The evolution of the natural killer complex; a comparison between mammals using new high-quality genome assemblies and targeted annotation.

Natural killer (NK) cells are a diverse population of lymphocytes with a range of biological roles including essential immune functions. NK cell diversity is in part created by the differential expression of cell surface receptors which modulate activation and function, including multiple subfamilies of C-type lectin receptors encoded within the NK complex (NKC). Little is known about the gene content of the NKC beyond rodent and primate lineages, other than it appears to be extremely variable between mammalian groups. We compared the NKC structure between mammalian species using new high-quality draft genome assemblies for cattle and goat; re-annotated sheep, pig, and horse genome assemblies; and the published human, rat, and mouse lemur NKC. The major NKC genes are largely in the equivalent positions in all eight species, with significant independent expansions and deletions between species, allowing us to propose a model for NKC evolution during mammalian radiation. The ruminant species, cattle and goats, have independently evolved a second KLRC locus flanked by KLRA and KLRJ, and a novel KLRH-like gene has acquired an activating tail. This novel gene has duplicated several times within cattle, while other activating receptor genes have been selectively disrupted. Targeted genome enrichment in cattle identified varying levels of allelic polymorphism between the NKC genes concentrated in the predicted extracellular ligand-binding domains. This novel recombination and allelic polymorphism is consistent with NKC evolution under balancing selection, suggesting that this diversity influences individual immune responses and may impact on differential outcomes of pathogen infection and vaccination

Fuel-Supply-Limited Stellar Relaxation Oscillations: Application to Multiple Rings around AGB Stars and Planetary Nebulae

We describe a new mechanism for pulsations in evolved stars: relaxation oscillations driven by a coupling between the luminosity-dependent mass-loss rate and the H fuel abundance in a nuclear-burning shell. When mass loss is included, the outward flow of matter can modulate the flow of fuel into the shell when the stellar luminosity is close to the Eddington luminosity $L_{\rm Edd}$. When the luminosity drops below $L_{\rm Edd}$, the mass outflow declines and the shell is re-supplied with fuel. This process can be repetitive. We demonstrate the existence of such oscillations and discuss the dependence of the results on the stellar parameters. In particular, we show that the oscillation period scales specifically with the mass of the H-burning relaxation shell (HBRS), defined as the part of the H-burning shell above the minimum radius at which the luminosity from below first exceeds the Eddington threshold at the onset of the mass loss phase. For a stellar mass M_*\sim 0.7\Msun, luminosity L_*\sim 10^4\Lsun, and mass loss rate |\dot M|\sim 10^{-5}\Msun yr$^{-1}$, the oscillations have a recurrence time $\sim 1400$ years $\sim 57\tau_{\rm fsm}$, where $\tau_{\rm fsm}$ is the timescale for modulation of the fuel supply in the HBRS by the varying mass-loss rate. This period agrees with the $\sim$ 1400-year period inferred for the spacings between the shells surrounding some planetary nebulae, and the the predictied shell thickness, of order 0.4 times the spacing, also agrees reasonably well.Comment: 15 pages TeX, 1 ps figure submitted to Ap

The Low CO Content of the Extremely Metal Poor Galaxy I Zw 18

We present sensitive molecular line observations of the metal-poor blue compact dwarf I Zw 18 obtained with the IRAM Plateau de Bure interferometer. These data constrain the CO J=1-0 luminosity within our 300 pc (FWHM) beam to be L_CO < 1 \times 10^5 K km s^-1 pc^2 (I_CO < 1 K km s^-1), an order of magnitude lower than previous limits. Although I Zw 18 is starbursting, it has a CO luminosity similar to or less than nearby low-mass irregulars (e.g. NGC 1569, the SMC, and NGC 6822). There is less CO in I Zw 18 relative to its B-band luminosity, HI mass, or star formation rate than in spiral or dwarf starburst galaxies (including the nearby dwarf starburst IC 10). Comparing the star formation rate to our CO upper limit reveals that unless molecular gas forms stars much more efficiently in I Zw 18 than in our own galaxy, it must have a very low CO-to-H_2 ratio, \sim 10^-2 times the Galactic value. We detect 3mm continuum emission, presumably due to thermal dust and free-free emission, towards the radio peak.Comment: 5 pages in emulateapj style, accepted by the Astrophysical Journa

Tissue engineering a fetal membrane

The aim of this study was to construct an artificial fetal membrane (FM) by combination of human amniotic epithelial stem cells (hAESCs) and a mechanically enhanced collagen scaffold containing encapsulated human amniotic stromal fibroblasts (hASFs). Such a tissue-engineered FM may have the potential to plug structural defects in the amniotic sac after antenatal interventions, or to prevent preterm premature rupture of the FM. The hAESCs and hASFs were isolated from human fetal amniotic membrane (AM). Magnetic cell sorting was used to enrich the hAESCs by positive ATP-binding cassette G2 selection. We investigated the use of a laminin/fibronectin (1:1)-coated compressed collagen gel as a novel scaffold to support the growth of hAESCs. A type I collagen gel was dehydrated to form a material mimicking the mechanical properties and ultra-structure of human AM. hAESCs successfully adhered to and formed a monolayer upon the biomimetic collagen scaffold. The resulting artificial membrane shared a high degree of similarity in cell morphology, protein expression profiles, and structure to normal fetal AM. This study provides the first line of evidence that a compacted collagen gel containing hASFs could adequately support hAESCs adhesion and differentiation to a degree that is comparable to the normal human fetal AM in terms of structure and maintenance of cell phenotype

MASE: A New Data--Reduction Pipeline for the Magellan Echellette Spectrograph

We introduce a data reduction package written in Interactive Data Language (IDL) for the Magellan Echellete Spectrograph (MAGE). MAGE is a medium-resolution (R ~4100), cross-dispersed, optical spectrograph, with coverage from ~3000-10000 Angstroms. The MAGE Spectral Extractor (MASE) incorporates the entire image reduction and calibration process, including bias subtraction, flat fielding, wavelength calibration, sky subtraction, object extraction and flux calibration of point sources. We include examples of the user interface and reduced spectra. We show that the wavelength calibration is sufficient to achieve ~5 km/s RMS accuracy and relative flux calibrations better than 10%. A light-weight version of the full reduction pipeline has been included for real-time source extraction and signal-to-noise estimation at the telescope.Comment: 10 pages (ApJ format), accepted PAS

Catalysis and chemical mechanisms of calcite dissolution in seawater

Near-equilibrium calcite dissolution in seawater contributes significantly to the regulation of atmospheric CO_2 on 1,000-y timescales. Despite many studies on far-from-equilibrium dissolution, little is known about the detailed mechanisms responsible for calcite dissolution in seawater. In this paper, we dissolve ^(13)C-labeled calcites in natural seawater. We show that the time-evolving enrichment of δ^(13)C in solution is a direct measure of both dissolution and precipitation reactions across a large range of saturation states. Secondary Ion Mass Spectrometer profiles into the ^(13)C-labeled solids confirm the presence of precipitated material even in undersaturated conditions. The close balance of precipitation and dissolution near equilibrium can alter the chemical composition of calcite deeper than one monolayer into the crystal. This balance of dissolution–precipitation shifts significantly toward a dissolution-dominated mechanism below about Ω= 0.7. Finally, we show that the enzyme carbonic anhydrase (CA) increases the dissolution rate across all saturation states, and the effect is most pronounced close to equilibrium. This finding suggests that the rate of hydration of CO_2 is a rate-limiting step for calcite dissolution in seawater. We then interpret our dissolution data in a framework that incorporates both solution chemistry and geometric constraints on the calcite solid. Near equilibrium, this framework demonstrates a lowered free energy barrier at the solid–solution interface in the presence of CA. This framework also indicates a significant change in dissolution mechanism at Ω= 0.7, which we interpret as the onset of homogeneous etch pit nucleation

Spitzer and z' Secondary Eclipse Observations of the Highly Irradiated Transiting Brown Dwarf KELT-1b

We present secondary eclipse observations of the highly irradiated transiting brown dwarf KELT-1b. These observations represent the first constraints on the atmospheric dynamics of a highly irradiated brown dwarf, and the atmospheres of irradiated giant planets at high surface gravity. Using the Spitzer Space Telescope, we measure secondary eclipse depths of 0.195+/-0.010% at 3.6um and 0.200+/-0.012% at 4.5um. We also find tentative evidence for the secondary eclipse in the z' band with a depth of 0.049+/-0.023%. These measured eclipse depths are most consistent with an atmosphere model in which there is a strong substellar hotspot, implying that heat redistribution in the atmosphere of KELT-1b is low. While models with a more mild hotspot or even with dayside heat redistribution are only marginally disfavored, models with complete heat redistribution are strongly ruled out. The eclipse depths also prefer an atmosphere with no TiO inversion layer, although a model with TiO inversion is permitted in the dayside heat redistribution case, and we consider the possibility of a day-night TiO cold trap in this object. For the first time, we compare the IRAC colors of brown dwarfs and hot Jupiters as a function of effective temperature. Importantly, our measurements reveal that KELT-1b has a [3.6]-[4.5] color of 0.07+/-0.11, identical to that of isolated brown dwarfs of similarly high temperature. In contrast, hot Jupiters generally show redder [3.6]-[4.5] colors of ~0.4, with a very large range from ~0 to ~1. Evidently, despite being more similar to hot Jupiters than to isolated brown dwarfs in terms of external forcing of the atmosphere by stellar insolation, KELT-1b has an atmosphere most like that of other brown dwarfs. This suggests that surface gravity is very important in controlling the atmospheric systems of substellar mass bodies.Comment: 14 pages, 3 tables, 11 figures. Accepted by ApJ. Updated to reflect the accepted versio

A Kinetic Pressure Effect on Calcite Dissolution in Seawater

This study provides laboratory data of calcite dissolution rate as a function of seawater undersaturation state (1-Ω) under variable pressure. ^(13)C-labeled calcite was dissolved in unlabeled seawater and the evolving δ^(13)C composition of the fluid was monitored over time to evaluate the dissolution rate. Results show that dissolution rates are enhanced by a factor of 2-4 at 700 dbar compared to dissolution at the same Ω under ambient pressure (10 dbar). This dissolution rate enhancement under pressure applies over an Ω range of 0.65 to 1 between 10 dbar and 700 dbar. Above 700 dbar (up to 2500 dbar), dissolution rates become independent of pressure. The observed enhancement is well beyond the uncertainty associated with the thermodynamic properties of calcite under pressure (partial molar volume ΔV), and thus should be interpreted as a kinetic pressure effect on calcite dissolution. Dissolution at ambient pressure and higher pressures yield non-linear dissolution kinetics, the pressure effect does not significantly change the reaction order n in Rate = k(1-Ω^)n, which is shown to vary from 3.1±0.3 to 3.8±0.5 from 10 dbar to 700 dbar over Ω = 0.65 to 0.9. Furthermore, two different dissolution mechanisms are indicated by a discontinuity in the rate-undersaturation relationship, and seen at both ambient and higher pressures. The discontinuity, Ω_(critical) = 0.87±0.05 and 0.90±0.03 at 10 dbar and 1050 dbar respectively, are similar within error. The reaction order, n, at Ω > 0.9 is 0.47±0.27 and 0.46±0.15 at 10 dbar and 700 dbar respectively. This Ω_(critical) is considered to be the threshold between step retreat dissolution and defect-assisted dissolution. The kinetic enhancement of dissolution rate at higher pressures is related to a decrease in the interfacial energy barrier at dissolution sites. The impact of pressure on the calcite dissolution kinetics implies that sinking particles would dissolve at shallower depth than previously thought

Cosmological parameters sigma_8, the baryon density, and the UV background intensity from a calibrated measurement of H I Lyman-alpha absorption at z = 1.9

We identify a concordant model for the intergalactic medium (IGM) at redshift z=1.9 that uses popular values for cosmological and astrophysical parameters and accounts for all baryons with an uncertainty of 6%. We have measured the amount of absorption, DA, in the Ly-alpha forest at redshift 1.9 in spectra of 77 QSO from the Kast spectrograph. We calibrated the continuum fits with realistic artificial spectra, and we found that averaged over all 77 QSOs the mean continuum level is within 1-2% of the correct value. Absorption from all lines in the Ly-alpha forest at z=1.9 removes DA=15.1 +/- 0.7% of the flux between 1070 and 1170 (rest) Angstroms. This is the first measurement using many QSOs at this z, and the first calibrated measurement at any redshift. Metal lines absorb 2.3 +/- 0.5%, and LLS absorb 1.0 +/- 0.4% leaving 11.8 +/- 1.0% from the lower density bulk of the IGM. Averaging over Delta z=0.1 or 154 Mpc, the dispersion is 6.1 +/- 0.3% including LLS and metal lines, or 3.9 (+0.5, -0.7)% for the lower density IGM alone, consistent with the usual description of large scale structure. LLS and metal lines are major contributors to the variation in the mean flux, and they make the flux field significantly non-Gaussian. We find that a hydrodynamic simulation on a 1024 cubed grid in a 75.7 Mpc box reproduces the observed DA from the low density IGM with parameters values H_o=71 km/s/Mpc, Omega_Lambda=0.73, Omega_m=0.27, Omega_b=0.044, sigma_8=0.9 and a UV background that has an ionization rate that is 1.08 +/- 0.08 times the prediction by Madau, Haardt & Rees (1999).Comment: Submitted to Ap

Comparing the EQ-5D-3 L and EQ-5D-5 L:studying measurement and scores in Indonesian type 2 diabetes mellitus patients

BACKGROUND: The EuroQoL five-dimensional instrument (EQ-5D) is the favoured preference-based instrument to measure health-related quality of life (HRQoL) in several countries. Two versions of the EQ-5D are available: the 3-level version (EQ-5D-3 L) and the 5-level version (EQ-5D-5 L). This study aims to compare specific measurement properties and scoring of the EQ-5D-3 L (3 L) and EQ-5D-5 L (5 L) in Indonesian type 2 diabetes mellitus (T2DM) outpatients.METHODS: A survey was conducted in a hospital and two primary healthcare centres on Sulawesi Island. Participants were asked to complete the two versions of the EQ-5D instruments. The 3 L and 5 L were compared in terms of distribution and ceiling, discriminative power and test-retest reliability. To determine the consistency of the participants' answers, we checked the redistribution pattern, i.e., the consistency of a participant's scores in both versions.RESULTS: A total of 198 T2DM outpatients (mean age 59.90 ± 11.06) completed the 3 L and 5 L surveys. A total of 46 health states for 3 L and 90 health states for 5 L were reported. The '11121' health state was reported most often: 17% in the 3 L and 13% in the 5 L. The results suggested a lower ceiling effect for 5 L (11%) than for 3 L (15%). Regarding redistribution, only 6.1% of responses were found to be inconsistent in this study. The 5 L had higher discriminative power than the 3 L version. Reliability as reflected by the index score was 0.64 for 3 L and 0.74 for 5 L. Pain/discomfort was the dimension mostly affected, whereas the self-care dimension was the least affected.CONCLUSIONS: This study suggests that the 5 L-version of the EQ-5D instrument performs better than the 3 L-version in T2DM outpatients in Indonesia, regarding measurement and scoring properties. As such, our study supports the use of the 5 L as the preferred health-related quality of life measurement tool. We did not do a trial but this study was approved by the Medical Ethics Committee of Universitas Gadjah Mada Yogyakarta, Indonesia (document number KE/FK/1188/EC, 12 November 2014, amended 16 March 2015).</p