USDA Stakeholder Workshop on Animal Bioinformatics: Summary and Recommendations

An electronic workshop was conducted on 4 November-13 December 2002 to discuss current issues and needs in animal bioinformatics. The electronic (e-mail listserver) format was chosen to provide a relatively speedy process that is broad in scope, cost-efficient and easily accessible to all participants. Approximately 40 panelists with diverse species and discipline expertise communicated through the panel e-mail listserver. The panel included scientists from academia, industry and government, in the USA, Australia and the UK. A second 'stakeholder' e-mail listserver was used to obtain input from a broad audience with general interests in animal genomics. The objectives of the electronic workshop were: (a) to define priorities for animal genome database development; and (b) to recommend ways in which the USDA could provide leadership in the area of animal genome database development. E-mail messages from panelists and stakeholders are archived at http://genome.cvm.umn.edu/bioinfo/. Priorities defined for animal genome database development included: (a) data repository; (b) tools for genome analysis; (c) annotation; (d) practical application of genomic data; and (e) a biological framework for DNA sequence. A stable source of funding, such as the USDA Agricultural Research Service (ARS), was recommended to support maintenance of data repositories and data curation. Continued support for competitive grants programs within the USDA Cooperative State Research, Education and Extension Service (CSREES) was recommended for tool development and hypothesis-driven research projects in genome analysis. Additional stakeholder input will be required to continuously refine priorities and maximize the use of limited resources for animal bioinformatics within the USDA.     

Public perceptions of reproductive biotechnologies: the case of farm animal breeding and reproduction in France and the United Kingdom

Results of previous qualitative and quantitative stages of the research project demonstrated that, although consumers had poor knowledge about breeding and reproduction procedures, they were concerned about the impact of breeding practices on their food items. They acknowledged breeding and reproduction to be at the very core of animal-based food chain process. Since however modern breeding programmers beg so much for genetics, their practices increasingly raised consumer concerns. This paper presents results of a research addressing this issue and based on interviews of livestock breeders and specialized scientists. This research was undertaken within the frame of an EU funded project (Sustainable Farm Animal Breeding and Reproduction Project, 2000-2003). Interviews were performed according to the methodology of focus groups and results were used to prepare a discussion guide, including definitions of breeding techniques such as artificial insemination, embryo transfer, in vitro fertilization, and molecular genetics. Farm animal breeding and reproduction methods raised high level of concerns in conventional terms like safety, healthiness and quality of food, factory farming and related consequences on environment, international issues, and cost. Several propositions were presented that deal with modern farm animal breeding and reproduction, EU regulation of breeding procedures, education of consumers on breeding methods, and labelling of products on breeding and reproduction grounds.     

2008—2017年度国家自然科学基金医学病原微生物与感染领域肝炎病毒相关项目申请与资助情况分析

本文对2008—2017年申请国家自然科学基金及获得资助的医学病原微生物与感染科学领域肝炎病毒相关项目进行回顾分析,介绍面上项目、青年科学基金和地区科学基金项目的申请数量、资助项目数量及资助强度,并对医学病原微生物与感染科学领域肝炎病毒相关项目的特点及存在的问题进行分析。     

2009-2018年度国家自然科学基金医学病原微生物与感染领域细菌相关项目申请与资助情况分析

本文对2009—2018年度国家自然科学基金医学病原微生物与感染领域细菌相关项目申请与资助情况进行回顾和分析,介绍面上项目、青年科学基金和地区科学基金的申请数量、资助项目数量及资助率,并对申请代码、依托单位情况进行总结,进一步探讨医学病原微生物与感染领域细菌相关项目的特点及存在的问题。     

Length rather than year‐round spawning,affects reproductive performance of RAS‐reared F‐generation pikeperch,Sander lucioperca (Linnaeus, 1758) – Insights from practice

The continuous production of large numbers of high quality gametes is essential for aquaculture, particularly in candidate species, such as pikeperch, Sander lucioperca (L.). The common practice of year‐round reproduction is under suspicion of inflicting adverse effects on the quality of the gametes through the disturbance of endogenous rhythms. We hypothesized that such perturbation does not affect RAS‐reared F‐generation broodstock. Reproductive performance (number of eggs) and gamete quality (fertilization and hatching rate) were assessed over the course of 3 years covering six independent, photothermal shifted spawning seasons in a commercial pikeperch hatchery (n = 31 egg batches of F‐generation fish in total). No substantial differences in fertilization or hatching rates could be detected between the individual spawning seasons. Fecundity varied, but there are indications for a size effect on female fecundity with intermediate sized females producing higher number of eggs (~65–70 cm). Low egg quality could be detected in batches of very large fish. In conclusion, size‐specific broodstock composition, but not year‐round reproduction of F‐generation pikeperch spawners affects the reproductive performance.     

Education and training for radiation scientists: radiation research program and American Society of Therapeutic Radiology and Oncology Workshop, Bethesda, Maryland, May 12-14, 2003

Current and potential shortfalls in the number of radiation scientists stand in sharp contrast to the emerging scientific opportunities and the need for new knowledge to address issues of cancer survivorship and radiological and nuclear terrorism. In response to these challenges, workshops organized by the Radiation Research Program (RRP), National Cancer Institute (NCI) (Radiat. Res. 157, 204-223, 2002; Radiat. Res. 159, 812-834, 2003), and National Institute of Allergy and Infectious Diseases (NIAID) (Nature, 421, 787, 2003) have engaged experts from a range of federal agencies, academia and industry. This workshop, Education and Training for Radiation Scientists, addressed the need to establish a sustainable pool of expertise and talent for a wide range of activities and careers related to radiation biology, oncology and epidemiology. Although fundamental radiation chemistry and physics are also critical to radiation sciences, this workshop did not address workforce needs in these areas. The recommendations include: (1) Establish a National Council of Radiation Sciences to develop a strategy for increasing the number of radiation scientists. The strategy includes NIH training grants, interagency cooperation, interinstitutional collaboration among universities, and active involvement of all stakeholders. (2) Create new and expanded training programs with sustained funding. These may take the form of regional Centers of Excellence for Radiation Sciences. (3) Continue and broaden educational efforts of the American Society for Therapeutic Radiology and Oncology (ASTRO), the American Association for Cancer Research (AACR), the Radiological Society of North America (RSNA), and the Radiation Research Society (RRS). (4) Foster education and training in the radiation sciences for the range of career opportunities including radiation oncology, radiation biology, radiation epidemiology, radiation safety, health/government policy, and industrial research. (5) Educate other scientists and the general public on the quantitative, basic, molecular, translational and applied aspects of radiation sciences.     

Proteomics' framework for success?

As Europe is rolling out its seventh Framework Program for funding research with some emphasis on post-genomics, initiatives are burgeoning in the community to establish a comprehensive resource of protein-affinity reagents. Will funding priorities and community-based efforts meet?     

Studying de-implementation in health: an analysis of funded research grants

Background

Studying de-implementation—defined herein as reducing or stopping the use of a health service or practice provided to patients by healthcare practitioners and systems—has gained traction in recent years. De-implementing ineffective, unproven, harmful, overused, inappropriate, and/or low-value health services and practices is important for mitigating patient harm, improving processes of care, and reducing healthcare costs. A better understanding of the state-of-the-science is needed to guide future objectives and funding initiatives. To this end, we characterized de-implementation research grants funded by the United States (US) National Institutes of Health (NIH) and the Agency for Healthcare Research and Quality (AHRQ).

Methods

We used systematic methods to search, identify, and describe de-implementation research grants funded across all 27 NIH Institutes and Centers (ICs) and AHRQ from fiscal year 2000 through 2017. Eleven key terms and three funding opportunity announcements were used to search for research grants in the NIH Query, View and Report (QVR) system. Two coders identified eligible grants based on inclusion/exclusion criteria. A codebook was developed, pilot tested, and revised before coding the full grant applications of the final sample.

Results

A total of 1277 grants were identified through the QVR system; 542 remained after removing duplicates. After the multistep eligibility assessment and review process, 20 grant applications were coded. Many grants were funded by NIH (n?=?15), with fewer funded by AHRQ, and a majority were funded between fiscal years 2015 and 2016 (n?=?11). Grant proposals focused on de-implementing a range of health services and practices (e.g., medications, therapies, screening tests) across various health areas (e.g., cancer, cardiovascular disease) and delivery settings (e.g., hospitals, nursing homes, schools). Grants proposed to use a variety of study designs and research methods (e.g., experimental, observational, mixed methods) to accomplish study aims.

Conclusions

Based on the systematic portfolio analysis of NIH- and AHRQ-funded research grants over the past 17 years, relatively few have focused on studying the de-implementation of ineffective, unproven, harmful, overused, inappropriate, and/or low-value health services and practices provided to patients by healthcare practitioners and systems. Strategies for raising the profile and growing the field of research on de-implementation are discussed.

     

Life Cycle Impact Assessment—where we are, trends, and next steps: a late report from a UNEP/SETAC Life Cycle Initiative workshop and a few updates from recent developments

Purpose

The paper provides a late report from the United Nations Environment Program (UNEP)/Society of Environmental Toxicology and Chemistry (SETAC) Life Cycle Initiative workshop “Life Cycle Impact Assessment (LCIA)—where we are, trends, and next steps;” it embeds this report into recent development with regard to the envisaged development of global guidance on environmental life cycle impact assessment indicators and related methodologies.

Methods

The document is the output of the UNEP/SETAC Life Cycle Initiative’s workshop on “Life Cycle Impact Assessment—where we are, trends, and next steps.” The presentations and discussions held during the workshop reviewed the first two phases of the Life Cycle Initiative and provided an overview of current LCIA activities being conducted by the Initiative, governments and academia, as well as corporate approaches. The outcomes of the workshop are reflected in light of the implementation of the strategy for Phase 3 of the Life Cycle Initiative.

Results

The range of views provided during the workshop indicated different user needs, with regards to, amongst other things, the required complexity of the LCIA methodology, associated costs, and the selection of LCIA categories depending on environmental priorities. The workshop’s results signified a number of potential focus areas for Phase 3 of the Initiative, including capacity building efforts concerning LCIA in developing countries and emerging economies, the preparation of training materials on LCIA, the production of global guidance on LCIA, and the potential development of a broader sustainability indicators framework.

Conclusions

These suggestions have been taken into account in the strategy for Phase 3 of the Life Cycle Initiative in two flagship projects, one on global capability development on life cycle approaches and the other on global guidance on environmental life cycle impact assessment indicators. In the context of the latter project, first activities are being organized and planned. Moreover, UNEP has included the recommendations in its Rio + 20 Voluntary Commitments: UNEP and SETAC through the UNEP/SETAC Life Cycle Initiative commit to facilitate improved access to good quality life cycle data and databases as well as expanded use of key environmental indicators that allows the measurement and monitoring of progress towards the environmental sustainability of selected product chains.     

Summary of final report: Space Life Sciences Planning Workshop (SLSPW). June 5-7, 2000 Mont Tremblant, Quebec

A Space Life Sciences Planning Workshop was sponsored by the Canadian Space Agency to identify key questions in the major research areas supported by the Life Sciences Program, to identify Canadian strengths and capabilities as they relate to these research areas, and to make recommendations for the future directions of the Life Sciences Program. The conclusions reached by the workshop participants have been presented to the Canadian Space Agency. This report is a summary of those conclusions.     

Frontiers in glycomics: bioinformatics and biomarkers in disease. An NIH white paper prepared from discussions by the focus groups at a workshop on the NIH campus, Bethesda MD (September 11-13, 2006)

Key issues relating to glycomics research were discussed after the workshop entitled "Frontiers in Glycomics: Bioinformatics and Biomarkers in Disease" by two focus groups nominated by the organizers. The groups focused on two themes: (i) glycomics as the new frontier for the discovery of biomarkers of disease and (ii) requirements for the development of informatics for glycomics and glycobiology. The mandate of the focus groups was to build consensus on these issues and develop a summary of findings and recommendations for presentation to the NIH and the greater scientific community. A list of scientific priorities was developed, presented, and discussed at the workshops. Additional suggestions were solicited from workshop participants and collected using the workshop mailing list. The results are summarized in this White Paper, authored by the co-chairs of the focus groups.     

Editorial: First Issue

‘ANIMAL – An International Journal of Animal Bioscience’ is the central element in a new and exciting collaborative venture between the European Federation for Animal Science (EAAP), Institut National de la Recherche Agronomique (INRA), and British Society of Animal Science (BSAS). It merges three high-quality and successful journals (Animal Science, Animal Research and Reproduction, Nutrition, Development) into a single forward-looking publication that will reduce fragmentation in the sector, improve synergies and, we hope, act as a catalyst for integrating process-level and systems science in the animal biosciences.     

Comparing Cutaneous Research Funded by the National Institute of Arthritis and Musculoskeletal and Skin Diseases with 2010 Global Burden of Disease Results

Importance

Disease burden data helps guide research prioritization.

Objective

To determine the extent to which grants issued by the National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS) reflect disease burden, measured by disability-adjusted life years (DALYs) from Global Burden of Disease (GBD) 2010 project.

Design

Two investigators independently assessed 15 skin conditions studied by GBD 2010 in the NIAMS database for grants issued in 2013. The 15 skin diseases were matched to their respective DALYs from GBD 2010.

Setting

The United States NIAMS database and GBD 2010 skin condition disability data.

Main Outcome(s) and Measure(s)

Relationship of NIAMS grant database topic funding with percent total GBD 2010 DALY and DALY rank for 15 skin conditions.

Results

During fiscal year 2013, 1,443 NIAMS grants were issued at a total value of $424 million. Of these grants, 17.7% covered skin topics. Of the total skin disease funding, 82% (91 grants) were categorized as “general cutaneous research.” Psoriasis, leprosy, and “other skin and subcutaneous diseases” (ie; immunobullous disorders, vitiligo, and hidradenitis suppurativa) were over-represented when funding was compared with disability. Conversely, cellulitis, decubitus ulcer, urticaria, acne vulgaris, viral skin diseases, fungal skin diseases, scabies, and melanoma were under-represented. Conditions for which disability and funding appeared well-matched were dermatitis, squamous and basal cell carcinoma, pruritus, bacterial skin diseases, and alopecia areata.

Conclusions and Relevance

Degree of representation in NIAMS is partly correlated with DALY metrics. Grant funding was well-matched with disability metrics for five of the 15 studied skin diseases, while two skin diseases were over-represented and seven were under-represented. Global burden estimates provide increasingly transparent and important information for investigating and prioritizing national research funding allocations.     

To Apply or Not to Apply: A Survey Analysis of Grant Writing Costs and Benefits

We surveyed 113 astronomers and 82 psychologists active in applying for federally funded research on their grant-writing history between January, 2009 and November, 2012. We collected demographic data, effort levels, success rates, and perceived non-financial benefits from writing grant proposals. We find that the average proposal takes 116 PI hours and 55 CI hours to write; although time spent writing was not related to whether the grant was funded. Effort did translate into success, however, as academics who wrote more grants received more funding. Participants indicated modest non-monetary benefits from grant writing, with psychologists reporting a somewhat greater benefit overall than astronomers. These perceptions of non-financial benefits were unrelated to how many grants investigators applied for, the number of grants they received, or the amount of time they devoted to writing their proposals. We also explored the number of years an investigator can afford to apply unsuccessfully for research grants and our analyses suggest that funding rates below approximately 20%, commensurate with current NIH and NSF funding, are likely to drive at least half of the active researchers away from federally funded research. We conclude with recommendations and suggestions for individual investigators and for department heads.     

Reproduction of river and lake populations of Hyridella depressa (Unionacea: Hyriidae) in New South Wales: implications for their conservation

The freshwater mussel Hyridella depressa is an important component of the macrobiota of freshwater systems of south-eastern Australia. This species has declined in river habitats but is abundant in impounded water storages. Reproduction of river and lake populations of H. depressa was investigated to document details of their gametogenic cycle and to determine when the females incubate embryos in their gill marsupia. Four populations in Lake Burragorang and two populations in the Hawkesbury-Nepean River were studied over two breeding seasons. Reproduction was documented by anatomical and histological examination of the gonads. The study sites differed in anthropogenic influence and trophic status and the influence of these factors on reproduction in H. depressa was assessed. A skewed sex ratio in favour of females was common in the populations and histology revealed that some of these females were microhermaphrodites. It appears that sexuality in H. depressa is labile with the potential for self-fertilisation by individuals that largely function as females. H. depressa is a long-term brooder with progeny present in the marsupia for up to eight months of the year from mid-winter to late summer. Across all sites brooding started in July or August and finished in January or February of the following year. In parallel with the prolonged spawning pattern, gametogenesis in H. depressa was continuous. At the eutrophic sites the gonads contained advanced gametes throughout the year. H. depressa at these sites had a high annual reproductive output with the females producing several clutches each year. In contrast, gametogenesis in mussels at the oligotrophic sites was more seasonal. At one of the oligotrophic sites reproductive failure was common and in 1996 most females failed to brood a single clutch. Implications of this research for conservation of H. depressa are discussed. This revised version was published online in July 2006 with corrections to the Cover Date.     

THE IMPORTANCE OF INTEGRATING ALGAL SYSTEMS INTO A BALANCE MANAGEMENT APPROACH TO AQUACULTURE

McVey, J. P. Program Director, National Sea Grant College Program, 1315 East West Highway, Silver Spring, Maryland, 20910, USA The National Oceanic and Atmospheric Administration (NOAA), through its National Marine Fisheries Service (NMFS) and National Sea Grant College Program (NSGCP) has developed a vision for how seafood will be produced in the USA which includes the proper management of natural fisheries, aquaculture and the management and involvement by human coastal communities. The concept of balanced ecosystem management is not only being talked about at national levels but active research programs are being planned and supported. The recent $5 million National Marine Aquaculture Initiative (NMAI) specifically called for proposals that study the “trophic level consequences of marine aquaculture and marine species enhancement”. Recent workshops at the World Aquaculture Society meeting in Orlando and at the regional aquaculture meeting held at Boston on the topic of “Aquaculture and the Environment” have focused on a balanced approach to both aquaculture and fisheries management. All of the workshops focused on the important role of plants in the aquatic community. The basic premise about a balanced ecosystem approach is to incorporate the biological functions of a diverse group of plants and animals into a unified system that maintains the natural interactions of species and allows an ecosystem to function. Models are useful in understanding the energy and nutrient flow within an ecosystem; as are GIS technologies that allow us to map biological and ecological regimes. Macroalgae and phytoplankton both convert nutrients to plant material and transform carbon dioxide to oxygen. In contrast, animals derive much of their nutrition from plants, in one way or another and transform oxygen to carbon dioxide. This presentation will discuss the need to incorporate the use of plants in ecosystem maintenance such that there is balance between the animal, including humans, and plant communities in coastal areas. This will all be related to new NOAA programs and funding opportunities for research support in this area.     

Billions for biodefense: federal agency biodefense funding, FY2008-FY2009

Since 2001, the United States government has spent substantial resources on preparing the nation against a bioterrorist attack. Earlier articles in this series analyzed civilian biodefense funding by the federal government from fiscal years 2001 through 2008. This article updates those figures with budgeted amounts for fiscal year 2009, specifically analyzing the budgets and allocations for biodefense at the Departments of Health and Human Services, Homeland Security, Defense, Agriculture, and State and the Environmental Protection Agency and the National Science Foundation.     

Billions for biodefense: federal agency biodefense budgeting, FY2005-FY2006

Since 2001, the United States government has spent substantial resources on preparing the nation against a bioterrorist attack. An earlier article analyzed the civilian biodefense funding by the federal government from fiscal years 2001 through 2005. This article updates those figures with budgeted amounts for fiscal year 2006, specifically analyzing the budgets and allocations for biodefense at the Department of Health and Human Services, the Department of Homeland Security, the Department of Agriculture, the Environmental Protection Agency, the National Science Foundation, and the Department of State.     

Impact of Publicly Sponsored Neutering Programs on Animal Population Dynamics at Animal Shelters: The New Hampshire and Austin Experiences

This study found that government-funded surgical sterilization of companion animals has been widely promoted as a means of decreasing shelter intake and euthanasia. However, little information is available about the true impact of these programs on community and shelter nonhuman animal population dynamics. This study estimated the impact of the Animal Population Control Program in New Hampshire by comparing shelter intake and euthanasia data before and after the onset of the neutering initiative. Regression analysis demonstrated a significant decrease in cat intake and euthanasia during the years after program onset, a trend that appears to begin prior to the program's initiation; however, there was no decrease in dog intake or euthanasia. This study also estimated the impact of the Austin-based EmanciPET Free Spay/Neuter Program by comparing shelter intake and euthanasia data from the targeted program areas versus nonprogram areas within the city. Regression analysis demonstrated a significantly lower rate of increase for dog and cat intake and euthanasia in the program areas. Prospective studies should determine the effectiveness and affordability of different models for funding and delivering neutering services.