bluuebunny/crossref_metadata_2025 huggingface dataset:
Expression-based prediction of human essential genes and candidate lncRNAs in cancer cells
Authors: Kuang Shuzhen , Wei Yanzhang , Wang Liangjiang
Published: August 2020

Motivation

Essential genes are required for the reproductive success at either cellular or organismal level. The identification of essential genes is important for understanding the core biological processes and identifying effective therapeutic drug targets. However, experimental identification of essential genes is costly, time consuming and labor intensive. Although several machine learning models have been developed to predict essential genes, these models are not readily applicable to lncRNAs. Moreover, the currently available models cannot be used to predict essential genes in a specific cancer type.

Results

In this study, we have developed a new machine learning approach, XGEP (eXpression-based Gene Essentiality Prediction), to predict essential genes and candidate lncRNAs in cancer cells. The novelty of XGEP lies in the utilization of relevant features derived from the TCGA transcriptome dataset through collaborative embedding. When evaluated on the pan-cancer dataset, XGEP was able to accurately predict human essential genes and achieve significantly higher performance than previous models. Notably, several candidate lncRNAs selected by XGEP are reported to promote cell proliferation and inhibit cell apoptosis. Moreover, XGEP also demonstrated superior performance on cancer-type-specific datasets to identify essential genes. The comprehensive lists of candidate essential genes in specific cancer types may be used to guide experimental characterization and facilitate the discovery of drug targets for cancer therapy.

Availability and implementation

The source code and datasets used in this study are freely available at https://github.com/BioDataLearning/XGEP.

Supplementary information

Supplementary data are available at Bioinformatics online.
Rapid Antiretroviral Therapy Among Individuals With Acute and Early HIV
Authors: Martin Thomas C S , Abrams Matthew , Anderson Christy , Little Susan J
Published: August 2020

HIV transmission is increased during acute and early HIV (AEH). Rapid antiretroviral therapy may shorten the duration of infectivity. We show rapid antiretroviral therapy in AEH is acceptable and effective, with 69.0% of participants starting ART within 7 days of HIV diagnosis disclosure, and 88.1% achieving suppression by 48 weeks.
Left ventricular thrombus on cardiovascular magnetic resonance imaging in non-ischaemic cardiomyopathy
Authors: Hooks Matthew , Okasha Osama , Velangi Pratik S , Nijjar Prabhjot S , Farzaneh-Far Afshin , Shenoy Chetan
Published: August 2020

Aims

Case reports have described left ventricular (LV) thrombus in patients with non-ischaemic cardiomyopathy (NICM). We aimed to systematically study the characteristics, predictors, and outcomes of LV thrombus in NICM.

Methods and results

Forty-eight patients with LV thrombus detected on late gadolinium enhancement cardiovascular magnetic resonance imaging (LGE CMR) in NICM were compared with 124 patients with LV thrombus in ischaemic cardiomyopathy (ICM), and 144 matched patients with no LV thrombus in NICM. The performance of echocardiography for the detection of LV thrombus was compared between NICM and ICM. The 12-month incidence of embolism was compared between the three study groups. Independent predictors of LV thrombus in NICM were LV ejection fraction (LVEF) [hazard ratio (HR) 1.36 per 5% decrease; P = 0.002], LGE presence (HR 6.30; P < 0.001), and LGE extent (HR 1.33 per 5% increase; P = 0.001). Compared with patients with LV thrombus in ICM, those with LV thrombus in NICM had a 10-fold higher prevalence of thrombi in other cardiac chambers. The performance of echocardiography for the detection of LV thrombus was not different between NICM and ICM. The 12-month incidence of embolism associated with LV thrombus was not different between NICM and ICM (8.7% vs. 6.8%; P = 0.69) but both were higher compared with no LV thrombus in NICM (1.5%).

Conclusion

Independent predictors of LV thrombus in NICM were lower LVEF, LGE presence, and greater LGE extent. The 12-month incidence of embolism associated with LV thrombus in NICM was not different compared with LV thrombus in ICM.
Beyond the ‘Sham’ Critique and the Narrative of Humanitarianism: A Rejoinder to Jochen von Bernstorff
Authors: Benvenisti Eyal , Lustig Doreen
Published: August 2020

We are very grateful to Professor von Bernstorff for taking the trouble to read and comment on our article,1 which is a segment of a larger research project. His feedback will be invaluable in taking this project successfully to its next stage. While we could not address each and every aspect of his critique, the following response addresses four elements: the assertion that we argued that international humanitarian law (IHL) is merely a sham; his description of our historical approach as focused on the domestic; the ramifications of our historical analysis for future interpretation of IHL; and the challenge of one’s Vorverständnis to historical research.
On the helicity characteristics and induced emf of magnetic-Coriolis wave packets
Authors: McDermott B R , Davidson P A
Published: August 2020

In a rapidly rotating Boussinesq fluid, buoyant anomalies radiate low-frequency inertial wave packets that disperse along the rotation axis. The wave packets lead to axially elongated vortices, which propagate negative (positive) kinetic helicity upwards (downwards) with respect to the rotation vector. The kinetic helicity carried by the inertial wave packets is near-maximal relative to the velocity and vorticity fields. In classical mean-field theory, kinetic helicity is often associated with the α-effect, which is thought to be an important ingredient for planetary dynamos. The modification of inertial wave packets in the presence of a transverse uniform magnetic field is investigated here, motivated by small-scale dynamics in planetary cores, where a large-scale magnetic field affects fluid motions. We study numerically the dispersion of wave packets from an isolated buoyant source and from a random layer of buoyant anomalies, while varying the Lehnert number Le—the ratio of the frequencies of Alfvén and inertial waves. We find that for Le < 0.1, the vortices are columnar and continue to segregate kinetic helicity so that it is negative (positive) above (below) the buoyant source. Importantly, the wave packets induce an α-effect, which remains strong and coherent for Earth-like values of the Lehnert number (Le < 0.1). The interaction of wave packets emitted by multiple neighbouring buoyant sources results in an α-effect that is stronger than the α-effect induced by wave packets launched from an isolated buoyant source, and we provide an analytical explanation for this. The coherence of the α-effect induced by the wave packets, for Earth-like values of the Lehnert number, lends support to the α2 dynamo model driven by helical waves.
Petrophysically and geologically guided multi-physics inversion using a dynamic Gaussian mixture model
Authors: Astic Thibaut , Heagy Lindsey J , Oldenburg Douglas W
Published: August 2020

In a previous paper, we introduced a framework for carrying out petrophysically and geologically guided geophysical inversions. In that framework, petrophysical and geological information is modelled with a Gaussian mixture model (GMM). In the inversion, the GMM serves as a prior for the geophysical model. The formulation and applications were confined to problems in which a single physical property model was sought, and a single geophysical data set was available. In this paper, we extend that framework to jointly invert multiple geophysical data sets that depend on multiple physical properties. The petrophysical and geological information is used to couple geophysical surveys that, otherwise, rely on independent physics. This requires advancements in two areas. First, an extension from a univariate to a multivariate analysis of the petrophysical data, and their inclusion within the inverse problem, is necessary. Secondly, we address the practical issues of simultaneously inverting data from multiple surveys and finding a solution that acceptably reproduces each one, along with the petrophysical and geological information. To illustrate the efficacy of our approach and the advantages of carrying out multi-physics inversions coupled with petrophysical and geological information, we invert synthetic gravity and magnetic data associated with a kimberlite deposit. The kimberlite pipe contains two distinct facies embedded in a host rock. Inverting the data sets individually, even with petrophysical information, leads to a binary geological model: background or undetermined kimberlite. A multi-physics inversion, with petrophysical information, differentiates between the two main kimberlite facies of the pipe. Through this example, we also highlight the capabilities of our framework to work with interpretive geological assumptions when minimal quantitative information is available. In those cases, the dynamic updates of the GMM allow us to perform multi-physics inversions by learning a petrophysical model.
Green windows of opportunity: latecomer development in the age of transformation toward sustainability
Authors: Lema Rasmus , Fu Xiaolan , Rabellotti Roberta
Published: August 2020

The world is in the early stages of a paradigm transition toward a global green economy. In this article, we propose the notion of green windows of opportunity, highlighting the importance of institutional changes in the creation of new opportunities for latecomer development. We emphasize how demand and mission-guided technical change influence the directionality of latecomer development and highlight the important role emerging economies may attain in the global green transformation. We provide important insights regarding opportunities for green development in emerging economies, how these opportunities emerge in different renewable energy sectors and their implications for the global green economy.
Early-life antibiotic use and risk of attention-deficit hyperactivity disorder and autism spectrum disorder: results of a discordant twin study
Authors: Slob Elise M A , Brew Bronwyn K , Vijverberg Susanne J H , Dijs Talitha , van Beijsterveldt Catharina E M , Koppelman Gerard H , Bartels Meike , Dolan Conor V , Larsson Henrik , Lundström Sebastian , Lichtenstein Paul , Gong Tong , Maitland-van der Zee Anke H , Kraneveld Aletta D , Almqvist Catarina , Boomsma Dorret I
Published: August 2020

Background

Development of the gut-brain axis in early life may be disturbed by antibiotic use. It has been hypothesized that this disturbance may contribute to development of neurodevelopmental disorders, including autism spectrum disorder and attention-deficit hyperactivity disorder. We aimed to assess the association between antibiotic use in early life and the risk of developing attention-deficit hyperactivity disorder or autism spectrum disorder, while controlling for shared genetic and environmental factors in a discordant twin design.

Methods

We conducted a cohort study in twins (7–12 years; 25 781 twins) from the Netherlands Twin Register (NTR) and a replication study in the Childhood and Adolescent Twin Study in Sweden (CATSS; 7946 9-year-old twins). Antibiotic use was recorded before age 2 years. Attention-deficit hyperactivity disorder and autism spectrum disorder were parent-reported in the Netherlands Twin Register and register-based in the Childhood and Adolescent Twin Study in Sweden.

Results

Early-life antibiotic use was associated with increased risk of attention-deficit hyperactivity disorder development [pooled odds ratio (OR) 1.10, 95% confidence interval (CI) 1.02-1.17] and autism spectrum disorder (pooled OR 1.15, 95% CI 1.06-1.25) in a case-control design. When restricting to monozygotic twin pairs discordant for the outcome, associations disappeared for both disorders in both cohorts (attention-deficit hyperactivity disorder OR 0.90, 95% CI 0.48-1.69 and OR 0.80, 95% CI 0.37-1.76, and autism spectrum disorder OR 0.66, 95% CI 0.38-1.16 and OR 0.29, 95% CI 0.02-4.50, respectively).

Conclusions

Our findings suggest that the association between early-life antibiotic use and risk of attention-deficit hyperactivity and autism spectrum disorder may be confounded by shared familial environment and genetics.
Multisectoral Approach to Address Chikungunya Outbreaks Driven by Human Mobility: A Systematic Review and Meta-Analysis
Authors: Abdul-Ghani Rashad , Fouque Florence , Mahdy Mohammed A K , Zhong Qingxia , Al-Eryani Samira M A , Alkwri Abdulsamad , Beier John C
Published: August 2020

Background

The role of human mobility in the epidemiology of emerging Aedes-transmitted viral diseases is recognized but not fully understood. The objective of this systematic review and meta-analysis was to examine how human mobility patterns are driving chikungunya outbreaks.

Methods

Literature was systematically reviewed for studies on chikungunya prevalence in countries/territories with high-level evidence of human mobility-driven outbreaks, based on: (1) emergence of chikungunya outbreaks with epidemic chikungunya virus genotypes among displaced/migrant populations and their hosting communities; and (2) identification of imported index case(s) with epidemic genotypes phylogenetically related to the genotypes circulating during emerging or subsequent outbreaks.

Results

The meta-analysis of extracted prevalence data revealed that a large proportion of the population in countries/territories afflicted by outbreaks is still at risk of infection during future outbreaks. On the other hand, approximately one-half of suspected chikungunya cases could be infected with other co-circulating acute febrile illnesses.

Conclusions

We discussed in this paper how human mobility-driven chikungunya outbreaks can be addressed, and how the involvement of several sectors in addition to the health sector in multisectoral approaches (MSAs) is important for prevention and control of chikungunya and other Aedes-transmitted arboviral outbreaks.
The Politics of Aspiration
Authors: Finnemore Martha , Jurkovich Michelle
Published: August 2020

Aspiration is an essential component of politics. It articulates goals, affirms identities and values, and structures action at all levels of social life. Yet political scientists have spent little time theorizing aspiration—what it is, how it relates to other concepts, and the kinds of effects it creates. In this article, we develop the concept theoretically and argue that aspiration creates a distinct “aspirational politics” that differs from our international relations models of both norm-driven social activism and interest-driven rational choice. We identify three core features of aspiration that undergird its theoretical utility: lofty goals, change over time, and transformation through imagination. In the hands of skilled political actors, aspiration does essential work in both facilitating agreement and mobilizing social action that create change in the world. However, aspiration also has a dark side and can be manipulated to dodge accountability, postpone action, and serve private, rather than public, goals.
In vivopharmacodynamics of new-generation β-lactamase inhibitor taniborbactam (formerly VNRX-5133) in combination with cefepime against serine-β-lactamase-producing Gram-negative bacteria
Authors: Abdelraouf Kamilia , Almarzoky Abuhussain Safa , Nicolau David P
Published: August 2020

Objectives

Cefepime/taniborbactam is a cephalosporin/cyclic boronate β-lactamase inhibitor combination under development for the treatment of infections due to MDR Enterobacterales and Pseudomonas aeruginosa. Using a neutropenic murine thigh infection model, we aimed to determine the pharmacokinetic/pharmacodynamic index, relative to taniborbactam exposure, that correlated most closely with the efficacy of the cefepime/taniborbactam combination and the magnitude of index required for efficacy against serine-β-lactamase-producing strains.

Methods

Twenty-six clinical Enterobacterales (expressing ESBLs, plasmid-mediated AmpC and/or carbapenemases of classes A or D; cefepime/taniborbactam combination MICs 0.06–16 mg/L) and 11 clinical P. aeruginosa (AmpC overproducing or KPC expressing; cefepime/taniborbactam combination MICs 1–16 mg/L) were evaluated. A cefepime human-simulated regimen (HSR) equivalent to a clinical dose of 2 g q8h as a 2 h infusion was given in combination with taniborbactam for 24 h. For a subset of P. aeruginosa isolates, a sub-therapeutic cefepime exposure was utilized.

Results

Dose-fractionation studies revealed that dosing frequency had no impact on taniborbactam potentiation of cefepime activity. Relative to the initial bacterial burden, the median taniborbactam fAUC0–24/MIC associated with 1 log kill in combination with the cefepime HSR for Enterobacterales and P. aeruginosa isolates was 2.62 and 0.46, respectively. In combination with sub-therapeutic cefepime, the median taniborbactam fAUC0–24/MIC associated with 1 and 2 log kill against AmpC-overproducing P. aeruginosa was 2.00 and 3.30, respectively, relative to the bacterial burden in the cefepime-treated groups. The taniborbactam HSR (equivalent to 0.5 g q8h as a 2 h infusion) was adequate to attain ≥1 log reduction against all test isolates.

Conclusions

Our data show that the cefepime/taniborbactam combination (2 g/0.5 g q8h as a 2 h infusion) exerts potent in vivo activity against cefepime-resistant isolates, including serine-carbapenemase producers.
Determining sample size and length of follow-up for smartphone-based digital phenotyping studies
Authors: Barnett Ian , Torous John , Reeder Harrison T , Baker Justin , Onnela Jukka-Pekka
Published: August 2020

Objective

Studies that use patient smartphones to collect ecological momentary assessment and sensor data, an approach frequently referred to as digital phenotyping, have increased in popularity in recent years. There is a lack of formal guidelines for the design of new digital phenotyping studies so that they are powered to detect both population-level longitudinal associations as well as individual-level change points in multivariate time series. In particular, determining the appropriate balance of sample size relative to the targeted duration of follow-up is a challenge.

Materials and Methods

We used data from 2 prior smartphone-based digital phenotyping studies to provide reasonable ranges of effect size and parameters. We considered likelihood ratio tests for generalized linear mixed models as well as for change point detection of individual-level multivariate time series.

Results

We propose a joint procedure for sequentially calculating first an appropriate length of follow-up and then a necessary minimum sample size required to provide adequate power. In addition, we developed an accompanying accessible sample size and power calculator.

Discussion

The 2-parameter problem of identifying both an appropriate sample size and duration of follow-up for a longitudinal study requires the simultaneous consideration of 2 analysis methods during study design.

Conclusion

The temporally dense longitudinal data collected by digital phenotyping studies may warrant a variety of applicable analysis choices. Our use of generalized linear mixed models as well as change point detection to guide sample size and study duration calculations provide a tool to effectively power new digital phenotyping studies.
Assessment of three-dimensional acetabular coverage angles
Authors: Upasani Vidyadhar V , Bomar James D , Bandaralage Harsha , Doan Joshua D , Farnsworth Christine L
Published: August 2020

The purpose of this article is to report the inter- and intra-observer reliability of a computerized objective technique to quantify patient-specific acetabular morphology. We describe the use of and provide the software code for a technique to better define the location and magnitude of acetabular pathology. We have developed software code that allows the end user to obtain detailed measurements of the acetabulum using traditional computed tomography data. We provide the code and detailed instructions on how to use it in this article. The methodology was validated by having an unbiased observer (that was not involved in this project but has been trained in this software measurement methodology) to perform the entire acquisition, reconstruction and analysis procedure and compare their measurements to the measurements of one of the authors. The author then repeated the procedure 2 months later to determine intra-observer reliability. Inter- and intra-observer reliability for version, tilt, surface area and total acetabular coverage angles ranged from an intra-class correlation coefficient of 0.805 to 0.997. The method provided in this manuscript gives a reproducible objective assessment of three-dimensional (3D) acetabular morphology that can be used to assist in the diagnosis of hip pathology and to compare the morphological parameters of subjects with and without hip pathology. It allows a surgeon to understand the 3D shape of each individual’s acetabulum, share these findings with patients and their parents to demonstrate the magnitude and location of the clinical abnormality and perform patient-specific surgical corrections to optimize the shape and coverage of the hip.
A new species of Rhagomys (Rodentia, Sigmodontinae) from southeastern Ecuador
Authors: Moreno Cárdenas Pablo A , Tinoco Nicolás , Albuja Luis , Patterson Bruce D
Published: August 2020

During a faunal survey in the foothills of the Ecuadoran Andes southwest of the Cordillera del Cóndor, a mouse of uncertain affinities was taken in a fishing net. Various external characters suggested that it was a member of the genus Rhagomys, previously unrecorded in Ecuador. Comparisons with the external, cranial, and dental morphology both of Rhagomys rufescens and R. longilingua identified a number of unique characters, including its long, narrow rostrum and incisive foramina and the reduced anterolingual conule on its M1 procingulum. We describe the mouse as a new species of Rhagomys; both its morphology and molecular analyses suggest that it is sister to R. longilingua. This record of Rhagomys in southern Ecuador extends the known distribution of the genus 700 km northward and adds yet another genus and species to Ecuador’s extensive list of rodent species.
Powering galactic superwinds with small-scale AGN winds
Authors: Costa Tiago , Pakmor Rüdiger , Springel Volker
Published: August 2020

We present a new implementation for active galactic nucleus (AGN) feedback through small-scale, ultrafast winds in the moving-mesh hydrodynamic code arepo. The wind is injected by prescribing mass, momentum, and energy fluxes across a spherical boundary centred on a supermassive black hole according to available constraints for accretion disc winds. After sweeping-up a mass equal to their own, small-scale winds thermalize, powering energy-driven outflows with dynamics, structure, and cooling properties in excellent agreement with those of analytic wind solutions. Momentum-driven solutions do not easily occur, because the Compton cooling radius is usually much smaller than the free-expansion radius of the small-scale winds. Through various convergence tests, we demonstrate that our implementation yields wind solutions, which are well converged down to the typical resolution achieved in cosmological simulations. We test our model in hydrodynamic simulations of isolated Milky Way – mass galaxies. Above a critical AGN luminosity, initially spherical, small-scale winds power bipolar, energy-driven superwinds that break out of the galactic nucleus, flowing at speeds $\gt 1000 \rm \, km \, s^{-1}$ out to $\sim 10 \, \rm kpc$. These energy-driven outflows result in moderate, but long-term, reduction in star formation, which becomes more pronounced for higher AGN luminosities and faster small-scale winds. Suppression of star formation proceeds through a rapid mode that involves the removal of the highest density, nuclear gas, and through a slower mode that effectively halts halo gas accretion. Our new implementation makes it possible to model AGN-driven winds in a physically meaningful and validated way in simulations of galaxy evolution, the interstellar medium and black hole accretion flows.
Profiling astrophysically relevant MgC4H chains. An attempt to aid astronomical observations
Authors: Bâldea Ioan
Published: August 2020

In this paper, we report results of an extensive theoretical study on MgC4H chains conducted at DFT and CCSD(T) levels motivated by the recent discovery of this species in IRC+10216. A detailed characterization of both neutral and charged species is presented, which include structural, chemical bonding and vibrational properties, rotational, centrifugal distortion and Watson l-type doubling constants, dipole moments, Fermi contact, and spin-rotation constants. In addition, we present ab initio estimates needed for subsequent astrochemical evolution modelling (e.g. dissociation energies, acidity, electron attachment, and ionization energies and related chemical reactivity indices). Possible formation pathways are also discussed. They comprise exchange, (radiative) association, dissociative recombination, and ion neutralization reactions. As an important result aiming at stimulating further observational searching, we suggest that MgC4H− anions should also be observable via rovibrational spectroscopy. The reason is twofold: (i) Neutral MgC4H0 chains possess a sufficiently large dipole moment consistent with dipole-bound anion states and large electron attachment cross-sections. (ii) MgC4H− anions possess a dipole substantially larger than MgC4H0 neutrals (and also larger than that estimated earlier for the longest astronomically detected C8H− anion). This makes MgC4H− anion intensities in rovibrational spectrum experimentally accessible even in the unlikely case of a relative abundance MgC4H−/MgC4H0 comparable to that of CH4, whose anion has the lowest relative abundance observed so far in space because weakly polar C4H0 chains do not support dipole-bound anion states. A suggestion on why, counterintuitively, the MgC2H abundance found in IRC+10216 was lower than that of the longer MgC4H is also presented.
New methods for identifying Lyman continuum leakers and reionization-epoch analogues
Authors: Katz Harley , Ďurovčíková Dominika , Kimm Taysun , Rosdahl Joki , Blaizot Jeremy , Haehnelt Martin G , Devriendt Julien , Slyz Adrianne , Ellis Richard , Laporte Nicolas
Published: August 2020

Identifying low-redshift galaxies that emit Lyman continuum radiation (LyC leakers) is one of the primary, indirect methods of studying galaxy formation in the epoch of reionization. However, not only has it proved challenging to identify such systems, it also remains uncertain whether the low-redshift LyC leakers are truly ‘analogues’ of the sources that reionized the Universe. Here, we use high-resolution cosmological radiation hydrodynamics simulations to examine whether simulated galaxies in the epoch of reionization share similar emission line properties to observed LyC leakers at z ∼ 3 and z ∼ 0. We find that the simulated galaxies with high LyC escape fractions (fesc) often exhibit high O32 and populate the same regions of the R23–O32 plane as z ∼ 3 LyC leakers. However, we show that viewing angle, metallicity, and ionization parameter can all impact where a galaxy resides on the O32–fesc plane. Based on emission line diagnostics and how they correlate with fesc, lower metallicity LyC leakers at z ∼ 3 appear to be good analogues of reionization-era galaxies. In contrast, local [S ii]-deficient galaxies do not overlap with the simulated high-redshift LyC leakers on the S ii Baldwin–Phillips–Terlevich (BPT) diagram; however, this diagnostic may still be useful for identifying leakers. We use our simulated galaxies to develop multiple new diagnostics to identify LyC leakers using infrared and nebular emission lines. We show that our model using only [C ii]158 μm and [O iii]88 μm can identify potential leakers from non-leakers from the local Dwarf Galaxy Survey. Finally, we apply this diagnostic to known high-redshift galaxies and find that MACS 1149_JD1 at z = 9.1 is the most likely galaxy to be actively contributing to the reionization of the Universe.
The collapse and expansion regimes of photoevaporated clumps
Authors: Raga A C , Cantó J , Estrella-Trujillo D , Velázquez P F
Published: August 2020

We present a model for dense clumps in photoionized regions in the ‘cometary plasmon’ regime. We consider that as these plasmons accelerate outwards from the external ionizing photon source (as a result of the back-reaction of the photoevaporated wind from the clumps), they move into regions of decreasing external ionizing photon fluxes (resulting from the geometrical dilution of the ionizing radiation, and possibly also from absorption due to intervening material). We find the presence of two regimes: a ‘vanishing plasmon’ regime, in which the clump rapidly accelerates, compresses, and becomes fully photoionized without travelling far from the photon source, and an ‘expanding plasmon’ regime, in which the clump travels over a considerable radial domain, and expands as a result of the lower impinging ionizing photon fluxes (before eventually decreasing in size and becoming fully photoionized). Interestingly, the cometary clumps of the Helix nebula are at the boundary between these two regimes, and therefore correspond to clumps that travel over a relatively extended radial domain while keeping an approximately constant size.
The effect of differential accretion on the gravitational wave background and the present-day MBH binary population
Authors: Siwek Magdalena S , Kelley Luke Zoltan , Hernquist Lars
Published: August 2020

Massive black hole binaries (MBHBs) form as a consequence of galaxy mergers. However, it is still unclear whether they typically merge within a Hubble time, and how accretion may affect their evolution. These questions will be addressed by pulsar timing arrays (PTAs), which aim to detect the gravitational wave (GW) background (GWB) emitted by MBHBs during the last Myr of inspiral. Here, we investigate the influence of differential accretion on MBHB merger rates, chirp masses, and the resulting GWB spectrum. We evolve an MBHB sample from the Illustris hydrodynamic cosmological simulation using semi-analytical models and for the first time self-consistently evolve their masses with binary accretion models. In all models, MBHBs coalesce with median total masses up to 1.5 × 108 M⊙, up to 3−4 times larger than in models neglecting accretion. In our model with the largest plausible impact, the median mass ratio of coalescing MBHBs increases by a factor 3.6, the coalescence rate by $52.3{{\ \rm per\ cent}}$, and the GWB amplitude by a factor 4.0, yielding a dimensionless GWB strain $A_{yr^{-1}} = 1 \times 10^{-15}$. Our model that favours accretion on to the primary MBH reduces the median mass ratio of coalescing MBHBs by a factor of 2.9, and yields a GWB amplitude $A_{yr^{-1}} = 3.1 \times 10^{-16}$. This is nearly indistinguishable from our model neglecting accretion, despite higher MBHB masses at coalescence. We further predict binary separation and mass ratio distributions of stalled MBHBs in the low-redshift Universe, and find that these depend sensitively on binary accretion models. This presents the potential for combined electromagnetic and GW observational constraints on merger rates and accretion models of MBHB populations.
Remdesivir Use Compared With Supportive Care in Hospitalized Patients With Severe COVID-19: A Single-Center Experience
Authors: Kalligeros Markos , Tashima Karen T , Mylona Evangelia K , Rybak Natasha , Flanigan Timothy P , Farmakiotis Dimitrios , Beckwith Curt G , Sanchez Martha , Neill Marguerite , Johnson Jennie E , Garland Joseph M , Aung Su , Byrd Katrina M , O’Brien Thomas , Pandita Aakriti , Aridi Jad , Macias Gil Raul , Larkin Jerome , Shehadeh Fadi , Mylonakis Eleftherios
Published: August 2020

Background

The US Food and Drug Administration issued an Emergency Use Authorization for remdesivir use in patients with severe COVID-19.

Methods

We utilized data from 2 quaternary acute care hospitals. The outcomes of interest were the impact of remdesivir on in-hospital death by day 28 and time to recovery, clinical improvement, and discharge. We utilized Cox proportional hazards models and stratified log-rank tests.

Results

Two hundred twenty-four patients were included in the study. The median age was 59 years; 67.0% were male; 17/125 patients (13.6%) who received supportive care and 7/99 patients (7.1%) who received remdesivir died. The unadjusted risk for 28-day in-hospital death was lower for patients who received remdesivir compared with patients who received supportive care (hazard ratio [HR], 0.42; 95% CI, 0.16–1.08). Although this trend remained the same after adjusting for age, sex, race, and oxygen requirements on admission (adjusted HR [aHR], 0.49; 95% CI, 0.19–1.28), as well as chronic comorbidities and use of corticosteroids (aHR, 0.44; 95% CI, 0.16–1.23), it did not reach statistical significance. The use of remdesivir was not associated with an increased risk of acute kidney injury (AKI) or liver test abnormalities. Although not statistically significant, the rate ratios for time to recovery, clinical improvement, and discharge were higher in women and black or African American patients.

Conclusions

Patients on remdesivir had lower, albeit not significant, all-cause in-hospital mortality, and the use of remdesivir did not increase the risk for AKI. Promising signals from this study need to be confirmed by future placebo-controlled randomized clinical trials.
Musical Canons
Authors: Weber William
Published: August 2020

This chapter analyzes the process by which separate musical canons emerged during the nineteenth century, dividing musical culture along lines still in existence today. Musical life expanded in both economic and aesthetic terms, creating a set of separate worlds governed by contrasting taste and cultural authority: orchestral and chamber music; operas in contrasting genres; and popular songs sung in public and private contexts. These cultural worlds developed separate canons and canonic repertories which interacted through competing ideologies. The opera world, which emerged as the main economic base of musical life, ended up focused on a repertory of old works in diverse genres. The classical music world took higher ground intellectually, with concerts by orchestras, string quartets, and vocal or instrumental. Popular music concerts related closely with the opera world, but developed their own events in the English music halls, French café-concerts, and German Variety shows.
Costa Rica
Authors: Molina Iván
Published: August 2020

From 1840 to the present, Costa Rica has sharedsimilar historical processes with its Central American neighbors, but differed from them by consolidating a stable democracy. The Costa Rican dominant groups never had the resources or sufficient means to subjugate the middle classes or the popular sectors, whose demands for policies that satisfied their interests shaped very early a culture and a state prone to social reform. In the long term, this modernizing trend played in favor of the social and cultural inclusion of the population, the reduction of inequalities, and the legitimacy of the political system.
Post-Executive Activities
Authors: Musella Fortunato
Published: August 2020

This chapter will focus on political careers of executive members after the end of their term in office, with particular reference to political leaders. After reviewing literature on post-executive political career, it will focus on more recent research directions in this field: (a) the attempt to extend the number of empirical observations by assuming systematic and large-N comparative research; (b) the move from an empiricist-individualistic conception of career patterns to an institutional one; (c) the investigation on new politics-market linkages in democratic regimes coming from the new activism of former leaders. Jointly considering these lines, the final part of the chapter will be devoted to delineate some lines of future research agenda on post-executive patterns and raise crucial questions concerning representative regimes.
CO Multi-line Imaging of Nearby Galaxies (COMING). X. Physical conditions of molecular gas and the local SFR–mass relation
Authors: Morokuma-Matsui Kana , Sorai Kazuo , Sato Yuya , Kuno Nario , Takeuchi Tsutomu T , Salak Dragan , Miyamoto Yusuke , Yajima Yoshiyuki , Muraoka Kazuyuki , Kaneko Hiroyuki
Published: August 2020

We investigate the molecular gas properties of galaxies across the main sequence of star-forming (SF) galaxies in the local Universe using 12CO(J = 1–0), hereafter 12CO, and 13CO(J = 1–0), hereafter 13CO, mapping data of 147 nearby galaxies obtained in the COMING project, a legacy project of the Nobeyama Radio Observatory. In order to improve the signal-to-noise ratios of both lines, we stack all the pixels where 12CO emission is detected after aligning the line center expected from the first-moment map of 12CO. As a result, 13CO emission is successfully detected in 80 galaxies with a signal-to-noise ratio larger than three. The error-weighted mean of the integrated-intensity ratio of 12CO to 13CO lines (R1213) of the 80 galaxies is 10.9, with a standard deviation of 7.0. We find that (1) R1213 positively correlates to specific star-formation rate (sSFR) with a correlation coefficient of 0.46, and (2) both the flux ratio of IRAS 60 μm to 100 μm (f60/f100) and the inclination-corrected linewidth of 12CO stacked spectra ($\sigma _{{\rm ^{12}CO},i}$) also correlate with sSFR for galaxies with the R1213 measurement. Our results support the scenario where R1213 variation is mainly caused by changes in molecular gas properties such as temperature and turbulence. The consequent variation of the CO-to-H2 conversion factor across the SF main sequence is not large enough to completely extinguish the known correlations between sSFR and Mmol/Mstar (μmol) or star-formation efficiency (SFE) reported in previous studies, while this variation would strengthen (weaken) the sSFR–SFE (sSFR–μmol) correlation.
Disentangling Sources of Gene Tree Discordance in Phylogenomic Data Sets: Testing Ancient Hybridizations in Amaranthaceae s.l
Authors: Morales-Briones Diego F , Kadereit Gudrun , Tefarikis Delphine T , Moore Michael J , Smith Stephen A , Brockington Samuel F , Timoneda Alfonso , Yim Won C , Cushman John C , Yang Ya
Published: August 2020

Gene tree discordance in large genomic data sets can be caused by evolutionary processes such as incomplete lineage sorting and hybridization, as well as model violation, and errors in data processing, orthology inference, and gene tree estimation. Species tree methods that identify and accommodate all sources of conflict are not available, but a combination of multiple approaches can help tease apart alternative sources of conflict. Here, using a phylotranscriptomic analysis in combination with reference genomes, we test a hypothesis of ancient hybridization events within the plant family Amaranthaceae s.l. that was previously supported by morphological, ecological, and Sanger-based molecular data. The data set included seven genomes and 88 transcriptomes, 17 generated for this study. We examined gene-tree discordance using coalescent-based species trees and network inference, gene tree discordance analyses, site pattern tests of introgression, topology tests, synteny analyses, and simulations. We found that a combination of processes might have generated the high levels of gene tree discordance in the backbone of Amaranthaceae s.l. Furthermore, we found evidence that three consecutive short internal branches produce anomalous trees contributing to the discordance. Overall, our results suggest that Amaranthaceae s.l. might be a product of an ancient and rapid lineage diversification, and remains, and probably will remain, unresolved. This work highlights the potential problems of identifiability associated with the sources of gene tree discordance including, in particular, phylogenetic network methods. Our results also demonstrate the importance of thoroughly testing for multiple sources of conflict in phylogenomic analyses, especially in the context of ancient, rapid radiations. We provide several recommendations for exploring conflicting signals in such situations. [Amaranthaceae; gene tree discordance; hybridization; incomplete lineage sorting; phylogenomics; species network; species tree; transcriptomics.]
Transcranial Alternating Current Stimulation of the Primary Motor Cortex after Skill Acquisition Improves Motor Memory Retention in Humans: A Double-Blinded Sham-Controlled Study
Authors: Yamaguchi Tomofumi , Svane Christian , Forman Christian Riis , Beck Mikkel Malling , Geertsen Svend Sparre , Lundbye-Jensen Jesper , Nielsen Jens Bo
Published: August 2020

Consolidation leading to retention of motor memory following motor practice involves activity-dependent plastic processes in the corticospinal system. To investigate whether beta-band transcranial alternating current stimulation (tACS) applied immediately following skill acquisition can enhance ongoing consolidation processes and thereby motor skill retention 20 adults participated in a randomized, double-blinded, sham-controlled study. Participants received tACS at peak beta-band corticomuscular coherence (CMC) frequency or sham tACS for 10 min following practice of a visuomotor ankle dorsiflexion task. Performance was measured as the average percentage time on target. Electroencephalograhy (EMG) was measured at Cz and EMG from the right tibialis anterior muscle. CMC and intramuscular coherence (IMC) were estimated during 2-min tonic dorsiflexion. Motor skill retention was tested 1 and 7 days after motor practice. From the end of motor practice to the retention tests, motor performance improved more in the tACS group compared with the sham tACS group after 1 (P = 0.05) and 7 days (P < 0.001). At both retention tests, beta-band IMC increased in the tACS group compared with post-tACS. Beta-band CMC increased in the tACS group at retention day 1 compared with post-tACS. Changes in CMC but not IMC were correlated with performance 1 and 7 days following practice. This study shows that tACS applied at beta-band CMC frequency improves consolidation following visuomotor practice and increases beta-band CMC and IMC. We propose that oscillatory beta activity in the corticospinal system may facilitate consolidation of the motor skill.
Identification of Differentially Methylated miRNA Genes During Compatible and Incompatible Interactions Between Soybean and Soybean Cyst Nematode
Authors: Rambani Aditi , Hu Yanfeng , Piya Sarbottam , Long Miao , Rice J. Hollis , Pantalone Vince , Hewezi Tarek
Published: August 2020

DNA methylation is a widespread epigenetic mark that affects gene expression and transposon mobility during plant development and stress responses. However, the role of DNA methylation in regulating the expression of microRNA (miRNA) genes remains largely unexplored. Here, we analyzed DNA methylation changes of miRNA genes using a pair of soybean (Glycine max) near-isogenic lines (NILs) differing in their response to soybean cyst nematode (SCN; Heterodera glycines). Differences in global DNA methylation levels over miRNA genes in response to SCN infection were observed between the isogenic lines. miRNA genes with significant changes in DNA methylation levels in the promoter and primary transcript-coding regions were detected in both lines. In the susceptible isogenic line (NIL-S), 82 differentially methylated miRNAs were identified in response to SCN infection whereas, in the resistant isogenic line (NIL-R), only 16 differentially methylated miRNAs were identified. Interestingly, gma-miR5032, gma-miR5043, gma-miR1520b, and gma-2107-ch16 showed opposite methylation patterns in the isogenic lines. In addition, the miRNA paralogs gma-miR5770a and gma-miR5770b showed hypermethylation and hypomethylation in NIL-S and NIL-R, respectively. Gene expression quantification of gma-miR5032, gma-miR5043, gma-miR1520b, and gma-miR5770a/b and their confirmed targets indicated a role of DNA methylation in regulating miRNA expression and, thus, their targets upon SCN infection. Furthermore, overexpression of these four miRNAs in NIL-S using transgenic hairy root system enhanced plant resistance to SCN to various degrees with a key role observed for miR5032. Together, our results provide new insights into the role of epigenetic mechanisms in controlling miRNA regulatory function during SCN–soybean interactions.

[Formula: see text] Copyright © 2020 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Impaired learning and memory ability induced by a bilaterally hippocampal injection of streptozotocin in mice: involved with the adaptive changes of synaptic plasticity
Authors: Qi Congcong , Chen Xingxing , Gao Xinran , Xu Jingxian , Liu Sen , Ge Jinfang
Published: August 2020

Background

Alzheimer’s disease (AD) is a neurodegenerative disease characterized by progressive cognitive decline, psychiatric symptoms and behavioral disorders, resulting in disability and loss of self-sufficiency.

Objective

To establish an AD mice model, investigate the behavioral performance, and explore the potential mechanism.

Methods

Streptozotocin (STZ, 3 mg/kg) was microinjected bilaterally into the dorsal hippocampus of C57BL /6 mice to establish the AD model. Behavioral changes (anhedonia and despair, balance and motor coordination, locomotion, and learning and memory) were examined and the serum concentrations of insulin and nesfatin-1 were measured by ELISA. The activation of hippocampal microglia was assessed by immunohistochemistry and the protein expression of several molecular associated with the regulation of synaptic plasticity in the hippocampus and the prefrontal cortex (PFC) was detected via western blotting.

Results

The STZ model mice showed a slower bodyweight gain and higher serum concentration of insulin and nesfatin-1. Although there was no significant difference between groups with regard to the ability of balance and motor coordination, the model mice presented a decline of spontaneous movement and exploratory behavior, together with an impairment of learning and memory ability. Increased activated microglia was aggregated in the hippocampal dentate gyrus of model mice. Moreover, the protein expression of NMDAR2A, NMDAR2B, SynGAP, PSD95, BDNF, and p-β-catenin/β-catenin were remarkably decreased in the hippocampus and the PFC of model mice, and the expression of p-GSK-3β (ser9)/GSK-3β were reduced in the hippocampus.

Conclusion

A bilateral hippocampal microinjection of STZ could successfully duplicate an AD mice model, as indicated by the impaired learning and memory and the alternated synaptic plasticity, together with the hyperactive inflammatory response in the hippocampus and the imbalanced abundance of serum insulin and nesfatin-1. Apart from these, the mechanism might be associated with the imbalanced expression of the key proteins of Wnt signaling pathway in the hippocampus and the PFC.

Graphical abstract