MRI On the Fly: Accelerating MRI Imaging Using LDA Classification with LDB Feature Extraction

To improve MRI acquisition time, we explored the uses of linear discriminant analysis (LDA), and local discriminant bases (LDB) for the task of classifying MRI images using a minimal set of signal acquisitions. Our algorithm has both off-line and on-line components. The off-line component uses the k-basis algorithm to partition a set of training images (all from a particular region of a patient) into classes. For each class, we find a basis by applying the best basis algorithm on the images in that class. We keep these bases to be used by the on-line process. We then apply LDB to the training set with the class assignments, determining the best discriminant basis for the set. We rank the basis coordinates according to discriminating power, and retain the top M coordinates for the on-line algorithm. We keep the top M coordinates, which index the basis functions with the most discriminating capability, for on-line purposes. Finally, we train LDA on these transformed coordinates, producing a classifier for the images. With the off-line requirements complete, we can take advantage of the simplicity and speed of the on-line mechanism to acquire an image in a similar region of the patient. We need acquire only the M important coordinates of the image in the discriminant basis to create a ``scout image.\u27\u27 This image, which can be acquired quickly since M is much much smaller than the number of measurements needed to fill in the values of the 256 by 256 pixels, is then sent through the map furnished by LDA which in turn assigns a class to the image. Returning to the list of bases that we kept from the k-bases algorithm, we find the optimal basis for the particular class at hand. We then acquire the image using that optimal basis, omitting the coefficients with the least truncation error. The complete image can then be quickly reconstructed using the inverse wavelet packet transform. The power of our algorithm is that the on-line task is fast and simple, while the computational complexity lies mostly in the off-line task that needs to be done only once for images in a certain region. In addition, our algorithm only makes use of the flexibility of MRI hardware, so no modifications in hardware design are needed

The genomes of two key bumblebee species with primitive eusocial organization

Background: The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats. Results: We report the high quality draft genome sequences of Bombus terrestris and Bombus impatiens, two ecologically dominant bumblebees and widely utilized study species. Comparing these new genomes to those of the highly eusocial honeybee Apis mellifera and other Hymenoptera, we identify deeply conserved similarities, as well as novelties key to the biology of these organisms. Some honeybee genome features thought to underpin advanced eusociality are also present in bumblebees, indicating an earlier evolution in the bee lineage. Xenobiotic detoxification and immune genes are similarly depauperate in bumblebees and honeybees, and multiple categories of genes linked to social organization, including development and behavior, show high conservation. Key differences identified include a bias in bumblebee chemoreception towards gustation from olfaction, and striking differences in microRNAs, potentially responsible for gene regulation underlying social and other traits. Conclusions: These two bumblebee genomes provide a foundation for post-genomic research on these key pollinators and insect societies. Overall, gene repertoires suggest that the route to advanced eusociality in bees was mediated by many small changes in many genes and processes, and not by notable expansion or depauperation

A Next-Generation Liquid Xenon Observatory for Dark Matter and Neutrino Physics

The nature of dark matter and properties of neutrinos are among the mostpressing issues in contemporary particle physics. The dual-phase xenontime-projection chamber is the leading technology to cover the availableparameter space for Weakly Interacting Massive Particles (WIMPs), whilefeaturing extensive sensitivity to many alternative dark matter candidates.These detectors can also study neutrinos through neutrinoless double-beta decayand through a variety of astrophysical sources. A next-generation xenon-baseddetector will therefore be a true multi-purpose observatory to significantlyadvance particle physics, nuclear physics, astrophysics, solar physics, andcosmology. This review article presents the science cases for such a detector.<br

How sulphate-reducing microorganisms cope with stress: lessons from systems biology

Sulphate-reducing microorganisms (SRMs) are a phylogenetically diverse group of anaerobes encompassing distinct physiologies with a broad ecological distribution. As SRMs have important roles in the biogeochemical cycling of carbon, nitrogen, sulphur and various metals, an understanding of how these organisms respond to environmental stresses is of fundamental and practical importance. In this Review, we highlight recent applications of systems biology tools in studying the stress responses of SRMs, particularly Desulfovibrio spp., at the cell, population, community and ecosystem levels. The syntrophic lifestyle of SRMs is also discussed, with a focus on system-level analyses of adaptive mechanisms. Such information is important for understanding the microbiology of the global sulphur cycle and for developing biotechnological applications of SRMs for environmental remediation, energy production, biocorrosion control, wastewater treatment and mineral recovery

A next-generation liquid xenon observatory for dark matter and neutrino physics

The nature of dark matter and properties of neutrinos are among the most pressing issues in contemporary particle physics. The dual-phase xenon time-projection chamber is the leading technology to cover the available parameter space for weakly interacting massive particles, while featuring extensive sensitivity to many alternative dark matter candidates. These detectors can also study neutrinos through neutrinoless double-beta decay and through a variety of astrophysical sources. A next-generation xenon-based detector will therefore be a true multi-purpose observatory to significantly advance particle physics, nuclear physics, astrophysics, solar physics, and cosmology. This review article presents the science cases for such a detector

Population genomic scan for candidate signatures of balancing selection to guide antigen characterization in malaria parasites.

Acquired immunity in vertebrates maintains polymorphisms in endemic pathogens, leading to identifiable signatures of balancing selection. To comprehensively survey for genes under such selection in the human malaria parasite Plasmodium falciparum, we generated paired-end short-read sequences of parasites in clinical isolates from an endemic Gambian population, which were mapped to the 3D7 strain reference genome to yield high-quality genome-wide coding sequence data for 65 isolates. A minority of genes did not map reliably, including the hypervariable var, rifin, and stevor families, but 5,056 genes (90.9% of all in the genome) had >70% sequence coverage with minimum read depth of 5 for at least 50 isolates, of which 2,853 genes contained 3 or more single nucleotide polymorphisms (SNPs) for analysis of polymorphic site frequency spectra. Against an overall background of negatively skewed frequencies, as expected from historical population expansion combined with purifying selection, the outlying minority of genes with signatures indicating exceptionally intermediate frequencies were identified. Comparing genes with different stage-specificity, such signatures were most common in those with peak expression at the merozoite stage that invades erythrocytes. Members of clag, PfMC-2TM, surfin, and msp3-like gene families were highly represented, the strongest signature being in the msp3-like gene PF10_0355. Analysis of msp3-like transcripts in 45 clinical and 11 laboratory adapted isolates grown to merozoite-containing schizont stages revealed surprisingly low expression of PF10_0355. In diverse clonal parasite lines the protein product was expressed in a minority of mature schizonts (<1% in most lines and ∼10% in clone HB3), and eight sub-clones of HB3 cultured separately had an intermediate spectrum of positive frequencies (0.9 to 7.5%), indicating phase variable expression of this polymorphic antigen. This and other identified targets of balancing selection are now prioritized for functional study

Common Data Elements for Subarachnoid Hemorrhage and Unruptured Intracranial Aneurysms: Recommendations from the Working Group on Subject Characteristics

Background: The National Institute of Neurological Disorders and Stroke (NINDS) Common Data Elements (CDEs) have been generated to standardize and define terms used by the scientific community. The widespread use of these CDEs promotes harmonized data collection in clinical research. The aim of the NINDS Unruptured Intracranial Aneurysms (UIA) and Subarachnoid Hemorrhage (SAH), and Subject Characteristics working group (WG) was to identify, define, and classify CDEs describing the characteristics of patients diagnosed with an UIA and SAH. Thus, “Participant/Subject characteristics” is a set of factors defining a population of selected individuals and allowing comparisons with a reference population and overtime. Methods: Based on standard terms defined by the United States’ Census Bureau, CDEs previously defined by several (Stroke, Epilepsy and Traumatic Brain Injury) NINDS CDE working groups literature and expert opinion of the WG, the “Participant/Subject characteristics” domain has been defined. Results: A set of 192 CDEs divided in 7 subsections: demographics (8 CDEs), social status (8 CDEs), behavioral status (22 CDEs), family and medical history (144 CDEs), pregnancy and perinatal history (8 CDEs), history data source reliability (3 CDEs), and prior functional status (3 CDEs) was defined. SAH is characterized by 6 core elements, all classified in the “Participant/Subject characteristics” domain. Four exploratory elements out of the 39 for SAH overall are in the “Participant/Subject characteristics” domain, and all remaining 182 CDEs in the “Participant/Subject characteristics” domain are classified as Supplemental-Highly Recommended elements. Conclusions: These CDEs would allow the development of best practice guidelines to standardize the assessment and reporting of observations concerning UIA and SAH