Methodological Aspects of Shift-Work Research

A major issue in shift-work research is to understand the possible ways in which shift work can impact performance and health. Nearly all body functions, from those of the cellular level to those of the entire body, are circadian rhythmic. Disturbances of these rhythms as well as the social consequences of odd work hours are of importance for the health and well-being of shift workers. This article reviews a number of common methodological issues which are of relevance to epidemiological studies in this area of research. It discusses conceptual problems regarding the use of the term “shift work,” and it underscores the need to develop models that explain the mechanisms of disease in shift workers.     

Methodological aspects of shift-work research

A major issue in shift-work research is to understand the possible ways in which shift work can impact performance and health. Nearly all body functions, from those of the cellular level to those of the entire body, are circadian rhythmic. Disturbances of these rhythms as well as the social consequences of odd work hours are of importance for the health and well-being of shift workers. This article reviews a number of common methodological issues which are of relevance to epidemiological studies in this area of research. It discusses conceptual problems regarding the use of the term "shift work," and it underscores the need to develop models that explain the mechanisms of disease in shift workers.     

Value of long‐term ecological studies

Long‐term ecological studies are critical for providing key insights in ecology, environmental change, natural resource management and biodiversity conservation. In this paper, we briefly discuss five key values of such studies. These are: (1) quantifying ecological responses to drivers of ecosystem change; (2) understanding complex ecosystem processes that occur over prolonged periods; (3) providing core ecological data that may be used to develop theoretical ecological models and to parameterize and validate simulation models; (4) acting as platforms for collaborative studies, thus promoting multidisciplinary research; and (5) providing data and understanding at scales relevant to management, and hence critically supporting evidence‐based policy, decision making and the management of ecosystems. We suggest that the ecological research community needs to put higher priority on communicating the benefits of long‐term ecological studies to resource managers, policy makers and the general public. Long‐term research will be especially important for tackling large‐scale emerging problems confronting humanity such as resource management for a rapidly increasing human population, mass species extinction, and climate change detection, mitigation and adaptation. While some ecologically relevant, long‐term data sets are now becoming more generally available, these are exceptions. This deficiency occurs because ecological studies can be difficult to maintain for long periods as they exceed the length of government administrations and funding cycles. We argue that the ecological research community will need to coordinate ongoing efforts in an open and collaborative way, to ensure that discoverable long‐term ecological studies do not become a long‐term deficiency. It is important to maintain publishing outlets for empirical field‐based ecology, while simultaneously developing new systems of recognition that reward ecologists for the use and collaborative sharing of their long‐term data sets. Funding schemes must be re‐crafted to emphasize collaborative partnerships between field‐based ecologists, theoreticians and modellers, and to provide financial support that is committed over commensurate time frames.     

Ethical issues in ageing and biography

The increasing use of biographical materials in research and intervention in the field of ageing gives rise to significant ethical issues. In this inquiry, four of these issues are explicated. First, the notion of informed consent is explored in relation to selected contexts of research and intervention in ageing and biography. Second, the issues of autonomy and competence are considered from the point of view of identifying contexts where biography is a prerequisite for ethically responsive action. The third ethical issue concerns respecting the groundrules of various biographical approaches. Finally, the notions of authenticity and truth in lifestories are explored in an attempt to clarify the limitations and expectations of ageing and biography. The discussion of these ethical issues proceeds on the basis of an argument that indicates the fundamental importance of biographical ageing or the stories we are.     

Effects of d‐galactose‐induced ageing on the heart and its potential interventions

Ageing is a strong independent risk factor for disability, morbidity and mortality. Post‐mitotic cells including those in the heart are a particular risk to age‐related deterioration. As the occurrence of heart disease is increasing rapidly with an ageing population, knowledge regarding the mechanisms of age‐related cardiac susceptibility and possible therapeutic interventions needs to be acquired to prevent advancing levels of heart disease. To understand more about the ageing heart, numerous aged animal models are being used to explore the underlying mechanisms. Due to time‐consuming for investigations involving naturally aged animals, mimetic ageing models are being utilized to assess the related effects of ageing on disease occurrence. d ‐galactose is one of the substances used to instigate ageing in various models, and techniques involving this have been widely used since 1991. However, the mechanism through which d ‐galactose induces ageing in the heart remains unclear. The aim of this review was to comprehensively summarize the current findings from in vitro and in vivo studies on the effects of d ‐galactose‐induced ageing on the heart, and possible therapeutic interventions against ageing heart models. From this review, we hope to provide invaluable information for future studies and based on the findings from experiments involving animals, we can inform possible therapeutic strategies for the prevention of age‐related heart diseases in clinical settings.     

Shared and unique features of mammalian sleep spindles – insights from new and old animal models

Sleep spindles are phasic events observed in mammalian non-rapid eye movement sleep. They are relevant today in the study of memory consolidation, sleep quality, mental health and ageing. We argue that our advanced understanding of their mechanisms has not exhausted the utility and need for animal model work. This is both because some topics, like cognitive ageing, have not yet been addressed sufficiently in comparative efforts and because the evolutionary history of this oscillation is still poorly understood. Comparisons across species often are either limited to referencing the classical cat and rodent models, or are over-inclusive, uncritically including reports of sleep spindles in rarely studied animals. In this review, we discuss the emergence of new (dog and sheep) models for sleep spindles and compare the strengths and shortcomings of new and old models based on the three validation criteria for animal models – face, predictive, and construct validity. We conclude that an emphasis on cognitive ageing might dictate the future of comparative sleep spindle studies, a development that is already becoming visible in studies on dogs. Moreover, reconstructing the evolutionary history of sleep spindles will require more stringent criteria for their identification, across more species. In particular, a stronger emphasis on construct and predictive validity can help verify if spindle-like events in other species are actual sleep spindles. Work in accordance with such stricter validation suggests that sleep spindles display more universally shared features, like defining frequency, than previously thought.     

Below-threshold mortality: implications for studies in evolution,ecology and demography

Evolutionary biologists, ecologists and experimental gerontologists have increasingly used estimates of age-specific mortality as a critical component in studies of a range of important biological processes. However, the analysis of age-specific mortality rates is plagued by specific statistical challenges caused by sampling error. Here we discuss the nature of this ‘demographic sampling error’, and the way in which it can bias our estimates of (1) rates of ageing, (2) age at onset of senescence, (3) costs of reproduction and (4) demographic tests of evolutionary models of ageing. We conducted simulations which suggest that using standard statistical techniques, we would need sample sizes on the order of tens of thousands in most experiments to effectively remove any bias due to sampling error. We argue that biologists should use much larger sample sizes than have previously been used. However, we also present simple maximum likelihood models that effectively remove biases due to demographic sampling error even at relatively small sample sizes.     

Accounting for Age Uncertainty in Growth Modeling,the Case Study of Yellowfin Tuna (Thunnus albacares) of the Indian Ocean

Age estimates, typically determined by counting periodic growth increments in calcified structures of vertebrates, are the basis of population dynamics models used for managing exploited or threatened species. In fisheries research, the use of otolith growth rings as an indicator of fish age has increased considerably in recent decades. However, otolith readings include various sources of uncertainty. Current ageing methods, which converts an average count of rings into age, only provide periodic age estimates in which the range of uncertainty is fully ignored. In this study, we describe a hierarchical model for estimating individual ages from repeated otolith readings. The model was developed within a Bayesian framework to explicitly represent the sources of uncertainty associated with age estimation, to allow for individual variations and to include knowledge on parameters from expertise. The performance of the proposed model was examined through simulations, and then it was coupled to a two-stanza somatic growth model to evaluate the impact of the age estimation method on the age composition of commercial fisheries catches. We illustrate our approach using the saggital otoliths of yellowfin tuna of the Indian Ocean collected through large-scale mark-recapture experiments. The simulation performance suggested that the ageing error model was able to estimate the ageing biases and provide accurate age estimates, regardless of the age of the fish. Coupled with the growth model, this approach appeared suitable for modeling the growth of Indian Ocean yellowfin and is consistent with findings of previous studies. The simulations showed that the choice of the ageing method can strongly affect growth estimates with subsequent implications for age-structured data used as inputs for population models. Finally, our modeling approach revealed particularly useful to reflect uncertainty around age estimates into the process of growth estimation and it can be applied to any study relying on age estimation.     

The rise of model protozoa

It is timely to evaluate the role of protozoa as model organisms given their diversity, abundance and versatility as well as the economic and ethical pressures placed on animal-based experimentation. We first define the term model organism and then examine through examples why protozoa make good models. Our examples reflect major issues including evolution, ecology, population and community biology, disease, the role of organelles, ageing, space travel, toxicity and teaching. We conclude by recognising that although protozoa may in some cases not completely mimic tissue- or whole-animal-level processes, they are extremely flexible and their use should be embraced. Finally, we offer advice on obtaining emergent model protozoa.     

Incorporating the impacts of climate change into infrastructure life cycle assessments: A case study of pavement service life performance

Climate change is expected to impact both the operational and structural performance of infrastructures such as roads, bridges, and buildings. However, most past life cycle assessment (LCA) studies do not consider how the operational/structural performance of infrastructure will be affected by a changing climate. The goal of this research was to develop a framework for integrating climate change impacts into LCA of infrastructure systems. To illustrate this framework, a flexible pavement case study was considered where life‐cycle environmental impacts were compared across a climate change scenario and several time horizons. The Mechanistic‐Empirical Pavement Design Guide (MEPDG) was utilized to capture the structural performance of each pavement performance scenario and performance distresses were used as inputs into a pavement LCA model that considered construction and maintenance/rehabilitation materials and activities, change in relative surface albedo, and impacts due to traffic. The results from the case study suggest that climate change will likely call for adaptive design requirements in the latter half of this century but in the near‐to‐mid term, the international roughness index (IRI) and total rutting degradation profile was very close to the historical climate run. While the inclusion of mechanistic performance models with climate change data as input introduces new uncertainties to infrastructure‐based LCA, sensitivity analyses runs were performed to better understand a comprehensive range of result outcomes. Through further infrastructure cases the framework could be streamlined to better suit specific infrastructures where only the infrastructure components with the greatest sensitivity to climate change are explicitly modeled using mechanistic‐empirical modeling routines.     

Coordinated approaches to quantify long‐term ecosystem dynamics in response to global change

Many serious ecosystem consequences of climate change will take decades or even centuries to emerge. Long‐term ecological responses to global change are strongly regulated by slow processes, such as changes in species composition, carbon dynamics in soil and by long‐lived plants, and accumulation of nutrient capitals. Understanding and predicting these processes require experiments on decadal time scales. But decadal experiments by themselves may not be adequate because many of the slow processes have characteristic time scales much longer than experiments can be maintained. This article promotes a coordinated approach that combines long‐term, large‐scale global change experiments with process studies and modeling. Long‐term global change manipulative experiments, especially in high‐priority ecosystems such as tropical forests and high‐latitude regions, are essential to maximize information gain concerning future states of the earth system. The long‐term experiments should be conducted in tandem with complementary process studies, such as those using model ecosystems, species replacements, laboratory incubations, isotope tracers, and greenhouse facilities. Models are essential to assimilate data from long‐term experiments and process studies together with information from long‐term observations, surveys, and space‐for‐time studies along environmental and biological gradients. Future research programs with coordinated long‐term experiments, process studies, and modeling have the potential to be the most effective strategy to gain the best information on long‐term ecosystem dynamics in response to global change.     

Laboratory animal science issues in the design and conduct of studies with endocrine-active compounds

The use of rodent models for research and testing on endocrine-active compounds necessitates an awareness of a number of laboratory animal science issues to standardize bioassay methods and facilitate reproducibility of results between laboratories. These issues are not unique to endocrine research but are particularly important in this field due to the complexities and interdependencies of the endocrine system, coupled with the inherently sensitive and variable nature of physiological endpoints. Standardization of animal models and the control of animal environments depend on the establishment of strong scientific partnerships between research investigators and laboratory animal scientists. Laboratory animal care and use programs are becoming increasingly complex and are constantly changing, fueled in part by technological advances, changes in regulations concerning animal care and use, and economic pressures. Since the early 1980s, many institutions have moved to centralization of animal facility operations concomitant with numerous changes in housing systems, barrier concepts, equipment, and engineering controls of the macro- and microenvironment. These and other changes can have an impact on animals and the conduct of endocrine experiments. Despite the potential impact of animal care and use procedures on research endpoints, many investigators are surprisingly naive to the animal facility conditions that can affect in vivo studies. Several key animal care and use issues that are important to consider in endocrine experiments with rodent models are described.     

On an infrastructure to support sharing and aggregating pre- and post-publication systems biology research data

The move towards in silico experimentation has resulted in the use of computational models, in addition to traditional experimental models, to generate the raw data that is analysed and published as research findings. This change requires new methods to be introduced to facilitate independent validation of the underlying models and the reported results. The promotion of co-operative research has the potential to help to both validate results and explore wider problem areas. In this paper we leverage and extend two existing software frameworks to develop an infrastructure that has the potential to both promote the sharing of data between researchers pre-publication and enable access to the data for interested parties post-publication. The pre-publication sharing of data would enable larger problem spaces to be explored by distributed research groups; enabling access to the data post-publication would allow reviewers and the wider community to independently verify the published results which would, in the longer term, help to increase confidence in published results. The framework is used to perform reproducible and numerically validated individual-based computational experiments into the onset of colorectal cancer. Existing results are verified and new insights into the top-down versus bottom-up hypothesis of colorectal crypt invasion are given.     

Applying the genetic theories of ageing to the cytoplasm: cytoplasmic genetic covariation for fitness and lifespan

Two genetic models exist to explain the evolution of ageing – mutation accumulation (MA) and antagonistic pleiotropy (AP). Under MA, a reduced intensity of selection with age results in accumulation of late‐acting deleterious mutations. Under AP, late‐acting deleterious mutations accumulate because they confer beneficial effects early in life. Recent studies suggest that the mitochondrial genome is a major player in ageing. It therefore seems plausible that the MA and AP models will be relevant to genomes within the cytoplasm. This possibility has not been considered previously. We explore whether patterns of covariation between fitness and ageing across 25 cytoplasmic lines, sampled from a population of Drosophila melanogaster, are consistent with the genetic associations predicted under MA or AP. We find negative covariation for fitness and the rate of ageing, and positive covariation for fitness and lifespan. Notably, the direction of these associations is opposite to that typically predicted under AP.     

Using Current Data to Define New Approach in Age Related Macular Degeneration: Need to Accelerate Translational Research

Age related macular degeneration (AMD) is one of the major retinal degenerative disease of ageing whose complex genetic basis remains undeciphered. The involvement of various other factors like mitochondrial genes, cytoskeletal proteins and the role of epigenetics has been described in this review. Several population based AMD genetic studies have been carried out worldwide. Despite the increased publication of reports, clinical translation still eludes this davastating disease. We suggest models to address roadblocks in clinical translation hoping that these would be beneficial to drive AMD research towards innovative biomarkers and therapeutics Therefore, addressing the need large autopsy studies and combining it with efficient use of bioinformatic tools, statistical modeling and probing SNP-biomarker association are key to time bound resolution of this disease.     

森林生态系统健康评估的一般性途径探讨

生态系统健康评估方法及指标体系成为21世纪生态系统健康研究的核心内容．作为陆地生态系统的重要组成部分,森林生态系统健康的评估研究引起了广泛的关注．学者们对森林生态系统健康的定义、测度、评估和管理开始做出积极的探讨和实践,提出了一些理论和应用上的评价方法、评估途径和框架,为解决陆地生态系统危机甚至全球环境问题提供了新的概念和一系列研究手段．但由于多种条件的限制,目前仍然没有通用有效的评估森林生态系统健康的一般模式．文中简要探讨了森林生态系统健康问题,提出有效评估森林健康的3个前提：1)清晰明确的概念框架;2)充分有效的数据信息;3)正确合理的研究途径和技术手段．并分别进行了探讨．在此基础上总结阐述了可用于森林生态系统健康评估研究的途径：长期研究和定位监测、时空互换、历史研究途径、经济价值评估及其途径等．     

禽流感的哺乳类动物模型研究进展

N1禽流感为新的人畜共患性疾病,建立良好的哺乳动物模型是进一步深入研究人禽流感防治的重要基础。本文报道了禽流感哺乳动物模型研究进展,对病原株、造模方法、模型的临床特征、病理变化、病毒复制等方面进行归纳,比较了小鼠模型、雪貂模型和非人灵长类动物模型特点。各种禽流感动物模型有各自的优点和缺点,应根据不同的实验目的和实验条件选择合适的病毒株和实验动物进行造模。     

Are zinc-bound metallothionein isoforms (I+II and III) involved in impaired thymulin production and thymic involution during ageing?

In the elderly, many alterations of both innate and clonotypic immunity have been described. Alterations to the immune system in the elderly are generally viewed as a deterioration of immunity, leading to the use of the term immunosenescence. However, although many immunological parameters are often notably reduced in the elderly, retained function of both innate and clonotypic immunity in the elderly is tightly correlated to health status. Recognising the important role of the immune system in ageing, over the last few years, journals oriented towards gerontology and geriatric sciences have increasingly published articles dealing with the immunology of ageing, but a specialised journal in this area does not exist. Immunity & Ageing is a new Open Access, peer reviewed journal that aims to cover all the topics dealing with innate and clonotypic immunity which are relevant to ageing. The journal will provide an opportunity to focus on this topic, which is emerging as one of the critical mechanisms of ageing. Furthermore, as an online, Open Access journal, Immunity & Ageing will promote immediate accessibility to research, which is generally not possible for articles published in printed journals. We hope this forum, concentrating on the themes of ageing and immunology with a strong focus on human studies, will create a new perspective for viewing a world that is inevitably becoming older.     

caGrid: design and implementation of the core architecture of the cancer biomedical informatics grid

MOTIVATION: The complexity of cancer is prompting researchers to find new ways to synthesize information from diverse data sources and to carry out coordinated research efforts that span multiple institutions. There is a need for standard applications, common data models, and software infrastructure to enable more efficient access to and sharing of distributed computational resources in cancer research. To address this need the National Cancer Institute (NCI) has initiated a national-scale effort, called the cancer Biomedical Informatics Grid (caBIGtrade mark), to develop a federation of interoperable research information systems. RESULTS: At the heart of the caBIG approach to federated interoperability effort is a Grid middleware infrastructure, called caGrid. In this paper we describe the caGrid framework and its current implementation, caGrid version 0.5. caGrid is a model-driven and service-oriented architecture that synthesizes and extends a number of technologies to provide a standardized framework for the advertising, discovery, and invocation of data and analytical resources. We expect caGrid to greatly facilitate the launch and ongoing management of coordinated cancer research studies involving multiple institutions, to provide the ability to manage and securely share information and analytic resources, and to spur a new generation of research applications that empower researchers to take a more integrative, trans-domain approach to data mining and analysis. AVAILABILITY: The caGrid version 0.5 release can be downloaded from https://cabig.nci.nih.gov/workspaces/Architecture/caGrid/. The operational test bed Grid can be accessed through the client included in the release, or through the caGrid-browser web application http://cagrid-browser.nci.nih.gov.