MinION Analysis and Reference Consortium: Phase 1 data release and analysis

The advent of a miniaturized DNA sequencing device with a high-throughput contextual sequencing capability embodies the next generation of large scale sequencing tools. The MinION™ Access Programme (MAP) was initiated by Oxford Nanopore Technologies™ in April 2014, giving public access to their USB-attached miniature sequencing device. The MinION Analysis and Reference Consortium (MARC) was formed by a subset of MAP participants, with the aim of evaluating and providing standard protocols and reference data to the community. Envisaged as a multi-phased project, this study provides the global community with the Phase 1 data from MARC, where the reproducibility of the performance of the MinION was evaluated at multiple sites. Five laboratories on two continents generated data using a control strain of Escherichia coli K-12, preparing and sequencing samples according to a revised ONT protocol. Here, we provide the details of the protocol used, along with a preliminary analysis of the characteristics of typical runs including the consistency, rate, volume and quality of data produced. Further analysis of the Phase 1 data presented here, and additional experiments in Phase 2 of E. coli from MARC are already underway to identify ways to improve and enhance MinION performance

Observing a column-dependent zeta in dense interstellar sources: the case of the Horsehead Nebula

Context: Observations of small carbon-bearing molecules such as CCH, C4H, c-C3H2, and HCO in the Horsehead Nebula have shown these species to have higher abundances towards the edge of the source than towards the center. Aims: Given the determination of a wide range of values for zeta (s-1), the total ionization rate of hydrogen atoms, and the proposal of a column-dependent zeta(N_H), where N_H is the total column of hydrogen nuclei, we desire to determine if the effects of zeta(N_H) in a single object with spatial variation can be observable. We chose the Horsehead Nebula because of its geometry and high density. Method: We model the Horsehead Nebula as a near edge-on photon dominated region (PDR), using several choices for zeta, both constant and as a function of column. The column-dependent zeta functions are determined by a Monte Carlo model of cosmic ray penetration, using a steep power-law spectrum and accounting for ionization and magnetic field effects. We consider a case with low-metal elemental abundances as well as a sulfur-rich case. Results: We show that use of a column-dependent zeta(N_H) of 5(-15) s-1 at the surface and 7.5(-16) s-1 at Av = 10 on balance improves agreement between measured and theoretical molecular abundances, compared with constant values of zeta.Comment: 12 pages, 6 figures, 5 tables, accepted in A&

Ion kinetic properties in Mercury's pre-midnight plasma sheet

With data from the Fast Imaging Plasma Spectrometer sensor on the MErcury Surface, Space ENvironment, GEochemistry, and Ranging spacecraft, we demonstrate that the average distributions for both solar wind and planetary ions in Mercury’s pre-midnight plasma sheet are well-described by hot Maxwell-Boltzmann distributions. Temperatures and densities of the H+ ranges ~1–10 cm3 and ~5–30 MK, respectively, maintain thermal pressures of ~1 nPa. The dominant planetary ion, Na+ abundances with respect to H+ and exhibit mass-proportional ion temperatures, indicative of a reconnection-dominated heating in the magnetosphere. Conversely, planetary ion species are accelerated to similar average energies greater by a factor of ~1.5 than that of H+ acceleration in an electric potential, consistent with the presence of a strong centrifugal acceleration process in Mercury’s magnetosphere

Observations of Mercury's northern cusp region with MESSENGER's Magnetometer

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/95510/1/grl29143.pd

A sharp image or a sharp knife: norms for the modality-exclusivity of 774 concept-property items

According to recent embodied cognition theories, mental concepts are represented by modality-specific sensory-motor systems. Much of the evidence for modality-specificity in conceptual processing comes from the property-verification task. When applying this and other tasks, it is important to select items based on their modality-exclusivity. We collected modality ratings for a set of 387 properties, each of which was paired with two different concepts, yielding a total of 774 concept-property items. For each item, participants rated the degree to which the property could be experienced through five perceptual modalities (vision, audition, touch, smell, and taste). Based on these ratings, we computed a measure of modality exclusivity, the degree to which a property is perceived exclusively through one sensory modality. In this paper, we briefly sketch the theoretical background of conceptual knowledge, discuss the use of the property-verification task in cognitive research, provide our norms and statistics, and validate the norms in a memory experiment. We conclude that our norms are important for researchers studying modality-specific effects in conceptual processing

MESSENGER and Mariner 10 flyby observations of magnetotail structure and dynamics at Mercury

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/94896/1/jgra21525.pd

Pickup ion measurements by MAVEN: A diagnostic of photochemical oxygen escape from Mars

A key process populating the oxygen exosphere at Mars is the dissociative recombination of ionospheric O 2 + , which produces fast oxygen atoms, some of which have speeds exceeding the escape speed and thus contribute to atmospheric loss. Theoretical studies of this escape process have been carried out and predictions made of the loss rate; however, directly measuring the escaping neutral oxygen is difficult but essential. This paper describes how energetic pickup ion measurements to be made near Mars by the SEP (Solar Energetic Particle) instrument on board the MAVEN (Mars Atmosphere and Volatile EvolutioN) spacecraft can be used to constrain models of photochemical oxygen escape. In certain solar wind conditions, neutral oxygen atoms in the distant Martian exosphere that are ionized and picked up by the solar wind can reach energies high enough to be detected near Mars by SEP. Key Points Photochemical hot oxygen escape rate at Mars is predicted Martian exospheric neutral oxygen model is constructed Pickup ion fluxes measured by SEP will constrain neutral oxygen escape from MarsPeer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/108375/1/grl51888.pd

The Interstellar Environment of our Galaxy

We review the current knowledge and understanding of the interstellar medium of our galaxy. We first present each of the three basic constituents - ordinary matter, cosmic rays, and magnetic fields - of the interstellar medium, laying emphasis on their physical and chemical properties inferred from a broad range of observations. We then position the different interstellar constituents, both with respect to each other and with respect to stars, within the general galactic ecosystem.Comment: 39 pages, 12 figures (including 3 figures in 2 parts

MESSENGER observations of Alfvénic and compressional waves during Mercury's substorms

MErcury Surface, Space ENviroment, GEochemistry, and Ranging (MESSENGER) magnetic field measurements during the substorm expansion phase in Mercury's magnetotail have been examined for evidence of low‐frequency plasma waves, e.g., Pi2‐like pulsations. It has been revealed that the By fluctuations accompanying substorm dipolarizations are consistent with pulses of field‐aligned currents near the high‐latitude edge of the plasma sheet. Detailed analysis of the By fluctuations reveals that they are near circularly polarized electromagnetic waves, most likely Alfvén waves. Soon afterward the plasma sheet thickened and MESSENGER detected a series of compressional waves. These Alfvénic and compressional waves have similar durations (10–20 s), suggesting that they may arise from the same source. Drawing on Pi2 pulsation models developed for Earth, we suggest that the Alfvénic and compressional waves reported here at Mercury may be generated by the quasi‐periodic sunward flow bursts in Mercury's plasma sheet. But because they are observed during the period with rapid magnetic field reconfiguration, we cannot fully exclude the possibility of standing Alfvén wave.Key PointsThe first observation of Pi2‐like pulsations during Mercury's substormAlfvénic and compressional waves were observed in the different regions of the plasma sheetWe proposed the sources for the plasma wavesPeer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/113132/1/grl53278.pd

Dopaminergic modulation of appetitive trace conditioning: the role of D1 receptors in medial prefrontal cortex

Rationale: Trace conditioning may provide a behavioural model suitable to examine the maintenance of ‘on line’ information and its underlying neural substrates. Objectives: Experiment la was run to establish trace conditioning in a shortened procedure which would be suitable to test the effects of dopamine (DA) D1 receptor agents administered by microinjection directly into the brain. Experiment lb examined the effects of the DA D1 agonist SKF81297 and the DA D1 antagonist SCH23390 following systemic administration in pre-trained animals. Experiment 2 went on to test the effects of systemically administered SKF81297 on the acquisition of trace conditioning. In experiment 3, SKF81297 was administered directly in prelimbic (PL) and infralimbic (IL) sub-regions of medial prefrontal cortex (mPFC) to compare the role of different mPFC sub-regions. Results: Whilst treatment with SCH23390 impaired motor responding and/or motivation, SKF81297 had relatively little effect in the pre-trained animals tested in experiment 1b. However, systemic SKF81297 depressed the acquisition function at the 2-s trace interval in experiment 2. Similarly, in experiment 3, SKF81297 (0.1 μg in 1.0 μl) microinjected into either PL or IL mPFC impaired appetitive conditioning at the 2-s trace interval. Conclusions: Impaired trace conditioning under SKF81297 is likely to be mediated in part (but not exclusively) within the IL and PL mPFC sub-regions. The finding that trace conditioning was impaired rather than enhanced under SKF81297 provides further evidence for the inverse U-function which has been suggested to be characteristic of mPFC DA function