Benchmarking database systems for Genomic Selection implementation

Motivation: With high-throughput genotyping systems now available, it has become feasible to fully integrate genotyping information into breeding programs. To make use of this information effectively requires DNA extraction facilities and marker production facilities that can efficiently deploy the desired set of markers across samples with a rapid turnaround time that allows for selection before crosses needed to be made. In reality, breeders often have a short window of time to make decisions by the time they are able to collect all their phenotyping data and receive corresponding genotyping data. This presents a challenge to organize information and utilize it in downstream analyses to support decisions made by breeders. In order to implement genomic selection routinely as part of breeding programs, one would need an efficient genotyping data storage system. We selected and benchmarked six popular open-source data storage systems, including relational database management and columnar storage systems. Results: We found that data extract times are greatly influenced by the orientation in which genotype data is stored in a system. HDF5 consistently performed best, in part because it can more efficiently work with both orientations of the allele matrix

Structure, transport, and seasonality of the Atlantic Water boundary current north of Svalbard: Results from a yearlong mooring array

Author Posting. © American Geophysical Union, 2019. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research-Oceans 124(3), (2019): 1679-1698, doi:10.1029/2018JC014759.The characteristics and seasonality of the Svalbard branch of the Atlantic Water (AW) boundary current in the Eurasian Basin are investigated using data from a six‐mooring array deployed near 30°E between September 2012 and September 2013. The instrument coverage extended to 1,200‐m depth and approximately 50 km offshore of the shelf break, which laterally bracketed the flow. Averaged over the year, the transport of the current over this depth range was 3.96 ± 0.32 Sv (1 Sv = 106 m3/s). The transport within the AW layer was 2.08 ± 0.24 Sv. The current was typically subsurface intensified, and its dominant variability was associated with pulsing rather than meandering. From late summer to early winter the AW was warmest and saltiest, and its eastward transport was strongest (2.44 ± 0.12 Sv), while from midspring to midsummer the AW was coldest and freshest and its transport was weakest (1.10 ± 0.06 Sv). Deep mixed layers developed through the winter, extending to 400‐ to 500‐m depth in early spring until the pack ice encroached the area from the north shutting off the air‐sea buoyancy forcing. This vertical mixing modified a significant portion of the AW layer, suggesting that, as the ice cover continues to decrease in the southern Eurasian Basin, the AW will be more extensively transformed via local ventilation.We are grateful to the crew of the R/V Lance for the collection of the data. The U.S. component of A‐TWAIN was funded by the National Science Foundation under grant ARC‐1264098 as well as a grant from the Steven Grossman Family Foundation. The Norwegian component of A‐TWAIN was funded by the “Arctic Ocean” flagship program at the Fram Centre. The data used in this study are available at http://atwain.whoi.edu and data.npolar.no (Sundfjord et al., 2017). The data from Fram Strait are available at https://doi.pangaea.de/10.1594/PANGAEA.8539022019-08-1

Two-sided bounds on minimum-error quantum measurement, on the reversibility of quantum dynamics, and on the maximum overlap problem using directional iterates

In a unified framework, we obtain two-sided estimates of the following quantities of interest in quantum information theory: 1.The minimum-error distinguishability of arbitrary ensembles of mixed quantum states. 2.The approximate reversibility of quantum dynamics in terms of entanglement fidelity. (This is also referred to as "channel-adapted quantum error recovery" when the reversed channel is the composition of an encoding operation and a noise channel.) 3.The maximum overlap between a bipartite pure quantum state and a bipartite mixed state that may be achieved by applying a local quantum operation to one part of the mixed state. 4. The conditional min-entropy of bipartite quantum states. A refined version of the author's techniques [J. Math. Phys. 50, 032016] for bounding the first quantity is employed to give two-sided estimates of the remaining three quantities. Our primary tool is "small angle" initialization of an abstract generalization of the iterative schemes for computing optimal measurements and quantum error recoveries introduced by Jezek-Rehacek-Fiurasek [Phys. Rev. A 65, 060301], Jezek-Fiurasek-Hradil [Phys. Rev. A 68, 012305], and Reimpell-Werner [Phys. Rev. Lett 94, 080501].Comment: Extensively revised & new content added. Improved min-entropy bounds. Notation made more accessible. Minimax theorem used to clarify relationship between "worst case" bounds and "single instance" bounds. Improved motivation of the choice of "small angle" guess. Eliminated spurious factor appearing when overlap bounds are applied to state distinction. Work connected to that of Beny and Oreshko

The effect of phase fluctuations on the single-particle properties of the underdoped cuprates

We study the effect of order parameter phase fluctuations on the single-particle properties of fermions in the underdoped cuprate superconductors using a phenomenological low-energy theory. We identify the fermion-phase field coupling as the Doppler-shift of the quasiparticle spectrum induced by the fluctuating superfluid velocity and we calculate the effect of these fluctuations on the fermion self-energy. We show that the vortex pair unbinding near the superconducting transition causes a significant broadening in the fermion spectral function, producing a pseudogap-like feature. We also discuss the specific heat and show that the phase fluctuation effect is visible due to the short coherence length.Comment: RevTex 11 pages; 11 epsf figures included. Added and updated reference

Faithful Squashed Entanglement

Squashed entanglement is a measure for the entanglement of bipartite quantum states. In this paper we present a lower bound for squashed entanglement in terms of a distance to the set of separable states. This implies that squashed entanglement is faithful, that is, strictly positive if and only if the state is entangled. We derive the bound on squashed entanglement from a bound on quantum conditional mutual information, which is used to define squashed entanglement and corresponds to the amount by which strong subadditivity of von Neumann entropy fails to be saturated. Our result therefore sheds light on the structure of states that almost satisfy strong subadditivity with equality. The proof is based on two recent results from quantum information theory: the operational interpretation of the quantum mutual information as the optimal rate for state redistribution and the interpretation of the regularised relative entropy of entanglement as an error exponent in hypothesis testing. The distance to the set of separable states is measured by the one-way LOCC norm, an operationally-motivated norm giving the optimal probability of distinguishing two bipartite quantum states, each shared by two parties, using any protocol formed by local quantum operations and one-directional classical communication between the parties. A similar result for the Frobenius or Euclidean norm follows immediately. The result has two applications in complexity theory. The first is a quasipolynomial-time algorithm solving the weak membership problem for the set of separable states in one-way LOCC or Euclidean norm. The second concerns quantum Merlin-Arthur games. Here we show that multiple provers are not more powerful than a single prover when the verifier is restricted to one-way LOCC operations thereby providing a new characterisation of the complexity class QMA.Comment: 24 pages, 1 figure, 1 table. Due to an error in the published version, claims have been weakened from the LOCC norm to the one-way LOCC nor

The One Ocean Expedition: Science and Sailing for the Ocean We Want

The One Ocean Expedition (OOE) was a 20-month long circumnavigation of the globe by the Norwegian sail training vessel Statsraad Lehmkuhl, and a recognised part of the UN decade of Ocean Science for Sustainable Development. The ship was equipped with modern instrumentation to collect high-quality data on ocean physics, chemistry, and biology. Many of the data series were available in near real time from an open repository. The scientific programme was executed along the sailing route of Statsraad Lehmkuhl, with occasional stops for stationary work. The aim of the data collection on board the vessel was to improve knowledge about the state of the world's ocean with regards to the distribution and diversity of organisms, environmental status, climate, and human pressures on the marine ecosystem. Another aim of the expedition was to educate ocean scientists and strengthen ocean literacy. The main types of instrumentation are sensors that measure continuously underway including echosounder, hydrophone, temperature and salinity probes, and various instruments that collect and analyse water sampled from an inlet in the ship's hull, including for environmental DNA and microplastic. Here, we describe the scientific instrumentation onboard Statsraad Lehmkuhl and present preliminary results from the Atlantic part of the expedition. While there are many challenges to using a sail ship for scientific purposes, there are also some key benefits as the vessel is quiet and has a low footprint. Furthermore, the use of a common set of instruments and procedures across the ocean also removes an uncertainty factor when comparing data between ocean areas.The One Ocean Expedition: Science and Sailing for the Ocean We WantpublishedVersio

The One Ocean Expedition: Science and Sailing for the Ocean We Want

Source at https://www.hi.no/hi.The One Ocean Expedition (OOE) was a 20-month long circumnavigation of the globe by the Norwegian sail training vessel Statsraad Lehmkuhl, and a recognised part of the UN decade of Ocean Science for Sustainable Development. The ship was equipped with modern instrumentation to collect high-quality data on ocean physics, chemistry, and biology. Many of the data series were available in near real time from an open repository. The scientific programme was executed along the sailing route of Statsraad Lehmkuhl, with occasional stops for stationary work. The aim of the data collection on board the vessel was to improve knowledge about the state of the world's ocean with regards to the distribution and diversity of organisms, environmental status, climate, and human pressures on the marine ecosystem. Another aim of the expedition was to educate ocean scientists and strengthen ocean literacy. The main types of instrumentation are sensors that measure continuously underway including echosounder, hydrophone, temperature and salinity probes, and various instruments that collect and analyse water sampled from an inlet in the ship's hull, including for environmental DNA and microplastic. Here, we describe the scientific instrumentation onboard Statsraad Lehmkuhl and present preliminary results from the Atlantic part of the expedition. While there are many challenges to using a sail ship for scientific purposes, there are also some key benefits as the vessel is quiet and has a low footprint. Furthermore, the use of a common set of instruments and procedures across the ocean also removes an uncertainty factor when comparing data between ocean areas

Large-Scale Evidence for the Effect of the COLIA1 Sp1 Polymorphism on Osteoporosis Outcomes: The GENOMOS Study

BACKGROUND: Osteoporosis and fracture risk are considered to be under genetic control. Extensive work is being performed to identify the exact genetic variants that determine this risk. Previous work has suggested that a G/T polymorphism affecting an Sp1 binding site in the COLIA1 gene is a genetic marker for low bone mineral density (BMD) and osteoporotic fracture, but there have been no very-large-scale studies of COLIA1 alleles in relation to these phenotypes. METHODS AND FINDINGS: Here we evaluated the role of COLIA1 Sp1 alleles as a predictor of BMD and fracture in a multicenter study involving 20,786 individuals from several European countries. At the femoral neck, the average (95% confidence interval [CI]) BMD values were 25 mg/cm (2) (CI, 16 to 34 mg/cm (2)) lower in TT homozygotes than the other genotype groups ( p < 0.001), and a similar difference was observed at the lumbar spine; 21 mg/cm (2) (CI, 1 to 42 mg/cm (2)), ( p = 0.039). These associations were unaltered after adjustment for potential confounding factors. There was no association with fracture overall (odds ratio [OR] = 1.01 [CI, 0.95 to 1.08]) in either unadjusted or adjusted analyses, but there was a non-significant trend for association with vertebral fracture and a nominally significant association with incident vertebral fractures in females (OR = 1.33 [CI, 1.00 to 1.77]) that was independent of BMD, and unaltered in adjusted analyses. CONCLUSIONS: Allowing for the inevitable heterogeneity between participating teams, this study—which to our knowledge is the largest ever performed in the field of osteoporosis genetics for a single gene—demonstrates that the COLIA1 Sp1 polymorphism is associated with reduced BMD and could predispose to incident vertebral fractures in women, independent of BMD. The associations we observed were modest however, demonstrating the importance of conducting studies that are adequately powered to detect and quantify the effects of common genetic variants on complex diseases