Engage the hodgepodge: management factors are essential when prioritizing areas for restoration and conservation action

Restoration and conservation initiatives, such as the eradication of invasive alien plants, should be guided by scientific evidence. Typically, ecological data alone is used to inform the decision‐making of these initiatives. Recent advances in the mapping of conservation opportunity include a diverse range of scientifically‐identified factors that determine the feasibility and likely effectiveness of conservation initiatives, and include, for example, data on the willingness and capacity of land managers to be effectively involved. Social research techniques such as interview surveys, phenomenology, and social network analysis are important approaches for securing useful human and social data. These approaches are yet to be widely adopted in restoration initiatives, but could be usefully applied to improve the effective implementation of these initiatives. Restoration and conservation planners will deliver spatial prioritisations which provide more effective and cost‐efficient decision‐making if they include not simply ecological data, but also data on economic, human, management, social and vulnerability factors that determine implementation effectiveness.     

HPSLPred: An Ensemble Multi‐Label Classifier for Human Protein Subcellular Location Prediction with Imbalanced Source

Predicting the subcellular localization of proteins is an important and challenging problem. Traditional experimental approaches are often expensive and time‐consuming. Consequently, a growing number of research efforts employ a series of machine learning approaches to predict the subcellular location of proteins. There are two main challenges among the state‐of‐the‐art prediction methods. First, most of the existing techniques are designed to deal with multi‐class rather than multi‐label classification, which ignores connections between multiple labels. In reality, multiple locations of particular proteins imply that there are vital and unique biological significances that deserve special focus and cannot be ignored. Second, techniques for handling imbalanced data in multi‐label classification problems are necessary, but never employed. For solving these two issues, we have developed an ensemble multi‐label classifier called HPSLPred, which can be applied for multi‐label classification with an imbalanced protein source. For convenience, a user‐friendly webserver has been established at http://server.malab.cn/HPSLPred.     

Detecting and adjusting for small-study effects in meta-analysis

Publication bias and related types of small-study effects threaten the validity of systematic reviews. The existence of small-study effects has been demonstrated in empirical studies. Small-study effects are graphically diagnosed by inspection of the funnel plot. Though observed funnel plot asymmetry cannot be easily linked to a specific reason, tests based on funnel plot asymmetry have been proposed. Beyond a vast range of funnel plot tests, there exist several methods for adjusting treatment effect estimates for these biases. In this article, we consider the trim-and-fill method, the Copas selection model, and more recent regression-based approaches. The methods are exemplified using a meta-analysis from the literature and compared in a simulation study, based on binary response data. They are also applied to a large set of meta-analyses. Some fundamental differences between the approaches are discussed. An assumption common to the trim-and-fill method and the Copas selection model is that the small-study effect is caused by selection. The trim-and-fill method corresponds to an unknown implicit model generated by the symmetry assumption, whereas the Copas selection model is a parametric statistical model. However, it requires a sensitivity analysis. Regression-based approaches are easier to implement and not based on a specific selection model. Both simulations and applications suggest that in the presence of strong selection both the trim-and-fill method and the Copas selection model may not fully eliminate bias, while regression-based approaches seem to be a promising alternative.     

Cross-disciplinary approaches for better research: The case of birds and bats

Across a wide range of disciplines, mounting evidence points to solutions for addressing the global biodiversity and climate crisis through sustainable land use development. Managing ecosystem services offers promising potential of combining environmental, economic, and social interests in this process. Achieving sustainability, however, requires collaboration across disciplines, or in short “cross-disciplinary” approaches. Multi-, inter- and transdisciplinary approaches are often used as synonyms, although they are defined by different levels of integrating results and perspectives. We highlight challenges and opportunities related to these cross-disciplinary approaches by using research on bird- and bat-mediated ecosystem services as a case - with a focus on sustainable agricultural development. Examples from transdisciplinary collaborations show how more integrative and inclusive approaches promote the implementation of basic and applied ecological research into land use practices. Realizing this opportunity requires strong partnerships between science, practice and policy, as well as integration of diverse skills and perspectives. If appropriately funded and guided, this effort is rewarded by improved data quality, more targeted concepts, as well as improvement implementation and impact of sustainability research and practice. We outline a stepwise approach for developing these processes and highlight case studies from bird and bat research to inspire cross-disciplinary approaches within and beyond ecology.     

Transgenesis procedures in Xenopus

Stable integration of foreign DNA into the frog genome has been the purpose of several studies aimed at generating transgenic animals or producing mutations of endogenous genes. Inserting DNA into a host genome can be achieved in a number of ways. In Xenopus, different strategies have been developed which exhibit specific molecular and technical features. Although several of these technologies were also applied in various model organizms, the attributes of each method have rarely been experimentally compared. Investigators are thus confronted with a difficult choice to discriminate which method would be best suited for their applications. To gain better understanding, a transgenesis workshop was organized by the X-omics consortium. Three procedures were assessed side-by-side, and the results obtained are used to illustrate this review. In addition, a number of reagents and tools have been set up for the purpose of gene expression and functional gene analyses. This not only improves the status of Xenopus as a powerful model for developmental studies, but also renders it suitable for sophisticated genetic approaches. Twenty years after the first reported transgenic Xenopus, we review the state of the art of transgenic research, focusing on the new perspectives in performing genetic studies in this species.     

Hydroxyproline‐rich Glycoproteins and Plant Defence

The distinguished plant cell wall component referred to as hydroxyproline‐rich glycoproteins (HRGPs) exists in two forms: soluble in the symplast and insoluble in the apoplast. Insolubilization of HRGPs in cell walls through oxidative cross‐linking which is elicited by stress represents a characteristic feature exhibited by two classes of HRGPs, namely, extensins and proline/HRGPs. Cross‐linking of these HRGPs is an important process to strengthen the cell walls that contributes to plant defence reactions. In this review, the available information on these proteins is analysed with respect to their roles in host‐pathosystems and the various techniques applied for their characterization. Future prospects on strengthening of cell walls through gene regulation and transgenic approaches are also addressed.     

Molecular genetic approaches to the cytoskeleton in Dictyostelium.

Recent advances in molecular genetic techniques are being applied in Dictyostelium to test and expand prevailing views on the functioning of the actin-based cytoskeleton. Current research involves the disruption, by homologous recombination, of genes encoding cytoskeletal elements. We suggest combining classical and molecular genetic approaches to supplement these investigations.     

New visions of dental tissue research: Tooth development,chemistry, and structure

Teeth are one of the best preserved and most commonly recovered elements in primate fossil assemblages. Taxonomic, functional, and phylogenetic hypotheses often rely on dental characters, despite considerable evidence of homoplasy in tooth form and large variation in tooth size within and among primates.^1,2 Recent studies have led to new areas of research centered on incremental tooth development, chemical composition, and internal structure. Due to rapid technological developments in imaging and elemental sampling, these new approaches have the potential to increase our understanding of developmental biology, including not only changes in the pace of growth and reproduction, but also our assessments of diets, migration patterns, environments, and taxonomy. The integration of these temporal, chemical, and structural approaches heralds a bright future for the role of dental tissue research in evolutionary anthropology. © 2008 Wiley‐Liss, Inc.     

Don't forget to look down – collaborative approaches to predator conservation

Finding effective ways of conserving large carnivores is widely recognised as a priority in conservation. However, there is disagreement about the most effective way to do this, with some favouring top‐down ‘command and control’ approaches and others favouring collaboration. Arguments for coercive top‐down approaches have been presented elsewhere; here we present arguments for collaboration. In many parts of the developed world, flexibility of approach is built into the legislation, so that conservation objectives are balanced with other legitimate goals. In the developing world, limited resources, poverty and weak governance mean that collaborative approaches are likely to play a particularly important part in carnivore conservation. In general, coercive policies may lead to the deterioration of political legitimacy and potentially to non‐compliance issues such as illegal killing, whereas collaborative approaches may lead to psychological ownership, enhanced trust, learning, and better social outcomes. Sustainable hunting/trapping plays a crucial part in the conservation and management of many large carnivores. There are many different models for how to conserve carnivores effectively across the world, research is now required to reduce uncertainty and examine the effectiveness of these approaches in different contexts.     

Targeted and Untargeted Proteomics Approaches in Biomarker Development

An enormous amount of research effort has been devoted to biomarker discovery and validation. With the completion of the human genome, proteomics is now playing an increasing role in this search for new and better biomarkers. Here, what leads to successful biomarker development is reviewed and how these features may be applied in the context of proteomic biomarker research is considered. The “fit‐for‐purpose” approach to biomarker development suggests that untargeted proteomic approaches may be better suited for early stages of biomarker discovery, while targeted approaches are preferred for validation and implementation. A systematic screening of published biomarker articles using MS‐based proteomics reveals that while both targeted and untargeted technologies are used in proteomic biomarker development, most researchers do not combine these approaches. i) The reasons for this discrepancy, (ii) how proteomic technologies can overcome technical challenges that seem to limit their translation into the clinic, and (iii) how MS can improve, complement, or replace existing clinically important assays in the future are discussed.     

Drosophila with postponed aging as a model for aging research.

Species of the genus Drosophila, commonly known as "fruitflies," are good model systems for research in aging. Drosophila are extremely well-known genetically, developmentally, and otherwise. They are also genetically analogous to mammalian species in most important respects. Previous work with Drosophila has been hampered by inbreeding depression, but more recent work using selection has created Drosophila with postponed aging that is inherited normally. Genetic transformation has also increased Drosophila life spans in some cases. Several biologic approaches have been applied to the analysis of genetically postponed aging in Drosophila: quantitative genetics, organismal physiology, and protein electrophoresis. Ultimately, these different approaches will be integrated into an overall analysis of aging in Drosophila, one that could be valuable for research with other taxa as well.     

Model collaboration for the improved assessment of biomass supply,demand, and impacts

Existing assessments of biomass supply and demand and their impacts face various types of limitations and uncertainties, partly due to the type of tools and methods applied (e.g., partial representation of sectors, lack of geographical details, and aggregated representation of technologies involved). Improved collaboration between existing modeling approaches may provide new, more comprehensive insights, especially into issues that involve multiple economic sectors, different temporal and spatial scales, or various impact categories. Model collaboration consists of aligning and harmonizing input data and scenarios, model comparison and/or model linkage. Improved collaboration between existing modeling approaches can help assess (i) the causes of differences and similarities in model output, which is important for interpreting the results for policy‐making and (ii) the linkages, feedbacks, and trade‐offs between different systems and impacts (e.g., economic and natural), which is key to a more comprehensive understanding of the impacts of biomass supply and demand. But, full consistency or integration in assumptions, structure, solution algorithms, dynamics and feedbacks can be difficult to achieve. And, if it is done, it frequently implies a trade‐off in terms of resolution (spatial, temporal, and structural) and/or computation. Three key research areas are selected to illustrate how model collaboration can provide additional ways for tackling some of the shortcomings and uncertainties in the assessment of biomass supply and demand and their impacts. These research areas are livestock production, agricultural residues, and greenhouse gas emissions from land‐use change. Describing how model collaboration might look like in these examples, we show how improved model collaboration can strengthen our ability to project biomass supply, demand, and impacts. This in turn can aid in improving the information for policy‐makers and in taking better‐informed decisions.     

Informal education and health promoting approaches in adult cancer survivors

This review looks at the available data relating to the informal education aspects and other health promoting approaches applied by adult cancer survivors to reduce the risk of cancer. The implications of such behavioral interventions on oncology practice are discussed. We also highlight areas of future research to pursue. Available data show that many cancer survivors remain engaged in risky health behaviors post-diagnosis, which are associated with an increased risk of disease's recurrence. However, over the last years patients seem to increasingly receive adequate risk-based medical care. The application of appropriate informal education approaches, such as diet, exercise, and cessation of former unhealthy habits, such as smoking and alcohol has facilitated behavioral changes in cancer survivors, thoroughly improving their well being and overall quality of life (QOL). Most of the research studies published to date have applied structured lifestyle interventions on intensive, individualized counseling sessions delivered by trained personnel or psychosocial-based mediations and reported that these approaches are largely effective in promoting the adoption of a healthier lifestyle in cancer survivors. These interventions have been reported to reduce the risk of cancer recurrence and thus to obtain an obvious positive impact on their well-being and overall QOL. However, there is still insufficient evidence to conclude and support with confidence the effectiveness of any of these behavioral interventions and therefore future interventions should be initiated to assess the long-term effects and validating outcomes of lifestyle and other psychosocial interventions.     

A critique for phytosociology

Abstract. Phytosociology is a subdiscipline of plant ecology that describes the co‐occurrence of plant species in communities. Gradient analysis and classification are its complementary tools. Various peculiarities and anachronisms of Central European phytosociology conceal its similarity with Anglo‐American approaches. Phytosociology deserves to be updated as a part of modern vegetation science that can build on a vast heritage of high‐quality data and the tools to store and analyse them in ways that go beyond syntaxonomy. By providing a context to more specialized pure and applied research, it has a crucial role to play in understanding community structure, ecosystem functioning and biological evolution.     

Single Material Solar Cells: the Next Frontier for Organic Photovoltaics?

An overview of various approaches for the realization of single‐material organic solar cells (SMOCs) is presented. Fullerene‐conjugated systems dyads, di‐block copolymers, and self‐organized donor‐acceptor molecules all represent different possible approaches towards SMOCs. Although each of them presents specific advantages and poses specific problems of design and synthesis, these different routes have witnessed significant progress in the past few years and SMOCs with efficiencies in the range of 1.50% have been realized. These performances are already higher than those of bi‐component bulk heterojunction solar cells some ten years ago, demonstrating that SMOCs can represent a credible approach towards efficient and simple organic solar cells. Possible directions for future research are discussed with the aim of stimulating further research on this exciting topic.     

Exploring proteasome complexes by proteomic approaches

The ubiquitin proteasome system (UPS) represents a major pathway for intracellular protein degradation. Proteasome dependent protein quality control participates in cell cycle, immune response and apoptosis. Therefore, the UPS is in focus of therapeutic investigations and the development of pharmaceutical agents. Detailed analyses on proteasome structure and function are the foundation for drug development and clinical studies. Proteomic approaches contributed significantly to our current knowledge in proteasome research. In particular, 2-DE has been essential in facilitating the development of current models on molecular composition and assembly of proteasome complexes. Furthermore, developments in MS enabled identification of UPS proteins and their PTMs at high accuracy and high-throughput. First results on global characterization of the UPS are also available. Although the UPS has been intensively investigated within the last two decades, its functional significance and contribution to the regulation of cell and tissue phenotypes remain to be explored. This review recapitulates a variety of applied proteomic approaches in proteasome exploration, and presents an overview of current technologies and their potential in driving further investigations.     

How a growing organismal perspective is adding new depth to integrative studies of morphological evolution

Over the past half century, the field of Evolutionary Developmental Biology, or Evo‐devo, has integrated diverse fields of biology into a more synthetic understanding of morphological diversity. This has resulted in numerous insights into how development can evolve and reciprocally influence morphological evolution, as well as generated several novel theoretical areas. Although comparative by default, there remains a great gap in our understanding of adaptive morphological diversification and how developmental mechanisms influence the shape and pattern of phenotypic variation. Herein we highlight areas of research that are in the process of filling this void, and areas, if investigated more fully, that will add new insights into the diversification of morphology. At the centre of our discussion is an explicit awareness of organismal biology. Here we discuss an organismal framework that is supported by three distinct pillars. First, there is a need for Evo‐devo to adopt a high‐resolution phylogenetic approach in the study of morphological variation and its developmental underpinnings. Secondly, we propose that to understand the dynamic nature of morphological evolution, investigators need to give more explicit attention to the processes that generate evolutionarily relevant variation at the population level. Finally, we emphasize the need to address more thoroughly the processes that structure variation at micro‐ and macroevolutionary scales including modularity, morphological integration, constraint, and plasticity. We illustrate the power of these three pillars using numerous examples from both invertebrates and vertebrates to emphasize that many of these approaches are already present within the field, but have yet to be formally integrated into many research programs. We feel that the most exciting new insights will come where the traditional experimental approaches to Evo‐devo are integrated more thoroughly with the principles of this organismal framework.     

SINGLE MATERIAL SOLAR CELLS: Single Material Solar Cells: the Next Frontier for Organic Photovoltaics? (Adv. Energy Mater. 2/2011)

An overview of various approaches for the realization of single‐material organic solar cells (SMOCs) is presented. Fullerene‐conjugated systems dyads, di‐block copolymers, and self‐organized donor‐acceptor molecules all represent different possible approaches towards SMOCs. Although each of them presents specific advantages and poses specific problems of design and synthesis, these different routes have witnessed significant progress in the past few years and SMOCs with efficiencies in the range of 1.50% have been realized. These performances are already higher than those of bi‐component bulk heterojunction solar cells some ten years ago, demonstrating that SMOCs can represent a credible approach towards efficient and simple organic solar cells. Possible directions for future research are discussed with the aim of stimulating further research on this exciting topic.     

Systems approaches in global change and biogeochemistry research

Systems approaches have great potential for application in predictive ecology. In this paper, we present a range of examples, where systems approaches are being developed and applied at a range of scales in the field of global change and biogeochemical cycling. Systems approaches range from Bayesian calibration techniques at plot scale, through data assimilation methods at regional to continental scales, to multi-disciplinary numerical model applications at country to global scales. We provide examples from a range of studies and show how these approaches are being used to address current topics in global change and biogeochemical research, such as the interaction between carbon and nitrogen cycles, terrestrial carbon feedbacks to climate change and the attribution of observed global changes to various drivers of change. We examine how transferable the methods and techniques might be to other areas of ecosystem science and ecology.