bluuebunny/crossref_metadata_2025 huggingface dataset:
First step toward a synthetic diagnostic for magnetic fluctuation measurements using cross-polarization scattering on DIII-D
Authors: Wang G. , Rhodes T. L. , Crocker N. A. , Peebles W. A. , Barada K.
Published: September 2018

Cross-polarization scattering (CPS) provides localized magnetic fluctuation (B̃) measurements in fusion plasmas based on the process where B̃ scatters electromagnetic radiation into the orthogonal polarization. The CPS system on DIII-D utilizes the probe beam of a Doppler backscattering (DBS) diagnostic combined with a cross-view CPS receiver system, which allows simultaneous density and B̃ measurements with good spatial and wavenumber coverage. The interpretation of the signals is challenging due to the complex plasma propagation of the DBS probe beam and CPS receive beams. A synthetic diagnostic for CPS is therefore essential to interpret data and perform detailed validation tests of non-linear turbulence simulations. This work reports a first step toward a synthetic diagnostic for CPS utilizing GENRAY, a 3-D ray tracing code, to simulate the propagation of the probe and scattered rays. The local B̃ wavenumber is calculated from the local O- and X-mode wavenumbers using the wave vector matching scattering condition. The CPS wavenumber values and spatial locations are determined by a complex consideration that includes the local density and B̃ level, receive antenna pattern and orientation, scattering volume, wavenumber values detected at the various scattering centers, and alignment of the magnetic wave vector with the plane perpendicular to the magnetic field. The issue of a spurious CPS signal due to polarization mismatches for launch and receive is also discussed. It is suggested that simultaneous O- and X-mode DBS measurements should be utilized for better understanding of the CPS signal contamination when the cutoff locations for both polarizations are close.
Atmospheric discharge plasma in aqueous solution: Importance of the generation of water vapor bubbles for plasma onset and physicochemical evolution
Authors: Yui Hiroharu , Someya Yuu , Kusama Yuta , Kanno Kenta , Banno Motohiro
Published: September 2018

Discharge plasma formed in aqueous solutions has attracted much attention for its applications in environmental purification and material syntheses. The onset and evolution of the discharge plasma in an aqueous solution and transient reactive species formed in it are successfully monitored with micrometer spatial resolution and nanosecond temporal resolution. The combination of a custom-made microscopic discharge system and a high-speed camera provides direct evidence that water vapor bubbles form before the discharge with the thermal phase transition of aqueous solution at the electrode tip. The water vapor bubbles, i.e., locally formed space in the gas phase, connect the gap between the tips of the opposed electrodes. The local gas area formed in aqueous solution plays a crucial role in the ignition and continuance of the discharge plasma. It is also found that the initially formed plasma lasts for under 100 ns and quenches rapidly. However, plasma regenerates in the water vapor bubble and successively bridges the opposing electrodes during the pulsed-voltage application (ca. 1 μs). These two temporally distinct generations of plasma, i.e., the initial plasma (IP) and the following successive plasma (SP), can be seen to correspond to the dielectric breakdown and glow-like plasma, respectively. These results provide an important picture for the proposed mechanism for plasma evolution in water and also important information for the efficient control of the discharge plasma with its applications in waste-water treatments, nanomaterial syntheses with plasma oxidation–reduction reactions, and the chemical modification of the material surfaces in aqueous solutions as a form of “green chemistry.”
The electrochemical oxidation of hydroquinone and catechol through polyaniline and poly(aspartic acid) thin films: A comparative study
Authors: Feng Ye , Zhao Cheng-Sen , Cao Shuo-Hui , Cai Shu-Hui , Sun Hui-Jun , Chen Zhong
Published: September 2018

Lately, polymers as electrochemical catalysts have attracted intense interest. As two promising candidates, herein, electrochemically deposited polyaniline and poly(aspartic acid) thin film materials have been fabricated on glassy carbon electrodes. Through multiple characterizations, including attenuated total reflection Fourier transform infrared spectrophotometry, cyclic voltammetry, electrochemical impedance spectroscopy, and proton nuclear magnetic resonance, essential properties of these two electro-synthesized polymers, especially the capacity in electrochemically catalyzing the oxidation of electro-active isomers of hydroquinone and catechol, have been investigated. The polymer-modified electrodes present improved conductivity, and diffusion-dominated redox behaviors of hydroquinone and catechol at both modified glassy carbon electrodes are observed. In addition, quantitative proton nuclear magnetic resonance spectra provide the evident information on the electrochemically induced molecular transformation, which confirms the better electrochemical activity of poly(aspartic acid).
Green laser sintering of copper oxide (CuO) nano particle (NP) film to form Cu conductive lines
Authors: Rahman Md. Khalilur , Lu Zhao , Kwon Kye-Si
Published: September 2018

Copper oxide (CuO) nanoparticle (NP) ink is a potential candidate for low-cost alternatives to other metal-based nano-particle inks (e.g., Au, Ag.) in printed electronics. To obtain Cu patterns from CuO NP ink, CuO NP inks should be converted to Cu particles, and be fused to form a connected conductive line. For this purpose, photonic sintering methods have been widely used, which generate the heat required for sintering via the absorption of light. In this study, we used continuous wave (CW) green laser with 532 nm wavelength, since the laser has the advantage of selective sintering by irradiation of light only on the target place. We investigated the optimal sintering parameters, such as laser power and scanning speed, using the green laser, in order to obtain low resistivity. We also investigated the pre-treatment conditions, such as pre-baking, which is required to evaporate solvents in the ink. We found that over-baking of deposited film will adversely affect the sintering, because film can be easily damaged from laser irradiation. As a result of laser sintering, we obtained the resistivity of (9.5 and 71.6) μΩ·cm when the pre-baked thicknesses of CuO films were (546 and 889) nm, respectively. In such cases, the thicknesses were significantly reduced to (141 and 270) nm, respectively.
A technique to measure the thermal resistance at the interface between a micron size particle and its matrix in composite materials
Authors: Goni Miguel , Patelka Maciej , Ikeda Sho , Hartman Terry , Sato Toshiyuki , Schmidt Aaron J.
Published: September 2018

Particle-matrix interfaces can play an important role in heat propagation through particulate composites. We investigated the possibility of using frequency domain thermoreflectance combined with a numerical thermal model to measure in situ the thermal resistance of the particle-matrix interface in particulate composite materials. We found that the sensitivity of the technique depended on the matrix thermal conductivity, the particle size, and the value of the interface thermal resistance. In general, high thermal conductivity matrix materials and small particles will present higher sensitivity to the interface thermal resistance. We tested the technique with diamond particles embedded in tin and showed that the interface thermal resistance could be measured for these samples.
Accurate lattice geometrical parameters and bulk moduli from a semilocal density functional
Authors: Mo Yuxiang , Tang Hong , Bansil Arun , Tao Jianmin
Published: September 2018

Accurate prediction of lattice constants is very important in applications of density functional theory. In this work, we assess the efficacy of a non-empirical meta-generalized gradient approximation proposed by Tao and Mo (TM) by calculating the lattice constants as well as bulk moduli of 33 crystalline semiconductors within the TM scheme. We find that the TM functional is able to produce very accurate lattice constants, with a mean absolute error of 0.038 Å, and bulk moduli with a mean absolute error of 3.2 GPa, improving upon commonly-used semilocal density functionals, such as the LSDA, PBE, SOGGA, PBEsol, TPSS, M06L, and SCAN. The high computational efficiency and remarkable agreements with the corresponding experimental values suggest that the TM functional can be a very competitive candidate in electronic structure theory. We attribute the accuracy of the TM functional to be the result of its satisfaction of many exact or nearly-exact conditions related to the exchange-correlation energy and the associated hole, leading to an improved description of the short- as well as intermediate-range van der Waals interactions.
Metalenses offer integrated focusing for infrared imaging devices
Authors: Cesare Chris
Published: September 2018

Etched subwavelength structures made from a commonly used semiconductor help to increase the sensitivity of focal plane arrays.
Electrochemical Reduction of 2,4-Dinitrotoluene in Room Temperature Ionic Liquids: A Mechanistic Investigation
Authors: Lee Junqiao , Hay Catherine E. , Silvester Debbie S.
Published: September 2018

The reduction mechanism of 2,4-dinitrotoluene (DNT) has been studied in eight room temperature ionic liquids (RTILs) using cyclic voltammetry (CV), square wave voltammetry (SWV), chronoamperometry, and digital simulation. Two distinctive peaks are observed in the voltammetry, corresponding to the stepwise reduction of the two nitro groups on the aromatic ring. Diffusion coefficients (D) and electron counts (n) were calculated from chronoamperometric transients, revealing an electron count of one in most RTILs, and a linear relationship between D and the inverse of viscosity. Focusing on the first reduction only, the peak appears to be chemically reversible at low concentrations. However, as the concentration increases, the current of the reverse peak diminishes, suggesting that one or more chemical steps occur after the electrochemical step. The results from digital simulation of the CVs in one of the RTILs reveal that the most likely mechanism involves a deprotonation of the methyl group of a parent DNT molecule by the electrogenerated radical anion and/or a dimerisation of two electrogenerated radical anions. Elucidation of the reduction mechanism of DNT (and other explosives) is vital if electrochemical techniques are to be employed to detect these types of compounds in the field.
Deconvolution of pro- and antiviral genomic responses in Zika virus-infected and bystander macrophages
Authors: Carlin Aaron F. , Vizcarra Edward A. , Branche Emilie , Viramontes Karla M. , Suarez-Amaran Lester , Ley Klaus , Heinz Sven , Benner Christopher , Shresta Sujan , Glass Christopher K.
Published: September 2018

Genome-wide investigations of host–pathogen interactions are often limited by analyses of mixed populations of infected and uninfected cells, which lower sensitivity and accuracy. To overcome these obstacles and identify key mechanisms by which Zika virus (ZIKV) manipulates host responses, we developed a system that enables simultaneous characterization of genome-wide transcriptional and epigenetic changes in ZIKV-infected and neighboring uninfected primary human macrophages. We demonstrate that transcriptional responses in ZIKV-infected macrophages differed radically from those in uninfected neighbors and that studying the cell population as a whole produces misleading results. Notably, the uninfected population of macrophages exhibits the most rapid and extensive changes in gene expression, related to type I IFN signaling. In contrast, infected macrophages exhibit a delayed and attenuated transcriptional response distinguished by preferential expression of
IFNB1
at late time points. Biochemical and genomic studies of infected macrophages indicate that ZIKV infection causes both a targeted defect in the type I IFN response due to degradation of STAT2 and reduces RNA polymerase II protein levels and DNA occupancy, particularly at genes required for macrophage identity. Simultaneous evaluation of transcriptomic and epigenetic features of infected and uninfected macrophages thereby reveals the coincident evolution of dominant proviral or antiviral mechanisms, respectively, that determine the outcome of ZIKV exposure.
A metaphysics for practical knowledge
Authors: Frost Kim
Published: September 2018

Is Anscombean practical knowledge independent of what the agent actually does on an occasion? Failure to understand Anscombe’s answer to this question is a major obstacle to appreciating the subtlety and plausibility of her view. I argue that Anscombe’s answer is negative, and turns on the nature of mistakes in performance, and reveals a distinctive implicit metaphysics of mind and knowledge, structured by related capacities and exercises of capacities. If my interpretation is correct, then practical knowledge shares features with knowledge-how and knowledge-that, but deserves its own epistemic category.
How to tell essence (when you sense one)
Authors: Ivanov Ivan V.
Published: September 2018

How could perceptual experiences reveal matters of essentiality? Answering this question is crucial for vindicating a thesis about the epistemic import of experience, commonly known as Revelation. The thesis comes in a weak and a strong version. Only on the strong one could it make up an authoritative piece of common sense. But this version also seems to demand too much of our experiences, namely that they can reveal essentiality. However, the impression that our experiences are not suited for this turns out to be due to a non-mandatory assumption about how the revelation of essentiality would work.
A concise synthesis of peramine, a metabolite of endophytic fungi
Authors: Ito Shinsaku , Yamamoto Yuta , Nishikawa Toshio
Published: September 2018

The total synthesis of peramine, a natural product isolated from an endophytic fungi, has been achieved in four steps and 34% overall yield from known compounds. The key step was the one-pot construction of the pyrrolopyrazinone ring from pyrrole amide and propargyl bromide. The preparation of peramine-d4 as an internal standard for quantitative analysis by MS is also described.
Methyl-β-cyclodextrin potentiates the BITC-induced anti-cancer effect through modulation of the Akt phosphorylation in human colorectal cancer cells
Authors: Yang Qifu , Miyagawa Miku , Liu Xiaoyang , Zhu Beiwei , Munemasa Shintaro , Nakamura Toshiyuki , Murata Yoshiyuki , Nakamura Yoshimasa
Published: September 2018

Methyl-β-cyclodextrin (MβCD) is an effective agent for the removal of plasma membrane cholesterol. In this study, we investigated the modulating effects of MβCD on the antiproliferation induced by benzyl isothiocyanate (BITC), an ITC compound mainly derived from papaya seeds. We confirmed that MβCD dose-dependently increased the cholesterol level in the medium, possibly through its removal from the plasma membrane of human colorectal cancer cells. The pretreatment with a non-toxic concentration (2.5 mM) of MβCD significantly enhanced the BITC-induced cytotoxicity and apoptosis induction, which was counteracted by the cholesterol supplementation. Although BITC activated the phosphoinositide 3-kinase (PI3K)/Akt pathway, MβCD dose-dependently inhibited the phosphorylation level of Akt. On the contrary, the treatment of MβCD enhanced the phosphorylation of mitogen activated protein kinases, but did not potentiate their BITC-induced phosphorylation. These results suggested that MβCD might potentiate the BITC-induced anti-cancer by cholesterol depletion and thus inhibition of the PI3K/Akt-dependent survival pathway.

Abbreviations: CDs: cyclodextrins; MβCD: methyl-β-cyclodextrin; ITCs: isothiocyanates; BITC: benzyl isothiocyanate; PI3K: phosphoinositide 3-kinase; PDK1: phosphoinositide-dependent kinase-1; MAPK: mitogen activated protein kinase; ERK1/2: extracellular signal-regulated kinase1/2; JNK: c-Jun N-terminal kinase; PI: propidium iodide; FBS: fatal bovine serum; TLC: thin-layer chromatography; PBS(-): phosphate-buffered saline without calcium and magnesium; MEK: MAPK/ERK kinase; PIP2: phosphatidylinositol-4,5-bisphosphate; PIP3: phosphatidylinositol-3,4,5-trisphosphate
Simultaneous collection of the portal and superior vena cava blood in conscious rats defined that intestinal epithelium is the major site of glucuronidation, but not sulfation and methylation, of quercetin
Authors: Tanaka Seiya , Oyama Manami , Nishikawa Miyu , Ikushiro Shinichi , Hara Hiroshi
Published: September 2018

Quercetin is a flavonoid with many physiological effects. Absorbed quercetin is rapidly conjugated in the intestinal epithelium and liver. Different positional isomers of quercetin conjugates have different physiological properties. However, the mechanisms of quercetin conjugation in the intestine are not fully clarified. We examined the regioselective quercetin conjugate formation in the intestine after oral administration of quercetin glycosides, by simultaneous sampling of blood from the portal vein and superior vena cava, and quantifying various positional isomers of quercetin glucuronides and sulfates in conscious rats. Concentrations of quercetin glucuronides were higher in blood from the portal vein than the superior vena cava, showing that glucuronidation mainly occurred in the intestine. Such differences were not observed for quercetin sulfates. Regioselectivity of the intestinal glucuronidation in quercetin hydroxyl groups were 7- >3′- >3- >4′-OH. Quercetin was mainly sulfated on 3′-OH at 30 min, but on 4′-OH at 240 min.
bcGST—an interactive bias-correction method to identify over-represented gene-sets in boutique arrays
Authors: Wang Kevin Y X , Menzies Alexander M , Silva Ines P , Wilmott James S , Yan Yibing , Wongchenko Matthew , Kefford Richard F , Scolyer Richard A , Long Georgina V , Tarr Garth , Mueller Samuel , Yang Jean Y H
Published: September 2018

Motivation

Gene annotation and pathway databases such as Gene Ontology and Kyoto Encyclopaedia of Genes and Genomes are important tools in Gene-Set Test (GST) that describe gene biological functions and associated pathways. GST aims to establish an association relationship between a gene-set of interest and an annotation. Importantly, GST tests for over-representation of genes in an annotation term. One implicit assumption of GST is that the gene expression platform captures the complete or a very large proportion of the genome. However, this assumption is neither satisfied for the increasingly popular boutique array nor the custom designed gene expression profiling platform. Specifically, conventional GST is no longer appropriate due to the gene-set selection bias induced during the construction of these platforms.

Results

We propose bcGST, a bias-corrected GST by introducing bias-correction terms in the contingency table needed for calculating the Fisher’s Exact Test. The adjustment method works by estimating the proportion of genes captured on the array with respect to the genome in order to assist filtration of annotation terms that would otherwise be falsely included or excluded. We illustrate the practicality of bcGST and its stability through multiple differential gene expression analyses in melanoma and the Cancer Genome Atlas cancer studies.

Availability and implementation

The bcGST method is made available as a Shiny web application at http://shiny.maths.usyd.edu.au/bcGST/.

Supplementary information

Supplementary data are available at Bioinformatics online.
GenomeFlow: a comprehensive graphical tool for modeling and analyzing 3D genome structure
Authors: Trieu Tuan , Oluwadare Oluwatosin , Wopata Julia , Cheng Jianlin
Published: September 2018

Motivation

Three-dimensional (3D) genome organization plays important functional roles in cells. User-friendly tools for reconstructing 3D genome models from chromosomal conformation capturing data and analyzing them are needed for the study of 3D genome organization.

Results

We built a comprehensive graphical tool (GenomeFlow) to facilitate the entire process of modeling and analysis of 3D genome organization. This process includes the mapping of Hi-C data to one-dimensional (1D) reference genomes, the generation, normalization and visualization of two-dimensional (2D) chromosomal contact maps, the reconstruction and the visualization of the 3D models of chromosome and genome, the analysis of 3D models and the integration of these models with functional genomics data. This graphical tool is the first of its kind in reconstructing, storing, analyzing and annotating 3D genome models. It can reconstruct 3D genome models from Hi-C data and visualize them in real-time. This tool also allows users to overlay gene annotation, gene expression data and genome methylation data on top of 3D genome models.

Availability and implementation

The source code and user manual: https://github.com/jianlin-cheng/GenomeFlow.

Supplementary information

Supplementary data are available at Bioinformatics online.
Azure-winged magpies solve string-pulling tasks by partial understanding of the physical cognition
Authors: Wang Lin , Luo Yunchao , Wang Xin , Maierdiyali Abudusaimaiti , Chang Hao , Li Zhongqiu
Published: September 2018

String-pulling is one of the most widely used paradigms in animal cognition research. We investigated how azure-winged magpies Cyanopica cyanus solve multiple-string problems that they have never encountered before. In Experiment 1, the strings were arranged in parallel, slanted, or crossed to investigate what rules azure-winged magpies use to solve multiple spatial relations of strings. Experiment 2 assessed whether the subjects understood the connection between the string and the bait while taking advantage of broken strings. In Experiment 3, the subjects were confronted with strings of different lengths attached to rewards in order to explore whether the string length, as a proxy for the pulling efficiency or reward distance, was crucial for the birds’ choice of which string to pull. Generally, the birds were successful in tasks where the reward was close to the correct string’s end, and they relied on a “proximity rule” in most cases. The results showed that azure-winged magpies had a partial understanding of the physical principles underlying the string-pulling but were stumped by complex spatial relations. They likely relied on simple strategies such as the proximity rule to solve the tasks. The effects of individual difference and experiential learning on string-pulling performance are also discussed.
Sharp and telling
Authors: Tybjerg Karin
Published: September 2018

Surgical instrument collections have been used in a multitude of ways – as tools, taxonomies, teaching aids, representation, historical highlights and public displays – and they provide a key to understanding the shifting relations between surgery, medical museums and medical history. Tracing the uses of the surgical instrument collections from the Royal Danish Academy of Surgery and the Medical Historical Museum at the University of Copenhagen reveals a network of disciplinary and institutional changes from the late nineteenth to early twenty-first century. The history of the collections maps relations between scientific and cultural historical collections and between medicine and history. In the same way as surgical instruments have connected the surgeon’s hand to the patients’ body, the surgical instrument collections connect together the public, medical practice and history.
Cardiac Microvascular Dysfunction in Women Living With HIV Is Associated With Cytomegalovirus Immunoglobulin G
Authors: Knudsen Andreas , Thorsteinsson Kristina , Christensen Thomas E , Hasbak Philip , Ripa Rasmus Sejersten , Panum Inge , Lebech Anne-Mette , Kjaer Andreas
Published: September 2018

Background

People living with HIV (PLWH) appear to be at increased risk of cardiovascular disease (CVD), and this is possibly more pronounced in women living with HIV (WLWH). In the general population, men are more likely to develop obstructive coronary artery disease (CAD), and women often present with a nonobstructive pattern with cardiac microvascular dysfunction. We investigated cardiac microvascular function in men and women living with HIV and tested for association with cytomegalovirus (CMV) immunoglobulin G (IgG), as this has been associated with CVD in PLWH.

Methods

In a cross-sectional study, 94 PLWH on antiretroviral therapy were scanned with 82Rb positron emission tomography/computed tomography at rest and during adenosine-induced stress, which enables the quantification of the myocardial flow reserve (MFR). CMV IgG was measured in plasma.

Results

WLWH had significantly lower MFR compared with men living with HIV (MLWH; P = .003), and >45% of the women had an MFR indicative of cardiac microvascular dysfunction, whereas this was only true for 24% of men (P = .03). CMV IgG concentrations were inversely associated with MFR among WLWH but not MLWH (P = .05 for interaction).

Conclusions

In this first study comparing MFR in women and men living with HIV, we found that WLWH had significantly lower MFR than MLWH and 45% of the women had cardiac microvascular dysfunction despite younger age and lower cardiovascular risk. Furthermore, CMV IgG was inversely associated with MFR among women but not men. This calls for attention to CVD among young WLWH even with low cardiovascular risk.
HIV-2 Primary Infection in a French 69-Year-Old Bisexual Man
Authors: Cazals Nicolas , Le Hingrat Quentin , Abraham Bruno , Da Silva Patricia , Guindre Laure , Goffart Sylvie , Damond Florence , Visseaux Benoît , Charpentier Charlotte , Ranger-Rogez Sylvie , Descamps Diane
Published: September 2018

More than 1 million individuals, mainly in West Africa, are thought to be infected with HIV-2. Acute HIV-2 infection is rarely observed, only 2 primary infections have been described to date. We report a detailed case of HIV-2 primary infection in a 69-year-old French bisexual Caucasian man, thereby providing valuable insights into HIV-2 early infection.
The Canadian Reference Power: Delegation to the Courts and the Navigation of Federalism
Authors: Puddister Kate
Published: September 2018

The Canadian reference power allows governments to ask appellate courts for an advisory opinion without a live dispute. Reference cases have been an important element of Canadian federalism since their creation in 1875 but have not been subject to a comprehensive analysis. Shifting the focus to understanding government decisions to rely on the courts to navigate federalism, this article has two objectives. First, through analysis of an original dataset of Canadian appellate reference cases from 1875 to 2017, the article provides an examination of how references have been used by governments, with particular attention to issues related to federalism. Second, the article considers how the reference power can be employed as a political strategy by governments. The reference power demonstrates clear support for the blame avoidance and credit-claiming thesis and provides compelling evidence on how the dynamics of intergovernmental relations can shape a government’s decision to delegate decision-making to the courts.
Harvest of Lettuce from Verticillium-Infested Fields Has Little Impact on Postharvest Quality
Authors: Puri Krishna D. , Vallad Gary E. , Qin Qing-Ming , Hayes Ryan J. , Subbarao Krishna V.
Published: September 2018

Verticillium wilt of lettuce, caused by the soilborne pathogen Verticillium dahliae, poses a serious threat to the California lettuce industry. Knowledge of disease development and its impact on postharvest marketability would facilitate better management of the affected fields. This study investigated postharvest marketability of 22 lettuce varieties harvested from two Verticillium-infested commercial lettuce fields in Salinas and Watsonville, CA, in 2005 using a randomized complete block design. Periodic sampling to monitor disease in several crisphead varieties in the field demonstrated that root symptoms developed quickly at later stages of heading, followed by the onset of foliar symptoms as the crop reached harvest maturity. Harvested marketable heads were vacuum cooled soon after harvest to about 4°C and maintained at this temperature in commercial coolers. The impact of V. dahliae on postharvest marketability was assessed based on the percentage of heads per case deemed marketable following 1, 2, and 3 weeks of refrigerated storage. Across both field experiments, the average disease incidence and postharvest marketability ranged from 4.2 to 87.5% and from 69.4 to 100.0%, respectively, among lettuce types and varieties. The Pearson correlation analysis detected no significant relationship between disease incidence and postharvest marketability across all varieties tested (r = 0.041, P = 0.727), or within lettuce types, even though V. dahliae was recovered from 34% of the plants harvested, and recovery ranged from 0 to 73.3% for V. dahliae and from 10 to 91.7% for non-V. dahliae (V. isaacii or V. klebahnii) species. These findings demonstrate that growers can harvest lettuce from an infested field before foliar symptoms develop with negligible impact by Verticillium spp. on postharvest marketability or quality.
Kinetics of Systemic Invasion and Latent and Incubation Periods of Tomato severe rugose virus and Tomato chlorosis virus in Single and Co-Infections in Tomato Plants
Authors: Favara Gabriel Madoglio , Bampi Daiana , Molina Juan Pablo Edwards , Rezende Jorge Alberto Marques
Published: September 2018

Tomato severe rugose virus (ToSRV) and Tomato chlorosis virus (ToCV) are among the major viruses that affect tomato (Solanum lycopersicum) development and yield in Brazil. ToSRV and ToCV are transmitted in a persistent circulative and semipersistent manner, respectively, by the whitefly Bemisia tabaci Middle East-Asia Minor 1, considered the main vector of these viruses. In this study, the kinetics of systemic invasion and the latent and incubation periods of ToSRV and ToCV were evaluated in singly and doubly infected tomato plants. Both viruses moved systemically into tomato plants as early as 1 day after inoculation. The mean ToCV latent periods in single infections and co-infections with ToSRV were 13 and 11 days, respectively, while incubation periods in single and co-infections were, on average, 30 and 31 days, respectively. For ToSRV, the mean latent period was 7 days in single infections and 6 days in co-infections with ToCV. Incubation periods were, on average, 18 and 17 days in single and co-infections, respectively. Because latent periods for both viruses were shorter than their respective incubation periods, field-infected tomato plants may act as sources of inocula soon after infection and before onset of symptoms.
Treatment of Ciprofloxacin-resistant Ear Infections
Authors: Noonan Kathryn Y. , Kim Soo Yeon , Wong Lye Yeng , Martin Isabella W. , Schwartzman Joseph D. , Saunders James E.
Published: September 2018

Objective:

Ciprofloxacin resistance has been reported in 4.5% of patients with otorrhea and is increasing in prevalence. Due to ototoxicity, only fluoroquinolones are Food and Drug Administration approved for topical therapy in the middle ear. Furthermore, there is an assumption that antibiotic resistance is less relevant to topical therapy due to in vivo concentrations much higher than the minimum inhibitory concentration used to determine resistance. This study investigates ciprofloxacin-resistant infections and seeks to develop a better understanding of treatment options and outcomes.

Study Design:

Retrospective review of 141 ciprofloxacin-resistant otologic infections.

Setting:

Tertiary-care hospital.

Patients:

Patients with culture-proven ciprofloxacin-resistant infections from 2008 to 2017.

Intervention(s):

Antibiotic treatment with ciprofloxacin topical drops, ciprofloxacin plus oral antibiotics, and nonciprofloxacin therapy.

Main Outcome Measure(s):

Bacteriology for ciprofloxacin-resistant infections and treatment effectiveness of various therapies.

Results:

Methicillin-resistant Staphylococcus aureus (33%), Corynebacterium striatum (19%), and non-Methicillin-resistant Staphylococcus aureus (11%) are the most frequent causes of ciprofloxacin-resistant infections. Topical ciprofloxacin monotherapy was successful in 2.7% of infections compared with a 64.7% success rate with the addition of an oral antibiotic (p < 0.001). Nonciprofloxacin drops are more effective with a 70% cure rate compared with the 2.7% of the ciprofloxacin drops p < 0.001. There was no difference in treatment efficacy when comparing nonciprofloxacin topical therapy (70% cure) to nonciprofloxacin topical therapy plus oral antibiotic (83% cure, p = 0.17).

Conclusions:

Using ciprofloxacin drops to treat ciprofloxacin-resistant bacteria is ineffective and patients do significantly better with alternative therapy. This finding supports the conclusion that high concentrations achieved in topical applications are not sufficient to overcome antibiotic resistance.
Phase resetting in human auditory cortex to visual speech
Authors: Mégevand Pierre , Mercier Manuel R. , Groppe David M. , Golumbic Elana Zion , Mesgarani Nima , Beauchamp Michael S. , Schroeder Charles E. , Mehta Ashesh D.
Published: September 2018

Natural conversation is multisensory: when we can see the speaker’s face, visual speech cues influence our perception of what is being said. The neuronal basis of this phenomenon remains unclear, though there is indication that phase modulation of neuronal oscillations—ongoing excitability fluctuations of neuronal populations in the brain—provides a mechanistic contribution. Investigating this question using naturalistic audiovisual speech with intracranial recordings in humans, we show that neuronal populations in auditory cortex track the temporal dynamics of unisensory visual speech using the phase of their slow oscillations and phase-related modulations in high-frequency activity. Auditory cortex thus builds a representation of the speech stream’s envelope based on visual speech alone, at least in part by resetting the phase of its ongoing oscillations. Phase reset could amplify the representation of the speech stream and organize the information contained in neuronal activity patterns.

SIGNIFICANCE STATEMENT

Watching the speaker can facilitate our understanding of what is being said. The mechanisms responsible for this influence of visual cues on the processing of speech remain incompletely understood. We studied those mechanisms by recording the human brain’s electrical activity through electrodes implanted surgically inside the skull. We found that some regions of cerebral cortex that process auditory speech also respond to visual speech even when it is shown as a silent movie without a soundtrack. This response can occur through a reset of the phase of ongoing oscillations, which helps augment the response of auditory cortex to audiovisual speech. Our results contribute to discover the mechanisms by which the brain merges auditory and visual speech into a unitary perception.
Classification and monomer-by-monomer annotation of suprachromosomal family 1 alpha satellite higher-order repeats in hg38 human genome assembly
Authors: Uralsky L. , Shepelev V.A. , Alexandrov A.A. , Yurov Y.B. , Rogaev E.I. , Alexandrov I.A.
Published: September 2018

In the latest hg38 human genome assembly, centromeric gaps has been filled in by alpha satellite (AS) reference models (RMs) which are statistical representations of homogeneous higher-order repeat (HOR) arrays that make up the bulk of the centromeric regions. We studied these models to compose an atlas of human HORs where each monomer of a HOR could be characterized and represented by a number of its polymorphic sequence variants. We further used these data and HMMER sequence analysis platform to annotate AS HORs in the assembly. This led to discovery and annotation of a new type of low copy number highly divergent HORs which were not represented by RMs. The annotation can be viewed as UCSC Genome Browser custom track (the HOR-track) and used together with our previous annotation of AS SFs in the same assembly where each AS monomer can be viewed in its genomic context together with its classification into one of the 5 major SFs (the SF-track). To catalog the diversity of AS HORs in the human genome we introduced a new naming system. Each HOR received a name which showed its SF, chromosomal location and index number. Here we present the first installment of the HOR-track covering only the 17 HORs that belong to SF1 which forms live functional centromeres in chromosomes 1, 3, 5, 6, 7, 10, 12, 16 and 19 and also a large number of minor dead HOR domains, both homogeneous (pseudo) and divergent (relic). The 4 newly discovered divergent SF1 HORs have provided the missing links in SF1 early evolution and substantiated its partition into 2 generations, archaic and modern, which we reported earlier. Additionally, we demonstrated that monomer-by-monomer HOR annotation was useful for mapping and quantification of various structural variants of AS HORs which would be important for studies of inter-individual polymorphism of AS including centromeric functional epialleles.
Integrative analysis of rare variants and pathway information shows convergent results between immune pathways, drug targets and epilepsy genes
Authors: Nguyen Hoang T. , Dobbyn Amanda , Charney Alexander W. , Bryois Julien , Kim April , Mcfadden Whitney , Skene Nathan G. , Huckins Laura M. , Wang Weiqing , Ruderfer Douglas M , Xu Xinyi , Fromer Menachem , Purcell Shaun M , Lage Kasper , Verhage Matthijs , Smit August B. , Hjerling-Leffler Jens , Buxbaum Joseph D. , Pinto Dalila , He Xin , Sullivan Patrick F , Stahl Eli A.
Published: September 2018

Trio family and case-control studies of next-generation sequencing data have proven integral to understanding the contribution of rare inherited andde novosingle-nucleotide variants to the genetic architecture of complex disease. Ideally, such studies should identify individual risk genes of moderate to large effect size to generate novel treatment hypotheses for further follow-up. However, due to insufficient power, gene set enrichment analyses have come to be relied upon for detecting differences between cases and controls, implicating sets of hundreds of genes rather than specific targets for further investigation. Here, we present a Bayesian statistical framework, termed gTADA, that integrates gene-set membership information with gene-levelde novoand rare inherited case-control counts, to prioritize risk genes with excess rare variant burden within enriched gene sets. Applying gTADA to available whole-exome sequencing datasets for several neuropsychiatric conditions, we replicated previously reported gene set enrichments and identified novel risk genes. For epilepsy, gTADA prioritized 40 risk genes (posterior probabilities > 0.95), 6 of which replicate in an independent whole-genome sequencing study. In addition, 30/40 genes are novel genes. We found that epilepsy genes had high protein-protein interaction (PPI) network connectivity, and show specific expression during human brain development. Some of the top prioritized EPI genes were connected to a PPI subnetwork of immune genes and show specific expression in prenatal microglia. We also identified multiple enriched drug-target gene sets for EPI which included immunostimulants as well as known antiepileptics. Immune biology was supported specifically by case-control variants from familial epilepsies rather than do novo mutations in generalized encephalitic epilepsy.
New genetic variants associated with major adverse cardiovascular events in patients with acute coronary syndromes and treated with clopidogrel and aspirin
Authors: Liu Xiaomin , Xu Hanshi , Xu Huaiqian , Geng Qingshan , Mak Wai-Ho , Ling Fei , Su Zheng , Yang Fang , Zhang Tao , Chen Jiyan , Yang Huanming , Wang Jian , Zhang Xiuqing , Xu Xun , Jia Huijue , Zhang Zhiwei , Liu Xiao , Zhong Shilong
Published: September 2018

Importance

Although a few studies have reported the effects of several polymorphisms on major adverse cardiovascular events (MACE) in patients with acute coronary syndromes (ACS) and those undergoing percutaneous coronary intervention (PCI), these genotypes account for only a small fraction of the variation and evidence is insufficient. This study aims to identify new genetic variants associated with MACE by large-scale sequencing data.

Objective

To identify the genetic variants that caused MACE.

Design

All patients in this study were allocated to dual antiplatelet therapy for up to 12 months and have the follow-up duration of 18 months.

Setting

A two-stage association study was performed.

Participants

We evaluated the associations of genetic variants and MACE in 1961 patients with ACS undergoing PCI (2009-2012), including high-depth whole exome sequencing of 168 patients in the discovery cohort and high-depth targeted sequencing of 1793 patients in the replication cohort.

Main Outcomes and Measure

The primary clinical efficacy endpoint was the major adverse cardiovascular events (MACE) composite endpoint, including cardiovascular death, myocardial infarction (MI), stroke (CT or MR scan confirmed) and repeated revascularization (RR).

Results

We discovered and confirmed six new genotypes associated with MACE in patients with ACS. Of which, rs17064642 at MYOM2 increased the risk of MACE (hazard ratio [HR] 2.76; P = 2.95 × 10-9) and reached genome-wide significance. The other five suggestive variants were KRTAP10-4 (rs201441480), WDR24 (rs11640115), ECHS1 (rs140410716), AGAP3 (rs75750968) and NECAB1 (rs74569896). Notably, the expressions of MYOM2 and ECHS1 are down-regulated in both animal models and patients with phenotypes related to MACE. Importantly, we developed the first superior classifier for predicting MACE and achieved high predictive accuracy (0.809).

Conclusions and Relevance

We identified six new genotypes associated with MACE and developed a superior classifier for predicting MACE. Our findings shed light on the pathogenesis of cardiovascular outcomes and may help clinician to make decision on the therapeutic intervention for ACS patients.

Trial Registration

This study has been registered in the Chinese Clinical Trial Registry (http://www.chictr.org.cn, Registration number: ChiCTR-OCH-11001198).
Learning Gene Networks Underlying Clinical Phenotypes Using SNP Perturbations
Authors: McCarter Calvin , Howrylak Judie , Kim Seyoung
Published: September 2018

Recent technologies are generating an abundance of genome sequence data and molecular and clinical phenotype data, providing an opportunity to understand the genetic architecture and molecular mechanisms underlying diseases. Previous approaches have largely focused on the co-localization of single-nucleotide polymorphisms (SNPs) associated with clinical and expression traits, each identified from genome-wide association studies and expression quantitative trait locus (eQTL) mapping, and thus have provided only limited capabilities for uncovering the molecular mechanisms behind the SNPs influencing clinical phenotypes. Here we aim to extract rich information on the functional role of trait-perturbing SNPs that goes far beyond this simple co-localization. We introduce a computational framework called Perturb-Net for learning the gene network that modulates the influence of SNPs on phenotypes, using SNPs as naturally occurring perturbation of a biological system. Perturb-Net uses a probabilistic graphical model to directly model both the cascade of perturbation from SNPs to the gene network to the phenotype network and the network at each layer of molecular and clinical phenotypes. Perturb-Net learns the entire model by solving a single optimization problem with an extremely fast algorithm that can analyze human genome-wide data within a few hours. In our analysis of asthma data, for a locus that was previously implicated in asthma susceptibility but for which little is known about the molecular mechanism underlying the association, Perturb-Net revealed the gene network modules that mediate the influence of the SNP on asthma phenotypes. Many genes in this network module were well supported in the literature as asthma-related.
Transmission mode is associated with environment type and taxa across bacteria-eukaryote symbioses
Authors: Russell Shelbi L
Published: September 2018

Symbiotic associations between bacteria and eukaryotes exhibit a range of transmission strategies. Anecdotal observations suggest that symbionts of terrestrial hosts tend to be strictly vertically inherited through host tissues, whereas symbionts of marine hosts tend towards horizontal transmission. Aside from a few cursory investigations, the rates and distributions of transmission modes have not been investigated in depth across associations, despite the consequences for symbiont and host evolution. To address this empirically and estimate the rate of each mode, I compiled data from the literature and for associations between transmission mode and the environment, transmission route, symbiont function, and taxa involved in the symbiosis. Of the 441 analyzed symbioses, 50.1% were strictly vertically transmitted, 34.0% exhibited some form of mixed mode transmission, and 15.9% were strictly horizontally transmitted. Binning symbioses by their environment revealed a significant skew towards vertical transmission on land and horizontal transmission in aquatic environments, with mixed modes abundant in both. However, host and symbiont taxa were not randomly distributed, which prevented the full separation of these variables. Overall, the data suggest that many symbiotic taxa are capable of horizontal transmission and barriers exist that reduce the rate of these events. Thus, both the environment type and host/symbiont taxa combined influence symbiont transmission mode evolution.

One sentence summary

Through an intensive analysis of the literature on symbiosis transmission modes, estimated rates for each transmission mode were calculated, revealing bias for horizontal transmission in the ocean and vertical transmission on land.