cutpoint are the point on the receiver operating characteristic curve closest to (0,1) and the Youden index, J. Both have sound intuitive interpretations--the point closest to perfect differentiation and the point farthest from none, respectively--and are generalizable to weighted sensitivity and specificity. Under the same weighting of sensitivity and specificity, these two methods identify the same cutpoint as "optimal" in certain situations but different cutpoints in others. In this paper, the authors examine situations in which the two criteria agree or disagree and show that J is the only "optimal" cutpoint for given weighting with respect to overall misclassification rates. A data-driven example is used to clarify and demonstrate the magnitude of the differences. The authors also demonstrate a slight alteration in the (0,1) criterion that retains its intuitive meaning while resulting in consistent agreement with J. In conclusion, the authors urge that great care be taken when establishing a biomarker cutpoint for clinical use.

Biomarkers↗
PubMed2026

CHITRA: an interactive visualization tool for comparative genomic rearrangement analysis.

MOTIVATION: The increasing availability of chromosome-scale genome assemblies has fuelled a renewed interest in studying chromosomal evolution and rearrangements. Synteny visualization plays a critical role in understanding genome organization, structural variations, and evolutionary relationships. However, existing tools often have steep learning curves, produce static plots, or are limited in their ability to analyse multiple genomes simultaneously. There is a growing need for an intuitive and interactive visualization tool that can effectively explore syntenic relationships and chromosomal rearrangements. RESULTS: Here, we present CHITRA, a web-based interactive tool designed to visualize synteny blocks, chromosomal rearrangements, and breakpoints in both linear and circular styles. CHITRA-enables real-time exploration of genome structural variations with an intuitive graphical interface, customizable visualization options, and high-resolution export capabilities for publication-ready figures. The tool supports chromosome- and scaffold-level assemblies and allows users to filter, highlight, and interactively examine syntenic relationships. AVAILABILITY AND IMPLEMENTATION: CHITRA is freely available at https://chitra.bioinformaticsonline.com/, with comprehensive documentation at https://chitra.bioinformaticsonline.com/docs. The source code is open-source and accessible on GitHub at https://github.com/pranjalpruthi/CHITRA.

Journal Article↗
PubMed1998

Combining evidence using p-values: application to sequence homology searches.

MOTIVATION: To illustrate an intuitive and statistically valid method for combining independent sources of evidence that yields a p-value for the complete evidence, and to apply it to the problem of detecting simultaneous matches to multiple patterns in sequence homology searches. RESULTS: In sequence analysis, two or more (approximately) independent measures of the membership of a sequence (or sequence region) in some class are often available. We would like to estimate the likelihood of the sequence being a member of the class in view of all the available evidence. An example is estimating the significance of the observed match of a macromolecular sequence (DNA or protein) to a set of patterns (motifs) that characterize a biological sequence family. An intuitive way to do this is to express each piece of evidence as a p-value, and then use the product of these p-values as the measure of membership in the family. We derive a formula and algorithm (QFAST) for calculating the statistical distribution of the product of n independent p-values. We demonstrate that sorting sequences by this p-value effectively combines the information present in multiple motifs, leading to highly accurate and sensitive sequence homology searches.

Algorithms↗
PubMed2004

An ontology for collaborative construction and analysis of cellular pathways.

MOTIVATION: As the scientific curiosity in genome studies shifts toward identification of functions of the genomes in large scale, data produced about cellular processes at molecular level has been accumulating with an accelerating rate. In this regard, it is essential to be able to store, integrate, access and analyze this data effectively with the help of software tools. Clearly this requires a strong ontology that is intuitive, comprehensive and uncomplicated. RESULTS: We define an ontology for an intuitive, comprehensive and uncomplicated representation of cellular events. The ontology presented here enables integration of fragmented or incomplete pathway information via collaboration, and supports manipulation of the stored data. In addition, it facilitates concurrent modifications to the data while maintaining its validity and consistency. Furthermore, novel structures for representation of multiple levels of abstraction for pathways and homologies is provided. Lastly, our ontology supports efficient querying of large amounts of data. We have also developed a software tool named pathway analysis tool for integration and knowledge acquisition (PATIKA) providing an integrated, multi-user environment for visualizing and manipulating network of cellular events. PATIKA implements the basics of our ontology.

Biopolymers↗
PubMed2004

The Global Error Assessment (GEA) model for the selection of differentially expressed genes in microarray data.

MOTIVATION: Microarray technology has become a powerful research tool in many fields of study; however, the cost of microarrays often results in the use of a low number of replicates (k). Under circumstances where k is low, it becomes difficult to perform standard statistical tests to extract the most biologically significant experimental results. Other more advanced statistical tests have been developed; however, their use and interpretation often remain difficult to implement in routine biological research. The present work outlines a method that achieves sufficient statistical power for selecting differentially expressed genes under conditions of low k, while remaining as an intuitive and computationally efficient procedure. RESULTS: The present study describes a Global Error Assessment (GEA) methodology to select differentially expressed genes in microarray datasets, and was developed using an in vitro experiment that compared control and interferon-gamma treated skin cells. In this experiment, up to nine replicates were used to confidently estimate error, thereby enabling methods of different statistical power to be compared. Gene expression results of a similar absolute expression are binned, so as to enable a highly accurate local estimate of the mean squared error within conditions. The model then relates variability of gene expression in each bin to absolute expression levels and uses this in a test derived from the classical ANOVA. The GEA selection method is compared with both the classical and permutational ANOVA tests, and demonstrates an increased stability, robustness and confidence in gene selection. A subset of the selected genes were validated by real-time reverse transcription-polymerase chain reaction (RT-PCR). All these results suggest that GEA methodology is (i) suitable for selection of differentially expressed genes in microarray data, (ii) intuitive and computationally efficient and (iii) especially advantageous under conditions of low k. AVAILABILITY: The GEA code for R software is freely available upon request to authors.

Algorithms↗
PubMed2004

DIVAA: analysis of amino acid diversity in multiple aligned protein sequences.

MOTIVATION: Multiple alignments of proteins are an effective way of identifying conserved amino acids that provide clues to functional relationships among proteins. Quantitation of the abundances of amino acids found at each position in a sequence motif can provide a basis for understanding the structural and functional constraints at each point. Distribution of information across a motif has been used previously, but the non-intuitive nature of the analysis has limited its impact. RESULTS: Here, we introduce a quantitative measure of amino acid sequence diversity (DIVAA) that has a simple, intuitive meaning. Diversity, as a measure of sequence conservation or variation, is inextricably linked to the probability of selecting identical pairs from a distribution. We demonstrate its utility through the analysis of four populations: ATP-binding P-loops, hypervariable domains of kappa light chains, signal sequences, and the N- and C- termini of proteins. DIVAA provides a simple means to generate hypotheses concerning the contribution of individual residues to the functional and evolutionary relationships among proteins. AVAILABILITY: Access to DIVAA software is available at RELIC (http://relic.bio.anl.gov).

Algorithms↗