Modelling the branching growth fractal pattern of the maize root system

Using the technique of L-systems, a growth model of the maize root system is developed. From the observation of the root systems developed under various soil density in eight root boxes, a spatial hierarchy of growth rules was extracted. The rules were divided into three categories: a meta-rule for describing features of an entire root system, a branching growth rule and a tip elongation rule. Some variations in the entire features of the root system, such as the outline and the root distribution, were confirmed by observation, and then the respective meta-rules were re-defined. The branching properties of first- and second-order lateral roots were statistically almost equal in the observations, and this lead us to set up a single stochastic branching growth rule. Tip elongation movement was not observed here; its rule had to be assumed by reference to data in the literature. A single set of branching growth and tip elongation rules were coupled with the respective meta-rules corresponding to the root samples observed, where a small scale rule was loosely governed by a large scale rule. Computer simulations offered optimized drawings of the observed root systems, and they also reproduced a typical anisotropic power distribution of roots similar to those observed.     

Use of blood typing to confirm principles of coat-color genetics in horses.

The chestnut rule in equine coat-color genetics asserts that the inter se mating of chestnut horses never produces bay, black, brown or gray offspring. The gray rule asserts that a gray offspring must have at least one gray parent. Nine alleged exceptions to the chestnut rule, all involving bay offspring, and eight alleged exceptions to the gray rule, including four offspring that were also exceptions to the chestnut rule, were examined for parent-offspring genetic incompatibilities in as many as 17 genetic systems of blood-group markers. In all except one of the 17 cases it was possible to show that parentage had been incorrectly assigned. In 9 of the 16 exclusions it was possible to exclude the stallion irrespective of the mare and in one of the 16 exclusions it was possible to exclude the mare irrespective of the stallion. The percentage of exclusions, i.e., 94, was closely in line with expectation based on the established efficacy of these tests, about 90 percent, in excluding the incorrect stallion or stallions in paternity cases. Although the results strongly uphold the validity of the chestnut and gray rules in equine coat-color inheritance, they do not completely exclude the possibility that there could be rare exceptions to one or the other or both color rules. Insofar as equine registries may be concerned, the results clearly indicate that no alleged exception to the color rules should be considered eligible for registry in the absence of these tests.     

Supernumerary teeth in Lynx lynx and the irreversibility of evolution

Supernumerary dental elements have been reported in Lynx lynx by several authors. These features have been given different evolutionary interpretations by different commentators. I note here that, since these features are absent in the plesiomorphic sister-groups of L. lynx , they represent a true evolutionary reversal. If they were simply a retention of an evolutionarily older phenotype, we should expect to see them developed in at least one plesiomorphic sister-group. Such development of a previously hidden character can occur if it is genetically linked to features selected for, until it becomes phenotypically expressed, whereupon selection can act on the character itself. Since Dollo's law, which is the theoretical issue behind the present discussion, is not a law, but a rule, and, like all rules based on probabilities, we should expect to find exceptions in the fossil record. Such exceptions are not rare, but few are as spectacular as the present one, in which the redeveloped feature is at least phenotypically identical with one which has been lost in the Felidae since the Miocene.     

Computational mate choice: theory and empirical evidence

The present review is based on the thesis that mate choice results from information-processing mechanisms governed by computational rules and that, to understand how females choose their mates, we should identify which are the sources of information and how they are used to make decisions. We describe mate choice as a three-step computational process and for each step we present theories and review empirical evidence. The first step is a perceptual process. It describes the acquisition of evidence, that is, how females use multiple cues and signals to assign an attractiveness value to prospective mates (the preference function hypothesis). The second step is a decisional process. It describes the construction of the decision variable (DV), which integrates evidence (private information by direct assessment), priors (public information), and value (perceived utility) of prospective mates into a quantity that is used by a decision rule (DR) to produce a choice. We make the assumption that females are optimal Bayesian decision makers and we derive a formal model of DV that can explain the effects of preference functions, mate copying, social context, and females' state and condition on the patterns of mate choice. The third step of mating decision is a deliberative process that depends on the DRs. We identify two main categories of DRs (absolute and comparative rules), and review the normative models of mate sampling tactics associated to them. We highlight the limits of the normative approach and present a class of computational models (sequential-sampling models) that are based on the assumption that DVs accumulate noisy evidence over time until a decision threshold is reached. These models force us to rethink the dichotomy between comparative and absolute decision rules, between discrimination and recognition, and even between rational and irrational choice. Since they have a robust biological basis, we think they may represent a useful theoretical tool for behavioural ecologist interested in integrating proximate and ultimate causes of mate choice.     

Community identity in a temporal network: A taxonomy proposal

Communities of nodes are one of the most important meso structures in a network. In static networks they are essentially characterized by the nodes they hold, how modular they are and how they connect to other communities. Once identified, they do not change. In networks that evolve over time, communities can shed and acquire new nodes. This generates new constructs and raises the question of community identity, and of the characterization of the events that define their lifecycle. Although researchers have devoted efforts to address some of these questions, we believe that a formalized classification and a principled method to identify community events is still lacking. In this paper we propose such a classification in the form of a robust taxonomy, supported by a similarity metric based on the Jaccard index but adjusted to chance, and a set of rules that unequivocally can track a community journey from ”cradle to grave”.     

Successional state dynamics: A novel approach to modeling nonequilibrium foodweb dynamics

Communities and ecosystems are often far from equilibrium, but our understanding of nonequilibrium dynamics has been hampered by a paucity of analytical tools. Here I describe a novel approach to modeling seasonally forced food webs, called “successional state dynamics” (SSD). It is applicable to communities where species dynamics are fast relative to the external forcing, such as plankton and other microbes, diseases, and some insect communities. The approach treats succession as a series of state transitions driven by both the internal dynamics of species interactions and external forcing. First, I motivate the approach with numerical solutions of a seasonally forced predator-prey model. Second, I describe how to set up and analyze an SSD model. Finally, I apply the techniques to three additional models of two-species interactions: resource competition (r-K selection), facilitation, and flip-flop competition (where the competitive hierarchy alternates over time). This approach allows easy and thorough exploration of how dynamics depend on the environmental forcing regime, and uncovers unexpected phenomena such as multiple stable annual trajectories and year-to-year irregularity in successional trajectories (chaos).     

Cooperation and Defection at the Crossroads

We study a simple traffic model with a non-signalized road intersection. In this model the car arriving from the right has precedence. The vehicle dynamics far from the crossing are governed by the rules introduced by Nagel and Paczuski, which define how drivers behave when braking or accelerating. We measure the average velocity of the ensemble of cars and its flow as a function of the density of cars on the roadway. An additional set of rules is defined to describe the dynamics at the intersection assuming a fraction of drivers that do not obey the rule of precedence. This problem is treated within a game-theory framework, where the drivers that obey the rule are cooperators and those who ignore it are defectors. We study the consequences of these behaviors as a function of the fraction of cooperators and defectors. The results show that cooperation is the best strategy because it maximizes the flow of vehicles and minimizes the number of accidents. A rather paradoxical effect is observed: for any percentage of defectors the number of accidents is larger when the density of cars is low because of the higher average velocity.     

Morphological variations in a widely distributed Eastern Asian passerine cannot be consistently explained by ecogeographic rules

Ecogeographic rules that describe quantitative relationships between morphologies and climate might help us predict how morphometrics of animals was shaped by local temperature or humidity. Although the ecogeographic rules had been widely tested in animals of Europe and North America, they had not been fully validated for species in regions that are less studied. Here, we investigate the morphometric variation of a widely distributed East Asian passerine, the vinous‐throated parrotbill (Sinosuthora webbiana), to test whether its morphological variation conforms to the prediction of Bergmann''s rule, Allen''s rules, and Gloger''s rule. We at first described the climatic niche of S. webbiana from occurrence records (n = 7838) and specimen records (n = 290). The results of analysis of covariance (ANCOVA) suggested that the plumage coloration of these parrotbills was darker in wetter/warmer environments following Gloger''s rule. However, their appendage size (culmen length, beak volume, tarsi length) was larger in colder environments, the opposite of the predictions of Allen''s rule. Similarly, their body size (wing length) was larger in warmer environments, the opposite of the predictions of Bergmann''s rule. Such disconformity to both Bergmann''s rule and Allen''s rule suggests that the evolution of morphological variations is likely governed by multiple selection forces rather than dominated by thermoregulation. Our results suggest that these ecogeographic rules should be validated prior to forecasting biological responses to climate change especially for species in less‐studied regions.     

Modulation of Arm Reaching Movements during Processing of Arm/Hand-Related Action Verbs with and without Emotional Connotation

The theory of embodied language states that language comprehension relies on an internal reenactment of the sensorimotor experience associated with the processed word or sentence. Most evidence in support of this hypothesis had been collected using linguistic material without any emotional connotation. For instance, it had been shown that processing of arm-related verbs, but not of those leg-related verbs, affects the planning and execution of reaching movements; however, at present it is unknown whether this effect is further modulated by verbs evoking an emotional experience. Showing such a modulation might shed light on a very debated issue, i.e. the way in which the emotional meaning of a word is processed. To this end, we assessed whether processing arm/hand-related verbs describing actions with negative connotations (e.g. to stab) affects reaching movements differently from arm/hand-related verbs describing actions with neutral connotation (e.g. to comb). We exploited a go/no-go paradigm in which healthy participants were required to perform arm-reaching movements toward a target when verbs expressing emotional hand actions, neutral hand actions or foot actions were shown, and to refrain from moving when no-effector-related verbs were presented. Reaction times and percentages of errors increased when the verb involved the same effector as used to give the response. However, we also found that the size of this interference decreased when the arm/hand-related verbs had a negative emotional connotation. Crucially, we show that such modulation only occurred when the verb semantics had to be retrieved. These results suggest that the comprehension of negatively valenced verbs might require the simultaneous reenactment of the neural circuitry associated with the processing of the emotion evoked by their meaning and of the neural circuitry associated with their motor features.     

Non-concatenative realization in the verbal inflection of Modern Hebrew

This paper examines the realization of inflectional paradigms in the Semitic root-and pattern morphological system of Modern Hebrew. In the first part of the paper, a system of realizational statements is proposed, in the spirit of the framework of Distributed Morphology (Halle and Marantz 1993). Two different, independent positions V1 and V2 are identified and defined relative to a basic discontinuous set of elements, the root. Employing the notion of default status, which is accorded to the vocalization of Type I verbs in the past, this move allows for an optimally economic set of rules for the realization of all active and passive verbs. In the second part of the paper, the account is extended to roots with a final underlying glide?/j/. Within the verbal system, such roots give rise to a set of mostly vowel-final verbal stems. It?is claimed that the traditional analysis, according to which the different realizations are synchronically the phonological reflex of this final /j/, is untenable, and especially so because these verbs have almost exactly the same realization in all Types. Realization rules are then formalized with the conditioning environment being this underlying final /j/, with [j] as the default realization of this element. Thus, a third element /j/ is both a class-marker??it gives rise to a set of phonologically-arbitrary realizations??and a simple phoneme.     

Coevolution of vocal communication and sociality in primates

Understanding the rules that link communication and social behaviour is an essential prerequisite for discerning how a communication system as complex as human language might have evolved. The comparative method offers a powerful tool for investigating the nature of these rules, since it provides a means to examine relationships between changes in communication abilities and changes in key aspects of social behaviour over evolutionary time. Here we present empirical evidence from phylogenetically controlled analyses indicating that evolutionary increases in the size of the vocal repertoire among non-human primate species were associated with increases in both group size and time spent grooming (our measure of extent of social bonding).     

A note on the selection of priority rules in software packages for project management

Various software packages for project management include a procedure for resource-constrained scheduling. In several packages, the user can influence this procedure by selecting a priority rule. However, the resource-allocation methods that are implemented in the procedures are proprietary information; therefore, the question of how the priority-rule selection impacts the performance of the procedures arises. We experimentally evaluate the resource-allocation methods of eight recent software packages using the 600 instances of the PSPLIB J120 test set. The results of our analysis indicate that applying the default rule tends to outperform a randomly selected rule, whereas applying two randomly selected rules tends to outperform the default rule. Applying a small set of more than two rules further improves the project durations considerably. However, a large number of rules must be applied to obtain the best possible project durations.     

Production and perception rules underlying visual patterns: effects of symmetry and hierarchy

Formal language theory has been extended to two-dimensional patterns, but little is known about two-dimensional pattern perception. We first examined spontaneous two-dimensional visual pattern production by humans, gathered using a novel touch screen approach. Both spontaneous creative production and subsequent aesthetic ratings show that humans prefer ordered, symmetrical patterns over random patterns. We then further explored pattern-parsing abilities in different human groups, and compared them with pigeons. We generated visual plane patterns based on rules varying in complexity. All human groups tested, including children and individuals diagnosed with autism spectrum disorder (ASD), were able to detect violations of all production rules tested. Our ASD participants detected pattern violations with the same speed and accuracy as matched controls. Children's ability to detect violations of a relatively complex rotational rule correlated with age, whereas their ability to detect violations of a simple translational rule did not. By contrast, even with extensive training, pigeons were unable to detect orientation-based structural violations, suggesting that, unlike humans, they did not learn the underlying structural rules. Visual two-dimensional patterns offer a promising new formally-grounded way to investigate pattern production and perception in general, widely applicable across species and age groups.     

Experimental evidence of gradual size‐dependent shifts in body size and growth of fish in response to warming

A challenge facing ecologists trying to predict responses to climate change is the few recent analogous conditions to use for comparison. For example, negative relationships between ectotherm body size and temperature are common both across natural thermal gradients and in small‐scale experiments. However, it is unknown if short‐term body size responses are representative of long‐term responses. Moreover, to understand population responses to warming, we must recognize that individual responses to temperature may vary over ontogeny. To enable predictions of how climate warming may affect natural populations, we therefore ask how body size and growth may shift in response to increased temperature over life history, and whether short‐ and long‐term growth responses differ. We addressed these questions using a unique setup with multidecadal artificial heating of an enclosed coastal bay in the Baltic Sea and an adjacent reference area (both with unexploited populations), using before‐after control‐impact paired time‐series analyses. We assembled individual growth trajectories of ~13,000 unique individuals of Eurasian perch and found that body growth increased substantially after warming, but the extent depended on body size: Only among small‐bodied perch did growth increase with temperature. Moreover, the strength of this response gradually increased over the 24 year warming period. Our study offers a unique example of how warming can affect fish populations over multiple generations, resulting in gradual changes in body growth, varying as organisms develop. Although increased juvenile growth rates are in line with predictions of the temperature–size rule, the fact that a larger body size at age was maintained over life history contrasts to that same rule. Because the artificially heated area is a contemporary system mimicking a warmer sea, our findings can aid predictions of fish responses to further warming, taking into account that growth responses may vary both over an individual's life history and over time.     

Latent Semantics of Action Verbs Reflect Phonetic Parameters of Intensity and Emotional Content

Conjuring up our thoughts, language reflects statistical patterns of word co-occurrences which in turn come to describe how we perceive the world. Whether counting how frequently nouns and verbs combine in Google search queries, or extracting eigenvectors from term document matrices made up of Wikipedia lines and Shakespeare plots, the resulting latent semantics capture not only the associative links which form concepts, but also spatial dimensions embedded within the surface structure of language. As both the shape and movements of objects have been found to be associated with phonetic contrasts already in toddlers, this study explores whether articulatory and acoustic parameters may likewise differentiate the latent semantics of action verbs. Selecting 3 × 20 emotion-, face-, and hand-related verbs known to activate premotor areas in the brain, their mutual cosine similarities were computed using latent semantic analysis LSA, and the resulting adjacency matrices were compared based on two different large scale text corpora: HAWIK and TASA. Applying hierarchical clustering to identify common structures across the two text corpora, the verbs largely divide into combined mouth and hand movements versus emotional expressions. Transforming the verbs into their constituent phonemes, and projecting them into an articulatory space framed by tongue height and formant frequencies, the clustered small and large size movements appear differentiated by front versus back vowels corresponding to increasing levels of arousal. Whereas the clustered emotional verbs seem characterized by sequences of close versus open jaw produced phonemes, generating up- or downwards shifts in formant frequencies that may influence their perceived valence. Suggesting, that the latent semantics of action verbs reflect parameters of intensity and emotional polarity that appear correlated with the articulatory contrasts and acoustic characteristics of phonemes.     

Population Dynamics of Active and Total Ciliate Populations in Arable Soil Amended with Wheat

Soil protozoa are characterized by their ability to produce cysts, which allows them to survive unfavorable conditions (e.g., desiccation) for extended periods. Under favorable conditions, they may rapidly excyst and begin feeding, but even under optimal conditions, a large proportion of the population may be encysted. The factors governing the dynamics of active and encysted cells in the soil are not well understood. Our objective was to determine the dynamics of active and encysted populations of ciliates during the decomposition of freshly added organic material. We monitored, in soil microcosms, the active and total populations of ciliates, their potential prey (bacteria and small protozoa), their potential competitors (amoebae, flagellates, and nematodes), and their potential predators (nematodes). We sampled with short time intervals (2 to 6 days) and generated a data set, suitable for mathematical modeling. Following the addition of fresh organic material, bacterial numbers increased more than 1,400-fold. There was a temporary increase in the number of active ciliates, followed by a rapid decline, although the size of the bacterial prey populations remained high. During this initial burst of ciliate growth, the population of cystic ciliates increased 100-fold. We suggest that internal population regulation is the major factor governing ciliate encystment and that the rate of encystment depends on ciliate density. This model provides a quantitative explanation of ciliatostasis and can explain why protozoan growth in soil is less than that in aquatic systems. Internally governed encystment may be an essential adaptation to an unpredictable environment in which individual protozoa cannot predict when the soil will dry out and will survive desiccation only if they have encysted in time.