Theory and practice of classical matrix-matrix multiplication for hierarchical memory architectures

Matrix-matrix multiplication is perhaps the most important operation used as a basic building block in dense linear algebra. A computer with a hierarchical memory architectures has memory that is organized in layers, with small and fast memories close to the processor, and big and slow memories further away from it. Classical matrix-matrix multiplication is an operation particularly suited for such architectures, as it exhibits a large degree of data reuse, so expensive data movements can be amortized over a lot of computation. This dissertation advances the theory of how to optimally reuse data during matrix-matrix multiplication on hierarchical memory architectures, and it uses this understanding to develop new practical algorithms for matrix-matrix multiplication that exhibit improved properties related to data movement.Computer Science

Sodium Atoms in the Lunar Exotail: Observed Velocity and Spatial Distributions

The lunar sodium tail extends long distances due to radiation pressure on sodium atoms in the lunar exosphere. Our earlier observations measured the average radial velocity of sodium atoms moving down the lunar tail beyond Earth (i.e., near the anti-lunar point) to be ~ 12.5 km/s. Here we use the Wisconsin H-alpha Mapper to obtain the first kinematically resolved maps of the intensity and velocity distribution of this emission over a 15 x 15 deg region on the sky near the anti-lunar point. We present both spatially and spectrally resolved observations obtained over four nights bracketing new Moon in October 2007. The spatial distribution of the sodium atoms is elongated along the ecliptic with the location of the peak intensity drifting 3 deg east along the ecliptic per night. Preliminary modeling results suggest the spatial and velocity distributions in the sodium exotail are sensitive to the near surface lunar sodium velocity distribution. Future observations of this sort along with detailed modeling offer new opportunities to describe the time history of lunar surface sputtering over several days

Grid-Based Atmospheric Retrievals for Reflected-Light Spectra of Exoplanets using PSGnest

Techniques to retrieve the atmospheric properties of exoplanets via direct observation of their reflected light have often been limited in scope due to computational constraints imposed by the forward-model calculations. We have developed a new set of techniques which significantly decreases the time required to perform a retrieval while maintaining accurate results. We constructed a grid of 1.4 million pre-computed geometric albedo spectra valued at discrete sets of parameter points. Spectra from this grid are used to produce models for a fast and efficient nested sampling routine called PSGnest. Beyond the upfront time to construct a spectral grid, the amount of time to complete a full retrieval using PSGnest is on the order of seconds to minutes using a personal computer. An extensive evaluation of the error induced from interpolating intermediate spectra from the grid indicates that this bias is insignificant compared to other retrieval error sources, with an average coefficient of determination between interpolated and true spectra of 0.998. We apply these new retrieval techniques to help constrain the optimal bandpass centers for retrieving various atmospheric and bulk parameters from a LuvEx-type mission observing several planetary archetypes. We show that spectral observations made using a 20\% bandpass centered at 0.73 microns can be used alongside our new techniques to make detections of $H_2O$ and $O_2$ without the need to increase observing time beyond what is necessary for a signal-to-noise ratio of 10. The methods introduced here will enable robust studies of the capabilities of future observatories to characterize exoplanets.Comment: 32 pages, 17 figures. Accepted for publication in The Astronomical Journa

Identification of candidate structured RNAs in the marine organism 'Candidatus Pelagibacter ubique'

<p>Abstract</p> <p>Background</p> <p>Metagenomic sequence data are proving to be a vast resource for the discovery of biological components. Yet analysis of this data to identify functional RNAs lags behind efforts to characterize protein diversity. The genome of '<it>Candidatus </it>Pelagibacter ubique' HTCC 1062 is the closest match for approximately 20% of marine metagenomic sequence reads. It is also small, contains little non-coding DNA, and has strikingly low GC content.</p> <p>Results</p> <p>To aid the discovery of RNA motifs within the marine metagenome we exploited the genomic properties of '<it>Cand</it>. P. ubique' by targeting our search to long intergenic regions (IGRs) with relatively high GC content. Analysis of known RNAs (rRNA, tRNA, riboswitches etc.) shows that structured RNAs are significantly enriched in such IGRs. To identify additional candidate structured RNAs, we examined other IGRs with similar characteristics from '<it>Cand</it>. P. ubique' using comparative genomics approaches in conjunction with marine metagenomic data. Employing this strategy, we discovered four candidate structured RNAs including a new riboswitch class as well as three additional likely <it>cis</it>-regulatory elements that precede genes encoding ribosomal proteins S2 and S12, and the cytoplasmic protein component of the signal recognition particle. We also describe four additional potential RNA motifs with few or no examples occurring outside the metagenomic data.</p> <p>Conclusion</p> <p>This work begins the process of identifying functional RNA motifs present in the metagenomic data and illustrates how existing completed genomes may be used to aid in this task.</p

Monolayer superconductivity and tunable topological electronic structure at the Fe(Te,Se)/Bi2Te3 interface

The interface between two-dimensional topological Dirac states and an s-wave superconductor is expected to support Majorana bound states that can be used for quantum computing applications. Realizing these novel states of matter and their applications requires control over superconductivity and spin-orbit coupling to achieve spin-momentum locked topological surface states which are simultaneously superconducting. While signatures of Majorana bound states have been observed in the magnetic vortex cores of bulk FeTe0.55Se0.45, inhomogeneity and disorder from doping makes these signatures unclear and inconsistent between vortices. Here we report superconductivity in monolayer FeTe1-ySey (Fe(Te,Se)) grown on Bi2Te3 by molecular beam epitaxy. Spin and angle resolved photoemission spectroscopy directly resolve the interfacial spin and electronic structure of Fe(Te,Se)/Bi2Te3 heterostructures. We find that for y = 0.25 the Fe(Te,Se) electronic structure overlaps with the topological Bi2Te3 interfacial states which disrupts the desired spin-momentum locking. In contrast, for y = 0.1 a smaller Fe(Te,Se) Fermi surface allows for clear spin-momentum locking observed in the topological states. Hence, we demonstrate the Fe(Te,Se)/Bi2Te3 system is a highly tunable platform for realizing Majorana bound states where reduced doping can improve characteristics important for Majorana interrogation and potential applications

Past Tense Formation in Williams Syndrome

It has been claimed that in the language systems of people with Williams syndrome (WS), syntax is intact but lexical memory is impaired. Evidence has come from past tense elicitation tasks with a small number of participants where individuals with WS are said to have a specific deficit in forming irregular past tenses. However, typically developing children also show poorer performance on irregulars than regulars in these tasks, and one of the central features of WS language development is that it is delayed. We compared the performance of 21 participants with WS on two past tense elicitation tasks with that of four typically developing control groups, at ages 6, 8, 10, and adult. When verbal mental age was controlled for, participants in the WS group displayed no selective deficit in irregular past tense performance. However, there was evidence for lower levels of generalisation to novel strings. This is consistent with the hypothesis that the WS language system is delayed because it has developed under different constraints, constraints that perhaps include atypical phonological representations. The results are discussed in relation to dual-mechanism and connectionist computational models of language development, and to the possible differential weight given to phonology versus semantics in WS development

Where genotype is not predictive of phenotype: towards an understanding of the molecular basis of reduced penetrance in human inherited disease

Some individuals with a particular disease-causing mutation or genotype fail to express most if not all features of the disease in question, a phenomenon that is known as ‘reduced (or incomplete) penetrance’. Reduced penetrance is not uncommon; indeed, there are many known examples of ‘disease-causing mutations’ that fail to cause disease in at least a proportion of the individuals who carry them. Reduced penetrance may therefore explain not only why genetic diseases are occasionally transmitted through unaffected parents, but also why healthy individuals can harbour quite large numbers of potentially disadvantageous variants in their genomes without suffering any obvious ill effects. Reduced penetrance can be a function of the specific mutation(s) involved or of allele dosage. It may also result from differential allelic expression, copy number variation or the modulating influence of additional genetic variants in cis or in trans. The penetrance of some pathogenic genotypes is known to be age- and/or sex-dependent. Variable penetrance may also reflect the action of unlinked modifier genes, epigenetic changes or environmental factors. At least in some cases, complete penetrance appears to require the presence of one or more genetic variants at other loci. In this review, we summarize the evidence for reduced penetrance being a widespread phenomenon in human genetics and explore some of the molecular mechanisms that may help to explain this enigmatic characteristic of human inherited disease

LSU rDNA based RFLP assays for the routine identification of Gambierdiscus species

© The Author(s), 2017. This is the author's version of the work. It is posted here under a nonexclusive, irrevocable, paid-up, worldwide license granted to WHOI. It is made available for personal use, not for redistribution. The definitive version was published in Harmful Algae 66 (2017): 20-28, doi:10.1016/j.hal.2017.04.009.Gambierdiscus is a genus of benthic dinoflagellates commonly associated with ciguatera fish poisoning (CFP), which is generally found in tropical or sub-tropical regions around the world. Morphologically similar species within the genus can vary in toxicity; however, species identifications are difficult or sometimes impossible using light microscopy. DNA sequencing of ribosomal RNA genes (rDNA) is thus often used to identify and describe Gambierdiscus species and ribotypes, but the expense and time can be prohibitive for routine culture screening and/or large-scale monitoring programs. This study describes a restriction fragment length polymorphism (RFLP) typing method based on analysis of the large subunit ribosomal RNA gene (rDNA) that can successfully identify at least nine of the described Gambierdiscus species and two Fukuyoa species. The software programs DNAMAN 6.0 and Restriction Enzyme Picker were used to identify a set of restriction enzymes (SpeI, HpyCH4IV, and TaqαI) capable of distinguishing most of the known Gambierdiscus species for which DNA sequences were available. This assay was tested using in silico analysis and cultured isolates, and species identifications of isolates assigned by RFLP typing were confirmed by DNA sequencing. To verify the assay and assess intra-specific heterogeneity in RFLP patterns, identifications of 63 Gambierdiscus isolates comprising ten Gambierdiscus species, one ribotype, and two Fukuyoa species were confirmed using RFLP typing, and this method was subsequently employed in the routine identification of isolates collected from the Caribbean Sea. The RFLP assay presented here reduces the time and cost associated with morphological identification via scanning electron microscopy and/or DNA sequencing, and provides a phylogenetically sensitive method for routine Gambierdiscus species assignment.Funding for this study was provided by the U.S. National Oceanic and Atmospheric Administration ECOHAB program (CiguaHAB; Cooperative Agreement NA11NOS4780060, NA11NOS4780028), the China Scholarship Council and Natural Science Foundation of China (No. 41606137, 41606136), and the Guangxi Natural Science Foundation (2015GXNSFCA139003, 2016GXNSFBA380037)