Revision of failed traditional fundoplication using EsophyX® transoral fundoplication

BACKGROUND: Laparoscopic revision of failed traditional fundoplication is difficult and involves risk of gastric, esophageal, and vagal nerve injury that is higher than that of the primary fundoplication. This study assessed feasibility and clinical outcomes of the transoral approach to revision of loose Nissen. METHODS: Between November 2009 and August 2011, a total of 11 patients underwent transoral repair as opposed to 70 patients who underwent laparoscopic or open revision of a failed fundoplication. Subjective and objective outcomes were evaluated with the GERD health-related quality of life (GERD-HRQL) questionnaire and the reflux symptom index (RSI) questionnaire and ambulatory pH testing. The competency of the new antireflux barrier was evaluated by endoscopy. Wilcoxon signed-rank test was used to compare pre- and postoperative variables. RESULTS: All 11 patients evidenced loosening of the Nissen fundoplication without evidence of hiatal failure. Mean age was 57 years, BMI was 25.1 kg/m(2), and 4 of 11 (36 %) were female. Indications for operation were abnormal pH-metry off PPIs (6), impedance/pH on PPIs (3), esophagitis (1), and evidence of free reflux on barium swallow (1). One patient developed a postoperative bleed requiring transfusion. Two patients had laparoscopic revision at 6 and 8 months after the transoral procedure. At a median follow-up of 14 (range = 6–28) months, 8/10 patients reported resolution of their primary symptoms. Eight patients had pH testing off PPIs both pre- and postoperatively; median % time with pH <4 improved by dropping from 8.1 % (21–4.8 %) to 0.6 % (13.4–0.01 %) (p = 0.008). Esophageal acid exposure normalized in 5/6 patients. Mean GERD-HRQL score improved significantly by dropping from 28.6 (10.6) preoperatively to 6.7 (6.1) post-TIF (p = 0.016). Mean RSI score improved more than 50 % in 5/7 patients. CONCLUSION: Transoral revision of failed traditional fundoplication without herniation is technically feasible. It results in symptomatic and objective improvement of GERD without the risks of laparoscopic dissection for a majority of patients

Non-equilibrium dynamics and floral trait interactions shape extant angiosperm diversity.

Why are some traits and trait combinations exceptionally common across the tree of life, whereas others are vanishingly rare? The distribution of trait diversity across a clade at any time depends on the ancestral state of the clade, the rate at which new phenotypes evolve, the differences in speciation and extinction rates across lineages, and whether an equilibrium has been reached. Here we examine the role of transition rates, differential diversification (speciation minus extinction) and non-equilibrium dynamics on the evolutionary history of angiosperms, a clade well known for the abundance of some trait combinations and the rarity of others. Our analysis reveals that three character states (corolla present, bilateral symmetry, reduced stamen number) act synergistically as a key innovation, doubling diversification rates for lineages in which this combination occurs. However, this combination is currently less common than predicted at equilibrium because the individual characters evolve infrequently. Simulations suggest that angiosperms will remain far from the equilibrium frequencies of character states well into the future. Such non-equilibrium dynamics may be common when major innovations evolve rarely, allowing lineages with ancestral forms to persist, and even outnumber those with diversification-enhancing states, for tens of millions of years

Submillimeter observations of IRAS and WISE debris disk candidates

A set of six debris disk candidates identified with IRAS or WISE excesses were observed at either 350 μm or 450 μm with the Caltech Submillimeter Observatory. Five of the targets – HIP 51658, HIP 68160, HIP 73512, HIP 76375, and HIP 112460 – have among the largest measured excess emission from cold dust from IRAS in the 25–100 μm bands. Single temperature blackbody fits to the excess dust emission of these sources predict 350–450 μm fluxes above 240 mJy. The final target – HIP 73165 – exhibits weak excess emission above the stellar photosphere from WISE measurements at 22 μm, indicative of a population of warm circumstellar dust. None of the six targets were detected, with 3σ upper limits ranging from 51–239 mJy. These limits are significantly below the expected fluxes from SED fitting. Two potential causes of the null detections were explored – companion stars and contamination. To investigate the possible influence of companion stars, imaging data were analyzed from new adaptive optics data from the ARIES instrument on the 6.5 m MMT and archival HST, Gemini NIRI, and POSS/2MASS data. The images are sensitive to all stellar companions beyond a radius of 1–94 AU, with the inner limit depending on the distance and brightness of each target. One target is identified as a binary system, but with a separation too large to impact the disk. While the gravitational effects of a companion do not appear to provide an explanation for the submm upper limits, the majority of the IRAS excess targets show evidence for contaminating sources, based on investigation of higher resolution WISE and archival Spitzer and Herschel images. Finally, the exploratory submm measurements of the WISE excess source suggest that the hot dust present around these targets is not matched by a comparable population of colder, outer dust. More extensive and more sensitive Herschel observations of WISE excess sources will build upon this initial example to further define the characteristics of warm debris disks sources

Supernova Simulations and Strategies For the Dark Energy Survey

We present an analysis of supernova light curves simulated for the upcoming Dark Energy Survey (DES) supernova search. The simulations employ a code suite that generates and fits realistic light curves in order to obtain distance modulus/redshift pairs that are passed to a cosmology fitter. We investigated several different survey strategies including field selection, supernova selection biases, and photometric redshift measurements. Using the results of this study, we chose a 30 square degree search area in the griz filter set. We forecast 1) that this survey will provide a homogeneous sample of up to 4000 Type Ia supernovae in the redshift range 0.05<z<1.2, and 2) that the increased red efficiency of the DES camera will significantly improve high-redshift color measurements. The redshift of each supernova with an identified host galaxy will be obtained from spectroscopic observations of the host. A supernova spectrum will be obtained for a subset of the sample, which will be utilized for control studies. In addition, we have investigated the use of combined photometric redshifts taking into account data from both the host and supernova. We have investigated and estimated the likely contamination from core-collapse supernovae based on photometric identification, and have found that a Type Ia supernova sample purity of up to 98% is obtainable given specific assumptions. Furthermore, we present systematic uncertainties due to sample purity, photometric calibration, dust extinction priors, filter-centroid shifts, and inter-calibration. We conclude by estimating the uncertainty on the cosmological parameters that will be measured from the DES supernova data.Comment: 46 pages, 30 figures, resubmitted to ApJ as Revision 2 (final author revision), which has subtle editorial differences compared to the published paper (ApJ, 753, 152). Note that this posting includes PDF only due to a bug in either the latex macros or the arXiv submission system. The source files are available in the DES document database: http://des-docdb.fnal.gov/cgi-bin/ShowDocument?docid=624

The Genomic Signature of Crop-Wild Introgression in Maize

The evolutionary significance of hybridization and subsequent introgression has long been appreciated, but evaluation of the genome-wide effects of these phenomena has only recently become possible. Crop-wild study systems represent ideal opportunities to examine evolution through hybridization. For example, maize and the conspecific wild teosinte Zea mays ssp. mexicana, (hereafter, mexicana) are known to hybridize in the fields of highland Mexico. Despite widespread evidence of gene flow, maize and mexicana maintain distinct morphologies and have done so in sympatry for thousands of years. Neither the genomic extent nor the evolutionary importance of introgression between these taxa is understood. In this study we assessed patterns of genome-wide introgression based on 39,029 single nucleotide polymorphisms genotyped in 189 individuals from nine sympatric maize-mexicana populations and reference allopatric populations. While portions of the maize and mexicana genomes were particularly resistant to introgression (notably near known cross-incompatibility and domestication loci), we detected widespread evidence for introgression in both directions of gene flow. Through further characterization of these regions and preliminary growth chamber experiments, we found evidence suggestive of the incorporation of adaptive mexicana alleles into maize during its expansion to the highlands of central Mexico. In contrast, very little evidence was found for adaptive introgression from maize to mexicana. The methods we have applied here can be replicated widely, and such analyses have the potential to greatly informing our understanding of evolution through introgressive hybridization. Crop species, due to their exceptional genomic resources and frequent histories of spread into sympatry with relatives, should be particularly influential in these studies

Ecological implications of a flower size/number trade-off in tropical forest trees

Peer reviewedPublisher PD

Essential versus accessory aspects of cell death: recommendations of the NCCD 2015

Cells exposed to extreme physicochemical or mechanical stimuli die in an uncontrollable manner, as a result of their immediate structural breakdown. Such an unavoidable variant of cellular demise is generally referred to as ‘accidental cell death’ (ACD). In most settings, however, cell death is initiated by a genetically encoded apparatus, correlating with the fact that its course can be altered by pharmacologic or genetic interventions. ‘Regulated cell death’ (RCD) can occur as part of physiologic programs or can be activated once adaptive responses to perturbations of the extracellular or intracellular microenvironment fail. The biochemical phenomena that accompany RCD may be harnessed to classify it into a few subtypes, which often (but not always) exhibit stereotyped morphologic features. Nonetheless, efficiently inhibiting the processes that are commonly thought to cause RCD, such as the activation of executioner caspases in the course of apoptosis, does not exert true cytoprotective effects in the mammalian system, but simply alters the kinetics of cellular demise as it shifts its morphologic and biochemical correlates. Conversely, bona fide cytoprotection can be achieved by inhibiting the transduction of lethal signals in the early phases of the process, when adaptive responses are still operational. Thus, the mechanisms that truly execute RCD may be less understood, less inhibitable and perhaps more homogeneous than previously thought. Here, the Nomenclature Committee on Cell Death formulates a set of recommendations to help scientists and researchers to discriminate between essential and accessory aspects of cell death

Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline

BACKGROUND: Sequencing technology and assembly algorithms have matured to the point that high-quality de novo assembly is possible for large, repetitive genomes. Current assemblies traverse transposable elements (TEs) and provide an opportunity for comprehensive annotation of TEs. Numerous methods exist for annotation of each class of TEs, but their relative performances have not been systematically compared. Moreover, a comprehensive pipeline is needed to produce a non-redundant library of TEs for species lacking this resource to generate whole-genome TE annotations. RESULTS: We benchmark existing programs based on a carefully curated library of rice TEs. We evaluate the performance of methods annotating long terminal repeat (LTR) retrotransposons, terminal inverted repeat (TIR) transposons, short TIR transposons known as miniature inverted transposable elements (MITEs), and Helitrons. Performance metrics include sensitivity, specificity, accuracy, precision, FDR, and F1. Using the most robust programs, we create a comprehensive pipeline called Extensive de-novo TE Annotator (EDTA) that produces a filtered non-redundant TE library for annotation of structurally intact and fragmented elements. EDTA also deconvolutes nested TE insertions frequently found in highly repetitive genomic regions. Using other model species with curated TE libraries (maize and Drosophila), EDTA is shown to be robust across both plant and animal species. CONCLUSIONS: The benchmarking results and pipeline developed here will greatly facilitate TE annotation in eukaryotic genomes. These annotations will promote a much more in-depth understanding of the diversity and evolution of TEs at both intra- and inter-species levels. EDTA is open-source and freely available: https://github.com/oushujun/EDTA

Conceptualising spirituality for medical research and health service provision

The need to take account of spirituality in research and health services provision is assuming ever greater importance. However the field has long been hampered by a lack of conceptual clarity about the nature of spirituality itself. We do not agree with the sceptical claim that it is impossible to conceptualise spirituality within a scientific paradigm. Our aims are to 1) provide a brief over-view of critical thinking that might form the basis for a useful definition of spirituality for research and clinical work and 2) demystify the language of spirituality for clinical practice and research