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PubMed2001

Lateral sensitivity modulation explains the flanker effect in contrast discrimination.

We used a dual-masking paradigm to study how contrast discrimination can be influenced by the presence of adjacent stimuli. The task of the observer was to detect a target superimposed on a pedestal in the presence of flankers. The flankers (i) reduce the target threshold at zero pedestal contrast, (ii) shift the target threshold versus pedestal contrast (TvC) function horizontally to the left on a log-log plot at high pedestal contrasts, and (iii) reduce the size of pedestal facilitation at low pedestal contrasts. The horizontal shift at high pedestal contrasts suggests that the flanker effect is a multiplicative factor that cannot be explained by previous models of contrast discrimination. We extend the divisive inhibition model of contrast discrimination by implementing the flanker effect as a lateral multiplicative sensitivity modulation. This extended model provides a good account of the data.

Adult↗

PubMed2002

A novel theory to explain species diversity in landscapes: positive frequency dependence and habitat suitability.

Theories to explain the diversity of species have required that individual species occupy unique niches and/or vary in their response to environmental factors. Positive interactions within a species, although common in communities, have not been thought to maintain species diversity because in non-spatial models the more abundant species always outcompetes the rarer species. Here, we show, using a stochastic spatial model, that positive intraspecific interactions such as those caused by positive frequency dependence and/or priority effects, can maintain species diversity if interactions between individuals are primarily local and the habitat contains areas that cannot be colonized by any species, such as boulders or other physical obstructions. When intraspecific interactions are primarily neutral, species diversity will eventually erode to a single species. When the landscape is homogeneous (i.e. does not contain areas that cannot be colonized by any species), the presence of strong intraspecific interactions will not maintain diversity.

Ecosystem↗

PubMed2003

Is neural filling-in necessary to explain the perceptual completion of motion and depth information?

Retinal activity is the first stage of visual perception. Retinal sampling is non-uniform and not continuous, yet visual experience is not characterized by holes and discontinuities in the world. How does the brain achieve this perceptual completion? Fifty years ago, it was suggested that visual perception involves a two-stage process of (i) edge detection followed by (ii) neural filling-in of surface properties. We examine whether this general hypothesis can account for the specific example of perceptual completion of a small target surrounded by dynamic dots (an 'artificial scotoma'), a phenomenon argued to provide insight into the mechanisms responsible for perception. We degrade the target's borders using first blur and then depth continuity, and find that border degradation does not influence time to target disappearance. This indicates that important information for the continuity of target perception is conveyed at a coarse spatial scale. We suggest that target disappearance could result from adaptation that is not specific to borders, and question the need to hypothesize an active filling-in process to explain this phenomenon.

Depth Perception↗

PubMed2003

Global patterns in endemism explained by past climatic change.

I propose that global patterns in numbers of range-restricted endemic species are caused by variation in the amplitude of climatic change occurring on time-scales of 10-100 thousand years (Milankovitch oscillations). The smaller the climatic shifts, the more probable it is that palaeoendemics survive and that diverging gene pools persist without going extinct or merging, favouring the evolution of neoendemics. Using the change in mean annual temperature since the last glacial maximum, estimated from global circulation models, I show that the higher the temperature change in an area, the fewer endemic species of mammals, birds, reptiles, amphibians and vascular plants it harbours. This relationship was robust to variation in area (for areas greater than 10(4) km2), latitudinal position, extent of former glaciation and whether or not areas are oceanic islands. Past climatic change was a better predictor of endemism than annual temperature range in all phylads except amphibians, suggesting that Rapoport's rule (i.e. species range sizes increase with latitude) is best explained by the increase in the amplitude of climatic oscillations towards the poles. Globally, endemic-rich areas are predicted to warm less in response to greenhouse-gas emissions, but the predicted warming would cause many habitats to disappear regionally, leading to species extinctions.

Adaptation, Physiological↗

PubMed2004

Different algal symbionts explain the vertical distribution of dominant reef corals in the eastern Pacific.

Symbiotic reef corals occupy the entire photic zone; however, most species have distinct zonation patterns within the light intensity gradient. It is hypothesized that the presence of specific symbionts adapted to different light regimes may determine the vertical distribution of particular hosts. We have tested this hypothesis by genetic and in situ physiological analyses of the algal populations occupying two dominant eastern Pacific corals, over their vertical distribution in the Gulf of California. Our findings indicate that each coral species hosts a distinct algal taxon adapted to a particular light regime. The differential use of light by specific symbiotic dinoflagellates constitutes an important axis for niche diversification and is sufficient to explain the vertical distribution patterns of these two coral species.

Adaptation, Physiological↗

PubMed2004

Can sunspot activity and ultraviolet-B radiation explain cyclic outbreaks of forest moth pest species?

Cyclic outbreaks of forest moth pest species have long remained a puzzle for foresters and ecologists. This paper presents time-series exhibiting a strong negative relationship between sunspot numbers and population indices of autumnal and winter moths, both in a mountain birch forest in central Norway and in a mixed lowland forest in southern Norway. In the latter area, also the population level of a moth species feeding entirely on lichens was negatively related to sunspot numbers. Low sunspot activity leads to a thinner ozone layer and thus higher surface ultraviolet (UV)-B radiation. As winter moth larvae prefer leaves subjected to enhanced UV-B radiation, we suggest that the causal relationship between sunspots and moths is that the metabolic costs of producing UV-B-protective pigments during periods of low sunspot activity reduce trees' and lichens' resistance to herbivores, and thus increase the survival of moth larvae. Higher peak densities of moth cycles in mountain forests could be explained by the general higher UV-B radiation at higher altitudes.

Animals↗

PubMed2006

Why do red and dark-coloured cars lure aquatic insects? The attraction of water insects to car paintwork explained by reflection-polarization signals.

We reveal here the visual ecological reasons for the phenomenon that aquatic insects often land on red, black and dark-coloured cars. Monitoring the numbers of aquatic beetles and bugs attracted to shiny black, white, red and yellow horizontal plastic sheets, we found that red and black reflectors are equally highly attractive to water insects, while yellow and white reflectors are unattractive. The reflection-polarization patterns of black, white, red and yellow cars were measured in the red, green and blue parts of the spectrum. In the blue and green, the degree of linear polarization p of light reflected from red and black cars is high and the direction of polarization of light reflected from red and black car roofs, bonnets and boots is nearly horizontal. Thus, the horizontal surfaces of red and black cars are highly attractive to red-blind polarotactic water insects. The p of light reflected from the horizontal surfaces of yellow and white cars is low and its direction of polarization is usually not horizontal. Consequently, yellow and white cars are unattractive to polarotactic water insects. The visual deception of aquatic insects by cars can be explained solely by the reflection-polarizational characteristics of the car paintwork.

Animals↗

PubMed2006

Compliant leg behaviour explains basic dynamics of walking and running.

The basic mechanics of human locomotion are associated with vaulting over stiff legs in walking and rebounding on compliant legs in running. However, while rebounding legs well explain the stance dynamics of running, stiff legs cannot reproduce that of walking. With a simple bipedal spring-mass model, we show that not stiff but compliant legs are essential to obtain the basic walking mechanics; incorporating the double support as an essential part of the walking motion, the model reproduces the characteristic stance dynamics that result in the observed small vertical oscillation of the body and the observed out-of-phase changes in forward kinetic and gravitational potential energies. Exploring the parameter space of this model, we further show that it not only combines the basic dynamics of walking and running in one mechanical system, but also reveals these gaits to be just two out of the many solutions to legged locomotion offered by compliant leg behaviour and accessed by energy or speed.

Biomechanical Phenomena↗

PubMed2002

The apparent clock-like evolution of Escherichia coli in glucose-limited chemostats is reproducible at large but not at small population sizes and can be explained with Monod kinetics.

To follow and model evolution of a microbial population in the chemostat, parameters are needed that give an indication of the absolute extent of evolution at a high resolution of time. In this study the evolution of the maximum specific growth rate ( micro (max)) and the residual glucose concentration was followed for populations of Escherichia coli K-12 under glucose-limited conditions at dilution rates of 0.1 x h(-1), 0.3 x h(-1) and 0.53 x h(-1) during 500-700 h in continuous culture. Whereas micro (max) improved only during the initial 150 h, the residual glucose concentration decreased constantly during 500 h of cultivation and therefore served as a convenient parameter to monitor the evolution of a population at a high time resolution with respect to its affinity for the growth-limiting substrate. The evolution of residual glucose concentrations was reproducible in independent chemostats with a population size of 10(11) cells, whereas no reproducibility was found in chemostats containing 10(7) cells. A model based on Monod kinetics assuming successive take-overs of mutants with improved kinetic parameters (primarily K(s)) was able to simulate the experimentally observed evolution of residual glucose concentrations. Similar values for the increase in glucose affinity of mutant phenotypes (K(s(mutant)) approximately equal 0.6 x K(s(parent))) and similar mutation rates per cell per generation leading to these mutant phenotypes (1-5 x1 0(-7)) were estimated in silico for all dilution rates. The model predicts a maximum rate of evolution at a dilution rate slightly below micro (max)/2. With increasing and decreasing dilution rates the evolution slows down, which also explains why in special cases a selection-driven evolution can exhibit apparent clock-like behaviour. The glucose affinity for WT cells was dependent on the dilution rate with highest values at dilution rates around micro (max)/2. Below 0.3 x h(-1) poorer affinity was mainly due to the effects of rpoS.

Adaptation, Physiological↗

PubMed2005

A functional CD8+ cell assay reveals individual variation in CD8+ cell antiviral efficacy and explains differences in human T-lymphotropic virus type 1 proviral load.

The CD8+ lymphocyte response is a main component of host immunity, yet it is difficult to quantify its contribution to the control of persistent viruses. Consequently, it remains controversial as to whether CD8+ cells have a biologically significant impact on viral burden and disease progression in infections such as human immunodeficiency virus-1 and human T-lymphotropic virus type I (HTLV-I). Experiments to ascertain the impact of CD8+ cells on viral burden based on CD8+ cell frequency or specificity alone give inconsistent results. Here, an alternative approach was developed that directly quantifies the impact of CD8+ lymphocytes on HTLV-I proviral burden by measuring the rate at which HTLV-I-infected CD4+ cells were cleared by autologous CD8+ cells ex vivo. It was demonstrated that CD8+ cells reduced the lifespan of infected CD4+ cells to 1 day, considerably shorter than the 30 day lifespan of uninfected cells in vivo. Furthermore, it was shown that HTLV-I-infected individuals vary considerably in the rate at which their CD8+ cells clear infected cells, and that this was a significant predictor of their HTLV-I proviral load. Forty to 50 % of between-individual variation in HTLV-I proviral load was explained by variation in the rate at which CD8+ cells cleared infected cells. This novel approach demonstrates that CD8+ cells are a major determinant of HTLV-I proviral load. This assay is applicable to quantifying the CD8+ cell response to other viruses and malignancies and may be of particular importance in assessing vaccines.

Adult↗

PubMed2025

Integrating explainable AI with multiomics systems biology and EHR data mining for personalized drug repurposing in Alzheimer's disease.

Alzheimer's disease (AD) is characterized by region- and patient-specific molecular heterogeneity, which hinders therapeutic design. In this study, we introduce PRISM-ML (PRecision-medicine using Interpretable Systems and Multiomics with Machine Learning), an open-source integrated analysis pipeline that combines interpretable machine learning with systems biology and electronic health record (EHR) data mining to elucidate the molecular diversity of AD and predict promising drug repurposing opportunities. First, we integrated and harmonized transcriptomic (bulk RNA-seq) and genomic (genome-wide association study) data from 2105 brain samples, each with matched data from the same individual (1363 AD patients, 742 controls; nine tissues), sourced from three independent studies. Random forest classifiers with SHapley Additive exPlanations (SHAP) identified patient-specific biomarkers; unsupervised clustering resolved 36 molecularly distinct "subtissues" (clusters of samples); and gene-gene co-expression networks prioritized 262 high-centrality bottleneck genes as putative regulators of dysregulated pathways. Next, knowledge graph-based drug repurposing predicted six FDA-approved drugs that simultaneously target multiple bottleneck genes and multiple AD-relevant pathways. Notably, in a large U.S. de-identified insurance-claims database (n = 364733), exposure to promethazine, one of the candidate drugs, was associated with a 57-62 % lower incidence of AD versus an active antihistamine comparator (adjusted hazard ratio 0.38; inverse-probability weighted 0.43; both p < 0.001), providing real-world support for its repurposing potential. In summary, PRISM-ML, as an explainable multi-omics analysis pipeline, is readily transferable to other complex diseases, advancing precision medicine.

Computational Biology↗

PubMed2001

Identification of wound healing/regeneration quantitative trait loci (QTL) at multiple time points that explain seventy percent of variance in (MRL/MpJ and SJL/J) mice F2 population.

Studies on genetic mechanisms of wound healing in mammals are very few, although injury is a leading cause of the global burden of disease. In this study, we performed a high-density, genome-wide scan using 633 (MRL/MPJ x SJL/J) F(2) intercross at multiple time points (days 15, 21, and 25) to identify quantitative trait loci (QTL) involved in wound healing/regeneration. The hypothesis of the study was that QTL and unique epistatic interactions are involved at each time point to promote wound healing/regeneration. Ten QTL were identified from chromosomes 1, 4, 6, 7, 9, and 13. Of the 10 QTL, eight from chromosomes 1, 4, 6, and 9 were novel as compared to QTL identified in the study. The 10 QTL altogether explained 70% of variance in F(2) mice. The same QTL were identified at each time point, with simple linear correlation between days 15, 21, and 25, showing very high significant relationships (R >0.92, P <0.0001). Unique epistatic interactions were identified at each time point except those from chromosomes 4, 6, 9, and 13 that were found at all three time points, showing that some loci are involved at all the three time points of wound healing (days 15, 21, and 25). Therefore, loci-to-loci interactions may play a major role in wound healing. Information from these studies may help in the identification of genes that could be involved in wound healing/regeneration.

Analysis of Variance↗

PubMed2002

Explaining the anomalous CDF (mu)gamma missing- E(T) events with supersymmetry.

The CDF Collaboration recently reported an excess of events in the (mu)gamma missing E(T) (E(T)) channel that disagrees with the standard model prediction. We explain the excess via resonant smuon production with a single dominant R-parity violating coupling lambda'211, in the context of models where the gravitino is the lightest supersymmetric particle. The slepton decays to the lightest neutralino and a muon followed by neutralino decaying to a gravitino and photon. We determine a viable region of parameter space that fits the kinematical distributions of the Run I excess and illustrate the effect by examining the best fit point in detail. We provide predictions for an excess in the E(T) and photon channel at Run I and Run II.

Journal Article↗

PubMed1991

Alpha-amylase inhibitor, not phytohemagglutinin, explains resistance of common bean seeds to cowpea weevil.

There are claims that phytohemagglutinin (PHA), the lectin of common bean, Phaseolus vulgaris, is toxic when fed to the cowpea weevil, Callosobruchus maculatus, and that PHA serves as the chemical defense against this seed-feeding bruchid beetle (DH Janzen, HB Juster, IE Liener [1976] Science 192: 795-796; AMR Gatehouse, FM Dewey, J Dove, KA Fenton, A Pusztai [1984] J Sci Food Agric 35: 373-380). However, our studies indicate that neither PHA nor its isolectins have detrimental effects when fed to the cowpea weevil. To explain these contradictory results we characterized the commercial lectin source used by A. M. R. Gatehouse, F. M. Dewey, J. Dove, K. A. Fenton, A. Pusztai (1984, J Sci Food Agric 35: 373-380). We demonstrate here that the toxic effects of PHA to cowpea weevil are due to an alpha-amylase inhibitor contaminant in the commercial preparation.

Journal Article↗

PubMed2001

Parents explain more often to boys than to girls during shared scientific thinking.

Young children's everyday scientific thinking often occurs in the context of parent-child interactions. In a study of naturally occurring family conversation, parents were three times more likely to explain science to boys than to girls while using interactive science exhibits in a museum. This difference in explanation occurred despite the fact that parents were equally likely to talk to their male and female children about how to use the exhibits and about the evidence generated by the exhibits. The findings suggest that parents engaged in informal science activities with their children may be unintentionally contributing to a gender gap in children's scientific literacy well before children encounter formal science instruction in grade school.

Chi-Square Distribution↗

PubMed2001

Explaining math: gesturing lightens the load.

Why is it that people cannot keep their hands still when they talk? One reason may be that gesturing actually lightens cognitive load while a person is thinking of what to say. We asked adults and children to remember a list of letters or words while explaining how they solved a math problem. Both groups remembered significantly more items when they gestured during their math explanations than when they did not gesture. Gesturing appeared to save the speakers' cognitive resources on the explanation task, permitting the speakers to allocate more resources to the memory task. It is widely accepted that gesturing reflects a speaker's cognitive state, but our observations suggest that, by reducing cognitive load, gesturing may also play a role in shaping that state.

Adult↗

PubMed2003

The ecology of eating: smaller portion sizes in France Than in the United States help explain the French paradox.

Part of the "French paradox" can be explained by the fact that the French eat less than Americans. We document that French portion sizes are smaller in comparable restaurants, in the sizes of individual portions of foods (but not other items) in supermarkets, in portions specified in cookbooks, and in the prominence of "all you can eat" restaurants in dining guides. We also present data, from observations at McDonald's, that the French take longer to eat than Americans. Our results suggest that in the domain of eating, and more generally, more attention should be paid to ecological factors, even though their mechanism of operation is transparent, and hence less revealing of fundamental psychological processes. Ironically, although the French eat less than Americans, they seem to eat for a longer period of time, and hence have more food experience. The French can have their cake and eat it as well.

Adult↗

PubMed2002

Ability to take an out-group's perspective in explaining positive and negative behaviors.

A total of 251 Latvian and Russian schoolteachers explained positive and negative behaviours from their own perspective and from the perspective of an ethnic out-group. The results were in line with the attributional pattern usually found in studies using Hewstone's direct perspective of judgement, when participants are asked to take the perspective of an ethnic out-group. That is, there was an outcome effect in causal attributions for in-group actors and a categorization effect for negative behaviour from the imagined (out-group's) perspective. The attributions from the direct perspective only partly replicated the commonly found pattern. The results support Montgomery's perspective theory.

Adult↗