bluuebunny/crossref_metadata_2025 huggingface dataset:
Robust chaos and the continuity of attractors
Authors: Glendinning Paul A , Simpson David J W
Published: July 2020

As the parameters of a map are varied an attractor may vary continuously in the Hausdorff metric. The purpose of this paper is to explore the continuation of chaotic attractors. We argue that this is not a helpful concept for smooth unimodal maps for which periodic windows fill parameter space densely, but that for many families of piecewise-smooth maps it provides a way to think about changing structures within parameter regions of robust chaos and form a stronger notion of robustness. We obtain conditions for the continuity of an attractor and demonstrate the results with coupled skew tent maps, the Lozi map and the border-collision normal form.
Harnessing Iron Acquisition Machinery to Target Enterobacteriaceae
Authors: Sargun Artur , Gerner Romana R , Raffatellu Manuela , Nolan Elizabeth M
Published: July 2020

Infections caused by Gram-negative bacteria can be challenging to treat due to the outer membrane permeability barrier and the increasing emergence of antibiotic resistance. During infection, Gram-negative pathogens must acquire iron, an essential nutrient, in the host. Many Gram-negative bacteria utilize sophisticated iron acquisition machineries based on siderophores, small molecules that bind iron with high affinity. In this review, we provide an overview of siderophore-mediated iron acquisition in Enterobacteriaceae and show how these systems provide a foundation for the conceptualization and development of approaches to prevent and/or treat bacterial infections. Differences between the siderophore-based iron uptake machineries of pathogenic Enterobacteriaceae and commensal microbes may lead to the development of selective “Trojan-horse” antimicrobials and immunization strategies that will not harm the host microbiota.
Expanding frontiers of risk management: care safety in nursing home during COVID-19 pandemic
Authors: Scopetti Matteo , Santurro Alessandro , Tartaglia Riccardo , Frati Paola , Fineschi Vittorio
Published: July 2020

Background

Nursing homes provide long-term care and have residential-oriented hospitalizations characterized by medical, nursing and social-care treatments for a typically geriatric population. In the current emergency phase, the problem of infections in residential structures for the elderly is taking on considerable importance in relation to the significant prevalence rates of coronavirus disease 2019 (COVID-19).

Safety improvement strategies

Prevention and control measures for severe acute respiratory syndrome coronavirus 2 infection in nursing homes should be planned before a possible outbreak of COVID-19 occurs and should be intensified during any exacerbation of the same. Each facility should identify a properly trained contact person—also external—for the prevention and control of infections, who can refer to a multidisciplinary support committee and who is in close contact with the local health authorities. The contact person should collaborate with professionals in order to prepare a prevention and intervention plan that considers national provisions and scientific evidence, the requirements for reporting patients with symptoms compatible with COVID-19 and the indications for the management of suspected, probable or confirmed cases of COVID-19.

Discussion

Adequate risk management in residential structures implies the establishment of a coordination committee with dedicated staff, the implementation of a surveillance program for the rapid recognition of the outbreaks, the identification of suitable premises and equipment, the application of universal precautions, the adaptation of care plans to reduce the possibility of contagion among residents and the protection of operators and staff training initiatives.
A genome-wide analysis of Escherichia coli responses to fosfomycin using TraDIS-Xpress reveals novel roles for phosphonate degradation and phosphate transport systems
Authors: Turner A Keith , Yasir Muhammad , Bastkowski Sarah , Telatin Andrea , Page Andrew J , Charles Ian G , Webber Mark A
Published: July 2020

Background

Fosfomycin is an antibiotic that has seen a revival in use due to its unique mechanism of action and efficacy against isolates resistant to many other antibiotics. In Escherichia coli, fosfomycin often selects for loss-of-function mutations within the genes encoding the sugar importers, GlpT and UhpT. There has, however, not been a genome-wide analysis of the basis for fosfomycin susceptibility reported to date.

Methods

Here we used TraDIS-Xpress, a high-density transposon mutagenesis approach, to assay the role of all genes in E. coli involved in fosfomycin susceptibility.

Results

The data confirmed known fosfomycin susceptibility mechanisms and identified new ones. The assay was able to identify domains within proteins of importance and revealed essential genes with roles in fosfomycin susceptibility based on expression changes. Novel mechanisms of fosfomycin susceptibility that were identified included those involved in glucose metabolism and phosphonate catabolism (phnC-M), and the phosphate importer, PstSACB. The impact of these genes on fosfomycin susceptibility was validated by measuring the susceptibility of defined inactivation mutants.

Conclusions

This work reveals a wider set of genes that contribute to fosfomycin susceptibility, including core sugar metabolism genes and two systems involved in phosphate uptake and metabolism previously unrecognized as having a role in fosfomycin susceptibility.
Local economic conditions and the nature of new housing supply
Authors: Hilber Christian A. L , Rouwendal Jan , Vermeulen Wouter
Published: July 2020

We explore the effects of local economic conditions on the type and size of newly constructed housing units in a city. Exploiting the 1984–2004 metro area samples of the American Housing Survey and US Census building permit data from 1980 to 2018, we find that positive local income shocks (i) increase a city’s share of multi-family housing in new construction and (ii) trigger the construction of smaller units. These responses are driven by migration. Our findings are consistent with a modified open monocentric city model that more realistically assumes land is available for conversion into new housing throughout the city.
Species-specific effects of moonlight on insectivorous bat activity in central Chile
Authors: Vásquez Diana A , Grez Audrey A , Rodríguez-San Pedro Annia
Published: July 2020

Moonlight intensity influences the activity patterns of bats. Some bat species reduce their activity levels during brighter nights, a phenomenon known as “lunar phobia.” While lunar phobia of bats has been extensively studied in tropical regions, the same is not the case of bats in temperate regions. By using acoustic detectors, we examined differences in the activity of insectivorous bats on nights with different moonlight intensity in an agricultural landscape of central Chile. We also examined the hourly activity patterns throughout the night and how these varied between full and new moon nights. All bat species modified their activity based on the moonlight intensity; however, their effects were species-specific. The activity of Lasiurus varius, L. villosissimus, Myotis chiloensis, and Histiotus montanus was lower during bright nights, while Tadarida brasiliensis was the only species whose activity was higher during bright nights. Hourly activity throughout the night differed between full moon nights and new moon nights in most bat species. During full moon, bats concentrated their activities in the early hours of the nights; a more homogeneous activity pattern was exhibited during new moon night. Our study demonstrates that moonlight affects the activity of bats in Chile, a factor that should be considered when studying bats.
Cytoskeleton—a crucial key in host cell for coronavirus infection
Authors: Wen Zeyu , Zhang Yue , Lin Zhekai , Shi Kun , Jiu Yaming
Published: July 2020

The emerging coronavirus (CoV) pandemic is threatening the public health all over the world. Cytoskeleton is an intricate network involved in controlling cell shape, cargo transport, signal transduction, and cell division. Infection biology studies have illuminated essential roles for cytoskeleton in mediating the outcome of host‒virus interactions. In this review, we discuss the dynamic interactions between actin filaments, microtubules, intermediate filaments, and CoVs. In one round of viral life cycle, CoVs surf along filopodia on the host membrane to the entry sites, utilize specific intermediate filament protein as co-receptor to enter target cells, hijack microtubules for transportation to replication and assembly sites, and promote actin filaments polymerization to provide forces for egress. During CoV infection, disruption of host cytoskeleton homeostasis and modification state is tightly connected to pathological processes, such as defective cytokinesis, demyelinating, cilia loss, and neuron necrosis. There are increasing mechanistic studies on cytoskeleton upon CoV infection, such as viral protein‒cytoskeleton interaction, changes in the expression and post-translation modification, related signaling pathways, and incorporation with other host factors. Collectively, these insights provide new concepts for fundamental virology and the control of CoV infection.
Lucky Me: The Amiable and Weighty Influences on My Career
Authors: Beauchamp Tom L
Published: July 2020

This autobiographical sketch is being published 50 years after I started as an assistant professor at Georgetown University in 1970. In this presentation, I cannot tell the full story of these 50 years. I write only about the formative years both before and after I was hired at Georgetown, and I emphasize two subjects. The first is the importance of the individuals who were massive influences on my intellectual development and aspirations. The second is the great importance of multidisciplinary work. I came from philosophy, a discipline that generally did not emphasize or particularly value multidisciplinary work, but I was transformed by individuals in other disciplines who directed me to this style of work. Almost sheer luck brought each of these influences into my life.
Common Susceptibility Loci for Male Breast Cancer
Authors: Maguire Sarah , Perraki Eleni , Tomczyk Katarzyna , Jones Michael E , Fletcher Olivia , Pugh Matthew , Winter Timothy , Thompson Kyle , Cooke Rosie ,   kConFab Consortium, Trainer Alison , James Paul , Bojesen Stig , Flyger Henrik , Nevanlinna Heli , Mattson Johanna , Friedman Eitan , Laitman Yael , Palli Domenico , Masala Giovanna , Zanna Ines , Ottini Laura , Silvestri Valentina , Hollestelle Antoinette , Hooning Maartje J , Novaković Srdjan , Krajc Mateja , Gago-Dominguez Manuela , Castelao Jose Esteban , Olsson Hakan , Hedenfalk Ingrid , Saloustros Emmanouil , Georgoulias Vasilios , Easton Douglas F , Pharoah Paul , Dunning Alison M , Bishop D Timothy , Neuhausen Susan L , Steele Linda , Ashworth Alan , Garcia Closas Montserrat , Houlston Richard , Swerdlow Anthony , Orr Nick
Published: July 2020

Background

The etiology of male breast cancer (MBC) is poorly understood. In particular, the extent to which the genetic basis of MBC differs from female breast cancer (FBC) is unknown. A previous genome-wide association study of MBC identified 2 predisposition loci for the disease, both of which were also associated with risk of FBC.

Methods

We performed genome-wide single nucleotide polymorphism genotyping of European ancestry MBC case subjects and controls in 3 stages. Associations between directly genotyped and imputed single nucleotide polymorphisms with MBC were assessed using fixed-effects meta-analysis of 1380 cases and 3620 controls. Replication genotyping of 810 cases and 1026 controls was used to validate variants with P values less than 1 × 10–06. Genetic correlation with FBC was evaluated using linkage disequilibrium score regression, by comprehensively examining the associations of published FBC risk loci with risk of MBC and by assessing associations between a FBC polygenic risk score and MBC. All statistical tests were 2-sided.

Results

The genome-wide association study identified 3 novel MBC susceptibility loci that attained genome-wide statistical significance (P < 5 × 10–08). Genetic correlation analysis revealed a strong shared genetic basis with estrogen receptor–positive FBC. Men in the top quintile of genetic risk had a fourfold increased risk of breast cancer relative to those in the bottom quintile (odds ratio = 3.86, 95% confidence interval = 3.07 to 4.87, P = 2.08 × 10–30).

Conclusions

These findings advance our understanding of the genetic basis of MBC, providing support for an overlapping genetic etiology with FBC and identifying a fourfold high-risk group of susceptible men.
Taking us to the Vulnerability Scene: Television News Coverage and Framing of Internally Displaced Persons in Nigeria
Authors: Apuke Oberiri Destiny , Tunca Elif Asude
Published: July 2020

Despite the growing interest in the internally displaced person's (IDPs) media coverage in developing countries, studies on visual coverage are still in their embryonic stages. In this view, we examined Television news coverage of IDPs in Nigeria. We studied two broadcasting channels; Channels TV and the Nigeria Television Authority (NTA) from October 2018 to October 2019. We also interviewed some journalists and editors who reported and edited stories on IDPs. We anchored our study on the framing theory. Results showed that the two media outlets covered (n = 102) stories of IDPs. However, the private media (Channels TV) paid more attention to IDPs. Also, the private press placed more IDPs stories on its headline and most of which appeared in the first two headlines. Additional findings showed a significant difference in the visual frames; the private media used more visual and motion footages. Results from the interviews suggest that media ownership and control, media sources, advertisers, lack of adequate training, insufficient remuneration/incentive, and competition/ deadline syndrome influence media framing and coverage of IDPs in Nigeria. We concluded with some theoretical and practical implications.
External α-carbonic anhydrase and solute carrier 4 are required for bicarbonate uptake in a freshwater angiosperm
Authors: Huang Wenmin , Han Shijuan , Jiang Hongsheng , Gu Shuping , Li Wei , Gontero Brigitte , Maberly Stephen C
Published: July 2020

The freshwater monocot Ottelia alismoides is the only known species to operate three CO2-concentrating mechanisms (CCMs): constitutive bicarbonate (HCO3–) use, C4 photosynthesis, and facultative Crassulacean acid metabolism, but the mechanism of HCO3– use is unknown. We found that the inhibitor of an anion exchange protein, 4,4'-diisothio-cyanatostilbene-2,2'-disulfonate (DIDS), prevented HCO3– use but also had a small effect on CO2 uptake. An inhibitor of external carbonic anhydrase (CA), acetazolamide (AZ), reduced the affinity for CO2 uptake but also prevented HCO3– use via an effect on the anion exchange protein. Analysis of mRNA transcripts identified a homologue of solute carrier 4 (SLC4) responsible for HCO3– transport, likely to be the target of DIDS, and a periplasmic α-carbonic anhydrase 1 (α-CA1). A model to quantify the contribution of the three different pathways involved in inorganic carbon uptake showed that passive CO2 diffusion dominates inorganic carbon uptake at high CO2 concentrations. However, as CO2 concentrations fall, two other pathways become predominant: conversion of HCO3– to CO2 at the plasmalemma by α-CA1 and transport of HCO3– across the plasmalemma by SLC4. These mechanisms allow access to a much larger proportion of the inorganic carbon pool and continued photosynthesis during periods of strong carbon depletion in productive ecosystems.
Level 1 Trauma Centers and OEF/OIF Emergency Departments: Comparison of Trauma Patient Populations
Authors: Savell Shelia C , Blessing Alexis , Shults Nicole M , Mora Alejandra G , Medellin Kimberly L , Muir Mark T , Kester Nurani , Maddry Joseph K
Published: July 2020

Introduction

Brooke Army Medical Center (BAMC), the largest military hospital and the only level 1 trauma center in the DoD, cares for active duty, retired uniformed services personnel, and beneficiaries. In addition, BAMC works in collaboration with the Southwest Texas Regional Advisory Council (STRAC) and University Hospital (UH), San Antonio’s other level 1 trauma center, to provide trauma care to residents of the city and 22 counties in southwest Texas from San Antonio to Mexico (26,000 square mile area). Civilian-military partnerships are shown to benefit the training of military medical personnel; however, to date, there are no published reports specific to military personnel experiences within emergency care. The purpose of the current study was to describe and compare the emergency department trauma patient populations of two level 1 trauma centers in one metropolitan city (BAMC and UH) as well as determine if DoD level 1 trauma cases were representative of patients treated in OEF/OIF emergency department settings.

Materials and Methods

We obtained a nonhuman subjects research determination for de-identified data from the US Air Force 59th Medical Wing and the University of Texas Health Science Center at San Antonio Institutional Review Boards. Data on emergency department patients treated between the years 2015 and 2017 were obtained from the two level 1 trauma centers (BAMC and UH, located in San Antonio, Texas); data included injury descriptors, ICU and hospital days, and department procedures.

Results

Two-proportion Z-tests indicated that trauma patients were similar across trauma centers on injury type, injury severity, and discharge status; yet trauma patients differed significantly in terms of mechanism of injury and regions of injury. BAMC received significantly greater proportions of patients injured from falls, firearms and with facial and head injuries than UH, which received significantly greater proportion of patients with thorax and abdominal injuries. In addition, a significantly greater proportion of patients spent more than 2 days in the ICU and greater than two total hospital days at BAMC than in UH. In comparison to military emergency departments in combat zones, BAMC had significantly lower rates of blood product administration and endotracheal intubations.

Conclusions

The trauma patients treated at a military level 1 trauma center were similar to those treated in the civilian level 1 trauma center in the same city, indicating the effectiveness of the only DoD Level 1 trauma center to provide experience comparable to that provided in civilian trauma centers. However, further research is needed to determine if the exposure rates to specific procedures are adequate to meet predeployment readiness requirements.
Live fast, die young: GMC lifetimes in the FIRE cosmological simulations of Milky Way mass galaxies
Authors: Benincasa Samantha M , Loebman Sarah R , Wetzel Andrew , Hopkins Philip F , Murray Norman , Bellardini Matthew A , Faucher-Giguère Claude-André , Guszejnov Dávid , Orr Matthew
Published: July 2020

We present the first measurement of the lifetimes of giant molecular clouds (GMCs) in cosmological simulations at z = 0, using the Latte suite of FIRE-2 simulations of Milky Way (MW) mass galaxies. We track GMCs with total gas mass ≳105 M⊙ at high spatial (∼1 pc), mass (7100 M⊙), and temporal (1 Myr) resolution. Our simulated GMCs are consistent with the distribution of masses for massive GMCs in the MW and nearby galaxies. We find GMC lifetimes of 5–7 Myr, or 1–2 freefall times, on average, with less than 2 per cent of clouds living longer than 20 Myr. We find decreasing GMC lifetimes with increasing virial parameter, and weakly increasing GMC lifetimes with galactocentric radius, implying that environment affects the evolutionary cycle of GMCs. However, our GMC lifetimes show no systematic dependence on GMC mass or amount of star formation. These results are broadly consistent with inferences from the literature and provide an initial investigation into ultimately understanding the physical processes that govern GMC lifetimes in a cosmological setting.
Constraining a neutron star merger origin for localized fast radio bursts
Authors: Gourdji K , Rowlinson A , Wijers R A M J , Goldstein A
Published: July 2020

What the progenitors of fast radio bursts (FRBs) are, and whether there are multiple types of progenitors are open questions. The advent of localized FRBs with host galaxy redshifts allows the various emission models to be directly tested for the first time. Given the recent localizations of two non-repeating FRBs (FRB 180924 and FRB 190523), we discuss a selection of FRB emission models and demonstrate how we can place constraints on key model parameters such as e magnetic field strength and age of the putative FRB-emitting neutron star. In particular, we focus on models related to compact binary merger events involving at least one neutron star, motivated by commonalities between the host galaxies of the FRBs and the hosts of such merger events/short gamma-ray bursts (SGRBs). We rule out the possibility that either FRB was produced during the final inspiral stage of a merging binary system. Where possible, we predict the light curve of electromagnetic emission associated with a given model and use it to recommend multiwavelength follow-up strategies that may help confirm or rule out models for future FRBs. In addition, we conduct a targeted sub-threshold search in Fermi Gamma-ray Burst Monitor data for potential SGRB candidates associated with either FRB, and show what a non-detection means for relevant models. The methodology presented in this study may be easily applied to future localized FRBs, and adapted to sources with possibly core-collapse supernova progenitors, to help constrain potential models for the FRB population at large.
Wide-angle effects for peculiar velocities
Authors: Castorina Emanuele , White Martin
Published: July 2020

The line-of-sight peculiar velocities of galaxies contribute to their observed redshifts, breaking the translational invariance of galaxy clustering down to a rotational invariance around the observer. This becomes important when the line-of-sight direction varies significantly across a survey, leading to what are known as ‘wide-angle’ effects in redshift-space distortions. Wide-angle effects will also be present in measurements of the momentum field, i.e. the galaxy density-weighted velocity field, in upcoming peculiar velocity surveys. In this work, we study how wide-angle effects modify the predicted correlation function and power spectrum for momentum statistics, both in autocorrelation and in cross-correlation with the density field. Using both linear theory and the Zel'dovich approximation, we find that deviations from the plane-parallel limit are large and could become important in data analysis for low-redshift surveys. We point out that even multipoles in the cross-correlation between density and momentum are non-zero regardless of the choice of line of sight, and therefore contain new cosmological information that could be exploited. We discuss configuration space, Fourier space, and spherical analyses; providing exact expressions in each case rather than relying on an expansion in small angles. We hope these expressions will be of use in the analysis of upcoming surveys for redshift-space distortions and peculiar velocities.
A method for checking high-redshift identification of radio AGNs
Authors: An Tao , Zhang Yingkang , Frey Sándor
Published: July 2020

In large-scale optical spectroscopic surveys, there are many objects found to have multiple redshift measurements due to the weakness of their emission lines and the different automatic identification algorithms used. These include some suspicious high-redshift $(z \gtrsim 5)$ active galactic nuclei (AGNs). Here, we present a method for inspecting the high-redshift identification of such sources provided that they are radio-loud and have very long baseline interferometry (VLBI) imaging observations of their milli-arcsec (mas) scale jet structure available at multiple epochs. The method is based on the determination of jet component proper motions, and the fact that the combination of jet physics (the observed maximal values of the bulk Lorentz factor) and cosmology (the time dilation of observed phenomena in the early Universe) constrain the possible values of apparent proper motions. As an example, we present the case of the quasar J2346 + 0705 that was reported with two different redshifts, z1 = 5.063 and z2 = 0.171, in the literature. We measured the apparent proper motions (μ) of three components identified in its radio jet by utilizing VLBI data taken from 2014 to 2018. We obtained μJ1 = 0.334 ± 0.099 mas yr−1, μJ2 = 0.116 ± 0.029 mas yr−1, and μJ3 = 0.060 ± 0.005 mas yr−1. The maximal proper motion is converted to an apparent transverse speed of $\beta _{\rm app} = 41.2\pm 12.2\, c$, if the source is at redshift 5.063. This value exceeds the blazar jet speeds known to date. This and other arguments suggest that J2346 + 0705 is hosted by a low-redshift galaxy. Our method may be applicable for other high-redshift AGN candidates lacking unambiguous spectroscopic redshift determination or having photometric redshift estimates only, but showing prominent radio jets allowing for VLBI measurements of fast jet proper motions.
Physical conditions in the diffuse interstellar medium of local and high-redshift galaxies: measurements based on the excitation of H2 rotational and C i  fine-structure levels
Authors: Klimenko V V , Balashev S A
Published: July 2020

We present the results of an analysis of the physical conditions (number density, intensity of UV field, kinetic temperature) in the cold H2-bearing interstellar medium of local and high-redshift galaxies. Our measurements are based on the fit to the observed population of H2 rotational levels and C i  fine-structure levels with the help of grids of numerical models calculated with the photon-dominated region (PDR) Meudon code. A joint analysis of low H2 rotational levels and C i  fine-structure levels breaks the degeneracy in the IUV−nH plane and provides significantly tighter constraints on the number density and intensity of the UV field. Using archive data from the VLT/UVES, KECK/HIRES, HST/STIS and FUSE telescopes, we selected 12 high-redshift damped Lyα systems (DLAs) in quasar spectra and 14 H2 absorption systems along the lines of sight towards stars in the Milky Way and the Magellanic Cloud galaxies. These systems have strong H2 components, with a column density log N(H2)/[cm−2] > 18 and associated C i  absorptions. We find that H2-bearing media in high-redshift DLAs and in local galaxies have similar values of the kinetic temperatures Tkin ∼ 100 K and number density 10−500 cm−3. However, the intensity of incident UV radiation in DLAs varies in a wide range (0.1−100 units of the Mathis field), while it is ∼0.1−3 units of the Mathis field for H2 systems in the Milky Way and Large and Small Magellanic Cloud galaxies. The large dispersion of measured UV flux in DLAs is probably a consequence of the fact that the DLA sample probes galaxies selected from the overall galaxy population at high redshift, and therefore corresponds to a wide range of physical conditions.
Iterative removal of redshift-space distortions from galaxy clustering
Authors: Wang Yuchan , Li Baojiu , Cautun Marius
Published: July 2020

Observations of galaxy clustering are made in redshift space, which results in distortions to the underlying isotropic distribution of galaxies. These redshift-space distortions (RSDs) not only degrade important features of the matter density field, such as the baryonic acoustic oscillation (BAO) peaks, but also pose challenges for the theoretical modelling of observational probes. Here, we introduce an iterative non-linear reconstruction algorithm to remove RSD effects from galaxy clustering measurements, and assess its performance by using mock galaxy catalogues. The new method is found to be able to recover the real-space galaxy correlation function with an accuracy of $\sim \!1{{\ \rm per\ cent}}$, and restore the quadrupole accurately to 0, on scales $s\gtrsim 20\,h^{-1}\, {\rm Mpc}$. It also leads to an improvement in the reconstruction of the initial density field, which could help to accurately locate the BAO peaks. An ‘internal calibration’ scheme is proposed to determine the values of cosmological parameters, as a part of the reconstruction process, and possibilities to break parameter degeneracies are discussed. RSD reconstruction can offer a potential way to simultaneously extract the cosmological parameters, initial density field, real-space galaxy positions, and large-scale peculiar velocity field (of the real Universe), making it an alternative to standard perturbative approaches in galaxy clustering analysis, bypassing the need for RSD modelling.
The VMC survey – XXXIX. Mapping metallicity trends in the Small Magellanic Cloud using near-infrared passbands
Authors: Choudhury Samyaday , de Grijs Richard , Rubele Stefano , Bekki Kenji , Cioni Maria-Rosa L , Ivanov Valentin D , van Loon Jacco Th , Niederhofer Florian , Oliveira Joana M , Ripepi Vincenzo
Published: July 2020

We have derived high-spatial-resolution metallicity maps covering ∼42 deg2 across the Small Magellanic Cloud (SMC) in an attempt to understand its metallicity distribution and gradients up to a radius of ∼4○. Using the near-infrared VISTA Survey of the Magellanic Clouds, our data cover a thrice larger area compared with previous studies. We identify red giant branch (RGB) stars in spatially distinct Y, (Y − Ks) colour–magnitude diagrams. In any of our selected subregions, the RGB slope is used as an indicator of the average metallicity, based on calibration to metallicity using spectroscopic data. The metallicity distribution across the SMC is unimodal and can be fitted by a Gaussian distribution with a peak at [Fe/H] = −0.97 dex (σ[Fe/H] = 0.05 dex). We find evidence of a shallow gradient in metallicity (−0.031 ± 0.005 dex deg−1) from the Galactic Centre to radii of 2○–2${_{.}^{\circ}}$5, followed by a flat metallicity trend from ∼3${_{.}^{\circ}}$5 to 4○. We find that the SMC’s metallicity gradient is radially asymmetric. It is flatter towards the east than to the west, hinting at mixing and/or distortion of the spatial metallicity distribution (within the inner 3○), presumably caused by tidal interactions between the Magellanic Clouds.
Seeding the second star – II. CEMP star formation enriched from faint supernovae
Authors: Chiaki Gen , Wise John H , Marassi Stefania , Schneider Raffaella , Limongi Marco , Chieffi Alessandro
Published: July 2020

Carbon-enhanced metal-poor (CEMP) stars are the living fossils holding records of chemical enrichment from early generations of stars. In this work, we perform a set of numerical simulations of the enrichment from a supernova (SN) of a first generation of metal-free (Pop III) star and the gravitational collapse of the enriched cloud, considering all relevant cooling/heating processes and chemical reactions as well as the growth of dust grains. We adopt faint SN models for the first time with progenitor masses MPopIII = 13–$80 \ {\rm M_{\bigodot }}$, which yield C-enhanced abundance patterns ([C/Fe] = 4.57–4.75) through mixing and fallback of innermost layers of the ejecta. This model also considers the formation and destruction of dust grains. We find that the metals ejected by the SN can be partly re-accreted by the same dark matter minihalo, and carbon abundance of the enriched cloud A(C) = 3.80–5.06 is lower than the abundance range of observed CEMP stars (A(C) ≳ 6) because the mass of the metals ejected by faint SNe is smaller than normal core-collapse SNe due to extensive fallback. We also find that cloud fragmentation is induced by gas cooling from carbonaceous grains for $M_{\rm Pop III}= 13 \ {\rm M_{\bigodot }}$ even with the lowest iron abundance [Fe/H] ∼ −9. This leads to the formation of low-mass stars, and these ‘giga metal-poor’ stars can survive until the present-day Universe and may be found by future observations.
Illuminating a tadpole’s metamorphosis III: quantifying past and present environmental impact
Authors: Reiter Megan , Haworth Thomas J , Guzmán Andrés E , Klaassen Pamela D , McLeod Anna F , Garay Guido
Published: July 2020

We combine Multi-Unit Spectroscopic Explorer and Atacama Large Millimeter/sub-millimeter Array observations with theoretical models to evaluate how a tadpole-shaped globule located in the Carina Nebula has been influenced by its environment. This globule is now relatively small (radius ∼2500 au), hosts a protostellar jet+outflow (HH 900), and, with a blueshifted velocity of ∼10 km s−1, is travelling faster than it should be if its kinematics were set by the turbulent velocity dispersion of the precursor cloud. Its outer layers are currently still subject to heating, but comparing the internal and external pressures implies that the globule is in a post-collapse phase. Intriguingly the outflow is bent, implying that the Young Stellar Object (YSO) responsible for launching it is comoving with the globule, which requires that the star formed after the globule was up to speed since otherwise it would have been left behind. We conclude that the most likely scenario is one in which the cloud was much larger before being subject to radiatively driven implosion, which accelerated the globule to the high observed speeds under the photoevaporative rocket effect and triggered the formation of the star responsible for the outflow. The globule may now be in a quasi-steady state following collapse. Finally, the HH 900 YSO is likely ≳1 M⊙ and may be the only star forming in the globule. It may be that this process of triggered star formation has prevented the globule from fragmenting to form multiple stars (e.g. due to heating) and has produced a single higher mass star.
Planet Microbe: a platform for marine microbiology to discover and analyze interconnected ‘omics and environmental data
Authors: Ponsero Alise J , Bomhoff Matthew , Blumberg Kai , Youens-Clark Ken , Herz Nina M , Wood-Charlson Elisha M , Delong Edward F , Hurwitz Bonnie L
Published: July 2020

In recent years, large-scale oceanic sequencing efforts have provided a deeper understanding of marine microbial communities and their dynamics. These research endeavors require the acquisition of complex and varied datasets through large, interdisciplinary and collaborative efforts. However, no unifying framework currently exists for the marine science community to integrate sequencing data with physical, geological, and geochemical datasets. Planet Microbe is a web-based platform that enables data discovery from curated historical and on-going oceanographic sequencing efforts. In Planet Microbe, each ‘omics sample is linked with other biological and physiochemical measurements collected for the same water samples or during the same sample collection event, to provide a broader environmental context. This work highlights the need for curated aggregation efforts that can enable new insights into high-quality metagenomic datasets. Planet Microbe is freely accessible from https://www.planetmicrobe.org/.
NetCore: a network propagation approach using node coreness
Authors: Barel Gal , Herwig Ralf
Published: July 2020

We present NetCore, a novel network propagation approach based on node coreness, for phenotype–genotype associations and module identification. NetCore addresses the node degree bias in PPI networks by using node coreness in the random walk with restart procedure, and achieves improved re-ranking of genes after propagation. Furthermore, NetCore implements a semi-supervised approach to identify phenotype-associated network modules, which anchors the identification of novel candidate genes at known genes associated with the phenotype. We evaluated NetCore on gene sets from 11 different GWAS traits and showed improved performance compared to the standard degree-based network propagation using cross-validation. Furthermore, we applied NetCore to identify disease genes and modules for Schizophrenia GWAS data and pan-cancer mutation data. We compared the novel approach to existing network propagation approaches and showed the benefits of using NetCore in comparison to those. We provide an easy-to-use implementation, together with a high confidence PPI network extracted from ConsensusPathDB, which can be applied to various types of genomics data in order to obtain a re-ranking of genes and functionally relevant network modules.
Transcriptome-wide stability analysis uncovers LARP4-mediated NFκB1 mRNA stabilization during T cell activation
Authors: Tian Yi , Zeng Zhouhao , Li Xiang , Wang Yiyin , Chen Runsen , Mattijssen Sandy , Gaidamakov Sergei , Wu Yuzhang , Maraia Richard J , Peng Weiqun , Zhu Jun
Published: July 2020

T cell activation is a well-established model for studying cellular responses to exogenous stimulation. Motivated by our previous finding that intron retention (IR) could lead to transcript instability, in this study, we performed BruChase-Seq to experimentally monitor the expression dynamics of nascent transcripts in resting and activated CD4+ T cells. Computational modeling was then applied to quantify the stability of spliced and intron-retained transcripts on a genome-wide scale. Beyond substantiating that intron-retained transcripts were considerably less stable than spliced transcripts, we found a global stabilization of spliced mRNAs upon T cell activation, although the stability of intron-retained transcripts remained relatively constant. In addition, we identified that La-related protein 4 (LARP4), an RNA-binding protein (RBP) known to enhance mRNA stability, was involved in T cell activation-dependent mRNA stabilization. Knocking out Larp4 in mice destabilized Nfκb1 mRNAs and reduced secretion of interleukin-2 (IL2) and interferon-gamma (IFNγ), two factors critical for T cell proliferation and function. We propose that coordination between splicing regulation and mRNA stability may provide a novel paradigm to control spatiotemporal gene expression during T cell activation.
Impact of outreach education program on outcomes of neonates with hypoxic ischemic encephalopathy
Authors: Mohammad Khorshid , Dharel Dinesh , Abou Mehrem Ayman , Esser Michael J , Paul Renee , Zein Hussein , Scott James N , Fiedrich Elsa , Murthy Prashanth , Dossani Salma , Kopores Kaley , Kowal Derek , Montpetit John , Al Awad Essa , Thomas Sumesh
Published: July 2020

Aim

To evaluate the impact of outreach education targeting neuroprotection on outcomes of outborn infants with moderate-to-severe hypoxic ischemic encephalopathy (HIE).

Methods

A retrospective cohort study of infants admitted with moderate-to-severe HIE was conducted following the implementation of outreach education in January 2016. Key interventions were early identification and referral of infants with encephalopathy utilizing telemedicine and a centralized communication system, hands-on simulation, and interactive case discussion and dissemination of clinical management guidelines and educational resources. The association between the intervention and a composite outcome of death and/or severe brain injury on brain magnetic resonance imaging (MRI) was tested controlling for the confounding factors.

Results

Of 165 neonates, 37 (22.4%) died and/or had a severe brain injury. This outcome decreased from 35% (27/77) to 11% (10/88) following the implementation of outreach education (P<0.001). Eligible infants not undergoing therapeutic hypothermia within 6 hours from birth decreased from 19.5% (15/77) to 4.5% (4/88). The use of inotropes decreased from 49.3% (38/77) to 19.6% (13/88). Any core temperature below 33°C was recorded for 20/53 (38%) before and 16/78 (21%) after, while those within the target range of 33°C to 34°C at admission to a tertiary care facility increased from (15/53) 28% to (51/88) 58%. Outreach education was independently associated with decreased composite outcome of death and/or severe brain injury on MRI (adjusted odds ratio 0.2; 95% confidence interval 0.07 to 0.52).

Conclusion

Outreach education targeting neuroprotection for infants with moderate-to-severe HIE was associated with a reduction in death and/or severe brain injury.
A Comparison of Perceptions of Reassurance in Patients with Nontraumatic Neck Pain and Whiplash-Associated Disorders in Consultations with Primary Care Practitioners—An Online Survey
Authors: Silva Guerrero Alma Viviana , Setchell Jenny , Maujean Annick , Sterling Michele
Published: July 2020

Objectives

Neck pain remains highly prevalent and costly worldwide. Although reassurance has been recommended as a first line of treatment, specific advice on the best ways to provide reassurance has not been provided due to lack of evidence. Pain symptoms and experiences differ between patients with whiplash-associated disorder (WAD) and those with nontraumatic neck pain (NTNP). The aims of this study were to 1) identify and compare the concerns, fears, and worries of patients with WAD and NTNP; and 2) determine if patients believe their concerns are addressed by primary care providers.

Methods

These questions were investigated through an online survey, with a convenience sample of 30 participants with NTNP and 20 with WAD.

Results

A thematic analysis of survey responses resulted in the following seven themes related to common concerns, and two regarding how well concerns were addressed. Common concerns expressed by both groups shared four themes: 1) further structural damage, 2) psychological distress, 3) concerns about the future, and 4) hardships that eventuate. Theme 5), pain/disability is long term, was specific to WAD. Themes 6), pain is current or reoccurring, and 7), interference with daily life, were specific to NTNP. Regarding how well patient concerns were addressed, two overarching themes were common to both conditions: 1) concerns were addressed, with both groups sharing the subthemes “successful treatment,” “reassurance,” and “trust”; and 2) concerns were not addressed, where all subthemes were shared with the exception of two unique to NTNP.

Conclusions

This detailed comparison provides information about neck pain patients’ concerns and fears, while providing health practitioners support for selecting strategies to promote reassurance appropriately for individual patient needs. Our findings from patients’ perspectives enhance the understanding for providing reassurance for neck pain as proposed by our analysis.
Secondary attack rate of COVID-19 in household contacts: a systematic review
Authors: Shah K , Saxena D , Mavalankar D
Published: July 2020

Coronavirus disease 2019 (COVID-19) is a novel virus with continuously evolving transmission trends. Contact tracing and quarantining of positive cases are chief strategies of disease control that has been accepted globally, though scientific knowledge regarding household transmission of the COVID-19 through contact of positive case is sparse. Current systematic review was planned to assess global statistics and characteristics of household secondary attack rate (SAR) of COVID-19. Eligible articles were retrieved through search of—MEDLINE, SCOPUS and EMBASE for the period December 2019 to 15 June 2020. Search terms were developed to identify articles reporting household SARs in various countries. After initial screening of 326 articles, 13 eligible studies were included in the final evidence synthesis. We found that SAR varies widely across countries with lowest reported rate as 4.6% and highest as 49.56%. The rates were unaffected by confounders such as population of the country, lockdown status and geographic location. Review suggested greater vulnerability of spouse and elderly population for secondary transmission than other household members. It was also observed that quarantining and isolation are most effective strategies for prevention of the secondary transmission of the disease. Symptomatic status of the index case emerged to be a critical factor, with very low transmission probability during asymptomatic phase. Present review findings recommend that adequate measures should be provided to protect the vulnerable population as only case tracing and quarantining might be insufficient. It should be combined with advisory for limiting household contacts and active surveillance for symptom onset.
Predictors of joint damage progression and stringent remission in patients with established rheumatoid arthritis in clinical remission
Authors: Møller-Bisgaard Signe , Georgiadis Stylianos , Hørslev-Petersen Kim , Ejbjerg Bo , Hetland Merete Lund , Ørnbjerg Lykke Midtbøll , Glinatsi Daniel , Møller Jakob , Boesen Mikael , Stengaard-Pedersen Kristian , Madsen Ole Rintek , Jensen Bente , Villadsen Jan Alexander , Hauge Ellen-Margrethe , Bennett Philip , Hendricks Oliver , Asmussen Karsten , Kowalski Marcin , Lindegaard Hanne , Bliddal Henning , Krogh Niels Steen , Ellingsen Torkell , Nielsen Agnete H. , Balding Lone , Jurik Anne Grethe , Thomsen Henrik S. , Østergaard Mikkel
Published: July 2020

Objectives

To study if clinical, radiographic and MRI markers can predict MRI and radiographic damage progression and achievement of stringent remission in patients with established RA in clinical remission followed by a targeted treatment strategy.

Methods

RA patients (DAS28-CRP <3.2, no swollen joints) receiving conventional synthetic DMARDs were randomized to conventional or MRI-targeted treat-to-target strategies with predefined algorithmic treatment escalations. Potentially predictive baseline variables were tested in multivariate logistic regression analyses.

Results

In the 171 patients included, baseline MRI osteitis independently predicted progression in MRI erosion [odds ratio (OR) 1.13 (95% CI 1.06, 1.22)], joint space narrowing [OR 1.15 (95% CI 1.07, 1.24)] and combined damage [OR 1.23 (95% CI 1.13, 1.37)], while tenosynovitis independently predicted MRI erosion progression [OR 1.13 (95% CI 1.03, 1.25)]. A predictor of radiographic erosion progression was age, while gender predicted progression in joint space narrowing. Following an MRI treat-to-target strategy predicted stringent remission across all remission definitions: Clinical Disease Activity Index remission OR 2.94 (95% CI 1.25, 7.52), Simplified Disease Activity Index remission OR 2.50 (95% CI 1.01, 6.66), ACR/EULAR Boolean remission OR 5.47 (95% CI 2.33, 14.13). Similarly, low tender joint count and low patient visual analogue scale pain and global independently predicted achievement of more stringent remission.

Conclusion

Baseline MRI osteitis and tenosynovitis were independent predictors of 2 year MRI damage progression in RA patients in clinical remission, while independent predictors of radiographic damage progression were age and gender. Following an MRI treat-to-target strategy, low scores of patient-reported outcomes and low tender joint count predicted achievement of stringent remission.

Trial registration

ClinicalTrials.gov (https://clinicaltrials.gov), NCT01656278.