bluuebunny/crossref_metadata_2025 huggingface dataset:
Investigating bifidobacteria and human milk oligosaccharide composition of lactating mothers
Authors: Lugli Gabriele Andrea , Duranti Sabrina , Milani Christian , Mancabelli Leonardo , Turroni Francesca , Alessandri Giulia , Longhi Giulia , Anzalone Rosaria , Viappinai Alice , Tarracchini Chiara , Bernasconi Sergio , Yonemitsu Chloe , Bode Lars , Goran Michael I , Ossiprandi Maria Cristina , van Sinderen Douwe , Ventura Marco
Published: March 2020

Human milk is known to carry its own microbiota, of which the precise origin remains obscure. Breastfeeding allows mother-to-baby transmission of microorganisms as well as the transfer of many other milk components, such as human milk oligosaccharides (HMOs), which act as metabolizable substrates for particular bacteria, such as bifidobacteria, residing in infant intestinal tract. In the current study, we report the HMO composition of 249 human milk samples, in 163 of which we quantified the abundance of members of the Bifidobacterium genus using a combination of metagenomic and flow cytometric approaches. Metagenomic data allowed us to identify four clusters dominated by Bifidobacterium adolescentis and Bifidobacterium pseudolongum, Bifidobacterium crudilactis or Bifidobacterium dentium, as well as a cluster represented by a heterogeneous mix of bifidobacterial species such as Bifidobacterium breve and Bifidobacterium longum. Furthermore, in vitro growth assays on HMOs coupled with in silico glycobiome analyses allowed us to elucidate that members of the Bifidobacterium bifidum and B. breve species exhibit the greatest ability to degrade and grow on HMOs. Altogether, these findings indicate that the bifidobacterial component of the human milk microbiota is not strictly correlated with their ability to metabolize HMOs.
Ecogenomics reveals community interactions in a long-term methanogenic bioreactor and a rapid switch to sulfate-reducing conditions
Authors: St. James Andrew R , Richardson Ruth E
Published: March 2020

The anaerobic digestion of wastes is globally important in the production of methane (CH4) as a biofuel. When sulfate is present, sulfate-reducing bacteria (SRB) are stimulated, competing with methanogens for common substrates, which decreases CH4 production and results in the formation of corrosive, odorous hydrogen sulfide gas (H2S). Here, we show that a population of SRB within a methanogenic bioreactor fed only butyrate for years immediately (within hours) responded to sulfate availability and shifted the microbial community dynamics within the bioreactor. By mapping shotgun metatranscriptomes to metagenome-assembled genomes, we shed light on the transcriptomic responses of key community members in response to increased sulfate provision. We link these short-term transcriptional responses to long-term niche partitioning using comparative metagenomic analyses. Our results suggest that sulfate provision supports a syntrophic butyrate oxidation community that disfavors poly-β-hydroxyalkanoate storage and that hydrogenotrophic SRB populations effectively exclude obligately hydrogenotrophic, but not aceticlastic, methanogens when sulfate is readily available. These findings elucidate key ecological dynamics between SRB, methanogens and syntrophic butyrate-oxidizing bacteria, which can be applied to a variety of engineered and natural systems.
Reconstructing the Phylogeny of Corynebacteriales while Accounting for Horizontal Gene Transfer
Authors: Coimbra Nilson Da Rocha , Goes-Neto Aristoteles , Azevedo Vasco , Ouangraoua Aïda
Published: March 2020

Horizontal gene transfer is a common mechanism in Bacteria that has contributed to the genomic content of existing organisms. Traditional methods for estimating bacterial phylogeny, however, assume only vertical inheritance in the evolution of homologous genes, which may result in errors in the estimated phylogenies. We present a new method for estimating bacterial phylogeny that accounts for the presence of genes acquired by horizontal gene transfer between genomes. The method identifies and corrects putative transferred genes in gene families, before applying a gene tree-based summary method to estimate bacterial species trees. The method was applied to estimate the phylogeny of the order Corynebacteriales, which is the largest clade in the phylum Actinobacteria. We report a collection of 14 phylogenetic trees on 360 Corynebacteriales genomes. All estimated trees display each genus as a monophyletic clade. The trees also display several relationships proposed by past studies, as well as new relevant relationships between and within the main genera of Corynebacteriales: Corynebacterium, Mycobacterium, Nocardia, Rhodococcus, and Gordonia. An implementation of the method in Python is available on GitHub at https://github.com/UdeS-CoBIUS/EXECT (last accessed April 2, 2020).
Reference Data and T-Scores of Lumbar Skeletal Muscle Area and Its Skeletal Muscle Indices Measured by CT Scan in a Healthy Korean Population
Authors: Kim Eun Hee , Kim Kyung Won , Shin Yongbin , Lee Jiwoo , Ko Yousun , Kim Ye-Jee , Lee Min Jung , Bae Sung-Jin , Park Sung Won , Choe Jaewon , Kim Hong-Kyu
Published: March 2020

Background

Although computed tomography (CT) is considered the gold standard for investigating skeletal muscles, diagnostic cutoff points for sarcopenia have not been established. We therefore suggested clinically relevant diagnostic cutoff points for sarcopenia based on reference values of skeletal muscle area (SMA) measured by CT scan in a large-sized healthy Asian population.

Methods

This cross-sectional analysis included 11,845 subjects (7,314 men, 4,531 women) who underwent abdominal CT scans in South Korea. SMA including all muscles on the selected axial images of the L3 lumbar vertebrae level was demarcated using predetermined thresholds (−29 to +150 Hounsfield units). SMA indices (height-, weight-, and body mass index [BMI]-adjusted) were calculated.

Results

When T-score < −2.0 was used as the cutoff for defining sarcopenia, the sex-specific cutoff points of SMA, SMA/height2, SMA/weight, and SMA/BMI were 119.3 and 74.2 cm2, 39.8 and 28.4 cm2/m2, 1.65 and 1.38 cm2/kg, and 4.97 and 3.46 in men and women, respectively. In both sexes, the SMA/BMI values peaked in the 20s and decreased gradually. The SMA/BMI yielded the highest diagnostic rate of sarcopenia (4.2% in men, 8.7% in women), while SMA/height2 provided the lowest yield (2.8% in men, 1.0% in women).

Conclusions

This is the first study to report the reference values of SMA and skeletal muscle indices (SMIs) measured on CT scans and to suggest cutoff points for diagnosis of sarcopenia based on T-score in Asian subjects. BMI-adjusted index (SMA/BMI) was the best index of CT-measured SMA to reflect the age-related muscle changes and to maximize the diagnostic yield for sarcopenia.
Two main rupture stages during the 2018 magnitude 7.5 Sulawesi earthquake
Authors: Li Qi , Zhao Bin , Tan Kai , Xu Wenbin
Published: March 2020

On 28 September 2018, a Mw 7.5 strike-slip earthquake occurred in Sulawesi Island, Indonesia, and it unexpectedly triggered a tsunami. To clearly understand the spatiotemporal evolution process of source rupture, we collected the far-field body wave data and utilized the back-projection method together with finite fault inversion method to investigate the rupture kinematics of this earthquake. Results obtained with the two methods have good consistency and complementarity. We hold that the rupture expanded from the epicentre and propagated bilaterally towards the north and south along the strike direction during the first 24 s, and then to the south. Therefore, the whole rupture process consists of two main stages. For the second stage, the fault segment experienced most of the moment release between 0 and 15 km depth, while the fault plane tended to slip at greater depth (down to 20 km) in the first stage. The total length of the rupture was about 200 km and the seismic moment was ∼2.48 × 1020 Nm, which was equivalent to Mw 7.5. The surface rupture was evident and the maximum slip of 6.24 m was observed in the Palu basin, which was close to Palu city. The rupture was dominated by left-lateral strike-slip with both normal and thrust components as well. The normal slip exhibited in the shallow part of the fault on the north side of Palu bay together with the special geographical location of Palu bay likely favored tsunami genesis.
CorPhU: an algorithm based on phase closure for the correction of unwrapping errors in SAR interferometry
Authors: Benoit Angélique , Pinel-Puysségur Béatrice , Jolivet Romain , Lasserre Cécile
Published: March 2020

Interferometric Synthetic Aperture Radar (InSAR) is commonly used in Earth Sciences to study surface displacements or construct high resolution topographic maps. Recent satellites such as those of the Sentinel-1 constellation allow to derive dense deformation maps with millimetric precision with high revisit frequency. However, InSAR is still limited by interferometric coherence. Interferometric phase noise resulting from a loss of coherence, due to changes in scattering properties between repeated SAR acquisitions, may lead to unwrapping errors, which then in turn lead to centimetric errors in time-series reconstruction. We present an algorithm based on interferometric phase closure to automatically correct unwrapping errors. We describe the algorithm and highlight its performances with two case studies, in Lebanon with Envisat satellite data and in Central Turkey with Sentinel-1 data. The first data set is particularly affected by unwrapping errors because of long spatial (500 m) and temporal baseline interferograms (6 yr) and decorrelation due, in particular, to vegetation. The second data set contains unwrapping errors because of temporal changes in the scattering properties of the ground. For these two examples, the algorithm allows the correction of almost all detectable unwrapping errors, without requiring visual inspection or manual deletions. Our algorithm is efficient especially on large data sets, such as with Sentinel-1 constellation, where interferometric phase is redundant and improves eventually the reconstruction of time-series.
Interventions improving health professionals’ practice for addressing patients’ weight management behaviours: systematic review of reviews
Authors: Yazdizadeh Bahareh , Walker Ruth , Skouteris Helen , Olander Ellinor K , Hill Briony
Published: March 2020

Health professionals require education and training to implement obesity management guidelines and ultimately impact on the health outcomes experienced by their patients. Therefore, a systematic review of systematic reviews that evaluated interventions designed to change the practice of health professionals when addressing diet and physical activity with their patients was conducted. MEDLINE Complete; Cochrane database of systematic reviews; PsycINFO; CINAHL Complete; Global Health; Embase; INFORMIT: Health Subset; Health System Evidence and RX for change were searched in March 2019, with no date or language limits. Identified references underwent screening, full-text analyses and data extraction in duplicate. The search identified 15 230 references. Five systematic reviews that provided a narrative syntheses of a combined 38 studies were included. Health professional participants generally reported being satisfied with the training interventions. Heterogeneity between and within included reviews, non-controlled designs of individual studies and low quality of evidence at an individual study level and review level made it difficult to draw firm conclusions regarding what interventions are most effective in changing health professionals’ knowledge, skills, self-efficacy, attitudes and practice. However, similar gaps in the literature were identified across included reviews. Key areas that could be addressed in future interventions including organization and system-level barriers to providing advice, health professionals’ attitudes and motivation and weight stigma have been highlighted. Health professionals and patients could be more involved in the planning and development of interventions that work towards improving diet and physical activity advice and support provided in healthcare.
Failure to achieve a satisfactory cardiac outcome after isolated coronary surgery in low-risk patients
Authors: Rubino Antonino S , Nicolini Francesco , Tauriainen Tuomas , Demal Till , De Feo Marisa , Onorati Francesco , Faggian Giuseppe , Bancone Ciro , Perrotti Andrea , Chocron Sidney , Dalén Magnus , Santarpino Giuseppe , Fischlein Theodor , Maselli Daniele , Musumeci Francesco , Santini Francesco , Salsano Antonio , Zanobini Marco , Saccocci Matteo , Bounader Karl , Gatti Giuseppe , Ruggieri Vito G , Mignosa Carmelo , Juvonen Tatu , Mariscalco Giovanni , Biancari Fausto
Published: March 2020

OBJECTIVES

This study aims to investigate the incidence and determinants of major early adverse events in low-risk patients undergoing isolated coronary artery bypass grafting (CABG).

METHODS

The multicentre E-CABG registry included 7352 consecutive patients who underwent isolated CABG from January 2015 to December 2016. Patients with an European System for Cardiac Operative Risk Evaluation (EuroSCORE) II of <2% and without any major comorbidity were the subjects of the present analysis.

RESULTS

Out of 2397 low-risk patients, 11 (0.46%) died during the index hospitalization or within 30 days from surgery. Five deaths were cardiac related, 4 of which were secondary to technical failures. We estimated that 8 out of 11 deaths were potentially preventable. Logistic regression model identified porcelain aorta [odds ratio (OR) 34.3, 95% confidence interval (CI) 1.3–346.3] and E-CABG bleeding grades 2–3 (OR 30.2, 95% CI 8.3–112.9) as independent predictors of hospital death.

CONCLUSIONS

Mortality and major complications, although infrequently, do occur even in low-risk patients undergoing CABG. Identification of modifiable causes of postoperative adverse events may be useful to develop preventative strategies to improve the quality of care of patients undergoing cardiac surgery.

Clinical Trial Registration

NCT02319083 (https://clinicaltrials.gov/ct2/show/NCT02319083).
Inequalities in all-cause and cause-specific mortality across the life course by wealth and income in Sweden: a register-based cohort study
Authors: Katikireddi S Vittal , Niedzwiedz Claire L , Dundas Ruth , Kondo Naoki , Leyland Alastair H , Rostila Mikael
Published: March 2020

Background

Wealth inequalities are increasing in many countries, but their relationship to health is little studied. We investigated the association between individual wealth and mortality across the adult life course in Sweden.

Methods

We studied the Swedish adult population using national registers. The amount of wealth tax paid in 1990 was the main exposure of interest and the cohort was followed up for 18 years. Relative indices of inequality (RII) summarize health inequalities across a population and were calculated for all-cause and cause-specific mortality for six different age groups, stratified by sex, using Poisson regression. Mortality inequalities by wealth were contrasted with those assessed by individual and household income. Attenuation by four other measures of socio-economic position and other covariates was investigated.

Results

Large inequalities in mortality by wealth were observed and their association with mortality remained more stable across the adult life course than inequalities by income-based measures. Men experienced greater inequalities across all ages (e.g. the RII for wealth was 2.58 [95% confidence interval (CI) 2.54–2.63) in men aged 55–64 years compared with 2.29 (95% CI 2.24–2.34) for women aged 55–64 years), except among the over 85s. Adjustment for covariates, including four other measures of socio-economic position, led to only modest reductions in the association between wealth and mortality.

Conclusions

Wealth is strongly associated with mortality throughout the adult life course, including early adulthood. Income redistribution may be insufficient to narrow health inequalities—addressing the increasingly unequal distribution of wealth in high-income countries should be considered.
Wall-Crossings for Hassett Descendant Potentials
Authors: Blankers Vance , Cavalieri Renzo
Published: March 2020

This paper solves the combinatorics relating the intersection theory of $\psi $-classes of Hassett spaces to that of $\overline{{\mathcal{M}}}_{g,n}$. A generating function for intersection numbers of $\psi $-classes on all Hassett spaces is obtained from the Gromov–Witten potential of a point via a non-invertible transformation of variables. When restricting to diagonal weights, the changes of variables are invertible and explicitly described as polynomial functions. Finally, the comparison of potentials is extended to the level of cycles: the pinwheel cycle potential, a generating function for tautological classes of rational tail type on $\overline{{\mathcal{M}}}_{g,n}$ is the right instrument to describe the pull-back to $\overline{{\mathcal{M}}}_{g,n}$ of all monomials of $\psi $-classes on Hassett spaces.
The Application of Cytokine Expression Assays to Differentiate Active From Previously Treated Syphilis
Authors: Kojima Noah , Siebert Janet C , Maecker Holden , Rosenberg-Hasson Yael , Leon Segundo R , Vargas Silver K , Konda Kelika A , Caceres Carlos F , Klausner Jeffrey D
Published: March 2020

To investigate the role of serum cytokine assays to distinguish between active from treated syphilis among serofast patients, we recruited individuals into a prospective cohort study. Participants underwent routine syphilis screening. We selected specimens from a majority cohort of serofast participants with treated and active syphilis. We analyzed specimens with a 62-cytokine multiplex bead-based enzyme-linked immunosorbent assay. Cytokines, brain-derived neurotrophic factor and tumor necrosis factor β, were most predictive. We built a decision tree that was 82.4% accurate, 100% (95% confidence interval, 82%–100%) sensitive, and 45% (18%–75%) specific. Our decision tree differentiated between serum specimens from serofast participants with treated syphilis versus active syphilis.
In vivo synergism of ampicillin, gentamicin, ceftaroline and ceftriaxone against Enterococcus faecalis assessed in the Galleria mellonella infection model
Authors: Thieme Lara , Hartung Anita , Makarewicz Oliwia , Pletz Mathias W
Published: March 2020

Background

The unfavourable safety profile of aminoglycosides and the synergistic effects observed in vitro have prompted the development of novel dual β-lactam therapies, e.g. ampicillin/ceftriaxone or ampicillin/ceftaroline, for the treatment of Enterococcus faecalis endocarditis.

Objectives

For comparison with in vitro chequerboard assay results, a partial chequerboard setup of ampicillin/gentamicin, ampicillin/ceftriaxone and ampicillin/ceftaroline against E. faecalis was established in the Galleria mellonella larval infection model.

Methods

Discrimination of synergistic and additive interactions was based on the evaluation of larval survival, bacterial quantity in the haemolymph and a pathology score index (internal to the workgroup). Single and multiple dosing schemes based on the half-life of ampicillin were applied. Pharmacokinetic data of the antibiotics in the larvae were determined via agar plate diffusion assays.

Results

Ampicillin and ceftriaxone exhibited strain-specific synergistic interactions in the larvae under both dosing regimens, while the other two combinations showed additive effects. Ampicillin/ceftaroline was inferior to ampicillin/ ceftriaxone. Not all synergistic effects observed in vitro could be replicated in the larvae.

Conclusions

Our results suggest superior efficacy of ampicillin/ceftriaxone for the treatment of high-inoculum enterococcal infections, for at least some strains, but question the benefit of the current standard of adding the nephrotoxic gentamicin compared with the safer ceftriaxone. This is the first study to develop a scheme for differentiation between additive and synergistic effects in larvae and apply a multiple-antibiotic dosing scheme based on the pharmacokinetics of ampicillin. The model allows the analysis of synergistic effects of antimicrobials in an in vivo setting, but the clinical correlation warrants further study.
Intergenerational Associations and the Fertility Transition
Authors: Vogl Tom S
Published: March 2020

Evolutionary theorists have long noted that intergenerational transmission in fertility may counteract aggregate fertility decline through a process of natural selection. I study this evolutionary process by estimating how intergenerational associations in fertility vary over the fertility transition and feed back into the level of average fertility. Microdata from 40 developing countries indicate that intergenerational persistence breaks down at the onset of the fertility transition but then strengthens as the transition progresses. These changes are attributable to a reversal of fertility differences by skill, as predicted by economic models of long-run demographic change. As fertility approaches the replacement level, rising intergenerational associations reweight the population to raise aggregate fertility rates, pushing back against aggregate fertility decline.
Genetic diversity, population structure, and immigration, in a partially hunted puma population of south-central Argentina
Authors: Gallo Orlando , Castillo Diego F , Godinho Raquel , Casanave Emma B
Published: March 2020

Carnivores are decreasing globally due in part to anthropogenic ecological disturbances. In Argentina, human activities have fragmented wildlife habitat, thereby intensifying puma–livestock conflict and leading to population control of the predator species by hunting. We investigated genetic variability and population structure of pumas (Puma concolor) from three south-central Argentine provinces with two different management policies for the species: full protection versus legal hunting. All genetic estimates were based on 83 individuals genotyped at 25 species-specific microsatellite loci. The overall genetic diversity was high (observed heterozygosity = 0.63), but lower than in other South American populations. Spatial analyses revealed the presence of two bottlenecked genetic clusters with very similar diversity and low gene flow (3% per generation) between them. However, analyses based on a priori separated groups showed that gene flow follows increasing values of hunting pressure, converging to the area with the greatest number of individuals harvested. Our results suggest that hunting pressure likely is contributing to the gene flow pattern, limiting pumas’ movements and creating a metapopulation dynamic among geographic subpopulations. Integrated demographic and genetic approaches are needed to better understand pumas’ movements across the landscape and adopt successful management plans to achieve long-term population viability.
Routes for COVID-19 importation in Brazil
Authors: Candido Darlan Da S , Watts Alexander , Abade Leandro , Kraemer Moritz U G , Pybus Oliver G , Croda Julio , de Oliveira Wanderson , Khan Kamran , Sabino Ester C , Faria Nuno R
Published: March 2020

The global outbreak caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has been declared a pandemic by the World Health Organization. As the number of imported SARS-CoV-2 cases is on the rise in Brazil, we use incidence and historical air travel data to estimate the most important routes of importation into the country.
High-throughput phenotyping using digital and hyperspectral imaging-derived biomarkers for genotypic nitrogen response
Authors: Banerjee Bikram P , Joshi Sameer , Thoday-Kennedy Emily , Pasam Raj K , Tibbits Josquin , Hayden Matthew , Spangenberg German , Kant Surya
Published: March 2020

The development of crop varieties with higher nitrogen use efficiency is crucial for sustainable crop production. Combining high-throughput genotyping and phenotyping will expedite the discovery of novel alleles for breeding crop varieties with higher nitrogen use efficiency. Digital and hyperspectral imaging techniques can efficiently evaluate the growth, biophysical, and biochemical performance of plant populations by quantifying canopy reflectance response. Here, these techniques were used to derive automated phenotyping of indicator biomarkers, biomass and chlorophyll levels, corresponding to different nitrogen levels. A detailed description of digital and hyperspectral imaging and the associated challenges and required considerations are provided, with application to delineate the nitrogen response in wheat. Computational approaches for spectrum calibration and rectification, plant area detection, and derivation of vegetation index analysis are presented. We developed a novel vegetation index with higher precision to estimate chlorophyll levels, underpinned by an image-processing algorithm that effectively removed background spectra. Digital shoot biomass and growth parameters were derived, enabling the efficient phenotyping of wheat plants at the vegetative stage, obviating the need for phenotyping until maturity. Overall, our results suggest value in the integration of high-throughput digital and spectral phenomics for rapid screening of large wheat populations for nitrogen response.
WHIRLY1 maintains leaf photosynthetic capacity in tomato by regulating the expression of RbcS1 under chilling stress
Authors: Zhuang Kunyang , Wang Jieyu , Jiao Baozhen , Chen Chong , Zhang Junjie , Ma Nana , Meng Qingwei
Published: March 2020

Rubisco, which consists of eight large subunits (RBCLs) and eight small subunits (RBCSs), is a major photosynthetic enzyme that is sensitive to chilling stress. However, it is largely unclear how plants maintain high Rubisco content under low temperature conditions. Here, we report that tomato WHIRLY1 (SlWHY1) positively regulates the Rubisco level under chilling stress by directly binding to the promoter region of SlRbcS1, resulting in the activation of SlRbcS1 expression. SlRbcS1-overexpressing lines had higher Rubisco contents and were more resistant to chilling stress compared with the wild type. Quantitative real-time PCR analyses showed that, among the five RbcS genes, only SlRbcS1 expression is up-regulated by chilling treatment. These results indicate that SlWHIRLY1 specifically enhances the levels of SlRbcS1 and confers tolerance to chilling stress. The amino acid sequence of SlRBCS1 shows 92.67% identity with those of another two RBCS proteins and three residues are specifically found in SlRBCS1. However, mutation of these residues to alanine in SlRBCS1 does not influence its function during cold adaptation. Thus, we conclude that high levels of Rubisco, but not the specific residues in SlRBCS1, play important roles in tolerance to chilling stress in tomato.
Danfrie Reconsidered. Philippe Danfrié's (d. 1606) Civilite Types
Authors: Vervliet Hendrik D L
Published: March 2020

Though little known to the general public, to type historians Philippe Danfrie (c. 1532–1606) will be recognized as a competitor to Robert Granjon’s claim for being the inventor of the first Civilité type, a mid-sixteenth-century gothic script type that superseded the French bâtarde. The bâtarde was the usual script for vernacular texts north of the Alps (with the exception of German speaking countries): authors such as Caxton or Rabelais were read in this script. In their Civilité Types (Oxford, 1966) Carter & Vervliet described five of Danfrie’s founts. This article aims to present an update of their work and to expand it with four more founts. Danfrie’s civil career is broadly documented and that may be a help for gaining a closer insight in the characteristics of a late sixteenth-century type production that balanced between an incunabular model of private type ownership and the seventeenth-century norm of sales of cast types through large monopolistic typefoundries.
Statistical issues arising in the Office of Federal Contract Compliance’s recent notice on nondiscrimination obligations’ of contractor’s and the concerns raised in the comments submitted by the U.S. Chamber of Commerce
Authors: Gastwirth Joseph L
Published: March 2020

A proposed rule announced by the Office of Federal Contract Compliance describing the way statistical tests will be used in compliance reviews led to the Chamber of Commerce filing a formal Comment. The comment raises several statistical issues, including the proper analysis of stratified data and the effect of large samples on tests of significance. The Chamber correctly pointed out that simple pooling of the data into one large sample can lead to misleading conclusions, so an appropriate analysis, combining the results of statistical analyses of the individual strata into an overall estimate and statistical test is described. Both the proposal and Comment state that practical significance should be considered but do not provide a clear definition of the term, although various definitions are referred to. Two alternative approaches to evaluating the practical significance are described. One assesses the financial impact of the disparity on a typical wage earner, while the second considers the number of employees affected by the disparity and estimates the effect of the disparity on their earnings during their expected time of employment.
Rising stars in the global race for skill? A comparative analysis of Brazil, India, and Malaysia
Authors: Cerna Lucie , Czaika Mathias
Published: March 2020

How do emerging economies compete for international skilled workers? To explore policies used by non-Western countries to attract or retain high-skilled workers in the context of the ‘race for talent’, this article analyses and compares governmental measures employed in three emerging economies: Brazil, India, and Malaysia. Based on insights from 17 expert interviews, we describe the practices and strategies of these three countries to reverse ‘brain drain’—that is, the loss of human capital through migration. The article argues that the design and development of migration and skill recruitment policies are at different stages and of varying relevance to respective national actors. While Malaysia has become an active player and innovator on the international talent recruitment market, the other two countries still consider themselves as ‘self-sufficient’, relying on either their domestically produced human resources or, in the case of India, their skilled diaspora. The three countries are situated at different, mostly early stages of a ‘migration policy transition’, with rising demand for human capital, but still insufficient legal, administrative, and economic provisions to recruit and admit many skilled foreign workers. The ‘global race for talent’ is less of a race for the global South as it is in the global North.
The effect of diffusive nuclear burning in neutron star envelopes on cooling in accreting systems
Authors: Wijngaarden M J P , Ho Wynn C G , Chang Philip , Page Dany , Wijnands Rudy , Ootes Laura S , Cumming Andrew , Degenaar Nathalie , Beznogov Mikhail
Published: March 2020

Valuable information about the neutron star (NS) interior can be obtained by comparing observations of thermal radiation from a cooling NS crust with theoretical models. Nuclear burning of lighter elements that diffuse to deeper layers of the envelope can alter the relation between surface and interior temperatures and can change the chemical composition over time. We calculate new temperature relations and consider two effects of diffusive nuclear burning (DNB) for H–C envelopes. First, we consider the effect of a changing envelope composition and find that hydrogen is consumed on short time-scales and our temperature evolution simulations correspond to those of a hydrogen-poor envelope within ∼100 d. The transition from a hydrogen-rich to a hydrogen-poor envelope is potentially observable in accreting NS systems as an additional initial decline in surface temperature at early times after the outburst. Second, we find that DNB can produce a non-negligible heat flux, such that the total luminosity can be dominated by DNB in the envelope rather than heat from the deep interior. However, without continual accretion, heating by DNB in H–C envelopes is only relevant for <1–80 d after the end of an accretion outburst, as the amount of light elements is rapidly depleted. Comparison to crust cooling data shows that DNB does not remove the need for an additional shallow heating source. We conclude that solving the time-dependent equations of the burning region in the envelope self-consistently in thermal evolution models instead of using static temperature relations would be valuable in future cooling studies.
Efficient acceleration of cylindrical jets: effects of radiative cooling and tangled magnetic field
Authors: Tanaka Shuta J , Toma Kenji
Published: March 2020

Diverging supersonic flows are accelerating, as in the case of a de Laval nozzle, and the same concept has been applied for acceleration of magnetohydrodynamic flows in the universe. Here, we study the dynamics of ‘non-diverging’ cylindrical supersonic flows and show that they can be accelerated by effects of radiative cooling and the tangled magnetic field. In addition to radiative cooling of the jet materials (cooling effect), conversion of the ordered magnetic field into the turbulent one (conversion effect) and dissipation of the turbulent magnetic field (dissipation effect) are formulated according to our study on pulsar wind nebulae. Although each of the cooling and conversion effects is an ineffective acceleration process, the terminal velocity of magnetized cylindrical jets attains about half of the maximum possible value when the cooling, conversion, and dissipation effects work simultaneously. The radiation efficiency is also about half of the total luminosity of the jet in the case of maximal acceleration. The concept for flow acceleration by the non-ideal magnetohydrodynamic effects may be useful for studying relativistic jets in active galactic nuclei, in which the region near the jet axis is expected to be cylindrical and kink unstable.
Properties of gamma-ray decay lines in 3D core-collapse supernova models, with application to SN 1987A and Cas A
Authors: Jerkstrand A , Wongwathanarat A , Janka H-T , Gabler M , Alp D , Diehl R , Maeda K , Larsson J , Fransson C , Menon A , Heger A
Published: March 2020

Comparison of theoretical line profiles to observations provides important tests for supernova explosion models. We study the shapes of radioactive decay lines predicted by current 3D core-collapse explosion simulations, and compare these to observations of SN 1987A and Cas A. Both the widths and shifts of decay lines vary by several thousand kilometres per second depending on viewing angle. The line profiles can be complex with multiple peaks. By combining observational constraints from 56Co decay lines, 44Ti decay lines, and Fe IR lines, we delineate a picture of the morphology of the explosive burning ashes in SN 1987A. For MZAMS = 15−20 M⊙ progenitors exploding with ∼1.5 × 1051 erg, ejecta structures suitable to reproduce the observations involve a bulk asymmetry of the 56Ni of at least ∼400 km s−1 and a bulk velocity of at least 1500 km s−1. By adding constraints to reproduce the UVOIR bolometric light curve of SN 1987A up to 600 d, an ejecta mass around 14 M⊙ is favoured. We also investigate whether observed decay lines can constrain the neutron star (NS) kick velocity. The model grid provides a constraint VNS > Vredshift, and applying this to SN 1987A gives a NS kick of at least 500 km s−1. For Cas A, our single model provides a satisfactory fit to the NuSTAR observations and reinforces the result that current neutrino-driven core-collapse SN models achieve enough bulk asymmetry in the explosive burning material. Finally, we investigate the internal gamma-ray field and energy deposition, and compare the 3D models to 1D approximations.
Artificial neural networks for selection of pulsar candidates from radio continuum surveys
Authors: Yonemaru Naoyuki , Takahashi Keitaro , Kumamoto Hiroki , Dai Shi , Yoshiura Shintaro , Ideguchi Shinsuke
Published: March 2020

It is very computationally expensive to search for pulsars using time-domain observations, and the volume of data will be enormous with next-generation telescopes such as the Square Kilometre Array. We use artificial neural networks (ANNs), a machine learning method, for the efficient selection of pulsar candidates from radio continuum surveys; this is much cheaper than using time-domain observations. With observed quantities such as radio fluxes, sky position and compactness as inputs, our ANNs output the ‘score’ that indicates the degree of likeliness that an object is a pulsar. We demonstrate ANNs based on existing survey data by the Tata Institute for Fundamental Research (TIFR) Giant Metrewave Radio Telescope (GMRT) Sky Survey (TGSS) and the National Radio Astronomy Observatory (NRAO) Very Large Array (VLA) Sky Survey (NVSS) and we test their performance. The precision, which is the ratio of the number of pulsars classified correctly as pulsars to the number of any objects classified as pulsars, is about $96 {{\ \rm per\ cent}}$. Finally, we apply the trained ANNs to unidentified radio sources and our fiducial ANN with five inputs (the galactic longitude and latitude, the TGSS and NVSS fluxes and compactness) generates 2436 pulsar candidates from 456 866 unidentified radio sources. We need to confirm whether these candidates are truly pulsars by using time-domain observations. More information, such as polarization, will narrow the number of candidates down further.
Mass-loss in tidally stripped systems: the energy-based truncation method
Authors: Drakos Nicole E , Taylor James E , Benson Andrew J
Published: March 2020

The ability to accurately predict the evolution of tidally stripped haloes is important for understanding galaxy formation and testing the properties of dark matter. Most studies of substructure evolution make predictions based on empirical models of tidal mass-loss that are calibrated using numerical simulations. This approach can be accurate in the cases considered, but lacks generality and does not provide a physical understanding of the processes involved. Recently, we demonstrated that truncating NFW distribution functions sharply in energy results in density profiles that resemble those of tidally stripped systems, offering a path to constructing physically motivated models of tidal mass-loss. In this work, we review calculations of mass-loss based on energy truncation alone, and then consider what secondary effects may modulate mass-loss beyond this. We find that a combination of dependence on additional orbital parameters and variations in individual particle energies over an orbit results in a less abrupt truncation in energy space as a subhalo loses mass. Combining the energy truncation approach with a simple prediction for the mass-loss rate, we construct a full model of mass-loss that can accurately predict the evolution of a subhalo in terms of a single parameter ηeff. This parameter can be fully determined from the initial orbital and halo properties, and does not require calibration with numerical simulations.
All-sky angular power spectrum – I. Estimating brightness temperature fluctuations using the 150-MHz TGSS survey
Authors: Choudhuri Samir , Ghosh Abhik , Roy Nirupam , Bharadwaj Somnath , Intema Huib T , Ali Sk Saiyad
Published: March 2020

Measurements of the Galactic synchrotron emission are important for the 21-cm studies of the epoch of reionization. The study of synchrotron emission is also useful for quantifying the fluctuations in the magnetic field and the cosmic-ray electron density of the turbulent interstellar medium (ISM) of our Galaxy. Here, we present the all-sky angular power spectrum (Cℓ) measurements of the diffuse synchrotron emission obtained using the TIFR GMRT Sky Survey (TGSS) at 150 MHz. We estimate Cℓ using visibility data both before and after subtracting the modelled point sources. The amplitude of the measured Cℓ decreases significantly after subtracting the point sources, and it is slightly higher in the Galactic plane for the residual data. The residual Cℓ is most likely to be dominated by the Galactic synchrotron emission. The amplitude of the residual Cℓ decreases significantly away from the Galactic plane. We find that the measurements are quite symmetric in the Northern and Southern hemispheres except in the latitude range 15°−30°, which is the transition region from the disc-dominated to the diffuse halo-dominated region. A comparison between this interferometric measurement and the scaled version of the Haslam rms map at 150 MHz shows that the correlation coefficient (r) is greater than 0.5 for most of the latitude ranges considered here. This indicates that the TGSS is quite sensitive to the diffuse Galactic synchrotron radiation.
CHEOPS observations of TESS primary mission monotransits
Authors: Cooke Benjamin F , Pollacco Don , Lendl Monika , Kuntzer Thibault , Fortier Andrea
Published: March 2020

We set out to look at the overlap between CHaracterizing ExOPlanets Satellite (CHEOPS) sky coverage and Transiting Exoplanet Survey Satellite (TESS) primary mission monotransits to determine what fraction of TESS monotransits may be observed by CHEOPS. We carry out a simulation of TESS transits based on the stellar population in TICv8 in the primary TESS mission. We then select the monotransiting candidates and determine their CHEOPS observing potential. We find that TESS will discover approximately 433 monotransits during its primary mission. Using a baseline observing efficiency of 40 per cent, we then find that 387 of these (∼89 per cent) will be observable by CHEOPS with an average observing time of ∼60 d yr−1. Based on the individual observing times and orbital periods of each system, we predict that CHEOPS could observe additional transits for approximately 302 of the 433 TESS primary mission monotransits (∼70 per cent). Given that CHEOPS will require some estimate of period before observing a target, we estimate that up to 250 (∼58 per cent) TESS primary mission monotransits could have solved periods prior to CHEOPS observations using a combination of photometry and spectroscopy.
Star formation law in the epoch of reionization from [C ii] and C iii] lines
Authors: Vallini L , Ferrara A , Pallottini A , Carniani S , Gallerani S
Published: March 2020

We present a novel method to simultaneously characterize the star formation law and the interstellar medium properties of galaxies in the epoch of reionization (EoR) through the combination of [C ii] 158 μm (and its known relation with star formation rate) and C iii] λ1909 Å emission line data. The method, based on a Markov chain Monte Carlo algorithm, allows us to determine the target galaxy average density, n, gas metallicity, Z, and ‘burstiness’ parameter, κs, quantifying deviations from the Kennicutt–Schmidt relation. As an application, we consider COS-3018 (z = 6.854), the only EoR Lyman Break Galaxy so far detected in both [C ii] and C iii]. We show that COS-3018 is a moderate starburst (κs ≈ 3), with $Z \approx 0.4 \, \mathrm{Z}_{\odot }$, and $n \approx 500\, {\rm cm^{-3}}$. Our method will be optimally applied to joint ALMA and James Webb Space Telescope targets.
Natalus mexicanus (Chiroptera: Natalidae)
Authors: López-Wilchis Ricardo , Torres-Flores José Williams , Arroyo-Cabrales Joaquin
Published: March 2020

Natalus mexicanus Miller, 1902 is the smallest species of Natalus and is commonly called the Mexican greater funnel-eared bat. This insectivorous bat is the most widely distributed species of Natalidae, occurring from northern Mexico to Panama, inhabiting mainly deciduous and semideciduous tropical forests, generally at elevations below 300 m. N. mexicanus, a cave-dwelling bat, is considered as a “Least Concern” species by the International Union for Conservation of Nature and Natural Resources, and some data indicate moderate population sizes in several caves, although the population status at other sites is currently unknown.
Efficient and risk-reduced genome editing using double nicks enhanced by bacterial recombination factors in multiple species
Authors: He Xiaozhen , Chen Wenfeng , Liu Zhen , Yu Guirong , Chen Youbang , Cai Yi-Jun , Sun Ling , Xu Wanli , Zhong Lili , Gao Caixi , Chen Jishen , Zhang Minjie , Yang Shengxi , Yao Yizhou , Zhang Zhiping , Ma Fujun , Zhang Chen-Chen , Lu Hui-Ping , Yu Bin , Cheng Tian-Lin , Qiu Juhui , Sheng Qing , Zhou Hai-Meng , Lv Zhi-Rong , Yan Junjun , Zhou Yongjian , Qiu Zilong , Cui Zongbin , Zhang Xi , Meng Anming , Sun Qiang , Yang Yufeng
Published: March 2020

Site-specific DNA double-strand breaks have been used to generate knock-in through the homology-dependent or -independent pathway. However, low efficiency and accompanying negative impacts such as undesirable indels or tumorigenic potential remain problematic. In this study, we present an enhanced reduced-risk genome editing strategy we named as NEO, which used either site-specific trans or cis double-nicking facilitated by four bacterial recombination factors (RecOFAR). In comparison to currently available approaches, NEO achieved higher knock-in (KI) germline transmission frequency (improving from zero to up to 10% efficiency with an average of 5-fold improvement for 8 loci) and ‘cleaner’ knock-in of long DNA fragments (up to 5.5 kb) into a variety of genome regions in zebrafish, mice and rats. Furthermore, NEO yielded up to 50% knock-in in monkey embryos and 20% relative integration efficiency in non-dividing primary human peripheral blood lymphocytes (hPBLCs). Remarkably, both on-target and off-target indels were effectively suppressed by NEO. NEO may also be used to introduce low-risk unrestricted point mutations effectively and precisely. Therefore, by balancing efficiency with safety and quality, the NEO method reported here shows substantial potential and improves the in vivo gene-editing strategies that have recently been developed.
MrDNA: a multi-resolution model for predicting the structure and dynamics of DNA systems
Authors: Maffeo Christopher , Aksimentiev Aleksei
Published: March 2020

Although the field of structural DNA nanotechnology has been advancing with an astonishing pace, de novo design of complex 3D nanostructures and functional devices remains a laborious and time-consuming process. One reason for that is the need for multiple cycles of experimental characterization to elucidate the effect of design choices on the actual shape and function of the self-assembled objects. Here, we demonstrate a multi-resolution simulation framework, mrdna, that, in 30 min or less, can produce an atomistic-resolution structure of a self-assembled DNA nanosystem. We demonstrate fidelity of our mrdna framework through direct comparison of the simulation results with the results of cryo-electron microscopy (cryo-EM) reconstruction of multiple 3D DNA origami objects. Furthermore, we show that our approach can characterize an ensemble of conformations adopted by dynamic DNA nanostructures, the equilibrium structure and dynamics of DNA objects constructed using off-lattice self-assembly principles, i.e. wireframe DNA objects, and to study the properties of DNA objects under a variety of environmental conditions, such as applied electric field. Implemented as an open source Python package, our framework can be extended by the community and integrated with DNA design and molecular graphics tools.