A genotyping protocol for multiple tissue types from the polyploid tree species Sequoia sempervirens (Cupressaceae).

Premise of the studyIdentifying clonal lineages in asexually reproducing plants using microsatellite markers is complicated by the possibility of nonidentical genotypes from the same clonal lineage due to somatic mutations, null alleles, and scoring errors. We developed and tested a clonal identification protocol that is robust to these issues for the asexually reproducing hexaploid tree species coast redwood (Sequoia sempervirens).MethodsMicrosatellite data from four previously published and two newly developed primers were scored using a modified protocol, and clones were identified using Bruvo genetic distances. The effectiveness of this clonal identification protocol was assessed using simulations and by genotyping a test set of paired samples of different tissue types from the same trees.ResultsData from simulations showed that our protocol allowed us to accurately identify clonal lineages. Multiple test samples from the same trees were identified correctly, although certain tissue type pairs had larger genetic distances on average.DiscussionThe methods described in this paper will allow for the accurate identification of coast redwood clones, facilitating future studies of the reproductive ecology of this species. The techniques used in this paper can be applied to studies of other clonal organisms as well

Back to Paper: A Case Study

Documents the developments in California, Colorado, Florida, New Mexico, and Ohio, where electronic voting machines were introduced after the 2000 election but are now being replaced by paper ballots. Also discusses trends among other states

The Miocene Bükkábrány Fossil Forest in Hungary – field observations and project outline

The oldest, standing forest preserved as wood has been found at Bükkábrány, Hungary. An open-pit mine working Upper Miocene (Pannonian) lignite revealed sixteen stumps, 1.8 to 3.6 m diameter at base, preserved up to 6 m height, standing on top of the coal bed. Suddenly rising water level of Lake Pannon drowned the forest 7 Ma ago. Sand of a prograding delta covered the landscape, preserving the trunks in waterlogged condition. A brief review of the environment allowing preservation is provided here, and investigations in progress are outlined

MCViNE -- An object oriented Monte Carlo neutron ray tracing simulation package

MCViNE (Monte-Carlo VIrtual Neutron Experiment) is a versatile Monte Carlo (MC) neutron ray-tracing program that provides researchers with tools for performing computer modeling and simulations that mirror real neutron scattering experiments. By adopting modern software engineering practices such as using composite and visitor design patterns for representing and accessing neutron scatterers, and using recursive algorithms for multiple scattering, MCViNE is flexible enough to handle sophisticated neutron scattering problems including, for example, neutron detection by complex detector systems, and single and multiple scattering events in a variety of samples and sample environments. In addition, MCViNE can take advantage of simulation components in linear-chain-based MC ray tracing packages widely used in instrument design and optimization, as well as NumPy-based components that make prototypes useful and easy to develop. These developments have enabled us to carry out detailed simulations of neutron scattering experiments with non-trivial samples in time-of-flight inelastic instruments at the Spallation Neutron Source. Examples of such simulations for powder and single-crystal samples with various scattering kernels, including kernels for phonon and magnon scattering, are presented. With simulations that closely reproduce experimental results, scattering mechanisms can be turned on and off to determine how they contribute to the measured scattering intensities, improving our understanding of the underlying physics.Comment: 34 pages, 14 figure

Robo-line storage: Low latency, high capacity storage systems over geographically distributed networks

Rapid advances in high performance computing are making possible more complete and accurate computer-based modeling of complex physical phenomena, such as weather front interactions, dynamics of chemical reactions, numerical aerodynamic analysis of airframes, and ocean-land-atmosphere interactions. Many of these 'grand challenge' applications are as demanding of the underlying storage system, in terms of their capacity and bandwidth requirements, as they are on the computational power of the processor. A global view of the Earth's ocean chlorophyll and land vegetation requires over 2 terabytes of raw satellite image data. In this paper, we describe our planned research program in high capacity, high bandwidth storage systems. The project has four overall goals. First, we will examine new methods for high capacity storage systems, made possible by low cost, small form factor magnetic and optical tape systems. Second, access to the storage system will be low latency and high bandwidth. To achieve this, we must interleave data transfer at all levels of the storage system, including devices, controllers, servers, and communications links. Latency will be reduced by extensive caching throughout the storage hierarchy. Third, we will provide effective management of a storage hierarchy, extending the techniques already developed for the Log Structured File System. Finally, we will construct a protototype high capacity file server, suitable for use on the National Research and Education Network (NREN). Such research must be a Cornerstone of any coherent program in high performance computing and communications

Spin pseudogap in Ni-doped SrCuO2

The S=1/2 spin chain material SrCuO2 doped with 1% S=1 Ni-impurities is studied by inelastic neutron scattering. At low temperatures, the spectrum shows a pseudogap \Delta ~ 8 meV, absent in the parent compound, and not related to any structural phase transition. The pseudogap is shown to be a generic feature of quantum spin chains with dilute defects. A simple model based on this idea quantitatively accounts for the exprimental data measured in the temperature range 2-300 K, and allows to represent the momentum-integrated dynamic structure factor in a universal scaling form.Comment: 5 pages, 3 figure

Moa and the multi-model architecture: a new perspective on XNF2

Advanced non-traditional application domains such as geographic information systems and digital library systems demand advanced data management support. In an effort to cope with this demand, we present the concept of a novel multi-model DBMS architecture which provides evaluation of queries on complexly structured data without sacrificing efficiency. A vital role in this architecture is played by the Moa language featuring a nested relational data model based on XNF2, in which we placed renewed interest. Furthermore, extensibility in Moa avoids optimization obstacles due to black-box treatment of ADTs. The combination of a mapping of queries on complexly structured data to an efficient physical algebra expression via a nested relational algebra, extensibility open to optimization, and the consequently better integration of domain-specific algorithms, makes that the Moa system can efficiently and effectively handle complex queries from non-traditional application domains

The Impact of Climate Change on Coastal Fog Hours of California\u27s Central Coast

This study used observations and downscaled model output from the Coupled Model Intercomparison Project 5 to investigate diurnal temperature differences and their relationship to the number of fog hours in the future along California’s central coast. The study area extended north-south from Bodega Bay to the Santa Lucia Range and east-west from the coast of California to the western flank of the Sierra Nevada Mountains. Analyses of Representative Concentration Pathway (RCP) scenarios 4.5 and 8.5 showed that most of California’s central coast will likely see minimal changes in the number of fog hours per day through the turn of the century. However, fog hours in the northern portion of the study area showed a reduction of up to an hour and a half per day, while southern areas showed an increase by more than an hour and a half per day by the turn of the century. The implications of these changes will vary depending on the timing of the increase or decrease. Further research is needed to look at timing of fog events