Towards a collaborative, global infrastructure for biodiversity assessment

Biodiversity data are rapidly becoming available over the Internet in common formats that promote sharing and exchange. Currently, these data are somewhat problematic, primarily with regard to geographic and taxonomic accuracy, for use in ecological research, natural resources management and conservation decision-making. However, web-based georeferencing tools that utilize best practices and gazetteer databases can be employed to improve geographic data. Taxonomic data quality can be improved through web-enabled valid taxon names databases and services, as well as more efficient mechanisms to return systematic research results and taxonomic misidentification rates back to the biodiversity community. Both of these are under construction. A separate but related challenge will be developing web-based visualization and analysis tools for tracking biodiversity change. Our aim was to discuss how such tools, combined with data of enhanced quality, will help transform today's portals to raw biodiversity data into nexuses of collaborative creation and sharing of biodiversity knowledge.     

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.     

European policy review: Biodiversity research to support European policy

Biodiversity research is essential to underpin the development, implementation and evaluation of policy that impacts on or protects biodiversity. An example is presented on how European terrestrial biodiversity research is being integrated to strengthen policy input. ALTER-Net is a Long-Term Biodiversity, Ecosystem and Awareness Research Network funded by the 6th European Union Framework Programme for Research and Development.     

Data standards: a call to action

Access to data is something that every molecular biologist takes for granted nowadays, but data alone is of little use unless it is made available in a useable form through the development and global uptake of data standards. The challenge of standards development has been taken up by grass-roots movements working within several different branches of the biomedical research community. Many of these initiatives are proving extremely successful; for example, the Gene Ontology, which provides a controlled vocabulary for describing the properties of gene products, the Microarray Gene Expression Data Society's standards for describing microarray experiments, and the emerging standards developed by the Proteomics Standards Initiative are gaining broad acceptance. Standards development now faces its greatest ever challenge--the integration of diverse data types to fulfill the goals of systems biology. Now is the time for the communities that are developing these standards, the funding bodies that have invested so heavily in high-throughput data generation, and the publishers of biomedical research papers to cooperate fully to make the goals of integrated data analysis a reality.     

Establishment of an efficient germ-free animal system to support functional microbiome research

正Germ-free animals are indispensable models for human and animal functional microbiome research Germ-free animals are animals that typically have no microorganisms living in or on them. These animals have become irreplaceable research tools for studying the relationships among single bacteria strains, multiple bacteria strains and hosts.     

Meeting threats to global health: a call for American leadership

Although the application of major biomedical advances has yielded spectacular results for individual health, there has been little improvement in the health of whole populations. There is a "back to the future" irony in the fact that at the inception of the 21st century, the eruption and spread of a multitude of "old" and "new" infectious diseases has become the most serious global threat to the health of humankind. At this historical juncture, the United States is the country with the most potential for favorably influencing global health and health care. Although there are historical, cultural, economic, and political factors that impede the United States from rising to this challenge, there is both a moral imperative and a rational long-term self-interest basis for the U.S. medical profession and government to exercise leadership in facing the health challenges of tragic and genocidal proportions that threaten everyone in an increasingly interdependent world.     

In the patient's best interest--a call to action,a call to balance

Nurses, physicians, and other healthcare professionals often complain that a loss of freedom or other obstacles hinder their ability to act in the best interest of the patient. These barriers cause professional burnout and moral outrage, and may contribute to a migration away from medicine or, more broadly, healthcare. Understanding the historical underpinnings of the phrase "in the patient's best interest," and realizing that healthcare, which is fundamentally a moral enterprise must be built on sound business principles can help healthcare professionals reframe the issue, and reclaim their original commitment to a difficult path.     

The DCCD: A digital data infrastructure for tree-ring research

Existing on-line databases for dendrochronology are not flexible in terms of user permissions, tree-ring data formats, metadata administration and language. This is why we developed the Digital Collaboratory for Cultural Dendrochronology (DCCD). This TRiDaS-based multi-lingual database allows users to control data access, to perform queries, to upload and download (meta)data in a variety of digital formats, and to edit metadata on line. The content of the DCCD conforms to EU best practices regarding the long-term preservation of digital research data.     

Race and racism: Towards a global future

There is a deepening and worldwide contradiction in the meaning and structure of race and racism. The age of empire is over; apartheid and Jim Crow have ended; a significant consensus exists that the concept of race lacks an objective basis; and yet the concept persists, as idea, as practice, as identity, and as social structure. This suggests that the global racial situation remains not only volatile but also seriously undertheorized. Five key racial problems of the twenty-first century are stressed: (1)Nonracialism vs. Race Consciousness; (2)Racial Genomics; (3)The Nation and its Peoples; (4)Race/Gender/Class “Intersectionality”; and (5) Empire, Race, and Neoconservatism. A radical pragmatist approach is proposed, stressing the ineluctable link between racialized experience and racialized social structure. This argument, that racial hegemony has not been secured, draws on the DuBoisian legacy as well as racial formation theory. Because racial rule is essential to rule itself, these contradictions are destined to deepen, not diminish.     

Building a data sharing model for global genomic research

Data sharing models designed to facilitate global business provide insights for improving transborder genomic data sharing. We argue that a flexible, externally endorsed, multilateral arrangement, combined with an objective third-party assurance mechanism, can effectively balance privacy with the need to share genomic data globally.     

Restoring physiology to the undergraduate biology curriculum: a call for action

The National Research Council-sponsored report, BIO 2010: Transforming Undergraduate Education for Future Research Biologists, describes a number of significant changes that should be made to the undergraduate biology curriculum if we are to adequately train students to become the researchers of the 21st century. What should be of concern to the physiology community is the lack of identifiable physiology in the proposed revisions. This article describes the report and suggests some steps that physiologists can take to enhance our discipline in the undergraduate biology curriculum.