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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]

Motivation: The biological literature is a major repository of knowledge. Many biological databases draw much of their content from a careful curation of this literature. However, as the volume of literature increases, the burden of curation increases. Text mining may provide useful tools to assist in the curation process. To date, the lack of standards has made it impossible to determine whether text mining techniques are sufficiently mature to be useful. Results: We report on a Challenge Evaluation task that we created for the Knowledge Discovery and Data Mining (KDD) Challenge Cup. We provided a training corpus of 862 articles consisting of journal articles curated in FlyBase, along with the associated lists of genes and gene products, as well as the relevant data fields from FlyBase. For the test, we provided a corpus of 213 new ('blind') articles; the 18 participating groups provided systems that flagged articles for curation, based on whether the article contained experimental evidence for gene expression products. We report on the evaluation results and describe the techniques used by the top performing groups. Contact: asy@mitre.org Keywords: text mining, evaluation, curation, genomics, data management [ABSTRACT FROM AUTHOR]

To celebrate the 40th anniversary of Molecular Biology and Evolution, the Society for Molecular Biology and Evolution (SMBE) is publishing a series of virtual issues in 2024. These virtual issues feature selected papers from the society's journals, Molecular Biology and Evolution and Genome Biology and Evolution. Each virtual issue is accompanied by a Perspective that highlights the contributions of the journals to a specific topic in molecular evolution. The August Perspective, titled "Lessons from extremophiles: genomic innovations and functional adaptations across the eukaryotic tree of life," was written by H.B. Rappaport and Angela M. Oliverio and appears in Genome Biology and Evolution. The virtual issues include noteworthy papers on Genomic Innovations in Extremophiles and can be found on SMBE's 40th anniversary site. [Extracted from the article]

Bed bugs are an important group of medical and urban insect pests. They are obligate blood-feeders. Their bites may cause skin irritation and allergic reactions and, under some circumstances, may lead to mental and other health issues. Despite numerous discoveries on the biology of these obnoxious pests and progress in control strategies over the last two decades, bed bugs continue to preferentially plague those from low socioeconomic communities because the poor generally could not afford effective control options. As a result, such infestations in poorer communities serve as a reservoir for wider society. This Special Collection of the Perspective on Biology and Management of Bed Bugs presents nine original research papers on bed bug detection, insecticide performance and resistance, nonchemical treatment, fungal biopesticides, and pest management procurement and contracts. We hope that these investigative findings will spur research on safer, more affordable, and effective control options in the future. [ABSTRACT FROM AUTHOR]

This article presents guidelines for authors for preparing manuscripts for the "Journal of Applied Microbiology." The aim of the Journal is to publish high quality papers within 4-5 months of receipt of a revised and accepted manuscript. Manuscripts should be prepared using a word-processor. Text must be double-spaced, and the right hand margin justification should be switched off. A helpline for technical support is accessible on the online submission site. The paper should have as its aim the development of concepts as well as the recording of facts. The manuscript should be prepared for a wide readership.

In an occasional series of articles, we will be publishing autobiographical sketches from some of those working in the field of genome evolution. The series will feature both the very eminent, but also researchers closer to their start of their career, and those from underrepresented groups. The series will show the unusual paths that academics sometimes take and the obstacles they have overcome. We start this series with one of the most influential researchers in the field of molecular evolution, Wen-Hsiung Li. Wen-Hsiung has contributed enormously to the field and published on a wide diversity of topics, as described in this autobiographical sketch; he also wrote two textbooks, one of them with Dan Graur, which for many years were the bibles of the field. He was awarded the Motoo Kimura prize by the Society of Molecular Biology and Evolution in 2019 in recognition of his contributions to our subject. [ABSTRACT FROM AUTHOR]

The article presents guidelines for authors who will submit article for the "Journal of Applied Microbiology." The guidelines include format of papers, submissions, full-length papers, layout of references, English usage, headings, materials and methods, nucleotide sequences, statistics, tables, figures, photographs and ethics of experimentation.

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]

Book Information Foundations of Tropical Forest Biology: Classic Papers with Commentaries. Edited by R.L. Chazdon and T.C. Whitmore. University of Chicago Press. 2002. Pp. xviii + 862. Hardback, £66.50, 0-226-10224-6. Paperback, £24.50, 0-226-10225-4. [ABSTRACT FROM AUTHOR]

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]

"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]

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]

Theory structure can be defined in a simple, useful form, and most theories taught in biology have a simple structure. Teaching can be promoted by identifying the postulates underlying a biological theory. Some suggestions and some postulate lists are given for those who wish to test for themselves my contention that concisely listed postulates are an aid to learning and understanding. (Accepted for publication 5 February 1982) [ABSTRACT FROM AUTHOR]

Lists books on biological sciences. 'Acidic Precipitation. vol. 5. International Overview and Assessment' edited by A.H.M. Bresser and W. Salomons; 'Activation and Desensitization of Transducing Pathways,' edited by T.M. Konijn and others; 'African Birds of Prey,' by P. Pickford and B. Pickford.

The European Society of Cardiology (ESC) has a working group called the Working Group on Atherosclerosis and Vascular Biology (WG AVB) that focuses on the study of the vasculature and its role in cardiovascular disease. The WG AVB consists of scientists and physicians from various specialties who come together to discuss and research vascular biology and disease. They aim to translate their findings into clinical applications to benefit patients. The WG AVB is involved in scientific sessions, awards for young researchers, position papers, a textbook, newsletters, and involvement in other ESC councils. They welcome members from all ages and nationalities and are working to increase the representation of women in their field. [Extracted from the article]

Pterostichus melanarius (Illiger, 1798) is a Palearctic generalist predator native to Europe. It was unintentionally introduced to North America at least twice in the mid 1920s and has since become widespread in Canada and the United States. Although P. melanarius is a valuable natural enemy in many different agricultural systems, we are not aware of any effort to compile in one publication details of its life history, diet, distribution, and factors that influence its populations. Some studies in North America have investigated the effects of P. melanarius on pest species and native carabid assemblages. Moreover, given that it is an exotic species whose range appears to still be expanding, it will be valuable to predict its potential distribution in North America. Therefore, the goals of this paper are to: 1) compile information on the life history and biology of P. melanarius, 2) review the effects of various agricultural practices on this species, and 3) use ecological niche modeling to determine the potential range of P. melanarius in the United States and which climate variables are most important for range expansion. Our review revealed that P. melanarius appears to provide benefits most consistently in diverse agricultural systems managed with no-till or reduced till methods, whereas our modeling revealed that P. melanarius likely occupies, or will occupy, more of the northern U.S. than is currently recognized, particularly in the Appalachian and Rocky Mountain regions. [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]

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]

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]

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]

This article presents a list of books related to biology. They include "Agriculture in the 21st Century," Anita M. Kelly and Jeffrey Silverstein, "The Alvin Pineal Gland: A Model of the Biological Clock," by Valér Csernus and Béla Mess, "The Biology of Temporary Waters," by D. Dudley Williams, "Birds, Mammals, and Reptiles of the Galápagos Islands: an Identification Guide," 2nd ed., by Andy Swash and Rob Still, and "Coexisting With Large Carnivores: Lessons From Greater Yellowstone," edited by Tim W. Clark, Murray B. Rutherford and Denise Casey.

Deals with the changes in "Integrative and Comparative Biology" of the Society for Integrative and Comparative Biology. Change in editorship and publisher; Overview of the changes in the process of submitting papers online; Expansion of the scope of the journal.

This section presents a list of books on biology, published as of August 2005.

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: 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]

This paper challenges proceduralized, rule-bound approaches to ethics and considers how social workers and teams can develop an attitude of compassionate concern and become more effective in dealing with ethical problems in their day-to-day practice. It introduces the work of Humberto Maturana, a widely respected theorist, whose work has received little attention in social work. The paper argues that Maturana's biology of cognition provides an approach to ethics that takes into account the spontaneous nature of everyday work in which social workers undertake their ethical actions. It stresses the importance of emotions, particularly love, and considers the way in which ethical action is shaped by culture. It emphasizes the importance of engaging in reflection on professional practices and team, professional and organizational culture in order for social workers to improve their awareness of ethical dilemmas and promote ethical practice. For those teaching ethics, this paper suggests an alternative to the rational consideration of moral dilemmas and proposes approaches to training that can help social workers become more attuned and responsive to ethical conflicts. [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]

Focuses on the understanding of adaptive dynamic (AD). Information about the sympatric speciation theory; Discussion on the predictions given by population genetics; Comparisons between AD model predictions and empirical data.

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]

Motivation Genomic instability is a hallmark of cancer, leading to many somatic alterations. Identifying which alterations have a system-wide impact is a challenging task. Nevertheless, this is an essential first step for prioritizing potential biomarkers. We developed CIBRA (Computational Identification of Biologically Relevant Alterations), a method that determines the system-wide impact of genomic alterations on tumor biology by integrating two distinct omics data types: one indicating genomic alterations (e.g. genomics), and another defining a system-wide expression response (e.g. transcriptomics). CIBRA was evaluated with genome-wide screens in 33 cancer types using primary and metastatic cancer data from the Cancer Genome Atlas and Hartwig Medical Foundation. Results We demonstrate the capability of CIBRA by successfully confirming the impact of point mutations in experimentally validated oncogenes and tumor suppressor genes (0.79 AUC). Surprisingly, many genes affected by structural variants were identified to have a strong system-wide impact (30.3%), suggesting that their role in cancer development has thus far been largely under-reported. Additionally, CIBRA can identify impact with only 10 cases and controls, providing a novel way to prioritize genomic alterations with a prominent role in cancer biology. Our findings demonstrate that CIBRA can identify cancer drivers by combining genomics and transcriptomics data. Moreover, our work shows an unexpected substantial system-wide impact of structural variants in cancer. Hence, CIBRA has the potential to preselect and refine current definitions of genomic alterations to derive more nuanced biomarkers for diagnostics, disease progression, and treatment response. Availability and implementation The R package CIBRA is available at https://github.com/AIT4LIFE-UU/CIBRA. [ABSTRACT FROM AUTHOR]

Discusses an increase in errors in publications of biological studies. Corrections, Errata, Addenda and Corrigenda, and Author's Note; Errors not detected or reported; Rate of errors for different scientific journals; Editorial policy and practice.

A list of books related to biology is presented. These include "Ecological Communities: Plant Mediation in Indirect Interaction Webs," edited by Takayuki Ohgushi, Timothy P. Craig and Peter W. Price, "Fruits and Nuts," edited by Chittaranjan Kole, and "An Introduction to Plant Breeding," by Jack Brown and Peter Caligari.

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]

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 Federation of African Immunological Societies (FAIS) Congress, held in Tunisia in November 2017, marked a significant scientific milestone. It enabled scientists from across the continent to promote immunology research and to showcase major achievements made by immunologists throughout Africa. This issue of the Journal of Leukocyte Biology (JLB) features manuscripts from the FAIS Congress. As noted in these papers, research in infectious diseases remains the focus of the African immunology community; however, increasingly noncommunicable diseases—such as autoimmunity, allergy, primary immunodeficiency, cancer and transplantation immunology—are also an emerging priority. This overview gives a brief history of the FAIS meeting, which also commemorated the 25th anniversary of the FAIS. It describes the current activities of the organization, as well as its history and the future opportunities for this Federation. In 25 years the African immunology fraternity has expanded to 15 countries and is producing quality research in regionally relevant topics. [ABSTRACT FROM AUTHOR]

A list of books related to biology and ecology is presented. They include "Principles of Animal Locomotion," by R. McNeill Alexander, "River and Stream Ecosystems of the World," by C. E. Cushing, K. W. Cummins, and G. W. Minshall and "Trends in Chronobiology Research," edited by Frank Columbus.

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]

Presents announcements from the Society for Systematic Biologists (SSB) and related societies recent as of 2004. Subscriptions to "Systematic Biology" journal from developing nations; Joint meetings of the SSB, Society for the Study of Evolution and the American Society of Naturalists; Calls for papers for the 2005 SSB symposia; Submissions for the Ernst Mayr Award in systematic biology research.

The article presents a list of books related to biology and ecology. These books include "The Altruism Equation: Seven Scientists Search for the Origins of Goodness," by Lee Alan Dugatkin, "Atlas of Woody Plant Stems: Evolution, Structure, and Environmental Modifications," by Fritz H. Schweingruber, Annett Börner, and Ernst-Detlef Schulze, and "Female Infidelity and Paternal Uncertainty: Evolutionary Perspectives on Male Anti-cuckoldry Tactics," by Steven M. Platek and Todd K. Shackelford.

Forensic entomology could provide valuable data for the minimum postmortem interval (PMImin) estimation and other relevant information, such as causes and circumstances of death. Some representatives of flesh flies are one of the dominant necrophagous insects during early stages of decomposition, demonstrating unique biological characteristics compared with other necrophagous flies. Moreover, they lead to global health concerns as carriers of various pathogenic micro-organisms, and dominantly result in the traumatic myiasis. Thus, sarcophagid flies are considered important in decomposition processes for PMImin estimation. However, the utility of sarcophagid flies has been seriously hampered by limited ecological, biological and taxonomic knowledge of them. The aim of this paper is to provide a brief review on the species, distribution and biological habit of forensically important sarcophagid flies. In addition, the relation between traumatic myiasis and flesh flies, molecular identification methods and developmental pattern of flesh flies are summarized. [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]

Biological sciences are currently in the cultural ascent, promising to provide a theory of everything in the natural and social worlds. Beginning with the decade of the brain in the USA in the 1990s, neuroscience was first onto the stage, but developments in genetics, known as epigenetics, have profound implications for society and culture, and the responses of the state to intimate family life and personal choices. Epigenetics provides an explanation of the mechanisms underpinning the interaction of the environment and the DNA blueprint, and thus invites an interest in the impact of adverse conditions, such as deprivation or normatively deficient parenting. The implications of this biology of social disadvantage for social work are far-reaching. Epigenetics is part of an increasingly political biology with the potential to affect the moral direction of social work. This paper reviews the state of the field and its immediate implications for the profession. [ABSTRACT FROM AUTHOR]

One of the greatest fears associated with the new genetics is the resurgence of eugenics, but too often this assumes the new genetics is eugenics without investigating the diverse definitions and interpretations of eugenics. The aim of this paper is to critically investigate the concept of eugenics in theory and in practice and to question whether the new genetics is a renewal, reform or return of eugenics. The discussion is oriented around six key arguments that illuminate the central points of convergence and divergence between the old eugenics and the new genetics. Ultimately, the paper concludes that despite significant procedural, legislative and administrative differences between the old eugenics and the new genetics, and despite significant spatial, temporal and cultural variations in interpretation and implementation, at the ideological level, there is essentially no difference. The old eugenics was genetics and the new genetics is eugenics. [ABSTRACT FROM AUTHOR]

Biology can be regarded as a science of networks: interactions between various biological entities (eg genes, proteins, metabolites) on different levels (eg gene regulation, cell signalling) can be represented as graphs and, thus, analysis of such networks might shed new light on the function of biological systems. Such biological networks can be obtained from different sources. The extraction of networks from text is an important technique that requires the integration of several different computational disciplines. This paper summarises the most important steps in network extraction and reviews common approaches and solutions for the extraction of biological networks from scientific literature. [ABSTRACT FROM AUTHOR]