University of Wisconsin-Madison

About: University of Wisconsin-Madison is a education organization based out in Madison, Wisconsin, United States. It is known for research contribution in the topics: Population & Poison control. The organization has 108707 authors who have published 237594 publications receiving 11883575 citations.

Multifacet's general execution-driven multiprocessor simulator (GEMS) toolset

Abstract: The Wisconsin Multifacet Project has created a simulation toolset to characterize and evaluate the performance of multiprocessor hardware systems commonly used as database and web servers. We leverage an existing full-system functional simulation infrastructure (Simics [14]) as the basis around which to build a set of timing simulator modules for modeling the timing of the memory system and microprocessors. This simulator infrastructure enables us to run architectural experiments using a suite of scaled-down commercial workloads [3]. To enable other researchers to more easily perform such research, we have released these timing simulator modules as the Multifacet General Execution-driven Multiprocessor Simulator (GEMS) Toolset, release 1.0, under GNU GPL [9].

Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells

Abstract: Induced pluripotent stem cells (iPSCs) offer immense potential for regenerative medicine and studies of disease and development. Somatic cell reprogramming involves epigenomic reconfiguration, conferring iPSCs with characteristics similar to embryonic stem (ES) cells. However, it remains unknown how complete the reestablishment of ES-cell-like DNA methylation patterns is throughout the genome. Here we report the first whole-genome profiles of DNA methylation at single-base resolution in five human iPSC lines, along with methylomes of ES cells, somatic cells, and differentiated iPSCs and ES cells. iPSCs show significant reprogramming variability, including somatic memory and aberrant reprogramming of DNA methylation. iPSCs share megabase-scale differentially methylated regions proximal to centromeres and telomeres that display incomplete reprogramming of non-CG methylation, and differences in CG methylation and histone modifications. Lastly, differentiation of iPSCs into trophoblast cells revealed that errors in reprogramming CG methylation are transmitted at a high frequency, providing an iPSC reprogramming signature that is maintained after differentiation.

Farming the planet: 2. Geographic distribution of crop areas, yields, physiological types, and net primary production in the year 2000

Abstract: [1] Croplands cover ∼15 million km2 of the planet and provide the bulk of the food and fiber essential to human well-being. Most global land cover data sets from satellites group croplands into just a few categories, thereby excluding information that is critical for answering key questions ranging from biodiversity conservation to food security to biogeochemical cycling. Information about agricultural land use practices like crop selection, yield, and fertilizer use is even more limited. Here we present land use data sets created by combining national, state, and county level census statistics with a recently updated global data set of croplands on a 5 min by 5 min (∼10 km by 10 km) latitude-longitude grid. The resulting land use data sets depict circa the year 2000 the area (harvested) and yield of 175 distinct crops of the world. We aggregate these individual crop maps to produce novel maps of 11 major crop groups, crop net primary production, and four physiologically based crop types: annuals/perennials, herbaceous/shrubs/trees, C3/C4, and leguminous/nonleguminous.

The Report of the Ecological Society of America Committee on the Scientific Basis for Ecosystem Management

Abstract: Ecosystem management is management driven by explicit goals, executed by policies, protocols, and practices, and made adaptable by monitoring and research based on our best understanding of the ecological interactions and processes necessary to sustain ecosystem composition, structure, and function. In recent years, sustainability has become an explicitly stated, even legislatively mandated, goal of natural resource management agencies. In practice, however, management approaches have often focused on maximizing short-term yield and economic gain rather than long-term sustainability. Several obstacles contribute to this disparity, including: (1) inadequate information on the biological diversity of environments; (2) widespread ignorance of the function and dynamics of ecosystems; (3) the openness and interconnectedness of ecosystems on scales that transcend management boundaries; (4) a prevailing public perception that the immediate economic and social value of supposedly renewable resources outweighs the risk of future ecosystem damage or the benefits of alternative management approaches. The goal of ecosystem management is to overcome these obstacles. Ecosystem management includes the following elements: (1) Sustainability. Ecosystem management does not focus primarily on deliverables" but rather regards intergenerational sustainability as a precondition. (2) Goals. Ecosystem management establishes measurable goals that specify future processes and outcomes necessary for sustainability. (3) Sound ecological models and understanding. Ecosystem management relies on research performed at all levels of ecological organization. (4) Complexity and connectedness. Ecosystem management recognizes that biological diversity and structural complexity strengthen ecosystems against disturbance and supply the genetic resources necessary to adapt to long-term change. (5) The dynamic character of ecosystems. Recognizing that change and evolution are inherent in ecosystem sustainability, ecosystem management avoids attempts to freeze" ecosystems in a particular state or configuration. (6) Context and scale. Ecosystem processes operate over a wide range of spatial and temporal scales, and their behavior at any given location is greatly affected by surrounding systems. Thus, there is no single appropriate scale or time frame for management. (7) Humans as ecosystem components. Ecosystem management values the active role of humans in achieving sustainable management goals. (8) Adaptability and accountability. Ecosystem management acknowledges that current knowledge and paradigms of ecosystem function are provisional, incomplete, and subject to change. Management approaches must be viewed as hypotheses to be tested by research and monitoring programs. The following are fundamental scientific precepts for ecosystem management. (1) Spatial and temporal scale are critical. Ecosystem function includes inputs, outputs, cycling of materials and energy, and the interactions of organisms. Boundaries defined for the study or management of one process are often inappropriate for the study of others; thus, ecosystem management requires a broad view. (2) Ecosystem function depends on its structure, diversity, and integrity. Ecosystem management seeks to maintain biological diversity as a critical component in strengthening ecosystems against disturbance. Thus, management of biological diversity requires a broad perspective and recognition that the complexity and function of any particular location is influenced heavily by the surrounding system. (3) Ecosystems are dynamic in space and time. Ecosystem management is challenging in part because ecosystems are constantly changing. Over time scales of decades or centuries, many landscapes are altered by natural disturbances that lead to mosaics of successional patches of different ages. Such patch dynamics are critical to ecosystem structure and function. (4) Uncertainty, surprise, and limits to knowledge. Ecosystem management acknowledges that, given sufficient time and space, unlikely events are certain to occur. Adaptive management addresses this uncertainty by combining democratic principles, scientific analysis, education, and institutional learning to increase our understanding of ecosystem processes and the consequences of management interventions, and to improve the quality of data upon which decisions must be made. Ecosystem management requires application of ecological science to natural resource actions. Moving from concepts to practice is a daunting challenge and will require the following steps and actions. (1) Defining sustainable goals and objectives. Sustainable strategies for the provision of ecosystem goods and services cannot take as their starting points statements of need or want such as mandated timber supply, water demand, or arbitrarily set harvests of shrimp or fish. Rather, sustainability must be the primary objective, and levels of commodity and amenity provision must be adjusted to meet that goal. (2) Reconciling spatial scales. Implementation of ecosystem management would be greatly simplified if management jurisdictions were spatially congruent with the behavior of ecosystem processes. Given the variation in spatial domain among processes, one perfect fit for all processes is virtually impossible; rather, ecosystem management must seek consensus among the various stakeholders within each ecosystem. (3) Reconciling temporal scales. Whereas management agencies are often forced to make decisions on a fiscal-year basis, ecosystem management must deal with time scales that transcend human lifetimes. Ecosystem management requires long-term planning and commitment. (4) Making the system adaptable and accountable. Successful ecosystem management requires institutions that are adaptable to changes in ecosystem characteristics and in our knowledge base. Adaptive management by definition requires the scientist's ongoing interaction with managers and the public. Communication must flow in both directions, and scientists must be willing to prioritize their research with regard to critical management needs. Scientists have much to offer in the development of monitoring programs, particularly in creating sampling approaches, statistical analyses, and scientific models. As our knowledge base evolves, scientists must develop new mechanisms to communicate research and management results. More professionals with an understanding of scientific, management, and social issues, and the ability to communicate with scientists, managers, and the public are needed. Ecosystem management is not a rejection of an anthropocentric for a totally biocentric worldview. Rather it is management that acknowledges the importance of human needs while at the same time confronting the reality that the capacity of our world to meet those needs in perpetuity has limits and depends on the functioning of ecosystems.

Biological Nitrogen Fixation

Abstract: Biological nitrogen fixation (BNF) is the process of the reduction of dinitrogen from the air to ammonia carried out by a large number of species of free-living and symbiotic microbes called diazotrophs. BNF presents an inexpensive and environmentally sound, sustainable approach to crop production and constitutes one of the most important Plant Growth Promotion (PGP) scenarios. Here I will summarize various aspects of BNF, including the dinitrogen reduction catalysed reaction carried out by “nitrogenase” and the enzymes/genes involved and their regulation, the inherent “oxygen paradox” , the identification of diazotrophs, sustainable agricultural uses of BNF, symbiotic plant-diazotroph interactions and endophytic diazotrophs, data from the field, and future prospects in BNF.