Importance of randomization in microarray experimental designs with Illumina platforms

Measurements of gene expression from microarray experiments are highly dependent on experimental design. Systematic noise can be introduced into the data at numerous steps. On Illumina BeadChips, multiple samples are assayed in an ordered series of arrays. Two experiments were performed using the same samples but different hybridization designs. An experiment confounding genotype with BeadChip and treatment with array position was compared to another experiment in which these factors were randomized to BeadChip and array position. An ordinal effect of array position on intensity values was observed in both experiments. We demonstrate that there is increased rate of false-positive results in the confounded design and that attempts to correct for confounded effects by statistical modeling reduce power of detection for true differential expression. Simple analysis models without post hoc corrections provide the best results possible for a given experimental design. Normalization improved differential expression testing in both experiments but randomization was the most important factor for establishing accurate results. We conclude that lack of randomization cannot be corrected by normalization or by analytical methods. Proper randomization is essential for successful microarray experiments

Effects of Ground Failure on Bridges, Roads, and Railroads

The long duration and strong velocity content of the motions produced by the 27 February 2010 Maule earthquake resulted in widespread liquefaction and lateral spreading in several urban and other regions of Chile. In particular, critical lifeline structures such as bridges, roadway embankments, and railroads were damaged by ground shaking and ground failure. This paper describes the effects that ground failure had on a number of bridges, roadway embankments, and railroads during this major earthquake

The STAGES view of red spirals and dusty red galaxies: Mass-dependent quenching of star-formation in cluster infall

We investigate the properties of optically passive spirals and dusty red galaxies in the A901/2 cluster complex at redshift ~0.17 using restframe near-UV-optical SEDs, 24 micron IR data and HST morphologies from the STAGES dataset. The cluster sample is based on COMBO-17 redshifts with an rms precision of sigma_cz~2000 km/sec. We find that 'dusty red galaxies' and 'optically passive spirals' in A901/2 are largely the same phenomenon, and that they form stars at a substantial rate, which is only 4x lower than that in blue spirals at fixed mass. This star formation is more obscured than in blue galaxies and its optical signatures are weak. They appear predominantly in the stellar mass range of log M*/Msol=[10,11] where they constitute over half of the star-forming galaxies in the cluster; they are thus a vital ingredient for understanding the overall picture of star formation quenching in clusters. We find that the mean specific SFR of star-forming galaxies in the cluster is clearly lower than in the field, in contrast to the specific SFR properties of blue galaxies alone, which appear similar in cluster and field. Such a rich red spiral population is best explained if quenching is a slow process and morphological transformation is delayed even more. At log M*/Msol<10, such galaxies are rare, suggesting that their quenching is fast and accompanied by morphological change. We note, that edge-on spirals play a minor role; despite being dust-reddened they form only a small fraction of spirals independent of environment.Comment: Accepted for publication in MNRA

The Astropy Problem

The Astropy Project (http://astropy.org) is, in its own words, "a community effort to develop a single core package for Astronomy in Python and foster interoperability between Python astronomy packages." For five years this project has been managed, written, and operated as a grassroots, self-organized, almost entirely volunteer effort while the software is used by the majority of the astronomical community. Despite this, the project has always been and remains to this day effectively unfunded. Further, contributors receive little or no formal recognition for creating and supporting what is now critical software. This paper explores the problem in detail, outlines possible solutions to correct this, and presents a few suggestions on how to address the sustainability of general purpose astronomical software

Glucose Transporter 1 and Monocarboxylate Transporters 1, 2, and 4 Localization within the Glial Cells of Shark Blood-Brain-Barriers

Although previous studies showed that glucose is used to support the metabolic activity of the cartilaginous fish brain, the distribution and expression levels of glucose transporter (GLUT) isoforms remained undetermined. Optic/ultrastructural immunohistochemistry approaches were used to determine the expression of GLUT1 in the glial blood-brain barrier (gBBB). GLUT1 was observed solely in glial cells; it was primarily located in end-feet processes of the gBBB. Western blot analysis showed a protein with a molecular mass of 50 kDa, and partial sequencing confirmed GLUT1 identity. Similar approaches were used to demonstrate increased GLUT1 polarization to both apical and basolateral membranes in choroid plexus epithelial cells. To explore monocarboxylate transporter (MCT) involvement in shark brain metabolism, the expression of MCTs was analyzed. MCT1, 2 and 4 were expressed in endothelial cells; however, only MCT1 and MCT4 were present in glial cells. In neurons, MCT2 was localized at the cell membrane whereas MCT1 was detected within mitochondria. Previous studies demonstrated that hypoxia modified GLUT and MCT expression in mammalian brain cells, which was mediated by the transcription factor, hypoxia inducible factor-1. Similarly, we observed that hypoxia modified MCT1 cellular distribution and MCT4 expression in shark telencephalic area and brain stem, confirming the role of these transporters in hypoxia adaptation. Finally, using three-dimensional ultrastructural microscopy, the interaction between glial end-feet and leaky blood vessels of shark brain was assessed in the present study. These data suggested that the brains of shark may take up glucose from blood using a different mechanism than that used by mammalian brains, which may induce astrocyte-neuron lactate shuttling and metabolic coupling as observed in mammalian brain. Our data suggested that the structural conditions and expression patterns of GLUT1, MCT1, MCT2 and MCT4 in shark brain may establish the molecular foundation of metabolic coupling between glia and neurons

Deciphering the Properties of Different Arctic Ice Types During the Growth Phase of MOSAiC: Implications for Future Studies on Gas Pathways

The increased fraction of first year ice (FYI) at the expense of old ice (second-year ice (SYI) and multi-year ice (MYI)) likely affects the permeability of the Arctic ice cover. This in turn influences the pathways of gases circulating therein and the exchange at interfaces with the atmosphere and ocean. We present sea ice temperature and salinity time series from different ice types relevant to temporal development of sea ice permeability and brine drainage efficiency from freeze-up in October to the onset of spring warming in May. Our study is based on a dataset collected during the Multidisciplinary drifting Observatory for the Study of Arctic Climate (MOSAiC) Expedition in 2019 and 2020. These physical properties were used to derive sea ice permeability and Rayleigh numbers. The main sites included FYI and SYI. The latter was composed of an upper layer of residual ice that had desalinated but survived the previous summer melt and became SYI. Below this ice a layer of new first-year ice formed. As the layer of new first-year ice has no direct contact with the atmosphere, we call it insulated first-year ice (IFYI). The residual/SYI-layer also contained refrozen melt ponds in some areas. During the freezing season, the residual/SYI-layer was consistently impermeable, acting as barrier for gas exchange between the atmosphere and ocean. While both FYI and SYI temperatures responded similarly to atmospheric warming events, SYI was more resilient to brine volume fraction changes because of its low salinity (< 2). Furthermore, later bottom ice growth during spring warming was observed for SYI in comparison to FYI. The projected increase in the fraction of more permeable FYI in autumn and spring in the coming decades may favor gas exchange at the atmosphere-ice interface when sea ice acts as a source relative to the atmosphere. While the areal extent of old ice is decreasing, so is its thickness at the onset of freeze-up. Our study sets the foundation for studies on gas dynamics within the ice column and the gas exchange at both ice interfaces, i.e. with the atmosphere and the ocean

Low exposure long-baseline neutrino oscillation sensitivity of the DUNE experiment

The Deep Underground Neutrino Experiment (DUNE) will produce world-leading neutrino oscillation measurements over the lifetime of the experiment. In this work, we explore DUNE's sensitivity to observe charge-parity violation (CPV) in the neutrino sector, and to resolve the mass ordering, for exposures of up to 100 kiloton-megawatt-years (kt-MW-yr). The analysis includes detailed uncertainties on the flux prediction, the neutrino interaction model, and detector effects. We demonstrate that DUNE will be able to unambiguously resolve the neutrino mass ordering at a 3$\sigma$ (5$\sigma$) level, with a 66 (100) kt-MW-yr far detector exposure, and has the ability to make strong statements at significantly shorter exposures depending on the true value of other oscillation parameters. We also show that DUNE has the potential to make a robust measurement of CPV at a 3$\sigma$ level with a 100 kt-MW-yr exposure for the maximally CP-violating values \delta_{\rm CP}} = \pm\pi/2. Additionally, the dependence of DUNE's sensitivity on the exposure taken in neutrino-enhanced and antineutrino-enhanced running is discussed. An equal fraction of exposure taken in each beam mode is found to be close to optimal when considered over the entire space of interest

Long-baseline neutrino oscillation physics potential of the DUNE experiment

The sensitivity of the Deep Underground Neutrino Experiment (DUNE) to neutrino oscillation is determined, based on a full simulation, reconstruction, and event selection of the far detector and a full simulation and parameterized analysis of the near detector. Detailed uncertainties due to the flux prediction, neutrino interaction model, and detector effects are included. DUNE will resolve the neutrino mass ordering to a precision of 5σ, for all ΑCP values, after 2 years of running with the nominal detector design and beam configuration. It has the potential to observe charge-parity violation in the neutrino sector to a precision of 3σ (5σ) after an exposure of 5 (10) years, for 50% of all ΑCP values. It will also make precise measurements of other parameters governing long-baseline neutrino oscillation, and after an exposure of 15 years will achieve a similar sensitivity to sin22θ13 to current reactor experiments

First results on ProtoDUNE-SP liquid argon time projection chamber performance from a beam test at the CERN Neutrino Platform

The ProtoDUNE-SP detector is a single-phase liquid argon time projection chamber with an active volume of 7.2× 6.1× 7.0 m3. It is installed at the CERN Neutrino Platform in a specially-constructed beam that delivers charged pions, kaons, protons, muons and electrons with momenta in the range 0.3 GeV/c to 7 GeV/c. Beam line instrumentation provides accurate momentum measurements and particle identification. The ProtoDUNE-SP detector is a prototype for the first far detector module of the Deep Underground Neutrino Experiment, and it incorporates full-size components as designed for that module. This paper describes the beam line, the time projection chamber, the photon detectors, the cosmic-ray tagger, the signal processing and particle reconstruction. It presents the first results on ProtoDUNE-SP\u27s performance, including noise and gain measurements, dE/dx calibration for muons, protons, pions and electrons, drift electron lifetime measurements, and photon detector noise, signal sensitivity and time resolution measurements. The measured values meet or exceed the specifications for the DUNE far detector, in several cases by large margins. ProtoDUNE-SP\u27s successful operation starting in 2018 and its production of large samples of high-quality data demonstrate the effectiveness of the single-phase far detector design

Long-baseline neutrino oscillation physics potential of the DUNE experiment

The sensitivity of the Deep Underground Neutrino Experiment (DUNE) to neutrino oscillation is determined, based on a full simulation, reconstruction, and event selection of the far detector and a full simulation and parameterized analysis of the near detector. Detailed uncertainties due to the flux prediction, neutrino interaction model, and detector effects are included. DUNE will resolve the neutrino mass ordering to a precision of 5σ, for all δ_(CP) values, after 2 years of running with the nominal detector design and beam configuration. It has the potential to observe charge-parity violation in the neutrino sector to a precision of 3σ (5σ) after an exposure of 5 (10) years, for 50% of all δ_(CP) values. It will also make precise measurements of other parameters governing long-baseline neutrino oscillation, and after an exposure of 15 years will achieve a similar sensitivity to sin²θ₁₃ to current reactor experiments