6,319 research outputs found

    An HMM-based Comparative Genomic Framework for Detecting Introgression in Eukaryotes

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    One outcome of interspecific hybridization and subsequent effects of evolutionary forces is introgression, which is the integration of genetic material from one species into the genome of an individual in another species. The evolution of several groups of eukaryotic species has involved hybridization, and cases of adaptation through introgression have been already established. In this work, we report on a new comparative genomic framework for detecting introgression in genomes, called PhyloNet-HMM, which combines phylogenetic networks, that capture reticulate evolutionary relationships among genomes, with hidden Markov models (HMMs), that capture dependencies within genomes. A novel aspect of our work is that it also accounts for incomplete lineage sorting and dependence across loci. Application of our model to variation data from chromosome 7 in the mouse (Mus musculus domesticus) genome detects a recently reported adaptive introgression event involving the rodent poison resistance gene Vkorc1, in addition to other newly detected introgression regions. Based on our analysis, it is estimated that about 12% of all sites withinchromosome 7 are of introgressive origin (these cover about 18 Mbp of chromosome 7, and over 300 genes). Further, our model detects no introgression in two negative control data sets. Our work provides a powerful framework for systematic analysis of introgression while simultaneously accounting for dependence across sites, point mutations, recombination, and ancestral polymorphism

    Time-Domain Isolated Phoneme Classification Using Reconstructed Phase Spaces

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    This paper introduces a novel time-domain approach to modeling and classifying speech phoneme waveforms. The approach is based on statistical models of reconstructed phase spaces, which offer significant theoretical benefits as representations that are known to be topologically equivalent to the state dynamics of the underlying production system. The lag and dimension parameters of the reconstruction process for speech are examined in detail, comparing common estimation heuristics for these parameters with corresponding maximum likelihood recognition accuracy over the TIMIT data set. Overall accuracies are compared with a Mel-frequency cepstral baseline system across five different phonetic classes within TIMIT, and a composite classifier using both cepstral and phase space features is developed. Results indicate that although the accuracy of the phase space approach by itself is still currently below that of baseline cepstral methods, a combined approach is capable of increasing speaker independent phoneme accuracy

    Determining the Student Services which Align with Undergraduate Student Expectations A Study of Student Perceptions and University Service Delivery

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    Extant research demonstrates that student support services are a vital link in the success of students and a major component in student per- sistence to graduation. This paper reports the results of an empirical study examining enrolled undergraduate student attitudes and expec- tations regarding student services at two-similarly-sized universities in a major metropolitan area in the southwestern United States. Using survey data and a sample of several hundred students at each school, it analyzes their knowledge of and attitudes about student services, such as health services, career counseling, computer laboratories, student organizations and clubs, and sporting events. This study compares student perspectives at private versus public universities and further analyzes possible differing student needs and expectations that may occur among various student demographic groups. The results of this study are important for several reasons. First, it compares student and administrator perspectives on university services to see if they are similar or if there are possible differences in their views. Since the data informs universities about student attitudes and expectations, the data can help universities to do a better job in aligning services to student perceived needs. Second, the study tests the view that students at private universities may have higher expectations of services versus public university students, and then we explore possible differences between various student demographic groups, clarifying how the needs and expectations may differ among these demographic groups. Finally, the results can help universities to determine the services that are viewed as most critical and invest in those services which are more successfully attracting and retaining those students

    Heavy Axion Opportunities at the DUNE Near Detector

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    While the QCD axion is often considered to be necessarily light (≲\lesssim eV), recent work has opened a viable and interesting parameter space for heavy axions, which solve both the Strong CP and the axion Quality Problems. These well-motivated heavy axions, as well as the generic axion-like-particles, call for explorations in the GeV mass realm at collider and beam dump environments. The primary upcoming neutrino experiment, Deep Underground Neutrino Experiment (DUNE), is simultaneously also a powerful beam dump experiment, enabled by its multipurpose Near Detector (ND) complex. In this study, we show with detailed analyses that the DUNE ND has a unique sensitivity to heavy axions for masses between 2020 MeV and 22 GeV, complementary to other future experiments.Comment: 16 pages, 12 figure

    Dynamic detection of electron spin accumulation in ferromagnet-semiconductor devices by ferromagnetic resonance

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    A distinguishing feature of spin accumulation in ferromagnet-semiconductor devices is precession of the non-equilibrium spin population of the semiconductor in a magnetic field. This is the basis for detection techniques such as the Hanle effect, but these approaches become less effective as the spin lifetime in the semiconductor decreases. For this reason, no electrical Hanle measurement has been demonstrated in GaAs at room temperature. We show here that by forcing the magnetization in the ferromagnet (the spin injector and detector) to precess at the ferromagnetic resonance frequency, an electrically generated spin accumulation can be detected from 30 to 300 K. At low temperatures, the distinct Larmor precession of the spin accumulation in the semiconductor can be detected by ferromagnetic resonance in an oblique field. We verify the effectiveness of this new spin detection technique by comparing the injection bias and temperature dependence of the measured spin signal to the results obtained using traditional methods. We further show that this new approach enables a measurement of short spin lifetimes (< 100 psec), a regime that is not accessible in semiconductors using traditional Hanle techniques.Comment: 4 figure
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