Fourmidable: a database for ant genomics.

BACKGROUND: Fourmidable is an infrastructure to curate and share the emerging genetic, molecular, and functional genomic data and protocols for ants. DESCRIPTION: The Fourmidable assembly pipeline groups nucleotide sequences into clusters before independently assembling each cluster. Subsequently, assembled sequences are annotated via Interproscan and BLAST against general and insect-specific databases. Gene-specific information can be retrieved using gene identifiers, searching for similar sequences or browsing through inferred Gene Ontology annotations. The database will readily scale as ultra-high throughput sequence data and sequences from additional species become available. CONCLUSION: Fourmidable currently houses EST data from two ant species and microarray gene expression data for one of these. Fourmidable is publicly available at http://fourmidable.unil.ch.

Midwest Transportation Consortium Annual Report, 2004-2005

The Midwest Transportation Consortium (MTC) recently completed its sixth year of operation. The MTC has become an established portion of the research and educational programs at ISU and its partner universities. The MTC continues to emphasize its primary focus of developing human capital. For example, this semester, Fall, 2005, ISU has graduate scholars in its educational program. However, we also recognize that the federal grant is an opportunity to build programs at our respective universities that continue after the U.S. DOT UTCP may end. An example of building a long lasting program is the University of Missouri – St. Louis’ (UMSL) and its development of a transportation Ph.D. program in their business college. Admittedly, this program could have been started regardless, but Dr. Ray Mundy, Director of UMSL’s Transportation Scholars Program, believes that the MTC support of the transportation educational program at UMSL was the essential component in establishing a Ph.D. program. At ISU, the MTC has been instrumental in establishing two research and outreach programs, and both have themes that are related to the MTC’s theme of “Transportation System Management and Operation.” The Center for Weather Impacts on Mobility and Safety (C-WIMS) was recently established, and the Center for Road Infrastructure Management and Operations (RIMO) is in the process of being established. The MTC has a critical role in establishing each of these two programs. As part of the on-going MTC program, we have established an effective network that promotes the education of future transportation professionals and the development of new knowledge on how to manage transportation infrastructure and services in a more sustainable manner. The MTC has a track record of developing outstanding students; these students are now becoming leaders in the private sector, government, and academia. The MTC has also supported the development of an extensive research portfolio related to sustainable transportation asset management. More research projects are in the pipeline. Finally, the MTC has dedicated itself to the dissemination of asset management research results through an ongoing technology transfer program. This document provides a progress for the latest fiscal year of operation of the MTC, which ran from October 2004 through September 2005.

Midwest Transportation Consortium Annual Report, 2005-2006

The Midwest Transportation Consortium (MTC) recently completed its sixth year of operation. The MTC has become an established portion of the research and educational programs at ISU and its partner universities. The MTC continues to emphasize its primary focus of developing human capital. For example, this semester, Fall, 2005, ISU has graduate scholars in its educational program. However, we also recognize that the federal grant is an opportunity to build programs at our respective universities that continue after the U.S. DOT UTCP may end. An example of building a long lasting program is the University of Missouri – St. Louis’ (UMSL) and its development of a transportation Ph.D. program in their business college. Admittedly, this program could have been started regardless, but Dr. Ray Mundy, Director of UMSL’s Transportation Scholars Program, believes that the MTC support of the transportation educational program at UMSL was the essential component in establishing a Ph.D. program. At ISU, the MTC has been instrumental in establishing two research and outreach programs, and both have themes that are related to the MTC’s theme of “Transportation System Management and Operation.” The Center for Weather Impacts on Mobility and Safety (C-WIMS) was recently established, and the Center for Road Infrastructure Management and Operations (RIMO) is in the process of being established. The MTC has a critical role in establishing each of these two programs. As part of the on-going MTC program, we have established an effective network that promotes the education of future transportation professionals and the development of new knowledge on how to manage transportation infrastructure and services in a more sustainable manner. The MTC has a track record of developing outstanding students; these students are now becoming leaders in the private sector, government, and academia. The MTC has also supported the development of an extensive research portfolio related to sustainable transportation asset management. More research projects are in the pipeline. Finally, the MTC has dedicated itself to the dissemination of asset management research results through an ongoing technology transfer program. This document provides a progress for the latest fiscal year of operation of the MTC, which ran from October 2004 through September 2005.

Midwest Transportation Consortium Annual Report, 2006-2007

The Midwest Transportation Consortium (MTC) recently completed its sixth year of operation. The MTC has become an established portion of the research and educational programs at ISU and its partner universities. The MTC continues to emphasize its primary focus of developing human capital. For example, this semester, Fall, 2005, ISU has graduate scholars in its educational program. However, we also recognize that the federal grant is an opportunity to build programs at our respective universities that continue after the U.S. DOT UTCP may end. An example of building a long lasting program is the University of Missouri – St. Louis’ (UMSL) and its development of a transportation Ph.D. program in their business college. Admittedly, this program could have been started regardless, but Dr. Ray Mundy, Director of UMSL’s Transportation Scholars Program, believes that the MTC support of the transportation educational program at UMSL was the essential component in establishing a Ph.D. program. At ISU, the MTC has been instrumental in establishing two research and outreach programs, and both have themes that are related to the MTC’s theme of “Transportation System Management and Operation.” The Center for Weather Impacts on Mobility and Safety (C-WIMS) was recently established, and the Center for Road Infrastructure Management and Operations (RIMO) is in the process of being established. The MTC has a critical role in establishing each of these two programs. As part of the on-going MTC program, we have established an effective network that promotes the education of future transportation professionals and the development of new knowledge on how to manage transportation infrastructure and services in a more sustainable manner. The MTC has a track record of developing outstanding students; these students are now becoming leaders in the private sector, government, and academia. The MTC has also supported the development of an extensive research portfolio related to sustainable transportation asset management. More research projects are in the pipeline. Finally, the MTC has dedicated itself to the dissemination of asset management research results through an ongoing technology transfer program. This document provides a progress for the latest fiscal year of operation of the MTC, which ran from October 2004 through September 2005.

Midwest Transportation Consortium Annual Report, 2007-2008

The Midwest Transportation Consortium (MTC) recently completed its sixth year of operation. The MTC has become an established portion of the research and educational programs at ISU and its partner universities. The MTC continues to emphasize its primary focus of developing human capital. For example, this semester, Fall, 2005, ISU has graduate scholars in its educational program. However, we also recognize that the federal grant is an opportunity to build programs at our respective universities that continue after the U.S. DOT UTCP may end. An example of building a long lasting program is the University of Missouri – St. Louis’ (UMSL) and its development of a transportation Ph.D. program in their business college. Admittedly, this program could have been started regardless, but Dr. Ray Mundy, Director of UMSL’s Transportation Scholars Program, believes that the MTC support of the transportation educational program at UMSL was the essential component in establishing a Ph.D. program. At ISU, the MTC has been instrumental in establishing two research and outreach programs, and both have themes that are related to the MTC’s theme of “Transportation System Management and Operation.” The Center for Weather Impacts on Mobility and Safety (C-WIMS) was recently established, and the Center for Road Infrastructure Management and Operations (RIMO) is in the process of being established. The MTC has a critical role in establishing each of these two programs. As part of the on-going MTC program, we have established an effective network that promotes the education of future transportation professionals and the development of new knowledge on how to manage transportation infrastructure and services in a more sustainable manner. The MTC has a track record of developing outstanding students; these students are now becoming leaders in the private sector, government, and academia. The MTC has also supported the development of an extensive research portfolio related to sustainable transportation asset management. More research projects are in the pipeline. Finally, the MTC has dedicated itself to the dissemination of asset management research results through an ongoing technology transfer program. This document provides a progress for the latest fiscal year of operation of the MTC, which ran from October 2004 through September 2005.

Midwest Transportation Consortium Annual Report, 2009

The Midwest Transportation Consortium (MTC) recently completed its sixth year of operation. The MTC has become an established portion of the research and educational programs at ISU and its partner universities. The MTC continues to emphasize its primary focus of developing human capital. For example, this semester, Fall, 2005, ISU has graduate scholars in its educational program. However, we also recognize that the federal grant is an opportunity to build programs at our respective universities that continue after the U.S. DOT UTCP may end. An example of building a long lasting program is the University of Missouri – St. Louis’ (UMSL) and its development of a transportation Ph.D. program in their business college. Admittedly, this program could have been started regardless, but Dr. Ray Mundy, Director of UMSL’s Transportation Scholars Program, believes that the MTC support of the transportation educational program at UMSL was the essential component in establishing a Ph.D. program. At ISU, the MTC has been instrumental in establishing two research and outreach programs, and both have themes that are related to the MTC’s theme of “Transportation System Management and Operation.” The Center for Weather Impacts on Mobility and Safety (C-WIMS) was recently established, and the Center for Road Infrastructure Management and Operations (RIMO) is in the process of being established. The MTC has a critical role in establishing each of these two programs. As part of the on-going MTC program, we have established an effective network that promotes the education of future transportation professionals and the development of new knowledge on how to manage transportation infrastructure and services in a more sustainable manner. The MTC has a track record of developing outstanding students; these students are now becoming leaders in the private sector, government, and academia. The MTC has also supported the development of an extensive research portfolio related to sustainable transportation asset management. More research projects are in the pipeline. Finally, the MTC has dedicated itself to the dissemination of asset management research results through an ongoing technology transfer program. This document provides a progress for the latest fiscal year of operation of the MTC, which ran from October 2004 through September 2005.

Midwest Transportation Consortium Annual Report, 2010

The Midwest Transportation Consortium (MTC) recently completed its sixth year of operation. The MTC has become an established portion of the research and educational programs at ISU and its partner universities. The MTC continues to emphasize its primary focus of developing human capital. For example, this semester, Fall, 2005, ISU has graduate scholars in its educational program. However, we also recognize that the federal grant is an opportunity to build programs at our respective universities that continue after the U.S. DOT UTCP may end. An example of building a long lasting program is the University of Missouri – St. Louis’ (UMSL) and its development of a transportation Ph.D. program in their business college. Admittedly, this program could have been started regardless, but Dr. Ray Mundy, Director of UMSL’s Transportation Scholars Program, believes that the MTC support of the transportation educational program at UMSL was the essential component in establishing a Ph.D. program. At ISU, the MTC has been instrumental in establishing two research and outreach programs, and both have themes that are related to the MTC’s theme of “Transportation System Management and Operation.” The Center for Weather Impacts on Mobility and Safety (C-WIMS) was recently established, and the Center for Road Infrastructure Management and Operations (RIMO) is in the process of being established. The MTC has a critical role in establishing each of these two programs. As part of the on-going MTC program, we have established an effective network that promotes the education of future transportation professionals and the development of new knowledge on how to manage transportation infrastructure and services in a more sustainable manner. The MTC has a track record of developing outstanding students; these students are now becoming leaders in the private sector, government, and academia. The MTC has also supported the development of an extensive research portfolio related to sustainable transportation asset management. More research projects are in the pipeline. Finally, the MTC has dedicated itself to the dissemination of asset management research results through an ongoing technology transfer program. This document provides a progress for the latest fiscal year of operation of the MTC, which ran from October 2004 through September 2005.

Midwest Transportation Consortium Annual Report, 2011

The Midwest Transportation Consortium (MTC) recently completed its sixth year of operation. The MTC has become an established portion of the research and educational programs at ISU and its partner universities. The MTC continues to emphasize its primary focus of developing human capital. For example, this semester, Fall, 2005, ISU has graduate scholars in its educational program. However, we also recognize that the federal grant is an opportunity to build programs at our respective universities that continue after the U.S. DOT UTCP may end. An example of building a long lasting program is the University of Missouri – St. Louis’ (UMSL) and its development of a transportation Ph.D. program in their business college. Admittedly, this program could have been started regardless, but Dr. Ray Mundy, Director of UMSL’s Transportation Scholars Program, believes that the MTC support of the transportation educational program at UMSL was the essential component in establishing a Ph.D. program. At ISU, the MTC has been instrumental in establishing two research and outreach programs, and both have themes that are related to the MTC’s theme of “Transportation System Management and Operation.” The Center for Weather Impacts on Mobility and Safety (C-WIMS) was recently established, and the Center for Road Infrastructure Management and Operations (RIMO) is in the process of being established. The MTC has a critical role in establishing each of these two programs. As part of the on-going MTC program, we have established an effective network that promotes the education of future transportation professionals and the development of new knowledge on how to manage transportation infrastructure and services in a more sustainable manner. The MTC has a track record of developing outstanding students; these students are now becoming leaders in the private sector, government, and academia. The MTC has also supported the development of an extensive research portfolio related to sustainable transportation asset management. More research projects are in the pipeline. Finally, the MTC has dedicated itself to the dissemination of asset management research results through an ongoing technology transfer program. This document provides a progress for the latest fiscal year of operation of the MTC, which ran from October 2004 through September 2005.

Automated scoring of AFLPs using RawGeno v 2.0, a free R CRAN library.

Amplified Fragment Length Polymorphisms (AFLPs) are a cheap and efficient protocol for generating large sets of genetic markers. This technique has become increasingly used during the last decade in various fields of biology, including population genomics, phylogeography, and genome mapping. Here, we present RawGeno, an R library dedicated to the automated scoring of AFLPs (i.e., the coding of electropherogram signals into ready-to-use datasets). Our program includes a complete suite of tools for binning, editing, visualizing, and exporting results obtained from AFLP experiments. RawGeno can either be used with command lines and program analysis routines or through a user-friendly graphical user interface. We describe the whole RawGeno pipeline along with recommendations for (a) setting the analysis of electropherograms in combination with PeakScanner, a program freely distributed by Applied Biosystems; (b) performing quality checks; (c) defining bins and proceeding to scoring; (d) filtering nonoptimal bins; and (e) exporting results in different formats.

An evaluation of volume-based morphometry for prediction of mild cognitive impairment and Alzheimer's disease.

Voxel-based morphometry from conventional T1-weighted images has proved effective to quantify Alzheimer's disease (AD) related brain atrophy and to enable fairly accurate automated classification of AD patients, mild cognitive impaired patients (MCI) and elderly controls. Little is known, however, about the classification power of volume-based morphometry, where features of interest consist of a few brain structure volumes (e.g. hippocampi, lobes, ventricles) as opposed to hundreds of thousands of voxel-wise gray matter concentrations. In this work, we experimentally evaluate two distinct volume-based morphometry algorithms (FreeSurfer and an in-house algorithm called MorphoBox) for automatic disease classification on a standardized data set from the Alzheimer's Disease Neuroimaging Initiative. Results indicate that both algorithms achieve classification accuracy comparable to the conventional whole-brain voxel-based morphometry pipeline using SPM for AD vs elderly controls and MCI vs controls, and higher accuracy for classification of AD vs MCI and early vs late AD converters, thereby demonstrating the potential of volume-based morphometry to assist diagnosis of mild cognitive impairment and Alzheimer's disease.

Fecal pellets collection as a method for assessing egesta of the marine cave-dwelling mysid Hemimysis speluncula

Egesta of a cave-dwelling mysid (Hemimysis speluncola Ledoyer, 1963) was studied in a submarine cave of Medes Islands, NW Mediterranean by in situ fecal pellet collecting. Fecal pellet production and gut fullness of mysids during incubation experiments are used to estimate mysid egestion rates. Intrinsic factors related with the natural history of this species such as population structure, density of mysids, daily rhythms and pellet decomposition rates are tested for their influence on the egestion rate. The effects of methodological artifacts, such as the stress induced by both incubation and preservation procedures, are also studied. An average mysid egests about 2.5 pellets per day into the cave. The time of day is the main factor affecting egestion. The highest deposition rate is between 2 to 4 hours after sunrise when about 38 % of the total daily pellet production becomes egested. Fecal pellet morphology changes with mysid demographic classes: immature mysids produce slender and thick pellets, whereas mature mysids produce only thick pellets. Immature classes show higher percentages of full guts than mature ones. Mysid density in the incubators does not affect the results on gut fullness, but it causes a decrease in the number of pellets collected after incubation. Coprorhexia seems to be the only plausible process to explain this paradox. The incubation procedure does not increase deposition rate significantly. Time of incubation is critical because the half-life of fecal pellets is about 2.5 hours. Fixation with liquid nitrogen decreases gut fullness and also deposition rates. Higher values are obtained with 70 % ethanol and 5 % formalin solutions which show very similar results for both gut fullness and pellet deposition rates. Nevertheless, ethanol is not suitable as fixative because it enhances the opacity of the body. Several suggestions are given in order to optimize the reliability of further in situ experiments for evaluation of egesta of Hemimysis speluncola in submarine caves.

On the origin of the North Pacific arcs

We present a new hypothesis that relates global plate tectonics to the formation of marginal basins, island arcs, spreading ridges and arc-shaped mountain belts around the North Pacific Ocean. According to our model, the ellipsoidal-shaped Paleogene basins of the South China Sea, Parece-Vela Basin, Shikoku Basin, Sea of Japan and the Sea of Okhotsk in addition to those of the North American Cordillera can be attributed to the change in plate convergence direction at 42 Ma between the Indoaustralian and Eurasian plates. The new direction of convergence was parallel to the eastern continental margin of Asia and resulted in widespread extension perpendicular to this margin and to the western margin of North America. Both margins form part of a circle parallel to the Indoaustralian-Eurasian direction of convergence.

Combined use of the GGSFT data base and on Board Marine Collected Data to Model the Moho Beneath the Powell Basin, Antarctica

The Powell Basin is a small oceanic basin located at the NE end of the Antarctic Peninsula developed during the Early Miocene and mostly surrounded by the continental crusts of the South Orkney Microcontinent, South Scotia Ridge and Antarctic Peninsula margins. Gravity data from the SCAN 97 cruise obtained with the R/V Hespérides and data from the Global Gravity Grid and Sea Floor Topography (GGSFT) database (Sandwell and Smith, 1997) are used to determine the 3D geometry of the crustal-mantle interface (CMI) by numerical inversion methods. Water layer contribution and sedimentary effects were eliminated from the Free Air anomaly to obtain the total anomaly. Sedimentary effects were obtained from the analysis of existing and new SCAN 97 multichannel seismic profiles (MCS). The regional anomaly was obtained after spectral and filtering processes. The smooth 3D geometry of the crustal mantle interface obtained after inversion of the regional anomaly shows an increase in the thickness of the crust towards the continental margins and a NW-SE oriented axis of symmetry coinciding with the position of an older oceanic spreading axis. This interface shows a moderate uplift towards the western part and depicts two main uplifts to the northern and eastern sectors.

Evidence for middle Cretaceous accretion at Santa Elena Peninsula (Santa Rosa Accretionary Complex), Costa Rica

An oceanic assemblage of alkaline basalts, radiolarites and polymictic breccias forms the tectonic substratum of the Santa Elena Nappe, which is constituted by extensive outcrops of ultramafic and mafic rocks of the Santa Elena Peninsula (NW Costa Rica). The undulating basal contact of this nappe defines several half-windows along the south shores of the Santa Elena Peninsula. Lithologically it is constituted by vesicular pillowed and massive alkaline basaltic flows, alkaline sills, ribbon-bedded and knobby radiolarites, muddy tuffaceous and detrital turbidites, debris flows and polymictic breccias and megabreccias. Sediments and basalt flows show predominant subvertical dips and occur in packages separated by roughly bed-parallel thrust planes. Individual packages reveal a coherent internal stratigraphy that records younging to the east in all packages and shows rapid coarsening upwards of the detrital facies. Alkaline basalt flows, pillow breccias and sills within radiolarite successions are genetically related to a mid-Cretaceous submarine seamount. Detrital sedimentary facies range form distal turbidites to proximal debris flows and culminate in megabreccias related to collapse and mass wasting in an accretionary prism. According to radiolarian dating, bedded radiolarites and soft-sediment- deformed clasts in the megabreccias formed in a short, late Aptian to Cenomanian time interval. Middle Jurassic to Lower Cretaceous radiolarian ages are found in clasts and blocks reworked from an older oceanic basement. We conclude that the oceanic assemblage beneath the Santa Elena Nappe does not represent a continuous stratigraphic succession. It is a pile of individual thrust sheets constituting an accretionary sequence, where intrusion and extrusion of alkaline basalts, sedimentation of radiolarites, turbidites and trench fill chaotic sediments occurred during the Aptian-Cenomanian. These thrust sheets formed shortly before the off-scraping and accretion of the complex. Here we define the Santa Rosa Accretionary Complex and propose a new hypothesis not considered in former interpretations. This hypothesis would be the basis for further research.

ConnectomeViewer - Multi-Modal Multi-Level Network Visualization and Analysis.

Introduction: The field of Connectomic research is growing rapidly, resulting from methodological advances in structural neuroimaging on many spatial scales. Especially progress in Diffusion MRI data acquisition and processing made available macroscopic structural connectivity maps in vivo through Connectome Mapping Pipelines (Hagmann et al, 2008) into so-called Connectomes (Hagmann 2005, Sporns et al, 2005). They exhibit both spatial and topological information that constrain functional imaging studies and are relevant in their interpretation. The need for a special-purpose software tool for both clinical researchers and neuroscientists to support investigations of such connectome data has grown. Methods: We developed the ConnectomeViewer, a powerful, extensible software tool for visualization and analysis in connectomic research. It uses the novel defined container-like Connectome File Format, specifying networks (GraphML), surfaces (Gifti), volumes (Nifti), track data (TrackVis) and metadata. Usage of Python as programming language allows it to by cross-platform and have access to a multitude of scientific libraries. Results: Using a flexible plugin architecture, it is possible to enhance functionality for specific purposes easily. Following features are already implemented: * Ready usage of libraries, e.g. for complex network analysis (NetworkX) and data plotting (Matplotlib). More brain connectivity measures will be implemented in a future release (Rubinov et al, 2009). * 3D View of networks with node positioning based on corresponding ROI surface patch. Other layouts possible. * Picking functionality to select nodes, select edges, get more node information (ConnectomeWiki), toggle surface representations * Interactive thresholding and modality selection of edge properties using filters * Arbitrary metadata can be stored for networks, thereby allowing e.g. group-based analysis or meta-analysis. * Python Shell for scripting. Application data is exposed and can be modified or used for further post-processing. * Visualization pipelines using filters and modules can be composed with Mayavi (Ramachandran et al, 2008). * Interface to TrackVis to visualize track data. Selected nodes are converted to ROIs for fiber filtering The Connectome Mapping Pipeline (Hagmann et al, 2008) processed 20 healthy subjects into an average Connectome dataset. The Figures show the ConnectomeViewer user interface using this dataset. Connections are shown that occur in all 20 subjects. The dataset is freely available from the homepage (connectomeviewer.org). Conclusions: The ConnectomeViewer is a cross-platform, open-source software tool that provides extensive visualization and analysis capabilities for connectomic research. It has a modular architecture, integrates relevant datatypes and is completely scriptable. Visit www.connectomics.org to get involved as user or developer.