Issues related to the use of animals in biocontainment research facilities

The expansion and improvement of high-containment animal facilities has been driven by terrorism, economics, the emergence of new pathogens, and the re-emergence of other pathogens in new areas. Working with highly infectious viral agents requires a team of trained scientists, laboratory technicians, veterinarians, animal care staff, biological safety officers, engineers, and physical plant staff to ensure safety, biocontainment, and the animals' well being, while providing essential scientific data. The challenges of working with infectious disease agents in high levels of containment, and some solutions to these challenges, are described from an animal care point of view.     

Applications submitted to regional research committees in 1976 and their outcome.

In 1976 regional research committees in England and their equivalent in the Welsh Office judged 608 proposals for funding under the locally organised research scheme. Of these, 521 were new proposals and 87 were resubmissions. Medically and dentally qualified applicants made 451 (87%) of the new proposals; nearly two-thirds came from teaching areas and 21% from staff of academic departments. Two hundred and ninety new proposals were approved, 154 rejected, and 77 were referred back for modification. Approval was commoner for applications from teaching areas, from medical staff, and for the less expensive projects. Some regional committees did not support research into the organisation of health services. Under a quarter of the resubmitted projects were rejected. The scheme is not yet used by a wide range of health-care professions. Medical staff in teaching areas still use it most. In some regions prospective researchers, especially those without previous experience, need a comprehensive and easily identifiable counselling service, so that the fund may be exploited in the way originally intended and the number of unsuccessful proposals reduced.     

The behavioral research program at the Washington Park Zoo

For the past decade, the Washington Park Zoo, Portland, Oregon, has had an active behavioral research program. The research department is both a zoo-supported research facility for visiting researchers and staff, and an educational facility that teaches practical behavioral research methods to undergraduates. The research education program utilizes students from any of a dozen local colleges and universities. Students receive academic credit for their participation. Active keeper-participation plays a major role in many research projects. Not only does keeper-cooperation facilitate research, but their knowledge of the individual animals often proves invaluable. In addition to involvement in student projects, keepers have also conducted their own research projects.     

Information management at the North Temperate Lakes Long-term Ecological Research site — Successful support of research in a large,diverse, and long running project

Information management has been an integral part of the research process at the North Temperate Lakes Long-term Ecological Research (NTL LTER) program for over 30 years. A combination of factors has made the information management system (IMS) at NTL very successful. Significant resources have been invested in the IMS from the beginning, the Information Manager has been part of the leadership team at NTL and later in various roles at the LTER network level; the NTL IMS was a very early adopter of database systems, standardized metadata, and a data delivery system based on those metadata. This approach has made data easily accessible to NTL researchers and the broader scientific community. Data management workflows have become increasingly more automated with adoption of modern technologies as they became available, making the system efficient enough to handle core data as well as all one-time research data generated within NTL and several related projects. More than three decades of core data from eleven lakes are reused extensively as critical background information and as the limnological go-to site for many synthesis projects within and beyond LTER.The NTL IMS continues to implement new technologies for improving data management efficiency, discovery, access, integration, and synthesis. Accordingly, the functionality of the original online data access system programmed in Java and JavaServer Pages (JSP) was ported to the modern content management system, Drupal and integrated into LTER's Drupal Ecological Information Management System (DEIMS). NTL has invested in sensor technology for studying lake conditions over the long term, which necessitated a sophisticated management system tailored to high frequency data streams. Several technologies have been used at different times for automation of management, quality control and archiving of these high volume data. Near real time lake conditions can be accessed on the NTL website and smart phone Apps.Easy access to long-term and sensor data in the NTL IMS has led NTL researchers to develop new analytical methods and the publication of several R statistical packages. Recent graduate students are now employed as data scientists helping define a new career path inspired by the availability of data.The NTL project has amassed one of the world's most comprehensive long-term datasets on lakes and their surrounding landscapes. The NTL IMS facilitates the use of these data by multiple groups for research, education, and communication of science to the public.     

Phenology research for natural resource management in the United States

Natural resource professionals in the United States recognize that climate-induced changes in phenology can substantially affect resource management. This is reflected in national climate change response plans recently released by major resource agencies. However, managers on-the-ground are often unclear about how to use phenological information to inform their management practices. Until recently, this was at least partially due to the lack of broad-based, standardized phenology data collection across taxa and geographic regions. Such efforts are now underway, albeit in very early stages. Nonetheless, a major hurdle still exists: phenology-linked climate change research has focused more on describing broad ecological changes rather than making direct connections to local to regional management concerns. To help researchers better design relevant research for use in conservation and management decision-making processes, we describe phenology-related research topics that facilitate “actionable” science. Examples include research on evolution and phenotypic plasticity related to vulnerability, the demographic consequences of trophic mismatch, the role of invasive species, and building robust ecological forecast models. Such efforts will increase phenology literacy among on-the-ground resource managers and provide information relevant for short- and long-term decision-making, particularly as related to climate response planning and implementing climate-informed monitoring in the context of adaptive management. In sum, we argue that phenological information is a crucial component of the resource management toolbox that facilitates identification and evaluation of strategies that will reduce the vulnerability of natural systems to climate change. Management-savvy researchers can play an important role in reaching this goal.     

Engaging the community in research: lessons learned from the malaria vaccine trial

When staff of the Papua New Guinea Institute of Medical Research first went into Wosera in 1979, to try and interest the community into participating in malaria research, the traditional warning sign of crossed bamboo sticks constantly blocked their path as they tried to enter the villages. In 2003, the site is a thriving research centre, with many projects under its belt, a successfully executed malaria vaccine trial to its credit, and approximately 13000 people from 29 villages currently participating in demographic surveillance and various research projects. It has been a long road from community suspicion to sustainable community participation, and the field workers have learned many important lessons along the way that can be applicable to research programs in other disease-endemic areas.     

Review by a local medical research ethics committee of the conduct of approved research projects,by examination of patients' case notes,consent forms,and research records and by interview.

OBJECTIVE: To monitor the conduct of medical research projects that have already been approved by the local medical research ethics committee. DESIGN: Follow up study of ethically approved studies (randomly selected from all the studies approved in the previous year) by examination of patients'' case notes, consent forms, and research records and by interview of the researchers at their workplace. SETTING: Tayside, Scotland (mixed rural and urban population). SUBJECTS: 30 research projects approved by Tayside local medical research ethics committee. MAIN OUTCOME MEASURES: Adherence to the agreed protocol, particularly for recruitment (obtaining and recording informed consent) and for specific requirements of the ethics committee, including notification of changes to the protocol and of adverse events. RESULTS: In one project only oral consent had been obtained, and in a quarter of the studies one or more consent forms were incorrectly completed. Inadequate filing of case notes in five studies and of consent forms in six made them unavailable for scrutiny. Adverse events were reported, but there was a general failure to report the abandoning or non-starting of projects in two studies the investigators failed to notify a change in the responsible researcher. CONCLUSIONS: Monitoring of medical research by local medical research ethics committees promotes and preserves ethical standards, protects subjects and researchers, discourages fraud, and has the support of investigators. We recommend that 10% of projects should undergo on-site review, with all others monitored by questionnaire. This would require about six person hours of time and a salary bill of 120 pounds per study monitored.     

Gift-Giving and Network Structure in Rural China: Utilizing Long-Term Spontaneous Gift Records

The tradition of keeping written records of gift received during household ceremonies in many countries offers researchers an underutilized means of data collection for social network analysis. This paper first summarizes unique features of the gift record data that circumvent five prevailing sampling and measurement issues in the literature, and we discuss their advantages over existing studies at both the individual level and the dyadic link level using previous data sources. We then document our research project in rural China that implements a multiple wave census-type household survey and a long-term gift record collection. The pattern of gift-giving in major household social events and its recent escalation is analyzed. There are significantly positive correlations between gift network centrality and various forms of informal insurance. Finally, economic inequality and competitive marriage market are among the main demographic and socioeconomic determinants of the observed gift network structure.     

北方农牧交错带农村居民食物消费特征

北方农牧交错带是我国典型生态脆弱区之一,恶劣的自然环境和落后的基础条件制约着生产和消费的发展。自2000年起,当地实施了一系列生态工程措施,引导农牧民由粗放型生产经营方式向集约型转变,改善区域生态环境的同时也优化了农牧业生产格局,居民食物消费结构随之改变。由于入户跟踪调查数据较难获取,现有食物消费研究缺少长时间尺度的消费特征变化研究,且农区和牧区的对比研究较少。以赤峰和鄂尔多斯为例,采用基于随机抽样调查方法收集的食物消费面板数据,对比研究2000—2020年典型农牧交错区的食物消费类型、结构及其数量变化。结果表明：生态工程实施以来,农牧居民食物消费种类趋于多样化,但消费结构不尽合理。赤峰趋于传统农区以谷类为主的消费结构,其谷类消费正在稳步减少,其他食物类型的消费增加;鄂尔多斯表现为多粮肉、少果蔬的消费结构,兼具农牧区的消费特点,其谷类和畜肉消费的年际波动较大,体现出传统牧区粗放式经营下产出不稳定的特点。食物消费总量持续增长,截至2020年,农牧居民谷类消费偏多,肉蛋类、豆类和食用油消费较为适度,薯类和果蔬类消费不足,奶类消费涨幅虽十分突出,但仍比我国膳食标准低20倍以上,因此减少谷类消...     

Status of knowledge,ongoing research,and research needs in Amazonian wetlands

Exploitation and exploration of the Amazon basin by Europeans started in the 17th century, but only since about 1970 has the Brazilian government given priority to the connection of the Amazon basin to the industrialized southern part of the country. This new policy required scientific research on the natural resources of the area. Wetlands cover about 20% of the Amazon basin. Inland fishery, fertile floodplain soils, and hydroelectric energy offer a large potential for economic development. Research concentrates on major wetlands and water bodies near the large cities. The Amazon River floodplain belongs to the best studied tropical river floodplains in the world. However, studies in other areas suffer from lack of wetland inventory and classification. Accelerated economic development is not adequately accompanied by wetland research. Insufficient knowledge about distribution, size, structure and function of many wetlands leads to increasing degradation and loss of biodiversity, for instance, by the construction of hydroelectric power plants, large scale deforestation for cattle ranching and agro-industrial projects, mining activities, the construction of navigation channels (hidrovias), etc. The low number of scientists working in the area and lack of funding require close cooperation in problem-oriented multidisciplinary projects (scientific clustering) to optimize scientific outcome. Intensive, long-term cooperation and scientific exchange with institutions from southern Brazil and from abroad is recommended to improve the scientific infrastructure in Amazonian institutions, to accelerate the transfer of new scientific methods and technology, and to intensify the training program for local human resources.This revised version was published online in March 2005 with corrections to the issue cover date.     

FAIR research data management as community approach in bioengineering

Research data management (RDM) requires standards, policies, and guidelines. Findable, accessible, interoperable, and reusable (FAIR) data management is critical for sustainable research. Therefore, collaborative approaches for managing FAIR-structured data are becoming increasingly important for long-term, sustainable RDM. However, they are rather hesitantly applied in bioengineering. One of the reasons may be found in the interdisciplinary character of the research field. In addition, bioengineering as application of principles of biology and tools of process engineering, often have to meet different criteria. In consequence, RDM is complicated by the fact that researchers from different scientific institutions must meet the criteria of their home institution, which can lead to additional conflicts. Therefore, centrally provided general repositories implementing a collaborative approach that enables data storage from the outset In a biotechnology research network with over 20 tandem projects, it was demonstrated how FAIR-RDM can be implemented through a collaborative approach and the use of a data structure. In addition, the importance of a structure within a repository was demonstrated to keep biotechnology research data available throughout the entire data lifecycle. Furthermore, the biotechnology research network highlighted the importance of a structure within a repository to keep research data available throughout the entire data lifecycle.     

Research priorities for wind energy and migratory wildlife

With upcoming global wind-energy build-out estimated in millions of units, cumulative environmental impacts must be considered and understood to promote responsible expansion of this renewable energy source. In June 2009, 30 wildlife scientists convened in Racine, Wisconsin, USA to identify key research priorities concerning wind energy's potential impacts on migratory wildlife (birds and bats). This working group suggested 4 areas where improved science is most needed to evaluate the impacts of wind-energy development on migrating animals more accurately than can be accomplished today: 1) standardized protocols and definitions; 2) new methods and models for assessing and forecasting risk; 3) documenting lethal and sub-lethal effects at existing wind facilities; and 4) improved facility-site access, data access, and data management for researchers. Focused research based on these priorities will both quantify potential risks associated with wind-energy development and help derive science-based, peer-reviewed, best-management practices for existing and future wind projects. © 2011 The Wildlife Society.     

基于文献计量的生态系统观测研究网络长期观测数据应用研究

基于CNKI数据库,采用文献计量和知识图谱的方法,通过对应用生态系统观测研究网络长期定位观测数据的文献进行分析,探讨长期观测数据的应用领域、具体用途、用户特点及不同生态站数据的应用状况与研究主题,以期为提高生态系统观测研究网络长期观测数据的共享服务能力、充分发挥长期观测数据的价值提供参考。分析结果表明:生态系统观测研究网络长期观测数据受到越来越多学者的关注,其应用学科领域以林业、农业基础科学为主,同时不断扩展到其他学科中,呈多元化态势;数据主要在生态系统服务研究、模型模拟、人工林研究、水污染研究、生物多样性研究、小麦玉米研究、土壤水分研究等方面发挥作用;数据的主要用户群体为高等院校和科研院所,不同机构应用长期观测数据开展的研究各有侧重;各生态站的长期观测数据能够为揭示其所代表生态区和生态系统类型的生态系统结构与功能、能量流动与养分循环的变化规律,分析主要生态环境问题的现状、动态变化及驱动机制等方面提供重要支撑。最后,对生态系统观测研究网络长期观测数据应用的相关方面提出几点建议:(1)健全数据引用机制,制定相应的科学数据引用和著录标准;(2)发挥生态网络长期观测数据优势,开展专题数据产品的生产,充分开发生态网络长期观测数据的潜在价值;(3)加大和稳定生态站的经费投入,提高生态站的观测能力和水平,同时还要完善、优化生态站布局。     

Ethical considerations in fish research

Fishes are used in a wide range of scientific studies, from conservation research with potential benefits to the species used to biomedical research with potential human benefits. Fish research can take place in both laboratories and field environments and methods used represent a continuum from non-invasive observations, handling, through to experimental manipulation. While some countries have legislation or guidance regarding the use of fish in research, many do not and there exists a diversity of scientific opinions on the sentience of fish and how we determine welfare. Nevertheless, there is a growing pressure on the scientific community to take more responsibility for the animals they work with through maximising the benefits of their research to humans or animals while minimising welfare or survival costs to their study animals. In this review, we focus primarily on the refinement of common methods used in fish research based on emerging knowledge with the aim of improving the welfare of fish used in scientific studies. We consider the use of anaesthetics and analgesics and how we mark individuals for identification purposes. We highlight the main ethical concerns facing researchers in both laboratory and field environments and identify areas that need urgent future research. We hope that this review will help inform those who wish to refine their ethical practices and stimulate thought among fish researchers for further avenues of refinement. Improved ethics and welfare of fishes will inevitably lead to increased scientific rigour and is in the best interests of both fishes and scientists.     

Data sharing by scientists: practices and perceptions

Background

Scientific research in the 21st century is more data intensive and collaborative than in the past. It is important to study the data practices of researchers – data accessibility, discovery, re-use, preservation and, particularly, data sharing. Data sharing is a valuable part of the scientific method allowing for verification of results and extending research from prior results.

Methodology/Principal Findings

A total of 1329 scientists participated in this survey exploring current data sharing practices and perceptions of the barriers and enablers of data sharing. Scientists do not make their data electronically available to others for various reasons, including insufficient time and lack of funding. Most respondents are satisfied with their current processes for the initial and short-term parts of the data or research lifecycle (collecting their research data; searching for, describing or cataloging, analyzing, and short-term storage of their data) but are not satisfied with long-term data preservation. Many organizations do not provide support to their researchers for data management both in the short- and long-term. If certain conditions are met (such as formal citation and sharing reprints) respondents agree they are willing to share their data. There are also significant differences and approaches in data management practices based on primary funding agency, subject discipline, age, work focus, and world region.

Conclusions/Significance

Barriers to effective data sharing and preservation are deeply rooted in the practices and culture of the research process as well as the researchers themselves. New mandates for data management plans from NSF and other federal agencies and world-wide attention to the need to share and preserve data could lead to changes. Large scale programs, such as the NSF-sponsored DataNET (including projects like DataONE) will both bring attention and resources to the issue and make it easier for scientists to apply sound data management principles.     

Tabular strategies for metadata in ecology,evolution, and the environmental sciences

Data support knowledge development and theory advances in ecology and evolution. We are increasingly reusing data within our teams and projects and through the global, openly archived datasets of others. Metadata can be challenging to write and interpret, but it is always crucial for reuse. The value metadata cannot be overstated—even as a relatively independent research object because it describes the work that has been done in a structured format. We advance a new perspective and classify methods for metadata curation and development with tables. Tables with templates can be effectively used to capture all components of an experiment or project in a single, easy‐to‐read file familiar to most scientists. If coupled with the R programming language, metadata from tables can then be rapidly and reproducibly converted to publication formats including extensible markup language files suitable for data repositories. Tables can also be used to summarize existing metadata and store metadata across many datasets. A case study is provided and the added benefits of tables for metadata, a priori, are developed to ensure a more streamlined publishing process for many data repositories used in ecology, evolution, and the environmental sciences. In ecology and evolution, researchers are often highly tabular thinkers from experimental data collection in the lab and/or field, and representations of metadata as a table will provide novel research and reuse insights.     

Conservation strategies for poorly surveyed taxa: a dung beetle (Coleoptera, Scarabaeidae) case study from southern Africa

Despite being the focus of an international research effort spanning decades, the spatial distribution of southern African scarab beetles remains poorly documented. As well as reinforcing the magnitude of the challenge facing biodiversity scientists, this raises real concerns about best practice conservation strategies in the absence of detailed distribution information. However, dung beetles appear to be well represented in established conservation areas. This apparent contradiction could be ascribed to anthropogenic transformation, successful conservation efforts, the presence of dung generalists and reserve-biased or mesic-biased dung beetle collection efforts. It is suggested that all of the above contribute to the observed pattern to varying degrees. The implications of selecting areas that are either rich in species, contain rare species or contain taxonomically distinct species from a group whose taxonomy is well known but for which inadequate distribution data exist are explored. Best practice, in the face of inadequate data, appears to revolve around a subtle interplay between advantages and disadvantages associated with data interpolation techniques, reserve selection algorithms that use criteria more robust than database rarity (such as taxonomic distinctiveness) and the long-term economic costs of proceeding with the data at hand versus investing in biological surveys.     

Transgenic Technology meeting 2008 in Toronto, Canada: a meeting report

In a history that goes back to 1999, the Transgenic Technology meetings started out in Sweden and over the years began to attract a growing community of technicians and researchers mainly from Europe. As the meetings started to attract an expanding worldwide audience, the community decided to found the International Society for Transgenic Technologies at the Barcelona meeting in 2005. The 2007 convention was held at Brisbane, Australia, and in 2008, the 8th Transgenic Technology meeting was held for the second time on behalf of ISTT and for the second time outside of Europe in Toronto, Canada. Due to its excellent program with over 400 participants the meeting was able to attract the highest number of delegates of all past TT meetings. With extended times for plenary discussions about technical and organizational aspects, as well as top level scientific presentations, both technicians and scientists enjoyed this as an extremely fruitful meeting from which they could take home solutions for daily routines as well as new insights and ideas for coming projects.     

Exploring methods for rapid assessment of woody vegetation in the Batemi Valley, North-central Tanzania

Conservation of local biological resources in remote areas requires efficient data and collection methods. This paper describes part of a local conservation initiative in Northern Tanzania in which an indigenous conservation group enlisted the support of outside scientists to explore means of preparing baseline ecological reports. Two factors are seen as important: one is local use of ecological resources and the other is local availability. This paper focuses on the second of these and considers woody species. A variety of ecological field methods, statistical analysis and remote sensing and mapping techniques are used to generate baseline ecological inventories. The fieldwork identified 101 woody species, representing 54 genera and 37 families in the Batemi area. There are three main vegetation types: Vangueria apiculata-Ficus sycomorus-Trichilia emetica type; Croton dictygamous-Euphorbia tirucalli-Grewia bicolor type; and Acacia tortilis-Balanites aegyptica-Euphorbia candelabrum type. The Landsat TM map identified four main land-cover classes: (1) bushland and woodland thicket, (2) woodland (3) wooded grassland, and (4) grassland with scattered trees, which includes agricultural areas and villages. The combination of these data and methods can be useful for conservation planning and long-term monitoring, but it is clear that ground-level local assessment is necessary to detect subtleties of human-environment interaction that are required for conservation planning.     

How to work with children and animals: A guide for school‐based citizen science in wildlife research

Engaging school students in wildlife research through citizen science projects can be a win–win for scientists and educators. Not only does it provide a way for scientists to gather new data, but it can also contribute to science education and help younger generations become more environmentally aware. However, wildlife research can be challenging in the best of circumstances, and there are few guidelines available to help scientists create successful citizen science projects for school students. This paper explores the opportunities and challenges faced when developing school‐based citizen science projects in wildlife research by synthesising two sources of information. First, we conducted a small, school‐based citizen science project that investigated the effects of supplementary feeding on urban birds as a case study. Second, we reviewed the literature to develop a database of school‐based citizen science projects that address questions in wildlife ecology and conservation. Based on these activities, we present five lessons for scientists considering a school‐based citizen science project. Overall, we found that school‐based citizen science projects must be carefully designed to ensure reliable data are collected, students remain engaged, and the project is achievable under the logistical constraints presented by conducting wildlife research in a school environment. Ultimately, we conclude that school‐based citizen science projects can be a powerful way of collecting wildlife data while also contributing to the education and development of environmentally aware students.