Revisiting wavefront construction with collective agents: an approach to foraging

We consider the problem of coordinating a team of agents that have to collect disseminated resources in an unknown environment. We are interested in approaches in which agents collectively explore the environment and build paths between home and resources. The originality of our approach is to simultaneously build an artificial potential field (APF) around the agents’ home while foraging. We propose a multi-agent model defining a distributed and asynchronous version of Barraquand et al. Wavefront algorithm. Agents need only to mark and read integers locally on a grid, that is, their environment. We prove that the construction converges to the optimal APF. This allows the definition of a complete parameter-free foraging algorithm, called c-marking agents. The algorithm is evaluated by simulation, while varying the foraging settings. Then we compare our approach to a pheromone-based algorithm. Finally, we discuss requirements for implementation in robotics.     

Isolation and identification of Photobacterium phosphoreum from an unexpected niche: migrating salmon

Six luminous bacteria were isolated from migrating salmon in the Yukon River, Alaska. All isolates were identified as Photobacterium phosphoreum. Previous studies suggest that P. phosphoreum is an exclusively marine bacterium, while our Alaskan isolates are from salmon which migrated up to 1,228 km from the marine environment.     

The conditional relationship between English language proficiency and earnings among US immigrants

Using the 2000 US census data for immigrants of twenty language groups resided in metropolitan areas, we test the hypothesis that the rate of returns (in earnings) to English proficiency is not constant but varies with the language environment (as defined by group size, segregation, linguistic heterogeneity and inequality) in which immigrants are embedded. Results from our hierarchical model indicate that while an increase in the size and segregation of the language group diminishes returns to English proficiency, a rise in linguistic heterogeneity and inequality in the metropolitan area has the opposite effects. This study expands the scope of the previous studies by identifying conditions under which returns to English proficiency among immigrants are modified by a set of contextual factors often overlooked.     

Adaptive evolution in ecological communities

Understanding how natural selection drives evolution is a key challenge in evolutionary biology. Most studies of adaptation focus on how a single environmental factor, such as increased temperature, affects evolution within a single species. The biological relevance of these experiments is limited because nature is infinitely more complex. Most species are embedded within communities containing many species that interact with one another and the physical environment. To understand the evolutionary significance of such ecological complexity, experiments must test the evolutionary impact of interactions among multiple species during adaptation. Here we highlight an experiment that manipulates species composition and tracks evolutionary responses within each species, while testing for the mechanisms by which species interact and adapt to their environment. We also discuss limitations of previous studies of adaptive evolution and emphasize how an experimental evolution approach can circumvent such shortcomings. Understanding how community composition acts as a selective force will improve our ability to predict how species adapt to natural and human-induced environmental change.     

Isolation and Identification of Photobacterium phosphoreum from an Unexpected Niche: Migrating Salmon

Six luminous bacteria were isolated from migrating salmon in the Yukon River, Alaska. All isolates were identified as Photobacterium phosphoreum. Previous studies suggest that P. phosphoreum is an exclusively marine bacterium, while our Alaskan isolates are from salmon which migrated up to 1,228 km from the marine environment.     

Foraging environment determines the genetic architecture and evolutionary potential of trophic morphology in cichlid fishes

Phenotypic plasticity allows organisms to change their phenotype in response to shifts in the environment. While a central topic in current discussions of evolutionary potential, a comprehensive understanding of the genetic underpinnings of plasticity is lacking in systems undergoing adaptive diversification. Here, we investigate the genetic basis of phenotypic plasticity in a textbook adaptive radiation, Lake Malawi cichlid fishes. Specifically, we crossed two divergent species to generate an F₃ hybrid mapping population. At early juvenile stages, hybrid families were split and reared in alternate foraging environments that mimicked benthic/scraping or limnetic/sucking modes of feeding. These alternate treatments produced a variation in morphology that was broadly similar to the major axis of divergence among Malawi cichlids, providing support for the flexible stem theory of adaptive radiation. Next, we found that the genetic architecture of several morphological traits was highly sensitive to the environment. In particular, of 22 significant quantitative trait loci (QTL), only one was shared between the environments. In addition, we identified QTL acting across environments with alternate alleles being differentially sensitive to the environment. Thus, our data suggest that while plasticity is largely determined by loci specific to a given environment, it may also be influenced by loci operating across environments. Finally, our mapping data provide evidence for the evolution of plasticity via genetic assimilation at an important regulatory locus, ptch1. In all, our data address long‐standing discussions about the genetic basis and evolution of plasticity. They also underscore the importance of the environment in affecting developmental outcomes, genetic architectures, morphological diversity and evolutionary potential.     

Combining parametric and nonparametric models to estimate treatment effects in observational studies

Performing causal inference in observational studies requires we assume confounding variables are correctly adjusted for. In settings with few discrete-valued confounders, standard models can be employed. However, as the number of confounders increases these models become less feasible as there are fewer observations available for each unique combination of confounding variables. In this paper, we propose a new model for estimating treatment effects in observational studies that incorporates both parametric and nonparametric outcome models. By conceptually splitting the data, we can combine these models while maintaining a conjugate framework, allowing us to avoid the use of Markov chain Monte Carlo (MCMC) methods. Approximations using the central limit theorem and random sampling allow our method to be scaled to high-dimensional confounders. Through simulation studies we show our method can be competitive with benchmark models while maintaining efficient computation, and illustrate the method on a large epidemiological health survey.     

Hearing sensitivity and amplitude coding in bats are differentially shaped by echolocation calls and social calls

Differences in auditory perception between species are influenced by phylogenetic origin and the perceptual challenges imposed by the natural environment, such as detecting prey- or predator-generated sounds and communication signals. Bats are well suited for comparative studies on auditory perception since they predominantly rely on echolocation to perceive the world, while their social calls and most environmental sounds have low frequencies. We tested if hearing sensitivity and stimulus level coding in bats differ between high and low-frequency ranges by measuring auditory brainstem responses (ABRs) of 86 bats belonging to 11 species. In most species, auditory sensitivity was equally good at both high- and low-frequency ranges, while amplitude was more finely coded for higher frequency ranges. Additionally, we conducted a phylogenetic comparative analysis by combining our ABR data with published data on 27 species. Species-specific peaks in hearing sensitivity correlated with peak frequencies of echolocation calls and pup isolation calls, suggesting that changes in hearing sensitivity evolved in response to frequency changes of echolocation and social calls. Overall, our study provides the most comprehensive comparative assessment of bat hearing capacities to date and highlights the evolutionary pressures acting on their sensory perception.     

Socially Driven Consistent Behavioural Differences during Development in Common Ravens and Carrion Crows

Consistent individual differences in behaviour, or ‘personality’, are likely to be influenced by development, social context, and species ecology, though few comparative, longitudinal studies exist. Here, we investigated the role of development and social context on personality variation in two identically reared, social corvids: common ravens and carrion crows. We repeatedly presented subjects with a variety of novel food and objects, while alone and in a primarily sibling subgroup, from fledging to sub-adulthood. We predicted that consistent individual differences would emerge later in development, and that conspecific presence would facilitate behavioural similarities. In contrast to our predictions, we found that individuals of both species were highly inconsistent in their behavioural responses throughout the development period. In line with our predictions, though in the ravens only, conspecific presence promoted behavioural similarities as individuals were strongly shaped by their subgroup, and it is likely that these effects were driven by social context rather than relatedness. We discuss these findings in relation to developmental steps and the role of social relations in these species. Overall, our findings highlight that these two species are highly adaptable in their behaviour, and the ravens in particular are strongly influenced by their social environment, which may facilitate cooperation and social learning.     

Competitive success of southern populations of Betula pendula and Sorbus aucuparia under simulated southern climate experiment in the subarctic

Global warming has been commonly accepted to facilitate species’ range shifts across latitudes. Cross‐latitudinal transplantations support this; many tree species can well adapt to new geographical areas. However, these studies fail to capture species’ adaptations to new light environment because the experiments were not designed to explicitly separate species’ responses to light and temperature. Here we tested reaction norms of tree seedlings in reciprocal transplantations 1,000 km apart from each other at two latitudes (60°N and 69°N). In contrast to past studies, we exposed our experimental plants to same temperature in both sites (temperature of 60°N growing site is recorded to adjust temperature of 69°N site in real time via Internet connection) while light environment (photoperiod, light quality) remained ambient. Shoot elongation and autumn coloration were studied in seedlings of two deciduous trees (Betula pendula and Sorbus aucuparia), which were expected to respond differently to day length. Sorbus as a member of Rosaceae family was assumed to be indifferent to photoperiod, while Betula responds strongly to day length. We hypothesized that (1) southern and northern populations of both species perform differently; (2) southern populations perform better in both sites; (3) autumn phenology of southern populations may delay in the northern site; (4) and Sorbus aucuparia is less dependent on light environment. According to the hypotheses, shoot elongation of northern population was inherently low in both species. An evolutionary consequence of this may be a competitive success of southern populations under warming climate. Southern population of B. pendula was delayed in autumn coloration, but not in growth cessation. Sorbus aucuparia was less responsive to light environment. The results suggest that light provides selection pressure in range shifts, but the response is species dependent.     

Effects of spaceflight, simulated spaceflight and countermeasures on single muscle fiber physiology

Since the first human flew in space in 1961, there has been extensive scientific interest in the responses of the human body and how it adapts to this unique environment. From the available data, it appears that all major systems in the human body undergo an adaptive change while in a microgravity environment. In particular the human muscle system appears to undergo loss of muscle mass and strength which greatly influences the maximal work capacity of the muscle. Recently, our research group has been involved in a series of whole muscle and cellular studies during periods of short duration space flight, bed rest, and unilateral lower limb suspension (ULLS) in an attempt to elucidate the changes that are occurring in the whole muscle and single muscle fiber contractile properties with unloading. In addition, various countermeasure activities for skeletal muscle have been part of the space flights and ground-based studies. The intention of this paper will be to briefly review our findings in whole muscle, cellular, and countermeasure effectiveness with human muscle.     

Domestic dogs and puppies can use human voice direction referentially

Domestic dogs are particularly skilled at using human visual signals to locate hidden food. This is, to our knowledge, the first series of studies that investigates the ability of dogs to use only auditory communicative acts to locate hidden food. In a first study, from behind a barrier, a human expressed excitement towards a baited box on either the right or left side, while sitting closer to the unbaited box. Dogs were successful in following the human''s voice direction and locating the food. In the two following control studies, we excluded the possibility that dogs could locate the box containing food just by relying on smell, and we showed that they would interpret a human''s voice direction in a referential manner only when they could locate a possible referent (i.e. one of the boxes) in the environment. Finally, in a fourth study, we tested 8–14-week-old puppies in the main experimental test and found that those with a reasonable amount of human experience performed overall even better than the adult dogs. These results suggest that domestic dogs’ skills in comprehending human communication are not based on visual cues alone, but are instead multi-modal and highly flexible. Moreover, the similarity between young and adult dogs’ performances has important implications for the domestication hypothesis.     

深海热液口Epsilon-变形菌的物种多样性与环境适应机理

Epsilon-变形菌是近年来宏基因组调查发现的深海极端环境如热液喷口富集的重要微生物类群,在海洋碳、氮、氢、硫循环中发挥重要作用。目前对这个纲的研究较少,主要来自于16S rRNA的分类鉴定以及深度测序拼接的基因组序列分析。本文总结了目前对Epsilon-变形菌纲的生态分布及多样性调查研究结果,并对深海热液喷口的Epsilon-变形菌的多种能量代谢方式、强大的趋化运动系统以及与底栖生物的共生关系进行了阐述。这些结果初步揭示了Epsilon-变形菌对深海极端环境的适应机制,并推动对这个极端环境富集的细菌分支的生物学特征认知与资源利用。     

Institutions and Cultural Diversity: Effects of Democratic and Propaganda Processes on Local Convergence and Global Diversity

In a connected world where people influence each other, what can cause a globalized monoculture, and which measures help to preserve the coexistence of cultures? Previous research has shown that factors such as homophily, population size, geography, mass media, and type of social influence play important roles. In the present paper, we investigate for the first time the impact that institutions have on cultural diversity. In our first three studies, we extend existing agent-based models and explore the effects of institutional influence and agent loyalty. We find that higher institutional influence increases cultural diversity, while individuals'' loyalty to their institutions has a small, preserving effect. In three further studies, we test how bottom-up and top-down processes of institutional influence impact our model. We find that bottom-up democratic practices, such as referenda, tend to produce convergence towards homogeneity, while top-down information dissemination practices, such as propaganda, further increase diversity. In our last model—an integration of bottom-up and top-down processes into a feedback loop of information—we find that when democratic processes are rare, the effects of propaganda are amplified, i.e., more diversity emerges; however, when democratic processes are common, they are able to neutralize or reverse this propaganda effect. Importantly, our models allow for control over the full spectrum of diversity, so that a manipulation of our parameters can result in preferred levels of diversity, which will be useful for the study of other factors in the future. We discuss possible mechanisms behind our results, applications, and implications for political and social sciences.     

Use of Collagen Gel as a Three-Dimensional In Vitro Model to Study Electropermeabilization and Gene Electrotransfer

Gene electrotransfer is a promising nonviral method that enables transfer of plasmid DNA into cells with electric pulses. Although many in vitro and in vivo studies have been performed, the question of the implied gene electrotransfer mechanisms is largely open. The main obstacle toward efficient gene electrotransfer in vivo is relatively poor mobility of DNA in tissues. Since cells are mechanically coupled to their extracellular environment and act differently compared to standard in vitro conditions, we developed a three-dimensional (3-D) in vitro model of CHO cells embedded in collagen gel as an ex vivo model of tissue to study electropermeabilization and different parameters of gene electrotransfer. For this purpose, we first used propidium iodide to detect electropermeabilization of CHO cells embedded in collagen gel. Then, we analyzed the influence of different concentrations of plasmid DNA and pulse duration on gene electrotransfer efficiency. Our results revealed that even if cells in collagen gel can be efficiently electropermeabilized, gene expression is significantly lower. Gene electrotransfer efficiency in our 3-D in vitro model had similar dependence on concentration of plasmid DNA and pulse duration comparable to in vivo studies, where longer (millisecond) pulses were shown to be more optimal compared to shorter (microsecond) pulses. The presented results demonstrate that our 3-D in vitro model resembles the in vivo situation more closely than conventional 2-D cell cultures and, thus, provides an environment closer to in vivo conditions to study mechanisms of gene electrotransfer.     

认知地图的神经环路基础

空间记忆是人类认识世界和改造世界的基本认知能力,与我们的生活息息相关.无论是寻找常用的生活物件,如钥匙和手机,还是外出上班、购物和约会,都依赖我们对周围环境的记忆.截止到目前已有大量研究从不同水平探讨大脑如何表征其周围环境,但仍然有很多未解的问题.本文系统综述了基于脑成像和神经电生理技术开展的空间记忆研究进展.通过梳理以往研究中有关生物体在构建认知地图的神经结构和神经活动规律,提出了海马结构和新皮层对空间记忆的编码环路和表征机制,并在此基础上对未来研究进行了展望.     

Testing and estimating gene-environment interactions in family-based association studies

Summary .   We propose robust and efficient tests and estimators for gene–environment/gene–drug interactions in family-based association studies in which haplotypes, dichotomous/quantitative phenotypes, and complex exposure/treatment variables are analyzed. Using causal inference methodology, we show that the tests and estimators are robust against unmeasured confounding due to population admixture and stratification, provided that Mendel's law of segregation holds and that the considered exposure/treatment variable is not affected by the candidate gene under study. We illustrate the practical relevance of our approach by an application to a chronic obstructive pulmonary disease study. The data analysis suggests a gene–environment interaction between a single nucleotide polymorphism in the Serpine2 gene and smoking status/pack-years of smoking. Simulation studies show that the proposed methodology is sufficiently powered for realistic sample sizes and that it provides valid tests and effect size estimators in the presence of admixture and stratification.     

The overall process of metastasis: From initiation to a new tumor

Metastasis—a process that involves the migration of cells from the primary site to distant organs—is the leading cause of cancer-associated death. Improved technology and in-depth research on tumors have furthered our understanding of the various mechanisms involved in tumor metastasis. Metastasis is initiated by cancer cells of a specific phenotype, which migrate with the assistance of extracellular components and metastatic traits conferred via epigenetic regulation while modifying their behavior in response to the complex and dynamic human internal environment. In this review, we have summarized the general steps involved in tumor metastasis and their characteristics, incorporating recent studies and topical issues, including epithelial-mesenchymal transition, cancer stem cells, neutrophil extracellular traps, pre-metastatic niche, extracellular vesicles, and dormancy. Several feasible treatment directions have also been summarized. In addition, the correlation between cancer metastasis and lifestyle factors, such as obesity and circadian rhythm, has been illustrated.     

Consistent contrast between eyelid and iris brightness supports a role for vigilance signalling in ducks

Signalling self‐ability to maintain vigilance may help in securing a mate, while providing accurate information about vigilance status may result in conspecifics adjusting their own scanning rate of the environment, potentially to the individual's benefit. In birds, vigilance is often associated with head‐up postures adopted within a bout of head‐down activity, and this can be used by conspecifics to assess the vigilance of their flock mates. However, vigilance behaviour is not always obvious and other cues may then be used to assess vigilance rates of conspecifics. Here we assess whether iris/eyelid/face patterns from 43 duck species are consistent with the hypothesis that eyelid brightness has evolved so as to contrast with iris brightness, which may then help in signalling individual vigilance status. Ducks generally flock when resting during the day, and because of their wide visual fields, individuals can monitor their environment while remaining in a resting head‐down position. Ducks also show a wide variety of plumage and iris patterns, with both light‐headed and dark‐headed species. Matching our prediction, most ducks with dark irises had pale eyelids, irrespective of head colour. Furthermore, the smaller number of species with a pale iris generally have darker eyelids. A phylogenetic analysis shows a clear and significant association in the evolution of eyelid and iris brightness patterns in both males and females. These data therefore provide support for the hypothesis that eyelid brightness has evolved to act as a contrast with iris brightness. Further studies are now needed to examine the extent to which and the way this is used in vigilance information transfer between individuals.