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Inflammation is an important driver of atherosclerosis, and the favourable outcomes of the Canakinumab Anti-inflammatory Thrombosis Outcome Study (CANTOS) trial revealed the large potential of anti-inflammatory drugs for the treatment of cardiovascular disease, especially in patients with a pro-inflammatory constitution. However, the complex immune reactions driving inflammation in the vascular wall in response to an atherosclerotic microenvironment are still being unravelled. Novel insights into the cellular processes driving immunity and inflammation revealed that alterations in intracellular metabolic pathways are strong drivers of survival, growth, and function of immune cells. Therefore, this position paper presents a brief overview of the recent developments in the immunometabolism field, focusing on its role in atherosclerosis. We will also highlight the potential impact of immunometabolic markers and targets in clinical cardiovascular medicine. [ABSTRACT FROM AUTHOR]

Rosa, R., and Seibel, B. A. 2010. Voyage of the argonauts in the pelagic realm: physiological and behavioural ecology of the rare paper nautilus, Argonauta nouryi. – ICES Journal of Marine Science, 67: 1494–1500.The metabolic demands of a rare paper nautilus, Argonauta nouryi, in the eastern tropical Pacific (ETP) are evaluated. After adjusting for temperature and size, the rates of oxygen consumption and of aerobic and anaerobic metabolic potential (as evidenced by citrate synthase and octopine dehydrogenase activities, respectively) of A. nouryi were much higher than those in holopelagic octopods that exhibit float-and-wait predation strategies. In fact, the rates were similar to those found in small epipelagic squids and benthic octopods. The critical oxygen partial pressure was 4.9 kPa at 20°C, suggesting that the strong oxygen minimum layer found at intermediate depths in the ETP may constrain the vertical distribution of A. nouryi to the upper few metres of the water column. We also report the occurrence of a chain of shelled females at the surface, in which each animal was attached, as if on the benthos, to the next individual in the chain. Although it may constitute an effective strategy to increase the rates of mate encounter in the vast open ocean, there may be an important ecological trade-off for such behaviour, namely the increase in visibility at the surface with concomitant attraction of predators. [ABSTRACT FROM PUBLISHER]

How did plant sexuality come to so hauntingly resemble human sexual formations? How did plant biology come to theorize plant sexuality with binary formulations of male/female, sex/gender, sperm/egg, active males and passive females—all of which resemble western categories of sex, gender, and sexuality? Tracing the extant language of sex and sexuality in plant reproductive biology, we examine the histories of science to explore how plant reproductive biology emerged historically from formations of colonial racial and sexual politics and how evolutionary biology was premised on the imaginations of racialized heterosexual romance. Drawing on key examples, the paper aims to (un)read plant sexuality and sexual anatomy and bodies to imagine new possibilities for plant sex, sexualities, and their relationalities. In short, plant sex and sexuality are not two different objects of inquiry but are intimately related—it is their inter-relation that is the focus of this essay. One of the key impulses from the humanities that we bring to this essay is a careful consideration of how terms and terminologies are related to each other historically and culturally. In anthropomorphizing plants, if plant sexuality were modeled on human sexual formations, might a re-imagination of plant sexuality open new vistas for the biological sciences? While our definitions of plant sexuality will always be informed by contemporary society and culture, interrogating the histories of our theories and terminologies can help us reimagine a biology that allows for new and more accurate understandings of plants, plant biology, and the evolution of reproduction. [ABSTRACT FROM AUTHOR]

"Scientific Papers Made Easy" by Stuart West and Lindsay Turnbull is a comprehensive guide to writing academic papers in biology. The book covers all aspects of constructing a paper, including abstracts, introductions, methods, results, and discussions. The authors emphasize the importance of clear and concise writing, and provide practical tips and examples to help researchers improve their writing skills. While the book is primarily aimed at biologists, scientists from other disciplines can also benefit from reading it. However, the book does not cover collaborative writing or other forms of scientific writing, such as blogging or op-eds. Overall, "Scientific Papers Made Easy" is a valuable resource for researchers looking to improve their scientific writing abilities. [Extracted from the article]

Comparative biologists have typically used one or more of the following methods to assist in evaluating the proposed functional and performance significance of individual traits: comparative phylogenetic analysis, direct interspecific comparison among species, genetic modification, experimental alteration of morphology (for example by surgically modifying traits), and ecological manipulation where individual organisms are transplanted to a different environment. But comparing organisms as the endpoints of an evolutionary process involves the ceteris paribus assumption: that all traits other than the one(s) of interest are held constant. In a properly controlled experimental study, only the variable of interest changes among the groups being compared. The theme of this paper is that the use of robotic or mechanical models offers an additional tool in comparative biology that helps to minimize the effect of uncontrolled variables by allowing direct manipulation of the trait of interest against a constant background. The structure and movement pattern of mechanical devices can be altered in ways not possible in studies of living animals, facilitating testing hypotheses of the functional and performance significance of individual traits. Robotic models of organismal design are particularly useful in three arenas: (1) controlling variation to allow modification only of the trait of interest, (2) the direct measurement of energetic costs of individual traits, and (3) quantification of the performance landscape. Obtaining data in these three areas is extremely difficult through the study of living organisms alone, and the use of robotic models can reveal unexpected effects. Controlling for all variables except for the length of a swimming flexible object reveals substantial non-linear effects that vary with stiffness. Quantification of the swimming performance surface reveals that there are two peaks with comparable efficiency, greatly complicating the inference of performance from morphology alone. Organisms and their ecological interactions are complex, and dissecting this complexity to understand the effects of individual traits is a grand challenge in ecology and evolutionary biology. Robotics has great promise as a "comparative method," allowing better-controlled comparative studies to analyze the many interacting elements that make up complex behaviors, ecological interactions, and evolutionary histories. [ABSTRACT FROM AUTHOR]

Like many scientific disciplines, the field of reproductive biology is subject to biases in terminology and research foci. For example, females are often described as coy and passive players in reproductive behaviors and are termed "promiscuous" if they engage in extra-pair copulations. Males on the other hand are viewed as actively holding territories and fighting with other males. Males are termed "multiply mating" if they mate with multiple females. Similarly, textbooks often illustrate meiosis as it occurs in males but not females. This edition of Integrative and Comparative Biology (ICB) includes a series of papers that focus on reproduction from the female perspective. These papers represent a subset of the work presented in our symposium and complementary sessions on female reproductive biology. In this round table discussion, we use a question and answer format to leverage the diverse perspectives and voices involved with the symposium in an exploration of theoretical, cultural, pedagogical, and scientific issues related to the study of female biology. We hope this dialog will provide a stepping-stone toward moving reproductive science and teaching to a more inclusive and objective framework. [ABSTRACT FROM AUTHOR]

Despite efforts to integrate research across different subdisciplines of biology, the scale of integration remains limited. We hypothesize that future generations of Artificial Intelligence (AI) technologies specifically adapted for biological sciences will help enable the reintegration of biology. AI technologies will allow us not only to collect, connect, and analyze data at unprecedented scales, but also to build comprehensive predictive models that span various subdisciplines. They will make possible both targeted (testing specific hypotheses) and untargeted discoveries. AI for biology will be the cross-cutting technology that will enhance our ability to do biological research at every scale. We expect AI to revolutionize biology in the 21st century much like statistics transformed biology in the 20th century. The difficulties, however, are many, including data curation and assembly, development of new science in the form of theories that connect the subdisciplines, and new predictive and interpretable AI models that are more suited to biology than existing machine learning and AI techniques. Development efforts will require strong collaborations between biological and computational scientists. This white paper provides a vision for AI for Biology and highlights some challenges. [ABSTRACT FROM AUTHOR]

The organization of the living world covers a vast range of spatiotemporal scales, from molecules to the biosphere, seconds to centuries. Biologists working within specialized subdisciplines tend to focus on different ranges of scales. Therefore, developing frameworks that enable testing questions and predictions of scaling requires sufficient understanding of complex processes across biological subdisciplines and spatiotemporal scales. Frameworks that enable scaling across subdisciplines would ideally allow us to test hypotheses about the degree to which explicit integration across spatiotemporal scales is needed for predicting the outcome of biological processes. For instance, how does genomic variation within populations allow us to explain community structure? How do the dynamics of cellular metabolism translate to our understanding of whole-ecosystem metabolism? Do patterns and processes operate seamlessly across biological scales, or are there fundamental laws of biological scaling that limit our ability to make predictions from one scale to another? Similarly, can sub-organismal structures and processes be sufficiently understood in isolation of potential feedbacks from the population, community, or ecosystem levels? And can we infer the sub-organismal processes from data on the population, community, or ecosystem scale? Concerted efforts to develop more cross-disciplinary frameworks will open doors to a more fully integrated field of biology. In this paper, we discuss how we might integrate across scales, specifically by (1) identifying scales and boundaries, (2) determining analogous units and processes across scales, (3) developing frameworks to unite multiple scales, and (4) extending frameworks to new empirical systems. [ABSTRACT FROM AUTHOR]

Two hallmarks of biological processes are complexity and time. While complexity can have many meanings, in this paper we propose an explicit link to the flow of time and how it is experienced by the organism. While the flow of time is rooted in constraints of fundamental physics, understanding the operation of biological systems in terms of processual flow and tempo is more elusive. Fortunately, the convergence of new computational and methodological perspectives will provide a means to transform complicated, nonlinear paths between related phenomena at different time scales into dynamic four-dimensional perspectives. According to the complex temporal biology approach, information flow between time scales of multiple lengths is a transformational process that acts to regulate life's complexity. Interactions between temporal intervals of differing magnitude and otherwise loosely-related mechanisms can be understood as inter-timescale information flow. We further propose that informational flow between time scales is the glue that binds the multiple vertical layers of biocomplexity, as well as yielding surprising outcomes ranging from complex behaviors to the persistence of lineages. Building a foundation of rules based on common interactions between orders of time and common experiential contexts would help to reintegrate biology. Emerging methodologies such as state-of-the-art imaging, visualization techniques, and computational data analysis can help us uncover these interactions. In conclusion, we propose educational and community-level changes that would better enable our vision. [ABSTRACT FROM AUTHOR]

Both mathematical models and biological model systems stand as tractable representations of complex biological systems or behaviors. They facilitate research and provide insights, and they can describe general rules. Models that represent biological processes or formalize general hypotheses are essential to any broad understanding. Mathematical or biological models necessarily omit details of the natural systems and thus may ultimately be "incorrect" representations. A key challenge is that tractability requires relatively simple models but simplification can result in models that are incorrect in their qualitative, broad implications if the abstracted details matter. Our paper discusses this tension, and how we can improve our inferences from models. We advocate for further efforts dedicated to model development, improvement, and acceptance by the scientific community, all of which may necessitate a more explicit discussion of the purpose and power of models. We argue that models should play a central role in reintegrating biology as a way to test our integrated understanding of how molecules, cells, organs, organisms, populations, and ecosystems function. [ABSTRACT FROM AUTHOR]

The goal of this vision paper is to investigate the possible role that advanced machine learning techniques, especially deep learning (DL), could play in the reintegration of various biological disciplines. To achieve this goal, a series of operational, but admittedly very simplistic, conceptualizations have been introduced: Life has been taken as a multidimensional phenomenon that inhabits three physical dimensions (time, space, and scale) and biological research as establishing connection between different points in the domain of life. Each of these points hence denotes a position in time, space, and scale at which a life phenomenon of interest takes place. Using these conceptualizations, fragmentation of biology can be seen as the result of too few and especially too short-ranged connections. Reintegrating biology could then be accomplished by establishing more, longer ranged connections. DL methods appear to be very well suited for addressing this particular need at this particular time. Notwithstanding the numerous unsubstantiated claims regarding the capabilities of AI, DL networks represent a major advance in the ability to find complex relationships inside large data sets that would have not been accessible with traditional data analytic methods or to a human observer. In addition, ongoing advances in the automation of taking measurements from phenomena on all levels of biological organization continue to increase the number of large quantitative data sets that are available. These increasingly common data sets could serve as anchor points for making long-range connections by virtue of DL. However, connections within the domain of life are likely to be structured in a highly nonuniform fashion and hence it is necessary to develop methods, for example, theoretical, computational, and experimental, to determine linkage of biological data sets most likely to provide useful insights on a biological problem using DL. Finally, specific DL approaches and architectures should be developed to match the needs of reintegrating biology. [ABSTRACT FROM AUTHOR]

Amyris is a fermentation product company that leverages synthetic biology and has been bringing novel fermentation products to the market since 2009. Driven by breakthroughs in genome editing, strain construction and testing, analytics, automation, data science, and process development, Amyris has commercialized nine separate fermentation products over the last decade. This has been accomplished by partnering with the teams at 17 different manufacturing sites around the world. This paper begins with the technology that drives Amyris, describes some key lessons learned from early scale-up experiences, and summarizes the technology transfer procedures and systems that have been built to enable moving more products to market faster. Finally, the breadth of the Amyris product portfolio continues to expand; thus the steps being taken to overcome current challenges (e.g. automated strain engineering can now outpace the rest of the product commercialization timeline) are described. [ABSTRACT FROM AUTHOR]

Background: Recently, using a counterfactual framework, a causal mediation analysis has been formalized to decompose the total effect of a time-fixed exposure on an outcome into four components that can be loosely defined as being components due to mediation only, interaction only, mediated interaction and neither. The interpretation of the estimated effect sizes is challenging when these components of the total effect are of the opposite sign compared with each other. Particularly, a negative mediated interaction might be intuitively difficult to conceptualize and, so far, lacks an easy-to-understand biological or mechanical interpretation.Methods: In this paper, we focus on negative mediated interaction, and propose an interpretation using biological examples. For negative mediated interaction to be present, the effect of interaction on the outcome and the effect of the exposure on the mediator should be in opposite directions.Results: In this article, we give examples of biological and biochemical processes that may exhibit negative mediated interaction, such as drug treatment in clinical practice, allosteric effects of enzymes, different adaptations in the cardiovascular system and its effect on brain health, and antibiotic drug-drug interactions.Conclusions: We aim to make researchers realize that negative-effect estimates might reflect relevant biological processes in the mechanism under study. [ABSTRACT FROM AUTHOR]

The DNA is the fundamental basis of genetic information, just as bits are for computers. Whenever computers are used to represent genetic data, the computational encoding must be efficient to allow the representation of processes driving the inheritance and variability. This is especially important across simulations in view of the increasing complexity and dimensions brought by genomics. This paper introduces a new binary representation of genetic information. Algorithms as bitwise operations that mimic the inheritance of a wide range of polymorphisms are also presented. Different kinds and mixtures of polymorphisms are discussed and exemplified. Proposed algorithms and data structures were implemented in C++ programming language and is available to end users in the R package "isqg" which is available at the R repository (CRAN). Supplementary data are available online. [ABSTRACT FROM AUTHOR]

Geckos are remarkable in their ability to reversibly adhere to smooth vertical, and even inverted surfaces. However, unraveling the precise mechanisms by which geckos do this has been a long process, involving various approaches over the last two centuries. Our understanding of the principles by which gecko adhesion operates has advanced rapidly over the past 20 years and, with this knowledge, material scientists have attempted to mimic the system to create artificial adhesives. From a biological perspective, recent studies have examined the diversity in morphology, performance, and real-world use of the adhesive apparatus. However, the lack of multidisciplinarity is likely a key roadblock to gaining new insights. Our goals in this paper are to 1) present a historical review of gecko adhesion research, 2) discuss the mechanisms and morphology of the adhesive apparatus, 3) discuss the origin and performance of the system in real-world contexts, 4) discuss advancement in bio-inspired design, and 5) present grand challenges in gecko adhesion research. To continue to improve our understanding, and to more effectively employ the principles of gecko adhesion for human applications, greater intensity and scope of interdisciplinary research are necessary. [ABSTRACT FROM AUTHOR]

Social Constructivism about the disease concept has generally been taken to ignore the fundamental biological reality underlying diseases, as well as to fall foul of several apparently compelling objections. In this paper, I explain how the metaphysical relation of grounding can be used to tie a socially constructed account of diseases and their classification to their underlying biological and behavioural states. I then generalize the position by disambiguating several varieties of normativism, including a particularly strong 'placeholder' version of social constructivism, and showing that the grounding approach is available to each. I go on to provide what I believe to be the first attempt at a full semantics for disease-talk and disagreement, before using the placeholder to demonstrate on that basis that the most troublesome objections to normativism can be avoided even by very strong versions of the position. [ABSTRACT FROM AUTHOR]

The 10th International Conference and Workshop on Lobster Biology and Management was held in Cancún, Mexico, in May 2014. The papers included in this supplementary issue of the ICES Journal of Marine Science are a sample of the multidisciplinary nature of the conference and provide new knowledge of the biology, ecology, fisheries, and management and aquaculture of clawed, spiny, and slipper lobsters. The emphasis of the conference was climate change and its consequences for lobster biology, population dynamics, ecology, and fisheries. As noted in several papers, climate change is already affecting different lobster species by altering growth rates, sizes at maturity, the timing of reproductive processes, duration of larval development, and the timing and levels of settlement; by affecting key benthic habitat-forming species in settlement habitats; by increasing the risk of disease and impacting the behavioural ecology of lobsters, and by changing the spatial distribution of the stocks and, hence, affecting catches and the territorial behaviour of fishers. Other issues addressed at the conference included aquaculture and enhancement—the holy grails of lobster management—sustainable management strategies, and a fascinating review of the use of lobsters through human history. In addition to their economic importance, lobsters continue to provide valuable information to understand different marine environments in a changing climate. [ABSTRACT FROM AUTHOR]

Stress and strain among adolescents have been investigated and discussed largely within three separate disciplines: mental health, where the focus has been on the negative effects of stress on emotional health; criminology, where the emphasis has been on the effects of strain on delinquency; and biology, where the focus has been to understand the effects of stress on physiology. Recently, scholars have called for increased multilevel developmental analyses of the bio-psychosocial nature of risk and protection for behaviors of individuals. This paper draws on several different but converging theoretical perspectives in an attempt to provide an overview of research relevant to stress in adolescence and puts forth a new framework that aims to provide both a common language and consilience by which future research can analyze the effects of multiple biological, social and environmental factors experienced during specific developmental periods, and cumulatively over time, on harmful behavior during adolescence. We present a framework to examine the effects of stress on diverse behavioral outcomes among adolescents, including substance use, suicidal behavior, self-inflicted harm, and delinquency. [ABSTRACT FROM AUTHOR]

This paper is motivated by the recent interest in the analysis of high-dimensional microbiome data. A key feature of these data is the presence of "structural zeros" which are microbes missing from an observation vector due to an underlying biological process and not due to error in measurement. Typical notions of missingness are unable to model these structural zeros. We define a general framework which allows for structural zeros in the model and propose methods of estimating sparse high-dimensional covariance and precision matrices under this setup. We establish error bounds in the spectral and Frobenius norms for the proposed estimators and empirically verify them with a simulation study. The proposed methodology is illustrated by applying it to the global gut microbiome data of Yatsunenko and others (2012. Human gut microbiome viewed across age and geography. Nature 486, 222-227). Using our methodology we classify subjects according to the geographical location on the basis of their gut microbiome. [ABSTRACT FROM AUTHOR]

Background: A little more than a decade ago a review entitled 'Biological basis for human capacitation' was published. A primary conclusion of the review was that with all the technological advances that have been made since the first experiments demonstrated the in vivo requirement of capacitation for fertilization, very little progress had since been made, most significantly for human.Objective and Rationale: The present review was carried out to provide an update on the biological basis for human capacitation. It briefly revisits the original schema, presents a review of the literature that urged research interest in human sperm capacitation and puts under the spotlight the original definition of capacitation balanced against the limitations of experiments in vitro to characterize a complex process that necessarily mandates a female component, and very recent findings in the mouse. It also includes proposed considerations for new thinking regarding capacitation, and progress toward understanding the biology of human capacitation.Search Methods: The PubMed, Google Scholar and Scopus literature databases were reviewed extensively using inclusive, broad and multispecies search terms without publication date limitation.Outcomes: Comprehensive screening of the literature database showed that no papers regarding human sperm capacitation in vivo have been published in the past 20 years. Recent experiments in the mouse have provided compelling and unanticipated data regarding capacitation and in vivo fertilization. Questions were posed and addressed regarding: stimuli for initiation of capacitation, capacitation relative to the cumulus-oocyte complex, comparison between in vivo and in vitro capacitation, and potential species-specific differences in location and timing of capacitation.Wider Implications: There has been no progress on the in vivo biology of human sperm capacitation since before the turn of the century. Human IVF and its technologies may likely have inhibited, and continue to hold back, any future in vivo experiments that would address one or more questions regarding acquisition of fertilizing capacity in human. The limiting factor for progress in the area is access to funding and human subjects. [ABSTRACT FROM AUTHOR]

In a recent paper, I proposed that natural selection should act to increase offspring number when diversification bet hedging is favoured. The simple underlying reasoning is that a target diversification strategy is more reliably generated with increasing sample size. The intention of opening a discussion has been realized; recent criticisms of the idea argue that selection does not act to increase offspring number when population size is large or infinite. Here I agree that criticisms have merit; indeed they are largely confined to the caveats discussed in my original paper. The critique, however, implies a verdict of outright rejection of the idea of selection on offspring number, which would be erroneous. Contrary to the assertions of the criticism, then, the importance of selection acting directly on offspring number remains an open question. [ABSTRACT FROM AUTHOR]

This paper considers the biological weapons problem as a post-disarmament issue requiring 'management' or 'governance' rather than 'disarmament' or 'arms control'. This allows for a broader analysis of the BW problem, one where a range of relevant issues, threats, challenges and actors can be examined, as well as nation-states, international treaties, terrorist groups and the like. The paper therefore provides a more accurate depiction of the wide range of current efforts to minimise the chances of biology being misused for hostile purposes. It aims to explain how and why networks and non-state actors have emerged to play a bigger role in the governance of biological technologies. [ABSTRACT FROM AUTHOR]

There is a profound need for the scientific community to be better aware of the policy context in which it operates. To address this need, Evolution has established a new Outlook feature section to include papers that explore the interface between society and evolutionary biology. This first paper in the series considers the strategic relevance of evolutionary biology. Support for scientific research in general is based on governmental or institutional expenditure that is an investment, and such investment is based on strategies designed to achieve particular outcomes, such as advance in particular areas of basic science or application. The scientific community can engage in the development of scientific strategies on a variety of levels, including workshops to explicitly develop research priorities and targeted funding initiatives to help define emerging scientific areas. Better understanding and communication of the scientific achievements of evolutionary biology, emphasizing immediate and potential societal relevance, are effective counters to challenges presented by the creationist agenda. Future papers in the Outlook feature section should assist the evolutionary biology community in achieving a better collective understanding of the societal relevance of their field. [ABSTRACT FROM AUTHOR]

Complex biological structures, such as the human eye, have been interpreted as evidence for a creator for over three centuries. This raises the question of whether random mutation can create such adaptations. In this article, we present an inquiry-based laboratory experiment that explores this question using paper airplanes as a model organism. The main task for students in this investigation is to figure out how to simulate paper airplane evolution (including reproduction, inheritance, mutation, and selection). In addition, the lab requires students to practice analytic thinking and to carefully delineate the implications of their results. [ABSTRACT FROM AUTHOR]

An elementary course in human heredity for students not planning to major in the sciences can be based on current scientific literature and on the popular media. Examinations are constructed from questions on recent abstracts obtained from PubMed. The course is designed to promote writing skills in the sciences, and students write two papers in the course of a quarter. In the first paper, students trace the primary source of media reports on genetics and attempt to evaluate the reporter's translation. In a second paper, students write popular articles on the basis of current primary sources. [ABSTRACT FROM AUTHOR]

Adaptive Dynamics is an approach to studying evolutionary change when fitness is density or frequency dependent. Modern papers identifying themselves as using this approach first appeared in the 1990s, and have greatly increased up to the present. However, because of the rather technical nature of many of the papers, the approach is not widely known or understood by evolutionary biologists. In this review we aim to remedy this situation by outlining the methodology and then examining its strengths and weaknesses. We carry this out by posing and answering 20 key questions on Adaptive Dynamics. We conclude that Adaptive Dynamics provides a set of useful approximations for studying various evolutionary questions. However, as with any approximate method, conclusions based on Adaptive Dynamics are valid only under some restrictions that we discuss. [ABSTRACT FROM AUTHOR]

Papers in this Special Feature were presented at a symposium on the social biology of rodents that was held in June 2001 at the 81st Annual Meeting of the American Society of Mammalogists. Our decision to host a symposium on this topic resulted from our realization that although rodents have played a vital role in research on social behavior, no recent summaries of the social biology of these animals were available. Given the number of biological disciplines, research strategies, and species that are relevant to this topic, a comprehensive review of rodent social biology was not possible. Instead, in structuring the symposium, we chose to focus on a subset of behavioral issues for which studies of rodents currently are providing exciting new insights. Topics selected for inclusion--communication, kin recognition, philopatry, and sociality--are timely and are of considerable interest to biologists studying a wide array of animal taxa. Thus, papers presented in the symposium reflect recent advances not only in our knowledge of rodent social biology but also in our conceptual understanding of animal social behavior. [ABSTRACT FROM AUTHOR]

Abstract In this paper, we predict the outcome of dispersal evolution in metapopulations based on the following assumptions: (i) population dynamics within patches are density-regulated by realistic growth functions; (ii) demographic stochasticity resulting from finite population sizes within patches is accounted for; and (iii) the transition of individuals between patches is explicitly modelled by a disperser pool. We show, first, that evolutionarily stable dispersal rates do not necessarily increase with rates for the local extinction of populations due to external disturbances in habitable patches. Second, we describe how demographic stochasticity affects the evolution of dispersal rates: evolutionarily stable dispersal rates remain high even when disturbance-related rates of local extinction are low, and a variety of qualitatively different responses of adapted dispersal rates to varied levels of disturbance become possible. This paper shows, for the first time, that evolution of dispersal rates may give rise to monotonically increasing or decreasing responses, as well as to intermediate maxima or minima. [ABSTRACT FROM AUTHOR]

Computational models have been of interest in biology for many years and have represented a particular approach to trying to understand biological processes and phenomena from a systems point of view. Much of the early work was rather abstract and high level and probably seemed to many to be of more philosophical than practical value. There have, however, been some advances in the development of more realistic models and the current state of computer science research provides us with new opportunities through both the emergence of models that can model seriously complex systems and also the support that modern software can give to the modelling process. This paper describes a few of the early simple models¹ and then goes on to look at some new ideas in the area with a particular application drawn from the world of mycology. Some general principles relating to how new and emerging computational techniques can help to represent and understand extremely complex models conclude the paper. [ABSTRACT FROM AUTHOR]

This paper describes an integrated laboratory project for intermediate to advanced undergraduate students. The project spans an entire academic quarter (10 weeks) and involves a series of operations that give students experience with fundamental techniques in cell biology, molecular biology, biochemistry, genomics, and bioinformatics. In the process, the student learning community is strengthened, students gain increasing confidence in their abilities in the laboratory, and data are collected toward the eventual sequencing of a cytoplasmic genome. The culmination of the project is the preparation by students of a paper written in the format of a particularly accessible online journal. [ABSTRACT FROM AUTHOR]

Flows driven by surface tension are both ubiquitous and diverse, involving the drinking of birds and bees, the flow of xylem in plants, the impact of raindrops on animals, respiration in humans, and the transmission of diseases in plants and animals, including humans. The fundamental physical principles underlying such flows provide a unifying framework to interpret the adaptations of the microorganisms, animals, and plants that rely upon them. The symposium on “Surface-Tension Phenomena in Organismal Biology” assembled an interdisciplinary group of researchers to address a large spectrum of topics, all articulated around the role of surface tension in shaping biology, health, and ecology. The contributions to the symposium and the papers in this issue are meant to be a starting point for novices to familiarize themselves with the fundamentals of flows driven by surface tension; to understand how they can play a governing role in many settings in organismal biology; and how such understanding of nature’s use of surface tension can, in turn, inspire humans to innovate. [ABSTRACT FROM AUTHOR]

Home ranges relate to all aspects of a mammal's biology. The 5 papers in this Special Feature provide statistical, economic, game theoretic, mechanistic, information dependent, and conceptual approaches to understanding home ranges and why animals have them. All the papers emphasize the importance of testing a priori hypotheses, especially hypotheses that elucidate why animals behave as they do. All the papers relate resources and habitat quality to home ranges. Finally, the authors oppose viewing home ranges as the product of measurements and suggest viewing home ranges as the cognitive maps that animals maintain and update. [ABSTRACT FROM AUTHOR]

Questions and problems that emerged during operational conservation of black-footed ferrets (Mustela nigripes) have been addressed by a wide variety of studies. Early results from such studies often were communicated orally during meetings of recovery groups and in written form using memoranda, unpublished reports, and theses. Typically, implementation of results preceded their publication in widely distributed journals. Many of these studies eventually were published in journals, and we briefly summarize the contents of 8 volumes and special features of journals that have been dedicated to the biology of ferrets and issues in ferret recovery. This year marks the 30th anniversary of rediscovery of the black-footed ferret, and the 7 papers of the following Special Feature summarize data collected over nearly that span of time. [ABSTRACT FROM AUTHOR]

Rates of phenotypic evolution derive from numerous interrelated processes acting at varying spatial and temporal scales and frequently differ substantially among lineages. Although current models employed in reconstructing ancestral character states permit independent rates for distinct types of transition (forward and reverse transitions and transitions between different states), these rates are typically assumed to be identical for all branches in a phylogeny. In this paper, I present a general model of character evolution enabling rate heterogeneity among branches. This model is employed in assessing the extent to which the assumption of uniform transition rates affects reconstructions of ancestral limb morphology in the scincid lizard clade Lerista and, accordingly, the potential for rate variability to mislead inferences of evolutionary patterns. Permitting rate variation among branches significantly improves model fit for both the manus and the pes. A constrained model in which the rate of digit acquisition is assumed to be effectively zero is strongly supported in each case; when compared with a model assuming unconstrained transition rates, this model provides a substantially better fit for the manus and a nearly identical fit for the pes. Ancestral states reconstructed assuming the constrained model imply patterns of limb evolution differing significantly from those implied by reconstructions for uniform-rate models, particularly for the pes; whereas ancestral states for the uniform-rate models consistently entail the reacquisition of pedal digits, those for the model incorporating among-lineage rate heterogeneity imply repeated, unreversed digit loss. These results indicate that the assumption of identical transition rates for all branches in a phylogeny may be inappropriate in modeling the evolution of phenotypic traits and emphasize the need for careful evaluation of phylogenetic tests of Dollo's law. [ABSTRACT FROM PUBLISHER]

This paper surveys the economic theory of bargaining with a view to applications in biology, using Roughgarden’s recent Genial Gene as a case study in mistakes to be avoided. [ABSTRACT FROM AUTHOR]

This article discusses Charles Darwin's interest in topics that may broadly be defined as ‘neurological’ in character. Using published and manuscript materials, it examines the sources of Darwin's knowledge of neurological matters and seeks to explain why questions concerning the relation of mind and brain both in humans and other animals were relevant to his wider concerns. The paper concludes with a discussion of Darwin's impact on late 19th and early 20th century neurological thought. The 150th anniversary of the publication of the Origin of Species and the 200th of the birth of its author afford an opportunity to reflect on Charles Darwin's relationship to neurology. The first section of this article considers the part played by what might broadly be defined as ‘neurological’ materials in the shaping of Darwin's theory. The following section provides a brief review of the impact that Darwin's ideas were to have upon subsequent neurological thought. [ABSTRACT FROM PUBLISHER]

Recent developments in ecological statistics have reached behavioral ecology, and an increasing number of studies now apply analytical tools that incorporate alternatives to the conventional null hypothesis testing based on significance levels. However, these approaches continue to receive mixed support in our field. Because our statistical choices can influence research design and the interpretation of data, there is a compelling case for reaching consensus on statistical philosophy and practice. Here, we provide a brief overview of the recently proposed approaches and open an online forum for future discussion (https://bestat.ecoinformatics.org/). From the perspective of practicing behavioral ecologists relying on either correlative or experimental data, we review the most relevant features of information theoretic approaches, Bayesian inference, and effect size statistics. We also discuss concerns about data quality, missing data, and repeatability. We emphasize the necessity of moving away from a heavy reliance on statistical significance while focusing attention on biological relevance and effect sizes, with the recognition that uncertainty is an inherent feature of biological data. Furthermore, we point to the importance of integrating previous knowledge in the current analysis, for which novel approaches offer a variety of tools. We note, however, that the drawbacks and benefits of these approaches have yet to be carefully examined in association with behavioral data. Therefore, we encourage a philosophical change in the interpretation of statistical outcomes, whereas we still retain a pluralistic perspective for making objective statistical choices given the uncertainties around different approaches in behavioral ecology. We provide recommendations on how these concepts could be made apparent in the presentation of statistical outputs in scientific papers. [ABSTRACT FROM PUBLISHER]

Ona, E., Mazauric, V., and Andersen, L. N. 2009. Calibration methods for two scientific multibeam systems. – ICES Journal of Marine Science, 66: 1326–1334.The new Simrad scientific multibeam systems, the MS70 sonar and the ME70 echosounder, each transmit over many electronically formed beams with centre frequencies spanning from 70 to 120 kHz. Calibrations of these systems are therefore more complex than for conventional split-beam echosounder systems. Two large tungsten-carbide spheres (75 and 84 mm diameter) were designed and manufactured to facilitate accurate field calibrations over the entire operational bandwidth. These are heavy and therefore stable when suspended beneath a ship, and have target strengths much larger than those of biological targets potentially within the measurement volume. This paper presents procedures for calibrating each system in the field and the results from two such experiments. Detailed inspections of the results for individual beams indicate that minor adjustments in the described procedures might further improve the reported calibration accuracy. [ABSTRACT FROM PUBLISHER]

Velasco recently criticized our formal definition of the species concept, arguing for its inappropriateness both in fundamental and practical aspects [Velasco JD (2008) Biological Journal of the Linnean Society, 93, 865–869]. Here, we clarify some misunderstandings that are at the basis of Velasco's paper. First, we show why and how the definition of the species concept can be grounded in the theory of evolution and what that implies. Then, we explain why Velasco's formal criticisms are unjustified. Finally, we point out the practical and methodological consequences of a rigorous conceptual framework for species study, and we show that today's development of species delimitation methods fully agrees with our proposal. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 97, 217–222. [ABSTRACT FROM AUTHOR]

About 50 years ago, the German entomologist Willi Hennig presented a new approach in biological systematics that he called a phylogenetic systematics. The main difference between his approach and traditional Linnean systematics was that he distinguished two new kinds of groups that he called mono- and paraphyletic groups, and whereof he considered only monophyletic groups to be natural groups. However, almost immediately after publication of his approach in English, some biological systematists commented that his monophyletic groups rather ought to be called holophyletic groups. The comment sparked a heated debate about the definition of the concept ‘monophyletic groups’, but the debate never reached consensus. In this paper, I claim that the controversy does not concern the definition of the concept monophyletic groups per se, but instead conceptualization of phylogenies (i.e. dichotomously branching processes) in a general sense. I discuss the relation between mono-, holo- and paraphyletic groups, and conclude that Hennig's conceptualization of phylogenies is both inconsistent and empirically wrong, whereas Linné's instead is consistent and correct. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 94, 217–220. [ABSTRACT FROM AUTHOR]

Over the years, numerous studies have investigated the mechanisms controlling nutrient availability and metabolism in the mammary gland and how dietary interventions can influence these processes. The development of in vivo and in vitro systems made it possible to explore the trafficking and metabolic fate of nutrients and how these are influenced by hormones. To improve the quality and safety of milk products, attention has focused on improving animal health in general and mammary gland health in particular and also on enhancing the milk content of natural bioactive milk components that promote the health of human neonates and adults. In the past, attempts to probe the relationship among nutrition, animal health, and animal products were limited to administering single dietary components and investigating their biochemical and metabolic effects. Today, we have genomics, proteomics, and related technologies that allow us to pursue more holistic investigational strategies. These new technologies are providing new insights into interactions among nutrition, lactation, and product quality. The aim of this paper is to review advances in nutritional support of mammary gland function and health as presented in 14 yr of Biology of Lactation in Farm Animals (BOLFA) meetings. [ABSTRACT FROM AUTHOR]

Bdelloid rotifers, darwinulid ostracods and some oribatid mites have been called ‘ancient asexuals’ as they speciated and survived over long-term evolutionary timescale without sexual recombination. Data on their genetic diversification are contrasting: within-species diversification is present mostly at a continental scale in a parthenogenetic oribatid mite, whereas almost no genetic diversification at all seems to occur within darwinulid ostracod species. Strangely enough, no clear data for bdelloid rotifers are available so far. In this paper, we analyse partial COI mtDNA sequences to show that a bdelloid rotifer, Philodina flaviceps, so far considered a single traditional morphological species, has actually been able to diversify into at least nine distinct evolutionary entities, with genetic distances between lineages comparable with those between different traditional species within the same genus. We discovered that local coexistence of such different independent lineages is very common: up to four lineages were found in a same stream, and up to three in a single moss sample of 5 cm2. In contrast to the large-scale geographic pattern that has recently been reported in the oribatid mite, the spatial distribution of the bdelloid lineages provided evidence of micro-phylogeographic patterns. If the mtDNA diversity indicates that the lineages are independent and represent sympatric cryptic species within P. flaviceps, then the actual bdelloid diversity can be expected to be much greater than that recognized today. [ABSTRACT FROM AUTHOR]

The analysis of diversification and character evolution using phylogenetic data attracts increasing interest from biologists. Recent statistical developments have resulted in a variety of tools for the inference of macroevolutionary processes in a phylogenetic context. In a recent paper Maddison (2006 Evolution, 60: 1743–1746) pointed out that uncareful use of some of these tools could lead to misleading conclusions on diversification or character evolution, and thus to difficulties in distinguishing both phenomena. I here present guidelines for the analyses of macroevolutionary data that may help to avoid these problems. The proper use of recently developed statistical methods may help to untangle diversification and character change, and so will allow us to address important evolutionary questions. [ABSTRACT FROM AUTHOR]

The outgroup method is widely used to root phylogenetic trees. An accurate root indication, however, strongly depends on the availability of a proper outgroup. An alternate rooting method is the midpoint rooting (MPR). In this case, the root is set at the midpoint between the two most divergent operational taxonomic units. Although the midpoint rooting algorithm has been extensively used, the efficiency of this method in retrieving the correct root remains untested. In the present study, we empirically tested the success rate of the MPR in obtaining the outgroup root for a given phylogenetic tree. This was carried out by eliminating outgroups in 50 selected data sets from 33 papers and rooting the trees with the midpoint method. We were thus able to compare the root position retrieved by each method. Data sets were separated into three categories with different root consistencies: data sets with a single outgroup taxon (54% success rate for MPR), data sets with multiple outgroup taxa that showed inconsistency in root position (82% success rate), and data sets with multiple outgroup taxa in which root position was consistent (94% success rate). Interestingly, the more consistent the outgroup root is, the more successful MPR appears to be. This is a strong indication that the MPR method is valuable, particularly for cases where a proper outgroup is unavailable. © 2007 The Linnean Society of London, Biological Journal of the Linnean Society, 2007, 92, 669–674. [ABSTRACT FROM AUTHOR]

Understanding the evolution of microbial diversity is an important and current problem in evolutionary ecology. In this paper, we investigated the role of two established biochemical trade-offs in microbial diversification using a model that connects ecological and evolutionary processes with fundamental aspects of biochemistry. The trade-offs that we investigated are as follows:(1) a trade-off between the rate and affinity of substrate transport; and (2) a trade-off between the rate and yield of ATP production. Our model shows that these biochemical trade-offs can drive evolutionary diversification under the simplest possible ecological conditions: a homogeneous environment containing a single limiting resource. We argue that the results of a number of microbial selection experiments are consistent with the predictions of our model. [ABSTRACT FROM AUTHOR]

Summary: A review of the recent literature on treatment modalities of adult thoracic empyema was conducted in order to expose the controversies and verify where consensus exists. Critical reading filtered through clinical experience was the method followed. The roles of surgical drainage, lavage techniques, debridement via VATS, decortication, thoracoplasty and open window thoracostomy were considered using the Oxford Center of Evidence Based Medicine criteria. The roles of the different therapeutical modalities were interpreted in the light of the triphasic nature of empyema thoracis. The randomised controlled trials came up with conflicting results. With two exceptions all of the papers reviewed provide level (2b) or below evidences. The lack of a single ideal treatment modality or policy reflects the complexity of the diagnosis and staging of this heterogeneous disease. Basic elements of intervention – drainage, different evacuation techniques, decortication, thoracoplasty and open window thoracostomy – are well-established technical modalities; however, neither a universally acceptable primary modality nor the gold standard of their sequence is available. Drainage remains to be the initial treatment modality in Phase I disease. Debridement via VATS is a safe, reliable and efficient method in the fibrinopurulent phase. Organised pleural callus requires formal decortication. Open window thoracostomy is a simple and safe procedure for high-risk patients and results in quick detoxication. Thoracoplasty kept its final role in pleural space management. Acute postoperative bronchial stump insufficiency requires immediate surgery. Evacuation of toxic material is mandatory. No single-stage procedure offers a solution. An optimised agressivity treatment modality should be tailored to the condition of the patient and to the potential of the persisting cavity. Decision-making involves a triad consisting of the aetiology of empyema (i.e. primary vs secondary), general condition of the patient and stage of disease, while considering the triphasic nature of development of thoracic empyema. The current attitudes show that the present concepts are based mainly on expert opinion. Flexibility and patience on behalf of the surgeon and nursing staff, the patient and the hospital management, as well as a good understanding of the complexity of this condition are the cornerstones of the treatment. No exclusive sequence of procedures leading to a uniformly predictable successful outcome is available. Individualised approaches can be recommended based on institutional practice and local protocols. Thoracic empyema in general seems to remain resilient to fit completely into the categories of evidence-based medical approach. [Copyright &y& Elsevier]

Theoretical quantitative genetics provides a framework for reconstructing past selection and predicting future patterns of phenotypic differentiation. However, the usefulness of the equations of quantitative genetics for evolutionary inference relies on the evolutionary stability of the additive genetic variance-covariance matrix (G matrix). A fruitful new approach for exploring the evolutionary dynamics of G involves the use of individual-based computer simulations. Previous studies have focused on the evolution of the eigenstructure of G. An alternative approach employed in this paper uses the multivariate response-to-selection equation to evaluate the stability of G. In this approach, I measure similarity by the correlation between response-to-selection vectors due to random selection gradients. I analyze the dynamics of G under several conditions of correlational mutation and selection. As found in a previous study, the eigenstructure of G is stabilized by correlational mutation and selection. However, over broad conditions, instability of G did not result in a decreased consistency of the response to selection. I also analyze the stability of G when the correlation coefficients of correlational mutation and selection and the effective population size change through time. To my knowledge, no prior study has used computer simulations to investigate the stability of G when correlational mutation and selection fluctuate. Under these conditions, the eigenstructure of G is unstable under some simulation conditions. Different results are obtained if G matrix stability is assessed by eigenanalysis or by the response to random selection gradients. In this case, the response to selection is most consistent when certain aspects of the eigenstructure of G are least stable and vice versa. [ABSTRACT FROM AUTHOR]

Adjustment factors to allow comparison of EPD from several breed associations for birth, weaning, and yearling weights have been available for more than 10 yr. This paper describes steps to calculate adjustment factors for EPD for 4 carcass traits: marbling score, fat thickness, ribeye area, and retail product percentage. The required information is the same as for the weight traits: 1) breed of sire solutions based on measurements on progeny at the US Meat Animal Research Center (USJVIARC) that have sires with breed association EPD, 2) mean EPD of sires weighted by number of progeny at USMARC (USMARC progeny not included in breed association EPD), and 3) mean EPD of nonparents from breed associations (defined as animals born 2 yr prior to calculation of EPD). Records at USMARC are adjusted to 100% heterozygosity because the purpose of the adjustment factors is to allow prediction of performance of progeny of sires mated to other breeds of dam. A critical step is to adjust breed of sire solutions, which are based on an earlier sample of sires, to the equivalent of a sample from a more recent nonparent group using the difference between mean EPD from information sources 2) and 3). The difference is multiplied by the coefficient of regression of USMARC progeny on EPD of their sires. With weight traits, these coefficients are not greatly different from unity. With the carcass traits, 2 sets of coefficients can be used depending on whether the EPD are based on carcass or ultrasound measurements. The regression coefficients also reflect differences in conditions for USMARC progeny (all steers) and factors associated with breed association EPD. Only for marbling score and ribeye area were any estimates of the regression coefficients near unity. For other traits, the coefficients ranged from 1.65 to 2.82. The solutions for breed of sire, differences in mean EPD, and regression coefficients are then used to calculate adjustment factors for EPD of 11 breeds including the arbitrary base breed, Angus. [ABSTRACT FROM AUTHOR]

This paper contains analysis of a recently formulated multiphase model for the growth of biological tissue that comprises motile cells and water inside a rigid scaffold material. The model is extended here to include a term describing cell proliferation which is mediated by the supply of a diffusible nutrient and to include the case where the scaffold porosity varies in space. Numerical solutions of the model equations are presented for different values of the parameters. Comparison is drawn between the different types of growth that arise when using static or dynamic methods for seeding the scaffold with cells. Analytical solutions are presented for the limiting cases in which the coefficient of drag between the cells and the scaffold is very large or zero. In the limit of large time, solutions reveal preferential tissue growth in the vicinity of the scaffold edge due to depletion of nutrient by the cells, consistent with experimental results. However, it is shown that reducing the coefficient of drag between the scaffold and the cells overcomes the effects of nutrient depletion by increasing cell mobility, thereby leading to improved uniformity of the cell distribution within the scaffold. [ABSTRACT FROM AUTHOR]

Two standard mathematical formulations of kin-selection models can be found. Inclusive fitness is an actor-centred approach, which calculates the fitness effect on a number of recipients of the behaviour of a single actor. Direct fitness is a recipient-centred approach, which calculates the fitness effect on the recipient of the behaviour of a number of actors. Inclusive fitness offers us a powerful heuristic, of choosing behaviour to maximize fitness, but direct fitness can be mathematically easier to work with and has recently emerged as the preferred approach of theoreticians. In this paper, we explore the fundamental connection between these two approaches in both homogeneous and class-structured populations, and we show that under simple assumptions (mainly fair meiosis and weak selection) they provide equivalent formulations, which correspond to the predictions of Price's equation for allele frequency change. We use a couple of examples to highlight differences in their conception and formulation, and we briefly discuss a two-species example in which we have a class of ‘actor’ that is never a ‘recipient’, which the standard direct fitness method can handle but the usual inclusive fitness cannot. [ABSTRACT FROM AUTHOR]