Streamlined mean field variational Bayes for longitudinal and multilevel data analysis

Streamlined mean field variational Bayes algorithms for efficient fitting and inference in large models for longitudinal and multilevel data analysis are obtained. The number of operations is linear in the number of groups at each level, which represents a two orders of magnitude improvement over the naïve approach. Storage requirements are also lessened considerably. We treat models for the Gaussian and binary response situations. Our algorithms allow the fastest ever approximate Bayesian analyses of arbitrarily large longitudinal and multilevel datasets, with little degradation in accuracy compared with Markov chain Monte Carlo. The modularity of mean field variational Bayes allows relatively simple extension to more complicated scenarios.     

Detection of apoptosis in tissue sections

During the last few years, detection of apoptosis has evolved from a predominantly morphological basis to the use of ever more specific techniques. The methods widely used to visualize DNA fragmentation in tissue sections are now supplemented by a variety of specific antisera against components of the cell death pathways. Essential requirements for apoptosis detection techniques include high sensitivity for apoptotic cells, the ability to differentiate between apoptotic and necrotic cell death and other forms of DNA damage, and the distinction between different stages of the cell death process. In this overview, we will focus on recent technical advances in apoptosis detection covering improvements of in situ DNA fragmentation techniques, as well as pointing out some of the new tools available for the detection of apoptotic cells in tissue.     

Bone grafts,bone substitutes and orthobiologics: The bridge between basic science and clinical advancements in fracture healing

The biology of fracture healing is better understood than ever before, with advancements such as the locking screw leading to more predictable and less eventful osseous healing. However, at times one’s intrinsic biological response, and even concurrent surgical stabilization, is inadequate. In hopes of facilitating osseous union, bone grafts, bone substitutes and orthobiologics are being relied on more than ever before. The osteoinductive, osteoconductive and osteogenic properties of these substrates have been elucidated in the basic science literature and validated in clinical orthopaedic practice. Furthermore, an industry built around these items is more successful and in demand than ever before. This review provides a comprehensive overview of the basic science, clinical utility and economics of bone grafts, bone substitutes and orthobiologics.     

Bone grafts,bone substitutes and orthobiologics

The biology of fracture healing is better understood than ever before, with advancements such as the locking screw leading to more predictable and less eventful osseous healing. However, at times one’s intrinsic biological response, and even concurrent surgical stabilization, is inadequate. In hopes of facilitating osseous union, bone grafts, bone substitutes and orthobiologics are being relied on more than ever before. The osteoinductive, osteoconductive and osteogenic properties of these substrates have been elucidated in the basic science literature and validated in clinical orthopaedic practice. Furthermore, an industry built around these items is more successful and in demand than ever before. This review provides a comprehensive overview of the basic science, clinical utility and economics of bone grafts, bone substitutes and orthobiologics.     

Comparative Absorption Readings Obtained with Spectrophotometers of Various Types

One of the most important means of identifying a dye is by spectrophotometry. This method has been used as a criterion for judging the samples of stains submitted by manufacturers ever since the certification plan for biological stains was adopted. All specifications that have been drawn up for biological stains, such as those given in the 7th edition of the National Formulary, have included spectrophotometry requirements.     

Progress in paediatric parasitology: a preface to a topic focusing on ever younger subjects

Without realizing it perhaps, the research activities of many parasitologists are often focused upon the study of parasites most commonly found in children. Though there is little recognition of paediatric parasitology as a separate topic within medical parasitology, with the global interest in promotion of maternal and child health, alleviation of diseases associated with poverty and requirements of 'child-sized' medicines, a more formal consideration is now timely. Recent research, for example, has highlighted that defining precisely the 'first-age' at which parasites interfere with a child's health, or normal developmental processes, is being revised. Attention is now drawn towards ever younger subjects, for parasites have the capacity to also influence the health of the foetus within the in utero environment, altering immune-development. These subtle, yet evolutionary profound interactions perhaps manifest themselves as to why some children are more prone to infection(s), develop overt disease and sadly die while others do not. Here, we address the growing importance of paediatric parasitology and its applications within disease control strategies as highlighted in the 2010 Autumn Symposium of the British Society of Parasitology.     

Learning to extract relations for protein annotation

MOTIVATION: Protein annotation is a task that describes protein X in terms of topic Y. Usually, this is constructed using information from the biomedical literature. Until now, most of literature-based protein annotation work has been done manually by human annotators. However, as the number of biomedical papers grows ever more rapidly, manual annotation becomes more difficult, and there is increasing need to automate the process. Recently, information extraction (IE) has been used to address this problem. Typically, IE requires pre-defined relations and hand-crafted IE rules or annotated corpora, and these requirements are difficult to satisfy in real-world scenarios such as in the biomedical domain. In this article, we describe an IE system that requires only sentences labelled according to their relevance or not to a given topic by domain experts. RESULTS: We applied our system to meet the annotation needs of a well-known protein family database; the results show that our IE system can annotate proteins with a set of extracted relations by learning relations and IE rules for disease, function and structure from only relevant and irrelevant sentences.     

Single mothers in Ontario: sociodemographic,physical and mental health characteristics

OBJECTIVE: To examine the sociodemographic, physical and mental health characteristics of single mothers in Ontario. DESIGN: Cross-sectional. SETTING: Ontario. PARTICIPANTS: Ontario residents aged 15 years or older who participated in the Ontario Health Supplement survey conducted between December 1990 and April 1991; of 9953 eligible participants, 1540 were mothers with at least 1 dependent child (less than 16 years of age). OUTCOME MEASURES: Prevalence rates of sociodemographic, physical and mental health characteristics. RESULTS: Single mothers were significantly more likely than the mothers in 2-parent families to be poor, to be 25 years of age or less, to have mental health problems (dissatisfaction with multiple aspects of life, affective disorder ever and 1 or more psychiatric disorders in the past year or ever) and to use mental health services. When compared by income level, poor single mothers had a higher prevalence of all mental health outcomes measured; the difference was significant for anxiety disorder in the past year or ever and for 1 or more psychiatric disorders in the past year or ever. In a logistic regression analysis, single-mother status was found to have the strongest independent effect on predicting mental health morbidity and utilization of mental health services; the next strongest was low income. CONCLUSIONS: Single mothers are more likely to be poor, to have an affective disorder and to use mental health services than mothers in 2-parent families. The risk of mental health problems is especially pronounced among poor single mothers. Further studies are needed to determine which aspects of single motherhood, apart from economic status, affect mental health outcomes.     

Modeling genomic data with type attributes, balancing stability and maintainability

Background  

Molecular biology (MB) is a dynamic research domain that benefits greatly from the use of modern software technology in preparing experiments, analyzing acquired data, and even performing "in-silico" analyses. As ever new findings change the face of this domain, software for MB has to be sufficiently flexible to accommodate these changes. At the same time, however, the efficient development of high-quality and interoperable software requires a stable model of concepts for the subject domain and their relations. The result of these two contradictory requirements is increased complexity in the development of MB software.     

A future for seafood point-of-origin testing using DNA and stable isotope signatures

Reviews in Fish Biology and Fisheries - Demand for seafood products is increasing worldwide, contributing to ever more complex supply chains and posing challenges to trace their origin and...     

Biofuels – for better or worse?

The present world population is largely fed by ‘industrialised agriculture’. This, in turn, depends on massive inputs of fossil fuels. While this energy expenditure is inescapable, it is an expensive way of ‘converting oil into potatoes'. Arguably, in view of global climate change, ever increasing population, ever increasing oil prices, ever diminishing availability of water and arable land, this is not sustainable. Despite the fact that biofuels inevitably compete for resources that might otherwise be used to grow, store and distribute food, they are frequently held to be desirable and feasible ‘green’ substitutes for fossil fuels and even that they spare carbon emissions to the atmosphere. This article challenges the absurdity of such ‘retro-agriculture’ (i.e. except in a few local circumstances) incurring yet more energy expenditure. It seeks to illustrate the misinformation on which some of the advocacy of biofuels has been based.     

Mayday - integrative analytics for expression data

Background  

DNA Microarrays have become the standard method for large scale analyses of gene expression and epigenomics. The increasing complexity and inherent noisiness of the generated data makes visual data exploration ever more important. Fast deployment of new methods as well as a combination of predefined, easy to apply methods with programmer's access to the data are important requirements for any analysis framework. Mayday is an open source platform with emphasis on visual data exploration and analysis. Many built-in methods for clustering, machine learning and classification are provided for dissecting complex datasets. Plugins can easily be written to extend Mayday's functionality in a large number of ways. As Java program, Mayday is platform-independent and can be used as Java WebStart application without any installation. Mayday can import data from several file formats, database connectivity is included for efficient data organization. Numerous interactive visualization tools, including box plots, profile plots, principal component plots and a heatmap are available, can be enhanced with metadata and exported as publication quality vector files.     

Biomaterials for High‐Energy Lithium‐Based Batteries: Strategies,Challenges, and Perspectives

Developing high‐performance batteries through applying renewable resources is of great significance for meeting ever‐growing energy demands and sustainability requirements. Biomaterials have overwhelming advantages in material abundance, environmental benignity, low cost, and more importantly, multifunctionalities from structural and compositional diversity. Therefore, significant and fruitful research on exploiting various natural biomaterials (e.g., soy protein, chitosan, cellulose, fungus, etc.) for boosting high‐energy lithium‐based batteries by means of making or modifying critical battery components (e.g., electrode, electrolyte, and separator) are reported. In this review, the recent advances and main strategies for adopting biomaterials in electrode, electrolyte, and separator engineering for high‐energy lithium‐based batteries are comprehensively summarized. The contributions of biomaterials to stabilizing electrodes, capturing electrochemical intermediates, and protecting lithium metal anodes/enhancing battery safety are specifically emphasized. Furthermore, advantages and challenges of various strategies for fabricating battery materials via biomaterials are described. Finally, future perspectives and possible solutions for further development of biomaterials for high‐energy lithium‐based batteries are proposed.     

Synthetic biology--putting engineering into biology

Synthetic biology is interpreted as the engineering-driven building of increasingly complex biological entities for novel applications. Encouraged by progress in the design of artificial gene networks, de novo DNA synthesis and protein engineering, we review the case for this emerging discipline. Key aspects of an engineering approach are purpose-orientation, deep insight into the underlying scientific principles, a hierarchy of abstraction including suitable interfaces between and within the levels of the hierarchy, standardization and the separation of design and fabrication. Synthetic biology investigates possibilities to implement these requirements into the process of engineering biological systems. This is illustrated on the DNA level by the implementation of engineering-inspired artificial operations such as toggle switching, oscillating or production of spatial patterns. On the protein level, the functionally self-contained domain structure of a number of proteins suggests possibilities for essentially Lego-like recombination which can be exploited for reprogramming DNA binding domain specificities or signaling pathways. Alternatively, computational design emerges to rationally reprogram enzyme function. Finally, the increasing facility of de novo DNA synthesis-synthetic biology's system fabrication process-supplies the possibility to implement novel designs for ever more complex systems. Some of these elements have merged to realize the first tangible synthetic biology applications in the area of manufacturing of pharmaceutical compounds.     

MULTI‐LEVEL SEXUAL SELECTION: INDIVIDUAL AND FAMILY‐LEVEL SELECTION FOR MATING SUCCESS IN A HISTORICAL HUMAN POPULATION

Precopulatory sexual selection is the association between fitness and traits associated with mate acquisition. Although sexual selection is generally recognized to be a powerful evolutionary force, most investigations are limited to characters belonging to individuals. A broader multilevel perspective acknowledges that individual fitness can be affected by aspects of mating success that are characters of groups, such as families. Parental mating success in polygynous or polyandrous human societies may exemplify traits under group‐level sexual selection. Using fitness measures that account for age‐structure, I measure multilevel selection for mate number over 55 years in a human population with declining rates of polygyny. Sexual selection had three components: individual‐level selection for ever‐mating (whether an individual mated) and individual‐ and family‐level selection for polyandry and polygyny. Family‐ and individual‐level selection for polygyny was equally strong, three times stronger than family‐level selection for polyandry and more than an order of magnitude stronger than individual‐level selection for polyandry. However, individual‐level selection for polyandry and polygyny was more effective at explaining relative fitness variance than family‐level selection. Selection for ever‐mating was the most important source of sexual selection for fitness; variation for ever‐mating explained 23% of relative fitness variance.     

Current status and future prospects for ion-mobility mass spectrometry in the biopharmaceutical industry

Detailed characterization of protein reagents and biopharmaceuticals is key in defining successful drug discovery campaigns, aimed at bringing molecules through different discovery stages up to development and commercialization. There are many challenges in this process, with complex and detailed analyses playing paramount roles in modern industry.Mass spectrometry (MS) has become an essential tool for characterization of proteins ever since the onset of soft ionization techniques and has taken the lead in quality assessment of biopharmaceutical molecules, and protein reagents, used in the drug discovery pipeline. MS use spans from identification of correct sequences, to intact molecule analyses, protein complexes and more recently epitope and paratope identification.MS toolkits could be incredibly diverse and with ever evolving instrumentation, increasingly novel MS-based techniques are becoming indispensable tools in the biopharmaceutical industry. Here we discuss application of Ion Mobility MS (IMMS) in an industrial setting, and what the current applications and outlook are for making IMMS more mainstream.     

Why media relations matter

There is a common misperception that only medium- and large-cap biotechs need to understand and interact with the media. As investor demands increase and partnering dynamics evolve, startups need to understand the art of media relations more now than ever before.     

Functional landscapes in cities: a systems approach

Human enterprise and endeavour increasingly influence global processes of change, from the planetary scale down to the very local. Cities are hubs of human activity, and as the places where the majority of the world’s population live we must, when looking into an uncertain future, consider how we think about urban design. Cities are densely inhabited, lived-in landscapes where human presence and perceptions are deeply enmeshed with biophysical and built infrastructures. As such, they present complex mosaics of different habitats and competing uses, ever changing in response to human and physical drivers. If designed properly, green infrastructure can contribute many important functions to a city. Efforts to strategically make use of green infrastructure can benefit considerably from a systems perspective where linkages and cross-boundary dynamics are at the very least as important as individual components. Design, planning and governance of requirements for green infrastructure also extend far beyond biophysical elements and components. Recognition of interconnections between individual green spaces, green infrastructure and the built environment, the physical environment and diverse actors, and formal and informal governance arrangements—as outlined in the four design principles in this article—is a first important step towards a more comprehensive and inclusive approach, not least to green infrastructure planning and design.