bluuebunny/crossref_metadata_2025 huggingface dataset:
Transgenic mice with an R342X mutation in Phf6 display clinical features of Börjeson–Forssman–Lehmann Syndrome
Authors: Ahmed Raies , Sarwar Shihab , Hu Jinghua , Cardin Valérie , Qiu Lily R , Zapata Gerardo , Vandeleur Lucianne , Yan Keqin , Lerch Jason P , Corbett Mark A , Gecz Jozef , Picketts David J
Published: March 2021

The PHF6 mutation c.1024C > T; p.R342X, is a recurrent cause of Börjeson–Forssman–Lehmann Syndrome (BFLS), a neurodevelopmental disorder characterized by moderate–severe intellectual disability, truncal obesity, gynecomastia, hypogonadism, long tapering fingers and large ears (MIM#301900). Here, we generated transgenic mice with the identical substitution (R342X mice) using CRISPR technology. We show that the p.R342X mutation causes a reduction in PHF6 protein levels, in both human and mice, from nonsense-mediated decay and nonsense-associated alternative splicing, respectively. Magnetic resonance imaging studies indicated that R342X mice had a reduced brain volume on a mixed genetic background but developed hydrocephaly and a high incidence of postnatal death on a C57BL/6 background. Cortical development proceeded normally, while hippocampus and hypothalamus relative brain volumes were altered. A hypoplastic anterior pituitary was also observed that likely contributes to the small size of the R342X mice. Behavior testing demonstrated deficits in associative learning, spatial memory and an anxiolytic phenotype. Taken together, the R342X mice represent a good preclinical model of BFLS that will allow further dissection of PHF6 function and disease pathogenesis.
Article 31, 31 Years On: Choice and Autonomy as a Framework for Implementing Children’s Right to Play in Early Childhood Services
Authors: Colliver Yeshe , Doel-Mackaway Holly
Published: March 2021

Article 31(1) of the Convention on the Rights of the Child (CRC) provides all children, everywhere, with the right to play. The CRC is the most widely ratified international human rights treaty, yet children’s right to play is considered ‘the forgotten right’. The widespread State inaction to fulfil this right could be partly due to continued uncertainty about how to define play. This Article argues for the application a large body of recent research with the group most qualified to determine whether activities are play or not: young children. This research demonstrates that choice and autonomy are two universal and essential indicia for an activity to be experienced as play. The Article contends that the fulfilment of young children’s right to play would significantly increase if early childhood education and care (ECEC) institutions within States utilised these two indicia within daily programmed activities and in ECEC policies.
Assessing the state of the Barents Sea using indicators: how, when, and where?
Authors: Hansen Cecilie , van der Meeren Gro I , Loeng Harald , Skogen Morten D
Published: March 2021

Two end-to-end ecosystem models, NORWECOM.E2E and NoBa Atlantis, have been used to explore a selection of indicators from the Barents Sea Management plans (BSMP). The indicators included in the BSMP are a combination of simple (e.g. temperature, biomass, and abundance) and complex (e.g. trophic level and biomass of functional groups). The abiotic indicators are found to serve more as a tool to report on climate trends rather than being ecological indicators. It is shown that the selected indicators give a good overview of the ecosystem state, but that overarching management targets and lack of connection between indicators and management actions makes it questionable if the indicator system is suitable for direct use in management as such. The lack of socio-economic and economic indicators prevents a holistic view of the system, and an inclusion of these in future management plans is recommended. The evaluated indicators perform well as an assessment of the ecosystem, but consistency and representativeness are extremely dependent on the time and in what area they are sampled. This conclusion strongly supports the inclusion of an observing system simulation experiment in management plans, to make sure that the observations represent the properties that the indicators need.
A putative structural variant and environmental variation associated with genomic divergence across the Northwest Atlantic in Atlantic Halibut
Authors: Kess Tony , Einfeldt Anthony L , Wringe Brendan , Lehnert Sarah J , Layton Kara K S , McBride Meghan C , Robert Dominique , Fisher Jonathan , Le Bris Arnault , den Heyer Cornelia , Shackell Nancy , Ruzzante Daniel E , Bentzen Paul , Bradbury Ian R
Published: March 2021

Characterizing the nature of genetic differentiation among individuals and populations and its distribution across the genome is increasingly important to inform both conservation and management of exploited species. Atlantic Halibut (Hippoglossus hippoglossus) is an ecologically and commercially important fish species, yet knowledge of population structure and genomic diversity in this species remains lacking. Here, we use restriction-site associated DNA sequencing and a chromosome-level genome assembly to identify over 86 000 single nucleotide polymorphisms mapped to 24 chromosome-sized scaffolds, genotyped in 734 individuals across the Northwest Atlantic. We describe subtle but significant genome-wide regional structuring between the Gulf of St. Lawrence and adjacent Atlantic continental shelf. However, the majority of genetic divergence is associated with a large putative chromosomal rearrangement (5.74 megabases) displaying high differentiation and linkage disequilibrium, but no evidence of geographic variation. Demographic reconstructions suggest periods of expansion coinciding with glacial retreat, and more recent declines in Ne. This work highlights the utility of genomic data to identify multiple sources of genetic structure and genomic diversity in commercially exploited marine species.
Residential exposure to traffic-borne pollution as a risk factor for acute cardiocerebrovascular events: a population-based retrospective cohort study in a highly urbanized area
Authors: Magnoni Pietro , Murtas Rossella , Russo Antonio Giampiero
Published: March 2021

Background

Long-term exposure to traffic-borne noise and air pollution has been variably associated with incidence of acute vascular events, namely acute myocardial infarction, ischaemic stroke and haemorrhagic stroke. This study aims at exploring this association within a highly urbanized city.

Methods

This is a population-based retrospective dynamic cohort study including all residents aged ≥ 35 years in the municipality of Milan over the years 2011–18 (1 087 110 inhabitants). Residential exposure to road traffic noise (day-evening-night levels) and nitrogen dioxide was estimated using a noise predictive model and a land use regression model, respectively. Cox proportional hazards regression analyses were performed to assess the incidence of acute vascular events and specific outcomes in single-exposure and two-exposure models including adjustment for sociodemographic confounders, fine particulate matter and surrounding greenness.

Results

A total of 27 282 subjects (2.5%) had an acute vascular event. Models using nitrogen dioxide produced inconsistent results. The strongest effect was observed for noise, with an optimal cut-off for dichotomization set at 70 dBA (hazard ratio 1.025, 95% confidence interval 1.000–1.050). This association was observed specifically for ischaemic and haemorrhagic stroke. When stratifying by age group and sex, a remarkable effect was found for haemorrhagic stroke in men aged <60 years (hazard ratio 1.439, 95% confidence interval 1.156–1.792).

Conclusions

Living by roads with a day-evening-night noise level above 70 dBA exerts a small but tangible independent effect on the risks of both ischaemic and haemorrhagic stroke. It is urgent to propose mitigation measures against pollution and noise originating from vehicular traffic in order to reduce their impact, especially in the population younger than 60 years.
Polygenic Risk Scores Differentiating Schizophrenia From Bipolar Disorder Are Associated With Premorbid Intelligence in Schizophrenia Patients and Healthy Subjects
Authors: Ohi Kazutaka , Nishizawa Daisuke , Sugiyama Shunsuke , Takai Kentaro , Kuramitsu Ayumi , Hasegawa Junko , Soda Midori , Kitaichi Kiyoyuki , Hashimoto Ryota , Ikeda Kazutaka , Shioiri Toshiki
Published: March 2021

Background

Impairments in intelligence are more severe in patients with schizophrenia (SCZ) than in patients with bipolar disorder (BD) despite clinical and genetic similarities between the disorders. Genetic loci differentiating SCZ from BD, that is, SCZ-specific risk, have been identified. Polygenetic [risk] scores (PGSs) for SCZ-specific risk are higher in SCZ patients than in healthy controls (HCs). However, the influence of genetic risk on impaired intelligence is poorly understood. Here, we investigated whether SCZ-specific risk could predict impairments in intelligence in SCZ patients and HCs.

Methods

Large-scale genome-wide association study datasets related to SCZ vs BD, childhood intelligence (CHI), and adulthood intelligence (n = 12 441–282 014) were utilized to compute PGSs. PGSs derived from the genome-wide association studies were calculated for 130 patients with SCZ and 146 HCs. Premorbid and current intelligence and the decline were measured in SCZ patients and HCs. Correlations between PGSs and intelligence functions were investigated.

Results

High PGSs for SCZ-specific risk were correlated with low premorbid intelligence in SCZ patients and HCs (β = −0.17, P = 4.12 × 10–3). The correlation was still significant after adjusting for diagnostic status (β = −0.13, P = .024). There were no significant correlations between PGSs for SCZ-specific risk and current intelligence or intelligence decline (P > .05). PGSs for CHI were lower in SCZ patients than in HCs (R2 = 0.025, P = .025), while the PGSs for CHI were not significantly correlated with premorbid and current intelligence, the decline, or the PGSs for SCZ-specific risk (P > .05).

Conclusions

These findings suggest that genetic factors differentiating SCZ from BD might affect the pathogenesis of SCZ and/or pathological differences between SCZ and BD via the impairment of premorbid intelligence, that is, crystallized intelligence, while genetic factors for CHI might affect the pathogenesis of SCZ but not via impairments in intelligence.
Finite element analysis for a diffusion equation on a harmonically evolving domain
Authors: Edelmann Dominik
Published: March 2021

We study convergence of the evolving finite element semidiscretization of a parabolic partial differential equation on an evolving bulk domain. The boundary of the domain evolves with a given velocity, which is then extended to the bulk by solving a Poisson equation. The numerical solution to the parabolic equation depends on the numerical evolution of the bulk, which yields the time-dependent mesh for the finite element method. The stability analysis works with the matrix–vector formulation of the semidiscretization only and does not require geometric arguments, which are then required in the proof of consistency estimates. We present various numerical experiments that illustrate the proven convergence rates.
Failure of Vitek2 to reliably detect vanB-mediated vancomycin resistance in Enterococcus faecium
Authors: Walker Sarah V , Wolke Martina , Plum Georg , Weber Robert E , Werner Guido , Hamprecht Axel
Published: March 2021

Objectives

The increasing prevalence of VRE necessitates their reliable detection, especially for low-level resistance mediated by vanB in Enterococcus faecium. In this prospective study we analysed if vanB-mediated vancomycin resistance can be reliably detected by Vitek2.

Methods

One thousand, three hundred and forty-four enterococcal isolates from routine clinical specimens were tested by Vitek2 (bioMérieux, Nürtingen, Germany). Additionally, a bacterial suspension (with a turbidity equivalent to that of a 0.5 McFarland standard) was inoculated on chromID VRE screening agar (bioMérieux) and incubated for 48 h. If vancomycin tested susceptible by Vitek2 but growth was detected on the screening agar, PCR for vanA/vanB was performed (GeneXpert vanA/B test, Cepheid, Frankfurt, Germany). For isolates that tested susceptible to vancomycin by Vitek2 but were vanA/B positive, MICs were determined before and after cultivation in broth with increasing concentrations of vancomycin.

Results

One hundred and fifty-six out of 491 E. faecium were VRE and were predominantly vanB positive (81.0%). Of these, Vitek2 did not identify 14 as VRE (sensitivity 91.0%). By broth microdilution 9/14 isolates demonstrated high MICs (≥32 mg/L) and 5/14 showed low vancomycin MICs, which did not increase despite vancomycin exposure. Three of the 14 isolates demonstrated growth on chromID VRE; after vancomycin exposure seven additional isolates were able to grow on chromID VRE.

Conclusions

Vitek2 fails to detect vanB-mediated vancomycin resistance consistently, especially, but not limited to, low-level resistance. As this may lead to treatment failure and further dissemination of vanB VRE, additional methods (e.g. culture on VRE screening agar or PCR) are necessary to reliably identify vanB-positive enterococci in clinical routine.
Privacy-protecting, reliable response data discovery using COVID-19 patient observations
Authors: Kim Jihoon , Neumann Larissa , Paul Paulina , Day Michele E , Aratow Michael , Bell Douglas S , Doctor Jason N , Hinske Ludwig C , Jiang Xiaoqian , Kim Katherine K , Matheny Michael E , Meeker Daniella , Pletcher Mark J , Schilling Lisa M , SooHoo Spencer , Xu Hua , Zheng Kai , Ohno-Machado Lucila ,   R2D2 Consortium, Anderson David M , Anderson Nicholas R , Balacha Chandrasekar , Bath Tyler , Baxter Sally L , Becker-Pennrich Andrea , Bernstam Elmer V , Carter William A , Chau Ngan , Choi Yong , Covington Steven , DuVall Scott , El-Kareh Robert , Florian Renato , Follett Robert W , Geisler Benjamin P , Ghigi Alessandro , Gottlieb Assaf , Hu Zhaoxian , Ir Diana , Knight Tara K , Koola Jejo D , Kuo Tsung-Ting , Lee Nelson , Mansmann Ulrich , Mou Zongyang , Murphy Robert E , Neumann Larissa , Nguyen Nghia H , Niedermayer Sebastian , Park Eunice , Perkins Amy M , Post Kai W , Rieder Clemens , Scherer Clemens , Soares Andrey , Soysal Ekin , Tep Brian , Toy Brian , Wang Baocheng , Wu Zhen R , Zhou Yujia , Zucker Rachel A
Published: March 2021

Objective

To utilize, in an individual and institutional privacy-preserving manner, electronic health record (EHR) data from 202 hospitals by analyzing answers to COVID-19-related questions and posting these answers online.

Materials and Methods

We developed a distributed, federated network of 12 health systems that harmonized their EHRs and submitted aggregate answers to consortia questions posted at https://www.covid19questions.org. Our consortium developed processes and implemented distributed algorithms to produce answers to a variety of questions. We were able to generate counts, descriptive statistics, and build a multivariate, iterative regression model without centralizing individual-level data.

Results

Our public website contains answers to various clinical questions, a web form for users to ask questions in natural language, and a list of items that are currently pending responses. The results show, for example, that patients who were taking angiotensin-converting enzyme inhibitors and angiotensin II receptor blockers, within the year before admission, had lower unadjusted in-hospital mortality rates. We also showed that, when adjusted for, age, sex, and ethnicity were not significantly associated with mortality. We demonstrated that it is possible to answer questions about COVID-19 using EHR data from systems that have different policies and must follow various regulations, without moving data out of their health systems.

Discussion and Conclusions

We present an alternative or a complement to centralized COVID-19 registries of EHR data. We can use multivariate distributed logistic regression on observations recorded in the process of care to generate results without transferring individual-level data outside the health systems.
Regenstrief teaching electronic medical record (tEMR) platform: a novel tool for teaching and evaluating applied health information technology
Authors: Takesue Blaine Y , Tierney William M , Embi Peter J , Mamlin Burke W , Warvel Jeff , Litzelman Debra K
Published: March 2021

The objective of this study is to provide an overview of the Regenstrief Teaching Electronic Medical Record (tEMR), how the tEMR could be used, and how it is currently being used in health professions education. The tEMR is a derivative of a real-world electronic health record (EHR), a large, pseudonymized patient database, and a population health tool designed to support curricular goals. The tEMR has been successfully adopted at 12 health professional, public health, and health information technology (HIT) schools, with over 11 800 unique student users and more than 74 000 logins, for case presentation, to develop diagnostic and therapeutic plans, and to practice documentation skills. With the exponential growth of health-related data and the impact of HIT on work-life balance, it is critical for students to get early EHR skills practice and understand how EHR’s work. The tEMR is a promising, scalable, flexible application to help health professional students learn about common HIT tools and issues.
Temperature Targets and State Obligations on the Mitigation of Climate Change
Authors: Mayer Benoit
Published: March 2021

The Supreme Court of the Netherlands in Urgenda held that States had a customary obligation to implement their ‘fair share’ in achieving the 2°C temperature limitation target they had agreed upon. Yet, this article argues, the notion that States must adopt or implement mitigation action in line with temperature targets finds no support in treaty or customary law. States’ acceptance of temperature targets as a collective objective is relevant to interpreting the standard of due diligence applicable to mitigation obligations only inasmuch as this objective is actually reflected in consistent State practice. At present, temperature targets represent essentially an agreement on a direction of travel: the need for more mitigation action. Over time, the acceptance of this objective could facilitate further legal developments as States agree on particular implications of temperature targets and on a requirement that each of them acts consistently with its interpretation of these targets.
High density and survival of a native small carnivore, the Florida spotted skunk (Spilogale putorius ambarvalis), in south-central Florida
Authors: Harris Stephen N , Froehly Jennifer L , Glass Stephen L , Hannon Christina L , Hewett Ragheb Erin L , Doonan Terry J , Jachowski David S
Published: March 2021

The eastern spotted skunk (Spilogale putorius) is a species of conservation concern across much of its range and has experienced a population decline since the 1940s. Little is known about the Florida spotted skunk (S. p. ambarvalis), a subspecies endemic to peninsular Florida, but previous studies and the frequency of incidental observations suggest that populations of this subspecies might be more abundant than the two eastern spotted skunk subspecies that occur elsewhere. To better understand the status and demography of the Florida spotted skunk, we assessed the density and survival of a population occurring predominantly in dry prairie habitat in south-central Florida. To obtain density estimates, we trapped spotted skunks on a mark–recapture grid over 11 independent 4-day trapping sessions from 2016 to 2018. To obtain survival estimates, we monitored weekly survival of 38 radiocollared spotted skunks (20 collared initially in 2016 and 18 collared initially in 2017) from February 2016 to August 2017. We captured a minimum of 91 unique spotted skunks on 404 occasions on the mark–recapture grid and our density estimates ranged from 6.52 ± 2.93 skunks/km2 to 23.29 ± 7.65 skunks/km2, depending on trapping session, but seasonal differences in density were not significant. The sex ratio of spotted skunks at our site was 1.0M:3.8F. Mean annual survival for all spotted skunks was 0.714 (0.503–0.925, 95% CI), and sex, season, and year did not have significant effects on survival. This survival estimate is the highest reported thus far for any skunk species. Collectively, the density and survival estimates from our study are higher than those of many other mephitids and mustelids of similar size, and these findings reinforce the value of studying locally abundant populations of small carnivores to better inform the conservation, management, and potential restoration of these species in the future.
Pediatric Global Health in Children with Very Early-Onset Inflammatory Bowel Disease
Authors: Holbein Christina E , Plevinsky Jill , Patel Trusha , Conrad Maire C , Kelsen Judith R
Published: March 2021

Objective 

Children with very early-onset inflammatory bowel disease (VEO-IBD) represent a distinct group of patients with IBD with unique phenotypic and genetic characteristics; however, they are frequently omitted from psychosocial research. This study used a novel, brief measure of pediatric global health to assess (1) overall health-related quality of life (HRQOL) in children with VEO-IBD, (2) HRQOL compared to healthy children, and (3) whether gastrointestinal symptoms account for the differences in HRQOL between these groups.

Methods 

Caregivers of 51 children with VEO-IBD (Mage = 4.26 years, 75% male) and 54 healthy children (Mage = 3.50 years, 54% male) completed the PROMIS Pediatric Global Health Scale (PGH-7) parent-proxy form to assess HRQOL and a questionnaire assessing gastrointestinal symptoms. Descriptive statistics, analysis of variance with covariates (ANCOVA), and meditation analyses with bootstrapping were conducted.

Results 

Caregivers of children with VEO-IBD rated their HRQOL as relatively positive, although children with greater disease yielded lower ratings on some PGH-7 items (e.g., fun with friends, physical health, sadness). Compared to healthy youth, children with VEO-IBD scored lower on the PGH-7, with significantly lower item-level scores on overall health, physical health, mental health, and quality of life. Gastrointestinal symptoms mediated the association between health status (i.e., VEO-IBD vs. healthy) and HRQOL, αβ = −2.84, 95% CI = −5.70, −0.34.

Conclusions 

While some children with VEO-IBD are at risk for deficits in HRQOL, many are quite resilient. Psychosocial screening is necessary for providing appropriate referrals to behavioral health services and learning more about psychosocial adjustment in children with VEO-IBD.
‘Sarajevo Is Not What It Used to Be’: Ex-Sarajevan Serbs and Their Ambivalent Relationship to Their Place of Origin
Authors: Žíla OndŘej
Published: March 2021

This article investigates the striking ambivalence of people who left reintegrated Sarajevo en masse after the Bosnian war and have still retained a connection to the city. While ex-Sarajevans identifying as Serbs have cultivated a strong emotional relationship to their place of origin and have maintained various temporal, material, and political linkages with the city, they have completely ruled out the idea of returning physically. By addressing their ambivalent relationship with their place of origin, this study posits that ex-Sarajevans do not embrace the idea of returning to a ‘point fixed in space’, but rather harbour a utopian dream of returning to a ‘point fixed in time’. Rather, it argues that instead of mourning the place itself, ex-Sarajevans truly miss the previous forms of sociability, which no longer exist in the post-war milieu.
A meta-analysis of mesophyll conductance to CO2 in relation to major abiotic stresses in poplar species
Authors: Elferjani Raed , Benomar Lahcen , Momayyezi Mina , Tognetti Roberto , Niinemets Ülo , Soolanayakanahally Raju Y , Théroux-Rancourt Guillaume , Tosens Tiina , Ripullone Francesco , Bilodeau-Gauthier Simon , Lamhamedi Mohammed S , Calfapietra Carlo , Lamara Mebarek
Published: March 2021

Mesophyll conductance (gm) determines the diffusion of CO2 from the substomatal cavities to the site of carboxylation in the chloroplasts and represents a critical component of the diffusive limitation of photosynthesis. In this study, we evaluated the average effect sizes of different environmental constraints on gm in Populus spp., a forest tree model. We collected raw data of 815 A–Ci response curves from 26 datasets to estimate gm, using a single curve-fitting method to alleviate method-related bias. We performed a meta-analysis to assess the effects of different abiotic stresses on gm. We found a significant increase in gm from the bottom to the top of the canopy that was concomitant with the increase of maximum rate of carboxylation and light-saturated photosynthetic rate (Amax). gm was positively associated with increases in soil moisture and nutrient availability, but was insensitive to increasing soil copper concentration and did not vary with atmospheric CO2 concentration. Our results showed that gm was strongly related to Amax and to a lesser extent to stomatal conductance (gs). Moreover, a negative exponential relationship was obtained between gm and specific leaf area, which may be used to scale-up gm within the canopy.
Incidence, scaling relations and physical conditions of ionized gas outflows in MaNGA
Authors: Avery Charlotte R , Wuyts Stijn , Förster Schreiber Natascha M , Villforth Carolin , Bertemes Caroline , Chang Wenjun , Hamer Stephen L , Toshikawa Jun , Zhang Junkai
Published: March 2021

In this work, we investigate the strength and impact of ionized gas outflows within z ∼ 0.04 MaNGA galaxies. We find evidence for outflows in 322 galaxies ($12{{\ \rm per\ cent}}$ of the analysed line-emitting sample), 185 of which show evidence for hosting an active galactic nucleus (AGN). Most outflows are centrally concentrated with a spatial extent that scales sublinearly with Re. The incidence of outflows is enhanced at higher masses, central surface densities, and deeper gravitational potentials, as well as at higher star formation rate (SFR) and AGN luminosity. We quantify strong correlations between mass outflow rates and the mechanical drivers of the outflow of the form $\dot{M}_{\rm out} \propto \rm SFR^{0.97}$ and $\dot{M}_{\rm out} \propto L_{\rm AGN}^{0.55}$. We derive a master scaling relation describing the mass outflow rate of ionized gas as a function of M⋆, SFR, Re, and LAGN. Most of the observed winds are anticipated to act as galactic fountains, with the fraction of galaxies with escaping winds increasing with decreasing potential well depth. We further investigate the physical properties of the outflowing gas finding evidence for enhanced attenuation in the outflow, possibly due to metal-enriched winds, and higher excitation compared to the gas in the galactic disc. Given that the majority of previous studies have focused on more extreme systems with higher SFRs and/or more luminous AGN, our study provides a unique view of the non-gravitational gaseous motions within ‘typical’ galaxies in the low-redshift Universe, where low-luminosity AGN and star formation contribute jointly to the observed outflow phenomenology.
The impact of inhomogeneous subgrid clumping on cosmic reionization – II. Modelling stochasticity
Authors: Bianco Michele , Iliev Ilian T , Ahn Kyungjin , Giri Sambit K , Mao Yi , Park Hyunbae , Shapiro Paul R
Published: March 2021

Small-scale density fluctuations can significantly affect reionization, but are typically modelled quite crudely. Unresolved fluctuations in numerical simulations and analytical calculations are included using a gas clumping factor, typically assumed to be independent of the local environment. In Paper I, we presented an improved, local density-dependent model for the sub-grid gas clumping. Here, we extend this using an empirical stochastic model based on the results from high-resolution numerical simulations which fully resolve all relevant fluctuations. Our model reproduces well both the mean density-clumping relation and its scatter. We applied our stochastic model, along with the mean clumping one and the Paper I deterministic model, to create large-volume realizations of the clumping field, and used these in radiative transfer simulations of cosmic reionization. Our results show that the simplistic mean clumping model delays reionization compared to local density-dependent models, despite producing fewer recombinations overall. This is due to the very different spatial distribution of clumping, resulting in much higher photoionization rates in the latter cases. The mean clumping model produces smaller H ii regions throughout most of reionization, but those percolate faster at late times. It also causes a significant delay in the 21-cm fluctuations peak and yields lower non-Gaussianity and many fewer bright pixels in the PDF distribution. The stochastic density-dependent model shows relatively minor differences from the deterministic one, mostly concentrated around overlap, where it significantly suppresses the 21-cm fluctuations, and at the bright tail of the 21-cm PDFs, where it produces noticeably more bright pixels.
Eight new millisecond pulsars from the first MeerKAT globular cluster census
Authors: Ridolfi A , Gautam T , Freire P C C , Ransom S M , Buchner S J , Possenti A , Venkatraman Krishnan V , Bailes M , Kramer M , Stappers B W , Abbate F , Barr E D , Burgay M , Camilo F , Corongiu A , Jameson A , Padmanabh P V , Vleeschower L , Champion D J , Chen W , Geyer M , Karastergiou A , Karuppusamy R , Parthasarathy A , Reardon D J , Serylak M , Shannon R M , Spiewak R
Published: March 2021

We have used the central 44 antennas of the new 64-dish MeerKAT radio telescope array to conduct a deep search for new pulsars in the core of nine globular clusters (GCs). This has led to the discovery of eight new millisecond pulsars in six different clusters. Two new binaries, 47 Tuc ac and 47 Tuc ad, are eclipsing ‘spiders’, featuring compact orbits (≲0.32 d), very low mass companions, and regular occultations of their pulsed emission. The other three new binary pulsars (NGC 6624G, M62G, and Ter 5 an) are in wider (>0.7 d) orbits, with companions that are likely to be white dwarfs or neutron stars. NGC 6624G has a large eccentricity of e ≃ 0.38, which enabled us to detect the rate of advance of periastron. This suggests that the system is massive, with a total mass of Mtot = 2.65 ± 0.07 M⊙. Likewise, for Ter 5 an, with e ≃ 0.0066, we obtain Mtot = 2.97 ± 0.52 M⊙. The other three new discoveries (NGC 6522D, NGC 6624H, and NGC 6752F) are faint isolated pulsars. Finally, we have used the whole MeerKAT array and synthesized 288 beams, covering an area of ∼2 arcmin in radius around the centre of NGC 6624. This has allowed us to localize many of the pulsars in the cluster, demonstrating the beamforming capabilities of the TRAPUM software backend and paving the way for the upcoming MeerKAT GC pulsar survey.
No velocity-kicks are required to explain large-distance offsets of Ca-rich supernovae and short-GRBs
Authors: Perets Hagai B , Beniamini Paz
Published: March 2021

Environments of supernovae (SNe) and gamma-ray bursts (GRBs) link their progenitors to the underlying stellar population, providing critical clues for their origins. However, various transients including Ca-rich SNe and short-GRBs, appear to be located at remote locations, far from the stellar population of their host galaxy, challenging our understanding of their origin and/or physical evolution. These findings instigated models suggesting that either large velocity-kicks were imparted to the transient progenitors, allowing them to propagate to large distances and attain their remote locations; or that they formed in dense globular-clusters residing in the haloes. Here we show that instead, large spatial-offsets of such transients are naturally explained by observations of highly extended stellar populations in (mostly early-type) galaxy haloes, typically missed since they can only be identified through ultra-deep/stacked images. Consequently, no large velocity kicks, nor halo globular–cluster environments are required in order to explain the origin of these transients. These findings support thermonuclear explosions on white-dwarfs, for the origins of Ca-rich SNe progenitors, and the existence of small (or zero) kick-velocities given to short-GRB progenitors. Furthermore, since stacked/ultra-deep imaging show that early-type galaxies are more extended than late-type galaxies, studies of transients’ offset-distribution (e.g. type Ia SNe or FRBs) should account for host galaxy-type. Since early-type galaxies contain older stellar populations, transient arising from older stellar populations would have larger fractions of early-type hosts, and consequently larger fractions of large-offset transients. In agreement with our results for short-GRBs and Ca-rich SNe showing different offset distributions in early versus late-type galaxies.
Model-independent calibrations of gamma-ray bursts using machine learning
Authors: Luongo Orlando , Muccino Marco
Published: March 2021

We alleviate the circularity problem, whereby gamma-ray bursts are not perfect distance indicators, by means of a new model-independent technique based on Bézier polynomials. We use the well consolidate Amati and Combo correlations. We consider improved calibrated catalogues of mock data from differential Hubble rate points. To get our mock data, we use those machine learning scenarios that well adapt to gamma-ray bursts, discussing in detail how we handle small amounts of data from our machine learning techniques. We explore only three machine learning treatments, i.e. linear regression, neural network, and random forest, emphasizing quantitative statistical motivations behind these choices. Our calibration strategy consists in taking Hubble’s data, creating the mock compilation using machine learning and calibrating the aforementioned correlations through Bézier polynomials with a standard chi-square analysis first and then by means of a hierarchical Bayesian regression procedure. The corresponding catalogues, built up from the two correlations, have been used to constrain dark energy scenarios. We thus employ Markov chain Monte Carlo numerical analyses based on the most recent Pantheon supernova data, baryonic acoustic oscillations, and our gamma-ray burst data. We test the standard ΛCDM model and the Chevallier–Polarski–Linder parametrization. We discuss the recent H0 tension in view of our results. Moreover, we highlight a further severe tension over Ωm and we conclude that a slight evolving dark energy model is possible.
Constraining the cosmic UV background at z > 3 with MUSE Lyman-α emission observations
Authors: Gallego Sofia G , Cantalupo Sebastiano , Sarpas Saeed , Duboeuf Bastien , Lilly Simon , Pezzulli Gabriele , Marino Raffaella Anna , Matthee Jorryt , Wisotzki Lutz , Schaye Joop , Richard Johan , Kusakabe Haruka , Mauerhofer Valentin
Published: March 2021

The intensity of the Cosmic UV background (UVB), coming from all sources of ionizing photons such as star-forming galaxies and quasars, determines the thermal evolution and ionization state of the intergalactic medium (IGM) and is, therefore, a critical ingredient for models of cosmic structure formation. Most of the previous estimates are based on the comparison between observed and simulated Lyman-α forest. We present the results of an independent method to constrain the product of the UVB photoionization rate and the covering fraction of Lyman limit systems (LLSs) by searching for the fluorescent Lyman-α emission produced by self-shielded clouds. Because the expected surface brightness is well below current sensitivity limits for direct imaging, we developed a new method based on 3D stacking of the IGM around Lyman-α emitting galaxies (LAEs) between 2.9 < z < 6.6 using deep MUSE observations. Combining our results with covering fractions of LLSs obtained from mock cubes extracted from the EAGLE simulation, we obtain new and independent constraints on the UVB at z > 3 that are consistent with previous measurements, with a preference for relatively low UVB intensities at z = 3, and which suggest a non-monotonic decrease of ΓH i with increasing redshift between 3 < z < 5. This could suggest a possible tension between some UVB models and current observations which however require deeper and wider observations in Lyman-α emission and absorption to be confirmed. Assuming instead a value of UVB from current models, our results constrain the covering fraction of LLSs at 3 < z < 4.5 to be less than 25 per cent within 150 kpc from LAEs.
Magnetic field orientation in self-gravitating turbulent molecular clouds
Authors: Barreto-Mota L , de Gouveia Dal Pino E M , Burkhart B , Melioli C , Santos-Lima R , Kadowaki L H S
Published: March 2021

Stars form inside molecular cloud filaments from the competition of gravitational forces with turbulence and magnetic fields. The exact orientation of these filaments with the magnetic fields depends on the strength of these fields, the gravitational potential, and the line of sight (LOS) relative to the mean field. To disentangle these effects we employ three-dimensional magnetohydrodynamical numerical simulations that explore a wide range of initial turbulent and magnetic states, i.e. sub-Alfvénic to super-Alfvénic turbulence, with and without gravity. We use histogram of relative orientation (HRO) and the associated projected Rayleigh statistics (PRS) to study the orientation of density and, in order to compare with observations, the integrated density relative to the magnetic field. We find that in sub-Alfvénic systems the initial coherence of the magnetic is maintained inside the cloud and filaments form perpendicular to the field. This trend is not observed in super-Alfvénic models, where the lines are dragged by gravity and turbulence and filaments are mainly aligned to the field. The PRS analysis of integrated maps shows that LOS effects are important only for sub-Alfvénic clouds. When the LOS is perpendicular to the initial field orientation most of the filaments are perpendicular to the projected magnetic field. The inclusion of gravity increases the number of dense structures perpendicular to the magnetic field, reflected as lower values of the PRS for denser regions, regardless of whether the model is sub- or super-Alfvénic. The comparison of our results with observed molecular clouds reveals that most are compatible with sub-Alfvénic models.
Convolutional neural network identification of galaxy post-mergers in UNIONS using IllustrisTNG
Authors: Bickley Robert W , Bottrell Connor , Hani Maan H , Ellison Sara L , Teimoorinia Hossen , Yi Kwang Moo , Wilkinson Scott , Gwyn Stephen , Hudson Michael J
Published: March 2021

The Canada–France Imaging Survey (CFIS) will consist of deep, high-resolution r-band imaging over ∼5000 deg2 of the sky, representing a first-rate opportunity to identify recently merged galaxies. Because of the large number of galaxies in CFIS, we investigate the use of a convolutional neural network (CNN) for automated merger classification. Training samples of post-merger and isolated galaxy images are generated from the IllustrisTNG simulation processed with the observational realism code RealSim. The CNN’s overall classification accuracy is 88 per cent, remaining stable over a wide range of intrinsic and environmental parameters. We generate a mock galaxy survey from IllustrisTNG in order to explore the expected purity of post-merger samples identified by the CNN. Despite the CNN’s good performance in training, the intrinsic rarity of post-mergers leads to a sample that is only ∼6 per cent pure when the default decision threshold is used. We investigate trade-offs in purity and completeness with a variable decision threshold and find that we recover the statistical distribution of merger-induced star formation rate enhancements. Finally, the performance of the CNN is compared with both traditional automated methods and human classifiers. The CNN is shown to outperform Gini–M20 and asymmetry methods by an order of magnitude in post-merger sample purity on the mock survey data. Although the CNN outperforms the human classifiers on sample completeness, the purity of the post-merger sample identified by humans is frequently higher, indicating that a hybrid approach to classifications may be an effective solution to merger classifications in large surveys.
RX J0529.8−6556: a BeXRB pulsar with an evolving optical period and out of phase X-ray outbursts
Authors: Treiber H , Vasilopoulos G , Bailyn C D , Haberl F , Gendreau K C , Ray P S , Maitra C , Maggi P , Jaisawal G K , Udalski A , Wilms J , Monageng I M , Buckley D A H , König O , Carpano S
Published: March 2021

We report the results of eROSITA and NICER observations of the 2020 June outburst of the Be/X-ray binary pulsar RX J0529.8−6556 in the Large Magellanic Cloud, along with the analysis of archival X-ray and optical data from this source. We find two anomalous features in the system’s behaviour. First, the pulse profile observed by NICER during maximum luminosity is similar to that observed by XMM–Newton in 2000, despite the fact that the X-ray luminosity was different by two orders of magnitude. In contrast, a modest decrease in luminosity in the 2020 observations generated a significant change in pulse profile. Secondly, we find that the historical optical outbursts are not strictly periodic, as would be expected if the outbursts were triggered by periastron passage, as is generally assumed. The optical peaks are also not coincident with the X-ray outbursts. We suggest that this behaviour may result from a misalignment of the Be star disc and the orbital plane, which might cause changes in the timing of the passage of the neutron star through the disc as it precesses. We conclude that the orbital period of the source remains unclear.
An XMM–Newton study of active–inactive galaxy pairs
Authors: Guainazzi Matteo , De Rosa Alessandra , Bianchi Stefano , Husemann Bernd , Bogdanovic Tamara , Komossa Stefanie , Loiseau Nora , Paragi Zsolt , Pérez-Torres Miguel , Piconcelli Enrico , Vignali Cristian
Published: March 2021

While theory and simulations indicate that galaxy mergers play an important role in the cosmological evolution of accreting black holes and their host galaxies, samples of active galactic nuclei (AGNs) in galaxies at close separations are still small. In order to increase the sample of AGN pairs, we undertook an archival project to investigate the X-ray properties of an SDSS-selected sample of 32 galaxy pairs with separations ≤150 kpc containing one optically identified AGN, which were serendipitously observed by XMM–Newton. We discovered only one X-ray counterpart among the optically classified non-active galaxies, with a weak X-ray luminosity (≃ 5 × 1041 erg s−1). 59 per cent (19 out of 32) of the AGNs in our galaxy pair sample exhibit an X-ray counterpart, covering a wide range in absorption-corrected X-ray luminosity (5 × 1041–2 × 1044 erg s−1). More than 79 per cent of these AGNs are obscured (column density NH > 1022 cm−2), with more than half thereof (i.e. about 47 per cent of the total AGN sample) being Compton-thick. AGN/no-AGN pairs are therefore more frequently X-ray obscured (by a factor ≃1.5) than isolated AGNs. When compared to a luminosity and redshift-matched sample of bona fide dual AGN, AGN/no-AGN pairs exhibit one order-of-magnitude lower X-ray column density in the same separation range (>10 kpc). A small sample (4 objects) of AGN/no-AGN pairs with sub-pc separation is all heavily obscured, driving a formal anticorrelation between the X-ray column density and the galaxy pair separation in these systems. These findings suggest that the galactic environment has a key influence on the triggering of nuclear activity in merging galaxies.
Rubisco Adaptation Is More Limited by Phylogenetic Constraint Than by Catalytic Trade-off
Authors: Bouvier Jacques W , Emms David M , Rhodes Timothy , Bolton Jai S , Brasnett Amelia , Eddershaw Alice , Nielsen Jochem R , Unitt Anastasia , Whitney Spencer M , Kelly Steven
Published: March 2021

Rubisco assimilates CO2 to form the sugars that fuel life on earth. Correlations between rubisco kinetic traits across species have led to the proposition that rubisco adaptation is highly constrained by catalytic trade-offs. However, these analyses did not consider the phylogenetic context of the enzymes that were analyzed. Thus, it is possible that the correlations observed were an artefact of the presence of phylogenetic signal in rubisco kinetics and the phylogenetic relationship between the species that were sampled. Here, we conducted a phylogenetically resolved analysis of rubisco kinetics and show that there is a significant phylogenetic signal in rubisco kinetic traits. We re-evaluated the extent of catalytic trade-offs accounting for this phylogenetic signal and found that all were attenuated. Following phylogenetic correction, the largest catalytic trade-offs were observed between the Michaelis constant for CO2 and carboxylase turnover (∼21–37%), and between the Michaelis constants for CO2 and O2 (∼9–19%), respectively. All other catalytic trade-offs were substantially attenuated such that they were marginal (<9%) or non-significant. This phylogenetically resolved analysis of rubisco kinetic evolution also identified kinetic changes that occur concomitant with the evolution of C4 photosynthesis. Finally, we show that phylogenetic constraints have played a larger role than catalytic trade-offs in limiting the evolution of rubisco kinetics. Thus, although there is strong evidence for some catalytic trade-offs, rubisco adaptation has been more limited by phylogenetic constraint than by the combined action of all catalytic trade-offs.
Genomic Signatures for Species-Specific Adaptation in Lake Victoria Cichlids Derived from Large-Scale Standing Genetic Variation
Authors: Nakamura Haruna , Aibara Mitsuto , Kajitani Rei , Mrosso Hillary D J , Mzighani Semvua I , Toyoda Atsushi , Itoh Takehiko , Okada Norihiro , Nikaido Masato
Published: March 2021

The cichlids of Lake Victoria are a textbook example of adaptive radiation, as >500 endemic species arose in just 14,600 years. The degree of genetic differentiation among species is very low due to the short period of time after the radiation, which allows us to ascertain highly differentiated genes that are strong candidates for driving speciation and adaptation. Previous studies have revealed the critical contribution of vision to speciation by showing the existence of highly differentiated alleles in the visual opsin gene among species with different habitat depths. In contrast, the processes of species-specific adaptation to different ecological backgrounds remain to be investigated. Here, we used genome-wide comparative analyses of three species of Lake Victoria cichlids that inhabit different environments—Haplochromis chilotes, H. sauvagei, and Lithochromis rufus—to elucidate the processes of adaptation by estimating population history and by searching for candidate genes that contribute to adaptation. The patterns of changes in population size were quite distinct among the species according to their habitats. We identified many novel adaptive candidate genes, some of which had surprisingly long divergent haplotypes between species, thus showing the footprint of selective sweep events. Molecular phylogenetic analyses revealed that a large fraction of the allelic diversity among Lake Victoria cichlids was derived from standing genetic variation that originated before the adaptive radiation. Our analyses uncovered the processes of species-specific adaptation of Lake Victoria cichlids and the complexity of the genomic substrate that facilitated this adaptation.