Projected Gromov-Witten varieties in cominuscule spaces

A projected Gromov-Witten variety is the union of all rational curves of fixed degree that meet two opposite Schubert varieties in a homogeneous space X = G/P. When X is cominuscule we prove that the map from a related Gromov-Witten variety is cohomologically trivial. This implies that all (3 point, genus zero) K-theoretic Gromov-Witten invariants of X are determined by the projected Gromov-Witten varieties, which extends an earlier result of Knutson, Lam, and Speyer. Our proof uses that any projected Gromov-Witten variety in a cominuscule space is also a projected Richardson variety.Comment: 13 page

Finiteness of cominuscule quantum K-theory

The product of two Schubert classes in the quantum K-theory ring of a homogeneous space X = G/P is a formal power series with coefficients in the Grothendieck ring of algebraic vector bundles on X. We show that if X is cominuscule, then this power series has only finitely many non-zero terms. The proof is based on a geometric study of boundary Gromov-Witten varieties in the Kontsevich moduli space, consisting of stable maps to X that take the marked points to general Schubert varieties and whose domains are reducible curves of genus zero. We show that all such varieties have rational singularities, and that boundary Gromov-Witten varieties defined by two Schubert varieties are either empty or unirational. We also prove a relative Kleiman-Bertini theorem for rational singularities, which is of independent interest. A key result is that when X is cominuscule, all boundary Gromov-Witten varieties defined by three single points in X are rationally connected.Comment: 16 pages; proofs slightly improved; explicit multiplications in QK(Cayley plane) from v1 no longer necessar

Neutron Diffraction Measurements and First Principles Study of Thermal Motion of Atoms in Select M_{n+1}AX_n and Binary MX Transition Metal Carbide Phases

Herein, we compare the thermal vibrations of atoms in select ternary carbides with the formula Mn+1AXn ("MAX phases," M = Ti, Cr; A = Al, Si, Ge; X = C, N) as determined from first principles phonon calculations to those obtained from high-temperature neutron powder diffraction studies. The transition metal carbides TiC, TaC, and WC are also studied to test our methodology on simpler carbides. Good qualitative and quantitative agreement is found between predicted and experimental values for the binary carbides. For all the MAX phases studied - Ti3SiC2, Ti3GeC2, Ti2AlN, Cr2GeC and Ti4AlN3 - density functional theory calculations predict that the A element vibrates with the highest amplitude and does so anisotropically with a higher amplitude within the basal plane, which is in line with earlier results from high-temperature neutron diffraction studies. In some cases, there are quantitative differences in the absolute values between the theoretical and experimental atomic displacement parameters, such as reversal of anisotropy or a systematic offset of temperature-dependent atomic displacement parameters. The mode-dependent Gr\"uneisen parameters are also computed to explore the anharmonicity in the system

Kinetic analysis of an efficient DNA-dependent TNA polymerase.

alpha-l-Threofuranosyl nucleoside triphosphates (tNTPs) are tetrafuranose nucleoside derivatives and potential progenitors of present-day beta-d-2'-deoxyribofuranosyl nucleoside triphosphates (dNTPs). Therminator DNA polymerase, a variant of the 9 degrees N DNA polymerase, is an efficient DNA-directed threosyl nucleic acid (TNA) polymerase. Here we report a detailed kinetic comparison of Therminator-catalyzed TNA and DNA syntheses. We examined the rate of single-nucleotide incorporation for all four tNTPs and dNTPs from a DNA primer-template complex and carried out parallel experiments with a chimeric DNA-TNA primer-DNA template containing five TNA residues at the primer 3'-terminus. Remarkably, no drop in the rate of TNA incorporation was observed in comparing the DNA-TNA primer to the all-DNA primer, suggesting that few primer-enzyme contacts are lost with a TNA primer. Moreover, comparison of the catalytic efficiency of TNA synthesis relative to DNA synthesis at the downstream positions reveals a difference of no greater than 5-fold in favor of the natural DNA substrate. This disparity becomes negligible when the TNA synthesis reaction mixture is supplemented with 1.25 mM MnCl(2). These results indicate that Therminator DNA polymerase can recognize both a TNA primer and tNTP substrates and is an effective catalyst of TNA polymerization despite changes in the geometry of the reactants

Genome-wide profiling of human cap-independent translation-enhancing elements.

We report an in vitro selection strategy to identify RNA sequences that mediate cap-independent initiation of translation. This method entails mRNA display of trillions of genomic fragments, selection for initiation of translation and high-throughput deep sequencing. We identified >12,000 translation-enhancing elements (TEEs) in the human genome, generated a high-resolution map of human TEE-bearing regions (TBRs), and validated the function of a subset of sequences in vitro and in cultured cells

Seasonal and spatial variations in the ocean-coupled ambient wavefield of the Ross Ice Shelf

© The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Baker, M. G., Aster, R. C., Anthony, R. E., Chaput, J., Wiens, D. A., Nyblade, A., Bromirski, P. D., Gerstoft, P., & Stephen, R. A. Seasonal and spatial variations in the ocean-coupled ambient wavefield of the Ross Ice Shelf. Journal of Glaciology, 65(254), (2019): 912-925, doi:10.1017/jog.2019.64.The Ross Ice Shelf (RIS) is host to a broadband, multimode seismic wavefield that is excited in response to atmospheric, oceanic and solid Earth source processes. A 34-station broadband seismographic network installed on the RIS from late 2014 through early 2017 produced continuous vibrational observations of Earth's largest ice shelf at both floating and grounded locations. We characterize temporal and spatial variations in broadband ambient wavefield power, with a focus on period bands associated with primary (10–20 s) and secondary (5–10 s) microseism signals, and an oceanic source process near the ice front (0.4–4.0 s). Horizontal component signals on floating stations overwhelmingly reflect oceanic excitations year-round due to near-complete isolation from solid Earth shear waves. The spectrum at all periods is shown to be strongly modulated by the concentration of sea ice near the ice shelf front. Contiguous and extensive sea ice damps ocean wave coupling sufficiently so that wintertime background levels can approach or surpass those of land-sited stations in Antarctica.This research was supported by NSF grants PLR-1142518, 1141916, 1142126, 1246151 and 1246416. JC was additionally supported by Yates funds in the Colorado State University Department of Mathematics. PDB also received support from the California Department of Parks and Recreation, Division of Boating and Waterways under contract 11-106-107. We thank Reinhard Flick and Patrick Shore for their support during field work, Tom Bolmer in locating stations and preparing maps, and the US Antarctic Program for logistical support. The seismic instruments were provided by the Incorporated Research Institutions for Seismology (IRIS) through the PASSCAL Instrument Center at New Mexico Tech. Data collected are available through the IRIS Data Management Center under RIS and DRIS network code XH. The PSD-PDFs presented in this study were processed with the IRIS Noise Tool Kit (Bahavar and others, 2013). The facilities of the IRIS Consortium are supported by the National Science Foundation under Cooperative Agreement EAR-1261681 and the DOE National Nuclear Security Administration. The authors appreciate the support of the University of Wisconsin-Madison Automatic Weather Station Program for the data set, data display and information; funded under NSF grant number ANT-1543305. The Ross Ice Shelf profiles were generated using the Antarctic Mapping Tools (Greene and others, 2017). Regional maps were generated with the Generic Mapping Tools (Wessel and Smith, 1998). Topography and bathymetry data for all maps in this study were sourced from the National Geophysical Data Center ETOPO1 Global Relief Model (doi:10.7289/V5C8276M). We thank two anonymous reviewers for suggestions on the scope and organization of this paper

Clinical Judgment Analysis

SUMMARY Judgment is central to the practice of medicine and occurs between making clinical observations and taking clinical decisions. Clinical judgment analysis has developed as a method of making statistically firm models of doctors' judgments. Computed models reveal the differential importance attached to items of clinical, social, or other data which are determinants of clinical decisions. These models can both reveal the causes of conflicts of judgment and may help resolve them in a way that unaided discussion cannot. Revealing experts' models to students speeds learning of diagnostic skills. Clinical judgment analysis offers a method of probing the judgments not just of students and doctors but also of patients who have shown systematic differences in their perceptions of risk and benefit. The power and relevance of clinical trials can be improved by the consistent application of judgment policies generated from both the trialists and those who will use their result

Distinct RNA profiles in subpopulations of extracellular vesicles: apoptotic bodies, microvesicles and exosomes

Introduction: In recent years, there has been an exponential increase in the number of studies aiming to understand the biology of exosomes, as well as other extracellular vesicles. However, classification of membrane vesicles and the appropriate protocols for their isolation are still under intense discussion and investigation. When isolating vesicles, it is crucial to use systems that are able to separate them, to avoid cross-contamination. Method: EVs released from three different kinds of cell lines: HMC-1, TF-1 and BV-2 were isolated using two centrifugation-based protocols. In protocol 1, apoptotic bodies were collected at 2,000×g, followed by filtering the supernatant through 0.8 µm pores and pelleting of microvesicles at 12,200×g. In protocol 2, apoptotic bodies and microvesicles were collected together at 16,500×g, followed by filtering of the supernatant through 0.2 µm pores and pelleting of exosomes at 120,000×g. Extracellular vesicles were analyzed by transmission electron microscopy, flow cytometry and the RNA profiles were investigated using a Bioanalyzer®. Results: RNA profiles showed that ribosomal RNA was primary detectable in apoptotic bodies and smaller RNAs without prominent ribosomal RNA peaks in exosomes. In contrast, microvesicles contained little or no RNA except for microvesicles collected from TF-1 cell cultures. The different vesicle pellets showed highly different distribution of size, shape and electron density with typical apoptotic body, microvesicle and exosome characteristics when analyzed by transmission electron microscopy. Flow cytometry revealed the presence of CD63 and CD81 in all vesicles investigated, as well as CD9 except in the TF-1-derived vesicles, as these cells do not express CD9. Conclusions: Our results demonstrate that centrifugation-based protocols are simple and fast systems to distinguish subpopulations of extracellular vesicles. Different vesicles show different RNA profiles and morphological characteristics, but they are indistinguishable using CD63-coated beads for flow cytometry analysis