bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

ABSTRACT
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

ABSTRACT
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

ABSTRACT
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 &gt; 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 (&gt;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

Abstract
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 (&lt;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

Abstract
The cichlids of Lake Victoria are a textbook example of adaptive radiation, as &gt;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.
NEK1 deficiency affects mitochondrial functions and the transcriptome of key DNA repair pathways
Authors: Martins Mariana Bonjiorno , Perez Arina Marina , Bohr Vilhelm A , Wilson David M , Kobarg Jörg 
Published: March 2021

AbstractPrevious studies have indicated important roles for NIMA-related kinase 1 (NEK1) in modulating DNA damage checkpoints and DNA repair capacity. To broadly assess the contributions of NEK1 to genotoxic stress and mitochondrial functions, we characterised several relevant phenotypes of NEK1 CRISPR knockout (KO) and wild-type (WT) HAP1 cells. Our studies revealed that NEK1 KO cells resulted in increased apoptosis and hypersensitivity to the alkylator methyl methanesulfonate, the radiomimetic bleomycin and UVC light, yet increased resistance to the crosslinker cisplatin. Mitochondrial functionalities were also altered in NEK1 KO cells, with phenotypes of reduced mitophagy, increased total mitochondria, elevated levels of reactive oxygen species, impaired complex I activity and higher amounts of mitochondrial DNA damage. RNA-seq transcriptome analysis coupled with quantitative real-time PCR studies comparing NEK1 KO cells with NEK1 overexpressing cells revealed that the expression of genes involved in DNA repair pathways, such as base excision repair, nucleotide excision repair and double-strand break repair, are altered in a way that might influence genotoxin resistance. Together, our studies underline and further support that NEK1 serves as a hub signalling kinase in response to DNA damage, modulating DNA repair capacity, mitochondrial activity and cell fate determination.
Escherichia coliRNase E can efficiently replace RNase Y inBacillus subtilis
Authors: Laalami Soumaya , Cavaiuolo Marina , Roque Sylvain , Chagneau Carine , Putzer Harald 
Published: March 2021

AbstractRNase Y and RNase E are disparate endoribonucleases that govern global mRNA turnover/processing in the two evolutionary distant bacteria Bacillus subtilis and Escherichia coli, respectively. The two enzymes share a similar in vitro cleavage specificity and subcellular localization. To evaluate the potential equivalence in biological function between the two enzymes in vivo we analyzed whether and to what extent RNase E is able to replace RNase Y in B. subtilis. Full-length RNase E almost completely restores wild type growth of the rny mutant. This is matched by a surprising reversal of transcript profiles both of individual genes and on a genome-wide scale. The single most important parameter to efficient complementation is the requirement for RNase E to localize to the inner membrane while truncation of the C-terminal sequences corresponding to the degradosome scaffold has only a minor effect. We also compared the in vitro cleavage activity for the major decay initiating ribonucleases Y, E and J and show that no conclusions can be drawn with respect to their activity in vivo. Our data confirm the notion that RNase Y and RNase E have evolved through convergent evolution towards a low specificity endonuclease activity universally important in bacteria.
Central bank purchases of sovereign bonds in the euro area, the random walk hypothesis, and different measures of risk
Authors: Belke Ansgar , Gros Daniel , Shamsfakhr Farzaneh 
Published: March 2021

AbstractThe large purchase of public sector bonds (PSPP) by the ECB constitutes an interesting special case of quantitative easing (QE). It involved the purchase of risky, peripheral euro area government bonds—not by the ECB itself but by the national central banks at their own risk. The PSPP can be assimilated into a buy-back financed with senior debt, which should reduce the value of the remaining debt. Theory thus suggests that the PSPP should not be expected to have a positive impact on peripheral risk spreads. Empirical studies try to measure the impact of the asset purchases of central banks (QE) using the market reaction at the announcement date. The announcement effects are taken to be permanent because long-term rates are assumed to follow a random walk. We show that this assumption is not warranted for the risk spreads on bonds or the credit default swaps of peripheral euro area countries.
The Science Behind Safe School Re-opening: Leveraging the Pillars of Infection Control to Support Safe Elementary and Secondary Education During the COVID-19 Pandemic
Authors: Schechter-Perkins Elissa M , van den Berg Polly , Branch-Elliman Westyn 
Published: March 2021

Abstract
There are limited tools for adapting coronavirus disease 2019 (COVID-19) infection control plans to school settings. We present an infection prevention model for optimizing safe re-opening for elementary and secondary schools during the global COVID-19 pandemic and review the current evidence behind various infection prevention interventions in school settings. The model is adapted from the Centers for Disease Control and Prevention fundamental pillars for infection prevention and includes 4 categories of intervention: epidemiologic controls (town prevalence metrics, diagnostic testing, quarantine strategies), administrative controls (state vaccination policies, alternative school models, symptom screens, quarantine breaks), engineering/environmental controls (distancing, outdoor space, ventilation), and personal protective equipment (PPE)/hand hygiene (face coverings, hand sanitizing).
The adapted infection control pillars model utilizes implementation science–informed considerations to maximize pragmatism and adherence by leveraging evidence-based strategies. It highlights the necessity of redundant infection prevention interventions, acknowledges the importance of community buy-in to achieve real-world effectiveness, and addresses tactics to overcome implementation barriers. Recommendations are grounded in the Dynamic Sustainability Framework and include suggestions to maintain infection prevention effectiveness over time to ensure ongoing safety.
Three-Dimensional-Printed Drill Guides for Occipitothoracic Fusion in a Pediatric Patient With Occipitocervical Instability
Authors: Pijpker Peter A J , Kuijlen Jos M A , Kaptein Bart L , Pondaag Willem 
Published: March 2021

Abstract

BACKGROUND
Pediatric occipitothoracic fusion can be challenging because of small size pedicles and thin occipital bone. Three-dimensional (3D) printing technology can help with accurate screw insertion but has not been described for occipital keel plate positioning so far.

OBJECTIVE
To describe the novel use of 3D technology to position occipital keel plates during pediatric occipitothoracic fixation.

METHODS
A young boy with segmental spinal dysgenesis presented with asymmetrical pyramidal paresis in all limbs. Developmental abnormities of the cervical spine caused a thinned spinal cord, and because of progressive spinal cord compression, surgical intervention by means of occipitothoracic fixation was indicated at the age of 3 yr.
Because of the small-size pedicles and thin occipital bone, the pedicle screws and occipital plates were planned meticulously using 3D virtual surgical planning technology. The rods were virtually bent in order to properly align with the planned screws. By means of 3D-printed guides, the surgical plan was transferred to the operating theater. For the occipital bone, a novel guide concept was developed, aiming for screw positions at maximal bone thickness.

RESULTS
The postoperative course was uneventful, and radiographs showed good cervical alignment. After superimposing the virtual plan with the intraoperative acquired computed tomography, it was confirmed that the occipital plate positions matched the virtual plan and that pedicle screws were accurately inserted without signs of breach.

CONCLUSION
The use of 3D technology has greatly facilitated the performance of the occipitothoracic fixation and could, in the future, contribute to safer pediatric spinal fixation procedures.
Plankton food webs in the oligotrophic Gulf of Mexico spawning grounds of Atlantic bluefin tuna
Authors: Stukel Michael R , Gerard Trika , Kelly Thomas B , Knapp Angela N , Laiz-Carrión Raúl , Lamkin John T , Landry Michael R , Malca Estrella , Selph Karen E , Shiroza Akihiro , Shropshire Taylor A , Swalethorp Rasmus 
Published: March 2021

AbstractWe used linear inverse ecosystem modeling techniques to assimilate data from extensive Lagrangian field experiments into a mass-balance constrained food web for the Gulf of Mexico open-ocean ecosystem. This region is highly oligotrophic, yet Atlantic bluefin tuna (ABT) travel long distances from feeding grounds in the North Atlantic to spawn there. Our results show extensive nutrient regeneration fueling primary productivity (mostly by cyanobacteria and other picophytoplankton) in the upper euphotic zone. The food web is dominated by the microbial loop (&gt;70% of net primary productivity is respired by heterotrophic bacteria and protists that feed on them). By contrast, herbivorous food web pathways from phytoplankton to metazoan zooplankton process &lt;10% of the net primary production in the mixed layer. Nevertheless, ABT larvae feed preferentially on podonid cladocerans and other suspension-feeding zooplankton, which in turn derive much of their nutrition from nano- and micro-phytoplankton (mixotrophic flagellates, and to a lesser extent, diatoms). This allows ABT larvae to maintain a comparatively low trophic level (~4.2 for preflexion and postflexion larvae), which increases trophic transfer from phytoplankton to larval fish.
Functional characterization of proton antiport regulation in the thylakoid membrane
Authors: Uflewski Michał , Mielke Sarah , Correa Galvis Viviana , von Bismarck Thekla , Chen Xiaoheng , Tietz Enrico , Ruß Jeremy , Luzarowski Marcin , Sokolowska Ewelina , Skirycz Aleksandra , Eirich Jürgen , Finkemeier Iris , Schöttler Mark Aurel , Armbruster Ute 
Published: March 2021

Abstract
During photosynthesis, energy is transiently stored as an electrochemical proton gradient across the thylakoid membrane. The resulting proton motive force (pmf) is composed of a membrane potential (ΔΨ) and a proton concentration gradient (ΔpH) and powers the synthesis of ATP. Light energy availability for photosynthesis can change very rapidly and frequently in nature. Thylakoid ion transport proteins buffer the effects that light fluctuations have on photosynthesis by adjusting pmf and its composition. Ion channel activities dissipate ΔΨ, thereby reducing charge recombinations within photosystem II. The dissipation of ΔΨ allows for increased accumulation of protons in the thylakoid lumen, generating the signal that activates feedback downregulation of photosynthesis. Proton export from the lumen via the thylakoid K+ exchange antiporter 3 (KEA3), instead, decreases the ΔpH fraction of the pmf and thereby reduces the regulatory feedback signal. Here, we reveal that the Arabidopsis (Arabidopsis thaliana) KEA3 protein homo-dimerizes via its C-terminal domain. This C-terminus has a regulatory function, which responds to light intensity transients. Plants carrying a C-terminus-less KEA3 variant show reduced feed-back downregulation of photosynthesis and suffer from increased photosystem damage under long-term high light stress. However, during photosynthetic induction in high light, KEA3 deregulation leads to an increase in carbon fixation rates. Together, the data reveal a trade-off between long-term photoprotection and a short-term boost in carbon fixation rates, which is under the control of the KEA3 C-terminus.
Incidence of Paget’s disease of bone in the UK: evidence of a continuing decline
Authors: Cook Michael J , Pye Stephen R , Lunt Mark , Dixon William G , Ashcroft Darren M , O’Neill Terence W 
Published: March 2021

Abstract

Objectives
To characterize the incidence of clinically diagnosed Paget’s disease of bone in the UK during 1999–2015 and to determine variations in the incidence of disease by age, sex, geography and level of deprivation.

Methods
Incident cases of Paget’s disease occurring between 1999 and 2015 were identified from primary care records. Overall crude incidence and incidence stratified by age and sex was calculated each year from 1999 to 2015. Direct age- and sex-standardized incidence was also calculated. We used Poisson regression to look at variations in incidence by deprivation and UK region.

Results
A total of 3592 incident cases of Paget’s disease were identified between 1999 and 2015. Incidence increased with age and at all ages was greater in men than women. In women and men, respectively, crude incidence increased from 0.037 and 0.074/10 000 population per year among those 45–49 years of age to 3.7 and 6.3/10 000 population per year among those ≥85 years. The overall standardized incidence decreased from 0.75/10 000 person-years in 1999 to 0.20/10 000 person-years in 2015. After adjustment for age and sex, incidence was &gt;30% higher in the most- compared with least-deprived quintile of deprivation. There was evidence of geographic variation, with the highest incidence in the North West of England, which persisted after adjustment for age, sex and level of deprivation.

Conclusion
The incidence of clinically diagnosed Paget’s disease has continued to decrease since 1999. The reason for the decline in incidence remains unknown, although the rapidity of change points to an alteration in one or more environmental determinants.
A review and roadmap of the skin, lung and gut microbiota in systemic sclerosis
Authors: Teaw Shannon , Hinchcliff Monique , Cheng Michelle 
Published: March 2021

AbstractAs our understanding of the genetic underpinnings of SSc increases, questions regarding the environmental trigger(s) that induce and propagate SSc in the genetically predisposed individual emerge. The interplay between the environment, the immune system, and the microbial species that inhabit the patient’s skin and gastrointestinal tract is a pathobiological frontier that is largely unexplored in SSc. The purpose of this review is to provide an overview of the methodologies, experimental study results and future roadmap for elucidating the relationship between the SSc host and his/her microbiome.