Second Set of Spaces

This document describes the Gloss infrastructure supporting implementation of location-aware services. The document is in two parts. The first part describes software architecture for the smart space. As described in D8, a local architecture provides a framework for constructing Gloss applications, termed assemblies, that run on individual physical nodes, whereas a global architecture defines an overlay network for linking individual assemblies. The second part outlines the hardware installation for local sensing. This describes the first phase of the installation in Strathclyde University

Segmentation of brain tumors in MRI images using three-dimensional active contour without edge

Brain tumor segmentation in magnetic resonance imaging (MRI) is considered a complex procedure because of the variability of tumor shapes and the complexity of determining the tumor location, size, and texture. Manual tumor segmentation is a time-consuming task highly prone to human error. Hence, this study proposes an automated method that can identify tumor slices and segment the tumor across all image slices in volumetric MRI brain scans. First, a set of algorithms in the pre-processing stage is used to clean and standardize the collected data. A modified gray-level co-occurrence matrix and Analysis of Variance (ANOVA) are employed for feature extraction and feature selection, respectively. A multi-layer perceptron neural network is adopted as a classifier, and a bounding 3D-box-based genetic algorithm is used to identify the location of pathological tissues in the MRI slices. Finally, the 3D active contour without edge is applied to segment the brain tumors in volumetric MRI scans. The experimental dataset consists of 165 patient images collected from the MRI Unit of Al-Kadhimiya Teaching Hospital in Iraq. Results of the tumor segmentation achieved an accuracy of 89% +/- 4.7% compared with manual processes

Status of Grauer’s Gorilla and Chimpanzees in Eastern Democratic Republic of Congo: Historical and Current Distribution and Abundance

This report summarises the current state of knowledge on the distribution, densities and trends in abundance of Grauer’s gorilla (Gorilla beringei graueri) and the eastern chimpanzee (Pan troglodytes schweinfurthii) in eastern Democratic Republic of Congo (DRC). It summarises the historical knowledge about the distribution of Grauer’s gorilla across its range and describes the development of a Conservation Action Plan (CAP) for these two ape species. A result of this CAP was funding to undertake an assessment of the current status of these apes across the range of Grauer’s gorilla. Wildlife Conservation Society (WCS) and Fauna & Flora International (FFI) worked with Institut Congolais pour la Conservation de la Nature (ICCN) and the Reserve managers of the Reserve des Gorilles de Punia (RGPU) and local communities to undertake surveys across the region using a variety of methods: line transects, recces along paths and patrol data from data collected by rangers while on patrol and entered into SMART software

Grain-Size Analysis of the Late Pleistocene Sediments in the Corinth Rift: Insights into Strait Influenced Hydrodynamics and Provenance of an Active Rift Basin

Under embargo until: 2023-12-08Grain-size analysis of the sediments in borehole M0079A, which is located in the Corinth Rift, was used to explore hydrodynamic conditions and provenance in the Late Pleistcene Corinth Rift. Grain-size populations that were sensitive to the sedimentary environments were characterized by frequency distribution, particle size-standard deviation, and probability cumulative curves. Our results indicate the grain-size population component in the range 0.15-0.25 μm may be used as a sensitive proxy for hyperpycnal flows, which have commonly been triggered by river floods from the southern margin of the rift since ca. 0.593-0.613 Ma. The high-density plumes derived from the longer rivers of the southern rift that were prevalent before ca. 0.593-0.613 Ma. When sediment is supplied as hemipelagic deposition, the proportion of the total grain-size population that is in the 0.3-0.5 μm range becomes an index for suspension fall-out deposits. The core shows coarser sediments during the marine periods and this may be linked to the current circulation related to the Ishtmia Strait opening. The study thus illustrates how the establishment of interbasinal straits can influence the details of sedimentary hydrodynamics in the deep- water axis of an adjacent depocenter.acceptedVersio

Automated simultaneous analysis phylogenetics (ASAP) : an enabling tool for phlyogenomics

© 2008 Sarkar et al. This is an Open Access article distributed under the terms of the Creative Commons Attribution License 2.0, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in BMC Bioinformatics 9 (2008): 103, doi:10.1186/1471-2105-9-103.The availability of sequences from whole genomes to reconstruct the tree of life has the potential to enable the development of phylogenomic hypotheses in ways that have not been before possible. A significant bottleneck in the analysis of genomic-scale views of the tree of life is the time required for manual curation of genomic data into multi-gene phylogenetic matrices. To keep pace with the exponentially growing volume of molecular data in the genomic era, we have developed an automated technique, ASAP (Automated Simultaneous Analysis Phylogenetics), to assemble these multigene/multi species matrices and to evaluate the significance of individual genes within the context of a given phylogenetic hypothesis. Applications of ASAP may enable scientists to re-evaluate species relationships and to develop new phylogenomic hypotheses based on genome-scale data.This work is funded in part by NSF DBI-0421604 to GC and RD. INS is supported in part by the Ellison Medical Foundation

Using Phylogenomic Patterns and Gene Ontology to Identify Proteins of Importance in Plant Evolution

We use measures of congruence on a combined expressed sequenced tag genome phylogeny to identify proteins that have potential significance in the evolution of seed plants. Relevant proteins are identified based on the direction of partitioned branch and hidden support on the hypothesis obtained on a 16-species tree, constructed from 2,557 concatenated orthologous genes. We provide a general method for detecting genes or groups of genes that may be under selection in directions that are in agreement with the phylogenetic pattern. Gene partitioning methods and estimates of the degree and direction of support of individual gene partitions to the overall data set are used. Using this approach, we correlate positive branch support of specific genes for key branches in the seed plant phylogeny. In addition to basic metabolic functions, such as photosynthesis or hormones, genes involved in posttranscriptional regulation by small RNAs were significantly overrepresented in key nodes of the phylogeny of seed plants. Two genes in our matrix are of critical importance as they are involved in RNA-dependent regulation, essential during embryo and leaf development. These are Argonaute and the RNA-dependent RNA polymerase 6 found to be overrepresented in the angiosperm clade. We use these genes as examples of our phylogenomics approach and show that identifying partitions or genes in this way provides a platform to explain some of the more interesting organismal differences among species, and in particular, in the evolution of plants

Catastrophic Decline of World's Largest Primate: 80% Loss of Grauer's Gorilla (Gorilla beringei graueri) Population Justifies Critically Endangered Status

Grauer's gorilla (Gorilla beringei graueri), the World's largest primate, is confined to eastern Democratic Republic of Congo (DRC) and is threatened by civil war and insecurity. During the war, armed groups in mining camps relied on hunting bushmeat, including gorillas. Insecurity and the presence of several militia groups across Grauer's gorilla's range made it very difficult to assess their population size. Here we use a novel method that enables rigorous assessment of local community and ranger-collected data on gorilla occupancy to evaluate the impacts of civil war on Grauer's gorilla, which prior to the war was estimated to number 16,900 individuals. We show that gorilla numbers in their stronghold of Kahuzi- Biega National Park have declined by 87%. Encounter rate data of gorilla nests at 10 sites across its range indicate declines of 82-100% at six of these sites. Spatial occupancy analysis identifies three key areas as the most critical sites for the remaining populations of this ape and that the range of this taxon is around 19,700 km2. We estimate that only 3,800 Grauer's gorillas remain in the wild, a 77% decline in one generation, justifying its elevation to Critically Endangered status on the IUCN Red List of Threatened Species

Biolabile ferrous iron bearing nanoparticles in glacial sediments

Glaciers and ice sheets are a significant source of nanoparticulate Fe, which is potentially important in sustaining the high productivity observed in the near-coastal regions proximal to terrestrial ice cover. However, the bioavailability of particulate iron is poorly understood, despite its importance in the ocean Fe inventory. We combined high-resolution imaging and spectroscopy to investigate the abundance, morphology and valence state of particulate iron in glacial sediments. Our results document the widespread occurrence of amorphous and Fe(II)-rich and Fe(II)-bearing nanoparticles in Arctic glacial meltwaters and iceberg debris, compared to Fe(III)-rich dominated particulates in an aeolian dust sample. Fe(II) is thought to be highly biolabile in marine environments. Our work shows that glacially derived Fe is more labile than previously assumed, and consequently that glaciers and ice sheets are therefore able to export potentially bioavailable Fe(II)-containing nanoparticulate material to downstream ecosystems, including those in a marine setting. Our findings provide further evidence that Greenland Ice Sheet meltwaters may provide biolabile particulate Fe that may fuel the large summer phytoplankton bloom in the Labrador Sea, and that Fe(II)-rich particulates from a region of very high productivity downstream of a polar ice sheet may be glacial in origin

Bacterial Causes of Empyema in Children, Australia, 2007–2009

Most infections were caused by non–7-valent pneumococcal conjugate vaccine serotypes