Generating Attributed Networks with Communities

In many modern applications data is represented in the form of nodes and their relationships, forming an information network. When nodes are described with a set of attributes we have an attributed network. Nodes and their relationships tend to naturally form into communities or clusters, and discovering these communities is paramount to many applications. Evaluating algorithms or comparing algorithms for automatic discovery of communities requires networks with known structures. Synthetic generators of networks have been proposed for this task but most solely focus on connectivity and their properties and overlook attribute values and the network properties vis-à-vis these attributes. In this paper, we propose a new generator for attributed networks with community structure that dependably follows the properties of real world networks.     

Relationships Between Adult Male and Maturing Mountain Gorillas (Gorilla beringei beringei) Persist Across Developmental Stages and Social Upheaval

Across the animal kingdom, long‐term social relationships outside the context of reproductive pair bonds are rare. However, they have been demonstrated in some mammals including primates, cetaceans, and social carnivores. The ontogeny of such relationships is likely to depend on the benefits individuals can gain by cultivating them. Previous studies demonstrated that young mountain gorillas (Gorilla beringei beringei) have strong relationships with adult males, but little is known about the longevity of these bonds. Here, we examine the temporal stability of proximity relationships between coresident adult male and maturing gorillas in the habituated population monitored by the Dian Fossey Gorilla Fund International's Karisoke Research Center in Volcanoes National Park, Rwanda. We used spatial proximity data to assess the strength of relationships between adult males and juveniles, and tracked these relationships as the juveniles matured into subadults (3–4 yr later; n = 229 dyads) and then young adults (7 yr later; n = 42 dyads). The proximity relationships of juveniles of both sexes predicted their proximity relationships with adult males in both subadulthood and young adulthood. However some young adult males who had lost their top adult male proximity partner from juvenilehood developed new relationships with older males that had risen in the dominance hierarchy. These data suggest that (1) kin selection may play a more important role in social relationships between potential fathers and adult female offspring than previously suspected, and (2) when maturing males' foremost adult male social partners remain available to them, their relationships can be stable past the age at which younger males become reproductive competitors.     

Neuroendocrine control in social relationships in non-human primates: Field based evidence

Primates maintain a variety of social relationships and these can have fitness consequences. Research has established that different types of social relationships are unpinned by different or interacting hormonal systems, for example, the neuropeptide oxytocin influences social bonding, the steroid hormone testosterone influences dominance relationships, and paternal care is characterized by high oxytocin and low testosterone. Although the oxytocinergic system influences social bonding, it can support different types of social bonds in different species, whether pair bonds, parent-offspring bonds or friendships. It seems that selection processes shape social and mating systems and their interactions with neuroendocrine pathways. Within species, there are individual differences in the development of the neuroendocrine system: the social environment individuals are exposed to during ontogeny alters their neuroendocrine and socio-cognitive development, and later, their social interactions as adults. Within individuals, neuroendocrine systems can also have short-term effects, impacting on social interactions, such as those during hunting, intergroup encounters or food sharing, or the likelihood of cooperating, winning or losing. To understand these highly dynamic processes, extending research beyond animals in laboratory settings to wild animals living within their natural social and ecological setting may bring insights that are otherwise unreachable. Field endocrinology with neuropeptides is still emerging. We review the current status of this research, informed by laboratory studies, and identify questions particularly suited to future field studies. We focus on primate social relationships, specifically social bonds (mother-offspring, father-offspring, cooperative breeders, pair bonds and adult platonic friendships), dominance, cooperation and in-group/out-group relationships, and examine evidence with respect to the ‘tend and defend’ hypothesis.     

寄生植物对寄主的选择和影响

寄生植物对寄主的选择性与寄主营养物质的含量、合成的次生物质和硬度有关.多寄主存在的条件下,有利于寄生植物的生长发育.通过改变寄主光合产物的流向和影响寄主叶片的气孔调节,寄生植物对寄主生理和形态产生显著的影响.寄生植物的存在使植物群落的生物量、组成多样性和动态发生改变.大量研究显示,寄生植物对寄主的选择和影响与植食性动物对取食植物的选择和影响有很多相似之处.气候变化对寄生植物与寄主关系影响的研究还刚刚起步,寄生植物对寄主选择和影响的研究对有害寄生植物的防除和有益寄生植物的利用有重要的价值,应该重视和加强.     

寄生植物对寄主的选择和影响

寄生植物对寄主的选择性与寄主营养物质的含量、合成的次生物质和硬度有关．多寄主存在的条件下,有利于寄生植物的生长发育．通过改变寄主光合产物的流向和影响寄主叶片的气孔调节,寄生植物对寄主生理和形态产生显著的影响．寄生植物的存在使植物群落的生物量、组成多样性和动态发生改变．大量研究显示．寄生植物对寄主的选择和影响与植食性动物对取食植物的选择和影响有很多相似之处．气候变化对寄生植物与寄主关系影响的研究还刚刚起步,寄生植物对寄主选择和影响的研究对有害寄生植物的防除和有益寄生植物的利用有重要的价值,应该重视和加强．     

Canine Evolution in Sabretoothed Carnivores: Natural Selection or Sexual Selection?

The remarkable elongated upper canines of extinct sabretoothed carnivorous mammals have been the subject of considerable speculation on their adaptive function, but the absence of living analogues prevents any direct inference about their evolution. We analysed scaling relationships of the upper canines of 20 sabretoothed feliform carnivores (Nimravidae, Barbourofelidae, Machairodontinae), representing both dirk-toothed and scimitar-toothed sabretooth ecomorphs, and 33 non-sabretoothed felids in relation to body size in order to characterize and identify the evolutionary processes driving their development, using the scaling relationships of carnassial teeth in both groups as a control. Carnassials display isometric allometry in both sabretooths and non-sabretooths, supporting their close relationship with meat-slicing, whereas the upper canines of both groups display positive allometry with body size. Whereas there is no statistical difference in allometry of upper canine height between dirk-toothed and scimitar-toothed sabretooth ecomorphs, the significantly stronger positive allometry of upper canine height shown by sabretooths as a whole compared to non-sabretooths reveals that different processes drove canine evolution in these groups. Although sabretoothed canines must still have been effective for prey capture and processing by hypercarnivorous predators, canine morphology in these extinct carnivores was likely to have been driven to a greater extent by sexual selection than in non-sabretooths. Scaling relationships therefore indicate the probable importance of sexual selection in the evolution of the hypertrophied sabretooth anterior dentition.     

Allocation tradeoffs and life histories: a conceptual and graphical framework

Tradeoffs – negative reciprocal causal relationships in net benefits between trait magnitudes – have not always been studied in depth appropriate to their central role in life‐history analysis. Here we focus on allocation tradeoffs, in which acquisition of a limiting resource requires allocation of resource to alternative traits. We identify the components of this allocation process and emphasize the importance of quantifying them. We then propose categorizing allocation tradeoffs into linear, concave and convex relationships based on the way that resource allocation yields trait magnitudes under the tradeoff. Linear relationships are over‐represented in the literature because of typically small data sets over restricted ranges of trait magnitudes, an emphasis on simple correlation analysis, and a failure to remove variation associated with acquisition of the limiting resource in characterizing the tradeoff. (We provide methods for controlling these acquisition effects.) Non‐linear relationships have been documented and are expected under plausible conditions that we summarize. We note ways that shifting environments and biological features yield plasticity of tradeoff graphs. Finally, we illustrate these points using case studies and close with priorities for future work.     

Patterns and processes in abundance-body size relationships for marine benthic invertebrates

1. The nature of abundance-body size relationships in animal communities, and especially the drivers behind the observed patterns, have been a focus of persistent debate in animal ecology. In a recent review, Allen et al. (2006) categorized five mechanistic explanations behind the commonly observed polymodality in these relationships: energetic constraints; phylogenetic constraints; biogeographical determinants; habitat structure; and community interactions. Progress in understanding of these patterns and the processes underlying them have been hindered by the use of a range of methods that differ in their validity and robustness. 2. Here, we used data on invertebrate body sizes from a variety of sandy beaches in the UK to test the hypothesis that these communities display modality in their abundance-body size relationships. We quantified modality in the relationships using kernel density estimation and smoothed bootstrap resampling and then evaluated the competing explanations for this modality based on the patterns identified in conjunction with measurements of the physical beach environment. 3. We found bimodal distributions in the body size spectrum for benthic invertebrates at nine of 16 sites. There was a consistent trough in the spectrum at around 0·5-1 mm diameter, which reflected the traditional split between meiofauna and macrofauna. Beaches with finer particle sizes and more heterogeneous macrofauna hosted communities with more than two modes. 4. Our results suggest that modality in sandy beach benthic communities is unlikely to be explained by any single hypothesis. There will be an interplay between physical and biological factors, with different explanations accounting for modality at different scales.     

Biochemical systems theory and metabolic control theory: 2. the role of summation and connectivity relationships

Perhaps the major obstacle to recognizing the relatedness of Biochemical Systems Theory (BST) and a subsequently developed approach some have called Metabolic Control Theory (MCT) is the summation and connectivity relationships. These are the most visible and central features of the MCT approach to the understanding of intact biochemical systems, whereas in the BST approach they appear to be invisible and peripheral. Generalized versions of these relationships are shown to be inherent to BST, and it is shown how their role differs from that within MCT. The significance of summation and connectivity relationships is shown to be historical and secondary in the sense that one can understand fully the integrated behavior of complex biochemical systems in steady state with BST and never explicitly invoke these relationships. It also is shown that the summation and connectivity relationships in MCT have inherent limitations that make them inadequate as the basis for a general theory of biochemical systems. The results in this paper, together with those in the previous paper, clearly demonstrate that MCT is a special case of BST.     

Association of enkephalin catabolism inhibitors and CCKB antagonists: A potential use in the management of pain and opioid addiction

The overlapping distribution of opioid and cholecystokinin (CCK) peptides and their receptors (μ and δ opioid receptors; CCK-A and CCK-B receptors) in the central nervous system have led to a large number of studies aimed at clarifying the functional relationships between these two neuropeptides. Most of the pharmacological studies devoted to the role of CCK and enkephalins have been focused on the control of pain. Recently the existence of regulatory mechanisms between both systems have been proposed, and the physiological antagonism between CCK and endogenous opioid systems has been definitely demonstrated by coadministration of CCK-B selective antagonists with RB 101, a systemically active inhibitor, which fully protects enkephalins from their degradation. Several studies have also been done to investigate the functional relationships between both systems in development of opioid side-effects and in behavioral responses. This article will review the experimental pharmacology of association of enkephalin-degrading enzyme inhibitors and CCK-B antagonists to demonstrate the interest of these molecules in the management of both pain and opioid addiction. Special issue dedicated to Dr. Eric J. Simon.     

Supporting upper-level undergraduate students in building a systems perspective in a botany course

Undergraduate biology majors require biological literacy about the critical and dynamic relationships between plants and ecosystems and the effect human-made processes have on these systems. To support students in understanding systems relationships, we redesigned an undergraduate botany course using an ecological framework and embedded systems modelling to support students in understanding the criticality of plant processes to the global carbon cycle. The class meetings included lectures, opportunities to develop systems models identifying the relationships between plant processes and other systems, reflections on their systems understanding and open-floor discussions about assigned primary and secondary readings that explored the relationships between plant systems, abiotic and biotic processes and global carbon cycling in their systems models. We used the systems models students developed at the beginning and end of the course to examine how their systems understanding grew. Our results suggest that at the beginning of term, students’ ideas about plants were egocentric identifying the purpose of plants was to support human life and they did not consider relationships between plants and global carbon systems. By the end of the term, their models and reflections identified elements of a systems perspective and the students considered human impact on this delicate balance.     

"In the Clique": Popular Culture, Constructions of Place, and the Everyday Lives of Urban Youth

This study focuses on two teens, Tony and Rufus, and how they used key popular texts to construct a sense of place in the small city where this research was conducted. These two teens mobilized these popular texts in very specific ways, both finding specific thematic links between and across them and also using them to index their relationships with biological and extended family in this city and "down South." This study highlights the complex, emergent, and messy relationships many young people have with popular culture.     

Protoflavones: a class of unusual flavonoids as promising novel anticancer agents

Protoflavones represent a less widespread, unique class of natural flavonoids with a non-aromatic B-ring and a hydroxyl group at C-1′. Due to their recently discovered anticancer activity, these compounds have gotten into the focus of biomedical research during the past few years. The present review aims to give a brief summary on the available literature data on this special class of flavonoids, including their occurrence in plants and their bioactivity. A special emphasis is given on the anticancer potential of these compounds. Attempts for the development of certain synthetic/semi-synthetic protoflavone analogs as anticancer drugs, and structure–activity relationships are also discussed.     

Stability and Durability of Intra- and Intersex Social Bonds of Captive Rhesus Macaques (Macaca mulatta)

Many social species maintain differentiated relationships with their group members. These social bonds may reflect short-term interactions satisfying immediate needs. Alternatively, individuals of some species may entertain stable and valuable bonds that last much longer than opportunistic interactions would predict. This claim is supported by recent research that revealed clear fitness benefits for long-lasting social bonds. Here, we investigated the stability and equitability of social relationships in captive rhesus macaques, measured using their proximity and grooming patterns over a 3-yr period. We show that, in general, proximity patterns of the whole group were stable over 3 yr. More specifically, each individual’s top two nonkin within and between sex relationships based on proximity were relatively stable and some of these relationships lasted the full 3 yr. Female grooming relationships within and between sex were also stable over 3 yr. Moreover, strong social bonds in females were not based on age similarity and were not sex specific, suggesting that a general underlying mechanism of social bonding in female rhesus macaques. In contrast, patterns of male grooming of other males and of females were relatively unstable and male social bonds were less equitable than those of females. The differences in stability of the relationships between the sexes may reflect the dispersal pattern of rhesus macaques, although we have limited data on non-natal males in our study. With these data we add to a growing body of literature describing the value and durability of relationships among primates and other species.     

Bacillus thuringiensis and Its Pesticidal Crystal Proteins

During the past decade the pesticidal bacterium Bacillus thuringiensis has been the subject of intensive research. These efforts have yielded considerable data about the complex relationships between the structure, mechanism of action, and genetics of the organism’s pesticidal crystal proteins, and a coherent picture of these relationships is beginning to emerge. Other studies have focused on the ecological role of the B. thuringiensis crystal proteins, their performance in agricultural and other natural settings, and the evolution of resistance mechanisms in target pests. Armed with this knowledge base and with the tools of modern biotechnology, researchers are now reporting promising results in engineering more-useful toxins and formulations, in creating transgenic plants that express pesticidal activity, and in constructing integrated management strategies to insure that these products are utilized with maximum efficiency and benefit.     

Macroevolutionary analyses of ciliates associated with hosts support high diversification rates

Ciliophora is a phylum that is comprised of extremely diverse microorganisms with regard to their morphology and ecology. They may be found in various environments, as free-living organisms or associated with metazoans. Such associations range from relationships with low metabolic dependence such as epibiosis, to more intimate relationships such as mutualism and parasitism. We know that symbiotic relationships occur along the whole phylogeny of the group, however, little is known about their evolution. Theoretical studies show that there are two routes for the development of parasitism, yet few authors have investigated the evolution of these characteristics using molecular tools. In the present study, we inferred a wide dated molecular phylogeny, based on the 18S rDNA gene, for the entire Ciliophora phylum, mapped life habits throughout the evolutionary time, and evaluated whether symbiotic relationships were linked to the variation in diversification rates and to the mode of evolution of ciliates. Our results showed that the last common ancestor for Ciliophora was likely a free-living organism, and that parasitism is a recent adaptation in ciliates, emerging more than once and independently via two distinct routes: (i) a free-living ciliate evolved into a mutualistic organism and, later, into a parasitic organism, and (ii) a free-living ciliate evolved directly into a parasitic organism. Furthermore, we have found a significant increase in the diversification rate of parasitic and mutualistic ciliates compared with their free-living conspecifics. The evolutionary success in different lineages of symbiont ciliates may be associated with many factors including type and colonization placement on their host, as well as physical and physiological conditions made available by the hosts.     

Utilizing logical relationships in genomic data to decipher cellular processes

The wealth of available genomic data has spawned a corresponding interest in computational methods that can impart biological meaning and context to these experiments. Traditional computational methods have drawn relationships between pairs of proteins or genes based on notions of equality or similarity between their patterns of occurrence or behavior. For example, two genes displaying similar variation in expression, over a number of experiments, may be predicted to be functionally related. We have introduced a natural extension of these approaches, instead identifying logical relationships involving triplets of proteins. Triplets provide for various discrete kinds of logic relationships, leading to detailed inferences about biological associations. For instance, a protein C might be encoded within an organism if, and only if, two other proteins A and B are also both encoded within the organism, thus suggesting that gene C is functionally related to genes A and B. The method has been applied fruitfully to both phylogenetic and microarray expression data, and has been used to associate logical combinations of protein activity with disease state phenotypes, revealing previously unknown ternary relationships among proteins, and illustrating the inherent complexities that arise in biological data.     

Optimal foraging and community structure: The allometry of herbivore food selection and competition

I address the selection of plants with different characteristics by herbivores of different body sizes by incorporating allometric relationships for herbivore foraging into optimal foraging models developed for herbivores. Herbivores may use two criteria in maximizing their nutritional intake when confronted with a range of food resources: a minimum digestibility and a minimum cropping rate. Minimum digestibility should depend on plant chemical characteristics and minimum cropping rate should depend on the density of plant items and their size (mass). If herbivores do select for these plant characteristics, then herbivores of different body sizes should select different ranges of these characteristics due to allometric relationships in digestive physiology, cropping ability and nutritional demands. This selectivity follows a regular pattern such that a herbivore of each body size can exclusively utilize some plants, while it must share other plants with herbivores of other body sizes. I empirically test this hypothesis of herbivore diet selectivity and the pattern of resource use that it produces in the field and experimentally. The findings have important implications for competition among herbivores and their population and community ecology. Furthermore, the results may have general applicability to other types of foragers, with general implications for how biodiversity is influenced.