CfAIR2: Near Infrared Light Curves of 94 Type Ia Supernovae

CfAIR2 is a large homogeneously reduced set of near-infrared (NIR) light curves for Type Ia supernovae (SN Ia) obtained with the 1.3m Peters Automated InfraRed Imaging TELescope (PAIRITEL). This data set includes 4607 measurements of 94 SN Ia and 4 additional SN Iax observed from 2005-2011 at the Fred Lawrence Whipple Observatory on Mount Hopkins, Arizona. CfAIR2 includes JHKs photometric measurements for 88 normal and 6 spectroscopically peculiar SN Ia in the nearby universe, with a median redshift of z~0.021 for the normal SN Ia. CfAIR2 data span the range from -13 days to +127 days from B-band maximum. More than half of the light curves begin before the time of maximum and the coverage typically contains ~13-18 epochs of observation, depending on the filter. We present extensive tests that verify the fidelity of the CfAIR2 data pipeline, including comparison to the excellent data of the Carnegie Supernova Project. CfAIR2 contributes to a firm local anchor for supernova cosmology studies in the NIR. Because SN Ia are more nearly standard candles in the NIR and are less vulnerable to the vexing problems of extinction by dust, CfAIR2 will help the supernova cosmology community develop more precise and accurate extragalactic distance probes to improve our knowledge of cosmological parameters, including dark energy and its potential time variation.Comment: 31 pages, 15 figures, 10 tables. Accepted to ApJS. v2 modified to more closely match journal versio

Transitions between Inherent Structures in Water

The energy landscape approach has been useful to help understand the dynamic properties of supercooled liquids and the connection between these properties and thermodynamics. The analysis in numerical models of the inherent structure (IS) trajectories -- the set of local minima visited by the liquid -- offers the possibility of filtering out the vibrational component of the motion of the system on the potential energy surface and thereby resolving the slow structural component more efficiently. Here we report an analysis of an IS trajectory for a widely-studied water model, focusing on the changes in hydrogen bond connectivity that give rise to many IS separated by relatively small energy barriers. We find that while the system \emph{travels} through these IS, the structure of the bond network continuously modifies, exchanging linear bonds for bifurcated bonds and usually reversing the exchange to return to nearly the same initial configuration. For the 216 molecule system we investigate, the time scale of these transitions is as small as the simulation time scale ($\approx 1$ fs). Hence for water, the transitions between each of these IS is relatively small and eventual relaxation of the system occurs only by many of these transitions. We find that during IS changes, the molecules with the greatest displacements move in small ``clusters'' of 1-10 molecules with displacements of $\approx 0.02-0.2$ nm, not unlike simpler liquids. However, for water these clusters appear to be somewhat more branched than the linear ``string-like'' clusters formed in a supercooled Lennar d-Jones system found by Glotzer and her collaborators.Comment: accepted in PR

Thermodynamic and structural aspects of the potential energy surface of simulated water

Relations between the thermodynamics and dynamics of supercooled liquids approaching a glass transition have been proposed over many years. The potential energy surface of model liquids has been increasingly studied since it provides a connection between the configurational component of the partition function on one hand, and the system dynamics on the other. This connection is most obvious at low temperatures, where the motion of the system can be partitioned into vibrations within a basin of attraction and infrequent inter-basin transitions. In this work, we present a description of the potential energy surface properties of supercooled liquid water. The dynamics of this model has been studied in great details in the last years. Specifically, we locate the minima sampled by the liquid by ``quenches'' from equilibrium configurations generated via molecular dynamics simulations. We calculate the temperature and density dependence of the basin energy, degeneracy, and shape. The temperature dependence of the energy of the minima is qualitatively similar to simple liquids, but has anomalous density dependence. The unusual density dependence is also reflected in the configurational entropy, the thermodynamic measure of degeneracy. Finally, we study the structure of simulated water at the minima, which provides insight on the progressive tetrahedral ordering of the liquid on cooling

Equilibration times in numerical simulation of structural glasses: Comparing parallel tempering and conventional molecular dynamics

Generation of equilibrium configurations is the major obstacle for numerical investigation of the slow dynamics in supercooled liquid states. The parallel tempering (PT) technique, originally proposed for the numerical equilibration of discrete spin-glass model configurations, has recently been applied in the study of supercooled structural glasses. We present an investigation of the ability of parallel tempering to properly sample the liquid configuration space at different temperatures, by mapping the PT dynamics into the dynamics of the closest local potential energy minima (inherent structures). Comparing the PT equilibration process with the standard molecular dynamics equilibration process we find that the PT does not increase the speed of equilibration of the (slow) configurational degrees of freedom.Comment: 5 pages, 3 figure

PTF10fqs: A Luminous Red Nova in the Spiral Galaxy Messier 99

The Palomar Transient Factory (PTF) is systematically charting the optical transient and variable sky. A primary science driver of PTF is building a complete inventory of transients in the local Universe (distance less than 200 Mpc). Here, we report the discovery of PTF10fqs, a transient in the luminosity "gap" between novae and supernovae. Located on a spiral arm of Messier 99, PTF 10fqs has a peak luminosity of Mr = -12.3, red color (g-r = 1.0) and is slowly evolving (decayed by 1 mag in 68 days). It has a spectrum dominated by intermediate-width H (930 km/s) and narrow calcium emission lines. The explosion signature (the light curve and spectra) is overall similar to thatof M85OT2006-1, SN2008S, and NGC300OT. The origin of these events is shrouded in mystery and controversy (and in some cases, in dust). PTF10fqs shows some evidence of a broad feature (around 8600A) that may suggest very large velocities (10,000 km/s) in this explosion. Ongoing surveys can be expected to find a few such events per year. Sensitive spectroscopy, infrared monitoring and statistics (e.g. disk versus bulge) will eventually make it possible for astronomers to unravel the nature of these mysterious explosions.Comment: 12 pages, 12 figures, Replaced with published versio

Single-molecule imaging to characterise the transport mechanism of the Nuclear Pore Complex

In the eukaryotic cell, a large macromolecular channel, known as the Nuclear Pore Complex (NPC), mediates all molecular transport between the nucleus and cytoplasm. In recent years, single-molecule fluorescence (SMF) imaging has emerged as a powerful tool to study the molecular mechanism of transport through the NPC. More recently, techniques such as Single-Molecule Localisation Microscopy (SMLM) have enabled the spatial and temporal distribution of cargos, transport receptors and even structural components of the NPC to be determined with nanometre accuracy. In this protocol, we describe a method to study the position and/or motion of individual molecules transiting through the NPC with high spatial and temporal precision

Scleral Buckling for Primary Retinal Detachment: Outcomes of Scleral Tunnels versus Scleral Sutures

Purpose: There are primarily two techniques for affixing the scleral buckle (SB) to the sclera in the repair of rhegmatogenous retinal detachment (RRD): scleral tunnels or scleral sutures. Methods: This retrospective study examined all patients with primary RRD who were treated with primary SB or SB combined with vitrectomy from January 1, 2015 through December 31, 2015 across six sites. Two cohorts were examined: SB affixed using scleral sutures versus scleral tunnels. Pre- and postoperative variables were evaluated including visual acuity, anatomic success, and postoperative strabismus. Results: The mean preoperative logMAR VA for the belt loop cohort was 1.05 ± 1.06 (Snellen 20/224) and for the scleral suture cohort was 1.03 ± 1.04 (Snellen 20/214, p = 0.846). The respective mean postoperative logMAR VAs were 0.45 ± 0.55 (Snellen 20/56) and 0.46 ± 0.59 (Snellen 20/58, p = 0.574). The single surgery success rate for the tunnel cohort was 87.3% versus 88.6% for the suture cohort (p = 0.601). Three patients (1.0%) in the scleral tunnel cohort developed postoperative strabismus, but only one patient (0.1%) in the suture cohort (p = 0.04, multivariate p = 0.76). All cases of strabismus occurred in eyes that underwent SB combined with PPV (p = 0.02). There were no differences in vision, anatomic success, or strabismus between scleral tunnels versus scleral sutures in eyes that underwent primary SB. Conclusion: Scleral tunnels and scleral sutures had similar postoperative outcomes. Combined PPV/SB in eyes with scleral tunnels might be a risk for strabismus post retinal detachment surgery

Neurology-related protein biomarkers are associated with cognitive ability and brain volume in older age

Funder: NIHR Blood and Transplant Research Unit in Donor Health and Genomics (NIHR BTRU-2014-10024)Abstract: Identifying biological correlates of late life cognitive function is important if we are to ascertain biomarkers for, and develop treatments to help reduce, age-related cognitive decline. Here, we investigated the associations between plasma levels of 90 neurology-related proteins (Olink® Proteomics) and general fluid cognitive ability in the Lothian Birth Cohort 1936 (LBC1936, N = 798), Lothian Birth Cohort 1921 (LBC1921, N = 165), and the INTERVAL BioResource (N = 4451). In the LBC1936, 22 of the proteins were significantly associated with general fluid cognitive ability (β between −0.11 and −0.17). MRI-assessed total brain volume partially mediated the association between 10 of these proteins and general fluid cognitive ability. In an age-matched subsample of INTERVAL, effect sizes for the 22 proteins, although smaller, were all in the same direction as in LBC1936. Plasma levels of a number of neurology-related proteins are associated with general fluid cognitive ability in later life, mediated by brain volume in some cases

Somatic Mutagenesis with a Sleeping Beauty Transposon System Leads to Solid Tumor Formation in Zebrafish

Large-scale sequencing of human cancer genomes and mouse transposon-induced tumors has identified a vast number of genes mutated in different cancers. One of the outstanding challenges in this field is to determine which genes, when mutated, contribute to cellular transformation and tumor progression. To identify new and conserved genes that drive tumorigenesis we have developed a novel cancer model in a distantly related vertebrate species, the zebrafish, Danio rerio. The Sleeping Beauty (SB) T2/Onc transposon system was adapted for somatic mutagenesis in zebrafish. The carp ß-actin promoter was cloned into T2/Onc to create T2/OncZ. Two transgenic zebrafish lines that contain large concatemers of T2/OncZ were isolated by injection of linear DNA into the zebrafish embryo. The T2/OncZ transposons were mobilized throughout the zebrafish genome from the transgene array by injecting SB11 transposase RNA at the 1-cell stage. Alternatively, the T2/OncZ zebrafish were crossed to a transgenic line that constitutively expresses SB11 transposase. T2/OncZ transposon integration sites were cloned by ligation-mediated PCR and sequenced on a Genome Analyzer II. Between 700–6800 unique integration events in individual fish were mapped to the zebrafish genome. The data show that introduction of transposase by transgene expression or RNA injection results in an even distribution of transposon re-integration events across the zebrafish genome. SB11 mRNA injection resulted in neoplasms in 10% of adult fish at ∼10 months of age. T2/OncZ-induced zebrafish tumors contain many mutated genes in common with human and mouse cancer genes. These analyses validate our mutagenesis approach and provide additional support for the involvement of these genes in human cancers. The zebrafish T2/OncZ cancer model will be useful for identifying novel and conserved genetic drivers of human cancers

Global economic burden of unmet surgical need for appendicitis

Background: There is a substantial gap in provision of adequate surgical care in many low-and middle-income countries. This study aimed to identify the economic burden of unmet surgical need for the common condition of appendicitis. Methods: Data on the incidence of appendicitis from 170 countries and two different approaches were used to estimate numbers of patients who do not receive surgery: as a fixed proportion of the total unmet surgical need per country (approach 1); and based on country income status (approach 2). Indirect costs with current levels of access and local quality, and those if quality were at the standards of high-income countries, were estimated. A human capital approach was applied, focusing on the economic burden resulting from premature death and absenteeism. Results: Excess mortality was 4185 per 100 000 cases of appendicitis using approach 1 and 3448 per 100 000 using approach 2. The economic burden of continuing current levels of access and local quality was US $92 492 million using approach 1 and$73 141 million using approach 2. The economic burden of not providing surgical care to the standards of high-income countries was $95 004 million using approach 1 and$75 666 million using approach 2. The largest share of these costs resulted from premature death (97.7 per cent) and lack of access (97.0 per cent) in contrast to lack of quality. Conclusion: For a comparatively non-complex emergency condition such as appendicitis, increasing access to care should be prioritized. Although improving quality of care should not be neglected, increasing provision of care at current standards could reduce societal costs substantially