Practical trapped-ion protocols for universal qudit-based quantum computing

The notion of universal quantum computation can be generalized to multi-level qudits, which offer advantages in resource usage and algorithmic efficiencies. Trapped ions, which are pristine and well-controlled quantum systems, offer an ideal platform to develop qudit-based quantum information processing. Previous work has not fully explored the practicality of implementing trapped-ion qudits accounting for known experimental error sources. Here, we describe a universal set of protocols for state preparation, single-qudit gates, a new generalization of the M\o{}lmer-S\o{}rensen gate for two-qudit gates, and a measurement scheme which utilizes shelving to a meta-stable state. We numerically simulate known sources of error from previous trapped ion experiments, and show that there are no fundamental limitations to achieving fidelities above $99\%$ for three-level qudits encoded in $^{137}\mathrm{Ba}^+$ ions. Our methods are extensible to higher-dimensional qudits, and our measurement and single-qudit gate protocols can achieve $99\%$ fidelities for five-level qudits. We identify avenues to further decrease errors in future work. Our results suggest that three-level trapped ion qudits will be a useful technology for quantum information processing

Relationships between variance in electroencephalography relative power and developmental status in infants with typical development and at risk for developmental disability: An observational study [version 2; referees: 2 approved]

Background: Electroencephalography (EEG) is a non-invasive tool that has the potential to identify and quantify atypical brain development. We introduce a new measure here, variance of relative power of resting-state EEG. We sought to assess whether variance of relative power of resting-state EEG could predict i) classification of infants as typical development (TD) or at risk (AR) for developmental disability, and ii) Bayley developmental scores at the same visit or future visits. Methods: A total of 22 infants with TD participated, aged between 38 and 203 days. In addition, 11 infants broadly at risk participated (6 high-risk pre-term, 4 low-risk pre-term, 1 high-risk full-term), aged between 40 and 225 days of age (adjusted for prematurity). We used EEG to measure resting-state brain function across months. We calculated variance of relative power as the standard deviation of the relative power across each of the 32 EEG electrodes. The Bayley Scales of Infant Development (3rd edition) was used to measure developmental level. Infants were measured 1-6 times each, with 1 month between measurements. Results: Our main findings were: i) variance of relative power of resting state EEG can predict classification of infants as TD or AR, and ii) variance of relative power of resting state EEG can predict Bayley developmental scores at the same visit (Bayley raw fine motor, Bayley raw cognitive, Bayley total raw score, Bayley motor composite score) and at a future visit (Bayley raw fine motor). Conclusions: This was a preliminary, exploratory, small study. Our results support variance of relative power of resting state EEG as an area of interest for future study as a biomarker of neurodevelopmental status and as a potential outcome measure for early intervention

Parsimony and likelihood reconstruction of human segmental duplications

Motivation: Segmental duplications > 1 kb in length with ≥ 90% sequence identity between copies comprise nearly 5% of the human genome. They are frequently found in large, contiguous regions known as duplication blocks that can contain mosaic patterns of thousands of segmental duplications. Reconstructing the evolutionary history of these complex genomic regions is a non-trivial, but important task

The Extended Environment of M17: A Star Formation History

M17 is one of the youngest and most massive nearby star-formation regions in the Galaxy. It features a bright H II region erupting as a blister from the side of a giant molecular cloud (GMC). Combining photometry from the Spitzer GLIMPSE survey with complementary infrared (IR) surveys, we identify candidate young stellar objects (YSOs) throughout a 1.5 deg x 1 deg field that includes the M17 complex. The long sightline through the Galaxy behind M17 creates significant contamination in our YSO sample from unassociated sources with similar IR colors. Removing contaminants, we produce a highly-reliable catalog of 96 candidate YSOs with a high probability of association with the M17 complex. We fit model spectral energy distributions to these sources and constrain their physical properties. Extrapolating the mass function of 62 intermediate-mass YSOs (M >3 Msun), we estimate that >1000 stars are in the process of forming in the extended outer regions of M17. From IR survey images from IRAS and GLIMPSE, we find that M17 lies on the rim of a large shell structure ~0.5 deg in diameter (~20 pc at 2.1 kpc). We present new maps of CO and 13CO (J=2-1) emission, which show that the shell is a coherent, kinematic structure associated with M17 at v = 19 km/s. The shell is an extended bubble outlining the photodissociation region of a faint, diffuse H II region several Myr old. We provide evidence that massive star formation has been triggered by the expansion of the bubble. The formation of the massive cluster ionizing the M17 H II region itself may have been similarly triggered. We conclude that the star formation history in the extended environment of M17 has been punctuated by successive waves of massive star formation propagating through a GMC complex.Comment: 31 pages, 15 figures, accepted for publication in ApJ. For a version with higher-quality figures, see http://www.astro.wisc.edu/glimpse/Povich2009_M17.pd

Efficient algorithms for analyzing segmental duplications with deletions and inversions in genomes

Background: Segmental duplications, or low-copy repeats, are common in mammalian genomes. In the human genome, most segmental duplications are mosaics comprised of multiple duplicated fragments. This complex genomic organization complicates analysis of the evolutionary history of these sequences. One model proposed to explain this mosaic patterns is a model of repeated aggregation and subsequent duplication of genomic sequences. Results: We describe a polynomial-time exact algorithm to compute duplication distance, a genomic distance defined as the most parsimonious way to build a target string by repeatedly copying substrings of a fixed source string. This distance models the process of repeated aggregation and duplication. We also describe extensions of this distance to include certain types of substring deletions and inversions. Finally, we provide an description of a sequence of duplication events as a context-free grammar (CFG). Conclusion: These new genomic distances will permit more biologically realistic analyses of segmental duplications in genomes.

Binary Quasars at High Redshift I: 24 New Quasar Pairs at z ~ 3-4

The clustering of quasars on small scales yields fundamental constraints on models of quasar evolution and the buildup of supermassive black holes. This paper describes the first systematic survey to discover high redshift binary quasars. Using color-selection and photometric redshift techniques, we searched 8142 deg^2 of SDSS imaging data for binary quasar candidates, and confirmed them with follow-up spectroscopy. Our sample of 27 high redshift binaries (24 of them new discoveries) at redshifts 2.9 < z < 4.3 with proper transverse separations 10 kpc < R_{\perp} < 650 kpc increases the number of such objects known by an order of magnitude. Eight members of this sample are very close pairs with R_{\perp} 3.5. The completeness and efficiency of our well-defined selection algorithm are quantified using simulated photometry and we find that our sample is ~ 50% complete. Our companion paper uses this knowledge to make the first measurement of the small scale clustering (R < 1 Mpc/h comoving) of high-redshift quasars. High redshift binaries constitute exponentially rare coincidences of two extreme (M >~ 10^9 Msun) supermassive black holes. At z ~ 4 there is about one close binary per 10 Gpc^3, thus these could be the highest sigma peaks, the analogs of superclusters, in the early Universe.Comment: Submitted to Ap

Diversity of Murine Norovirus Strains Isolated from Asymptomatic Mice of Different Genetic Backgrounds within a Single U.S. Research Institute

Antibody prevalence studies in laboratory mice indicate that murine norovirus (MNV) infections are common, but the natural history of these viruses has not been fully established. This study examined the extent of genetic diversity of murine noroviruses isolated from healthy laboratory mice housed in multiple animal facilities within a single, large research institute- the National Institute of Allergy and Infectious Diseases of the National Institutes of Health (NIAID-NIH) in Bethesda, Maryland, U.S. Ten distinct murine norovirus strains were isolated from various tissues and feces of asymptomatic wild type sentinel mice as well as asymptomatic immunodeficient (RAG 2−/−) mice. The NIH MNV isolates showed little cytopathic effect in permissive RAW264.7 cells in early passages, but all isolates examined could be adapted to efficient growth in cell culture by serial passage. The viruses, although closely related in genome sequence, were distinguishable from each other according to facility location, likely due to the introduction of new viruses into each facility from separate sources or vendors at different times. Our study indicates that the murine noroviruses are widespread in these animal facilities, despite rigorous guidelines for animal care and maintenance

The evolutionarily conserved long non‐coding RNA <i>LINC00261</i> drives neuroendocrine prostate cancer proliferation and metastasis <i>via</i> distinct nuclear and cytoplasmic mechanisms

Metastatic neuroendocrine prostate cancer (NEPC) is a highly aggressive disease, whose incidence is rising. Long noncoding RNAs (lncRNAs) represent a large family of disease- and tissue-specific transcripts, most of which are still functionally uncharacterized. Thus, we set out to identify the highly conserved lncRNAs that play a central role in NEPC pathogenesis. To this end, we performed transcriptomic analyses of donor-matched patient-derived xenograft models (PDXs) with immunohistologic features of prostate adenocarcinoma (AR+/PSA+) or NEPC (AR-/SYN+/CHGA+ ) and through differential expression analyses identified lncRNAs that were upregulated upon neuroendocrine transdifferentiation. These genes were prioritized for functional assessment based on the level of conservation in vertebrates. Here, LINC00261 emerged as the top gene with over 3229-fold upregulation in NEPC. Consistently, LINC00261 expression was significantly upregulated in NEPC specimens in multiple patient cohorts. Knockdown of LINC00261 in PC-3 cells dramatically attenuated its proliferative and metastatic abilities, which are explained by parallel downregulation of CBX2 and FOXA2 through distinct molecular mechanisms. In the cell cytoplasm, LINC00261 binds to and sequesters miR-8485 from targeting the CBX2 mRNA, while inside the nucleus, LINC00261 functions as a transcriptional scaffold to induce SMAD-driven expression of the FOXA2 gene. For the first time, these results demonstrate hyperactivation of the LINC00261-CBX2-FOXA2 axes in NEPC to drive proliferation and metastasis, and that LINC00261 may be utilized as a therapeutic target and a biomarker for this incurable disease

Exposure to extreme heat and precipitation events associated with increased risk of hospitalization for asthma in Maryland, U.S.A.

Several studies have investigated the association between asthma exacerbations and exposures to ambient temperature and precipitation. However, limited data exists regarding how extreme events, projected to grow in frequency, intensity, and duration in the future in response to our changing climate, will impact the risk of hospitalization for asthma. The objective of our study was to quantify the association between frequency of extreme heat and precipitation events and increased risk of hospitalization for asthma in Maryland between 2000 and 2012. We used a time-stratified case-crossover design to examine the association between exposure to extreme heat and precipitation events and risk of hospitalization for asthma (ICD-9 code 493, n = 115,923). Occurrence of extreme heat events in Maryland increased the risk of same day hospitalization for asthma (lag 0) by 3 % (Odds Ratio (OR): 1.03, 95 % Confidence Interval (CI): 1.00, 1.07), with a considerably higher risk observed for extreme heat events that occur during summer months (OR: 1.23, 95 % CI: 1.15, 1.33). Likewise, summertime extreme precipitation events increased the risk of hospitalization for asthma by 11 % in Maryland (OR: 1.11, 95 % CI: 1.06, 1.17). Across age groups, increase in risk for asthma hospitalization from exposure to extreme heat event during the summer months was most pronounced among youth and adults, while those related to extreme precipitation event was highest among ≤4 year olds. Exposure to extreme heat and extreme precipitation events, particularly during summertime, is associated with increased risk of hospitalization for asthma in Maryland. Our results suggest that projected increases in frequency of extreme heat and precipitation event will have significant impact on public health.https://doi.org/10.1186/s12940-016-0142-