bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimal probabilistic catalogue matching for radio sources
Authors: Fan Dongwei , Budavári Tamás , Norris Ray P , Basu Amitabh 
Published: August 2020

ABSTRACT
Cross-matching catalogues from radio surveys to catalogues of sources at other wavelengths is extremely hard, because radio sources are often extended, often consist of several spatially separated components, and often no radio component is coincident with the optical/infrared host galaxy. Traditionally, the cross-matching is done by eye, but this does not scale to the millions of radio sources expected from the next generation of radio surveys. We present an innovative automated procedure, using Bayesian hypothesis testing, that models trial radio-source morphologies with putative positions of the host galaxy. This new algorithm differs from an earlier version by allowing more complex radio-source morphologies, and performing a simultaneous fit over a large field. We show that this technique performs well in an unsupervised mode.
Kraken reveals itself – the merger history of the Milky Way reconstructed with the E-MOSAICS simulations
Authors: Kruijssen J M Diederik , Pfeffer Joel L , Chevance Mélanie , Bonaca Ana , Trujillo-Gomez Sebastian , Bastian Nate , Reina-Campos Marta , Crain Robert A , Hughes Meghan E 
Published: August 2020

ABSTRACT
Globular clusters (GCs) formed when the Milky Way experienced a phase of rapid assembly. We use the wealth of information contained in the Galactic GC population to quantify the properties of the satellite galaxies from which the Milky Way assembled. To achieve this, we train an artificial neural network on the E-MOSAICS cosmological simulations of the co-formation and co-evolution of GCs and their host galaxies. The network uses the ages, metallicities, and orbital properties of GCs that formed in the same progenitor galaxies to predict the stellar masses and accretion redshifts of these progenitors. We apply the network to Galactic GCs associated with five progenitors: Gaia-Enceladus, the Helmi streams, Sequoia, Sagittarius, and the recently discovered ‘low-energy’ GCs, which provide an excellent match to the predicted properties of the enigmatic galaxy ‘Kraken’. The five galaxies cover a narrow stellar mass range [M⋆ = (0.6–4.6) × 108 M⊙], but have widely different accretion redshifts ($\mbox{$z_{\rm acc}$}=0.57\!-\!2.65$). All accretion events represent minor mergers, but Kraken likely represents the most major merger ever experienced by the Milky Way, with stellar and virial mass ratios of $\mbox{$r_{M_\star }$}=1$:$31^{+34}_{-16}$ and $\mbox{$r_{M_{\rm h}}$}=1$:$7^{+4}_{-2}$, respectively. The progenitors match the z = 0 relation between GC number and halo virial mass, but have elevated specific frequencies, suggesting an evolution with redshift. Even though these progenitors likely were the Milky Way’s most massive accretion events, they contributed a total mass of only log (M⋆, tot/M⊙) = 9.0 ± 0.1, similar to the stellar halo. This implies that the Milky Way grew its stellar mass mostly by in-situ star formation. We conclude by organizing these accretion events into the most detailed reconstruction to date of the Milky Way’s merger tree.
Life and Death of Selfish Genes: Comparative Genomics Reveals the Dynamic Evolution of Cytoplasmic Incompatibility
Authors: Martinez Julien , Klasson Lisa , Welch John J , Jiggins Francis M 
Published: August 2020

AbstractCytoplasmic incompatibility is a selfish reproductive manipulation induced by the endosymbiont Wolbachia in arthropods. In males Wolbachia modifies sperm, leading to embryonic mortality in crosses with Wolbachia-free females. In females, Wolbachia rescues the cross and allows development to proceed normally. This provides a reproductive advantage to infected females, allowing the maternally transmitted symbiont to spread rapidly through host populations. We identified homologs of the genes underlying this phenotype, cifA and cifB, in 52 of 71 new and published Wolbachia genome sequences. They are strongly associated with cytoplasmic incompatibility. There are up to seven copies of the genes in each genome, and phylogenetic analysis shows that Wolbachia frequently acquires new copies due to pervasive horizontal transfer between strains. In many cases, the genes have subsequently acquired loss-of-function mutations to become pseudogenes. As predicted by theory, this tends to occur first in cifB, whose sole function is to modify sperm, and then in cifA, which is required to rescue the cross in females. Although cif genes recombine, recombination is largely restricted to closely related homologs. This is predicted under a model of coevolution between sperm modification and embryonic rescue, where recombination between distantly related pairs of genes would create a self-incompatible strain. Together, these patterns of gene gain, loss, and recombination support evolutionary models of cytoplasmic incompatibility.
Effective Population Size Predicts Local Rates but Not Local Mitigation of Read-through Errors
Authors: Ho Alexander T , Hurst Laurence D 
Published: August 2020

Abstract
In correctly predicting that selection efficiency is positively correlated with the effective population size (Ne), the nearly neutral theory provides a coherent understanding of between-species variation in numerous genomic parameters, including heritable error (germline mutation) rates. Does the same theory also explain variation in phenotypic error rates and in abundance of error mitigation mechanisms? Translational read-through provides a model to investigate both issues as it is common, mostly nonadaptive, and has good proxy for rate (TAA being the least leaky stop codon) and potential error mitigation via “fail-safe” 3′ additional stop codons (ASCs). Prior theory of translational read-through has suggested that when population sizes are high, weak selection for local mitigation can be effective thus predicting a positive correlation between ASC enrichment and Ne. Contra to prediction, we find that ASC enrichment is not correlated with Ne. ASC enrichment, although highly phylogenetically patchy, is, however, more common both in unicellular species and in genes expressed in unicellular modes in multicellular species. By contrast, Ne does positively correlate with TAA enrichment. These results imply that local phenotypic error rates, not local mitigation rates, are consistent with a drift barrier/nearly neutral model.
Structural basis for DNA recognition and allosteric control of the retinoic acid receptors RAR–RXR
Authors: Osz Judit , McEwen Alastair G , Bourguet Maxime , Przybilla Frédéric , Peluso-Iltis Carole , Poussin-Courmontagne Pierre , Mély Yves , Cianférani Sarah , Jeffries Cy M , Svergun Dmitri I , Rochel Natacha 
Published: August 2020

AbstractRetinoic acid receptors (RARs) as a functional heterodimer with retinoid X receptors (RXRs), bind a diverse series of RA-response elements (RAREs) in regulated genes. Among them, the non-canonical DR0 elements are bound by RXR–RAR with comparable affinities to DR5 elements but DR0 elements do not act transcriptionally as independent RAREs. In this work, we present structural insights for the recognition of DR5 and DR0 elements by RXR–RAR heterodimer using x-ray crystallography, small angle x-ray scattering, and hydrogen/deuterium exchange coupled to mass spectrometry. We solved the crystal structures of RXR–RAR DNA-binding domain in complex with the Rarb2 DR5 and RXR–RXR DNA-binding domain in complex with Hoxb13 DR0. While cooperative binding was observed on DR5, the two molecules bound non-cooperatively on DR0 on opposite sides of the DNA. In addition, our data unveil the structural organization and dynamics of the multi-domain RXR–RAR DNA complexes providing evidence for DNA-dependent allosteric communication between domains. Differential binding modes between DR0 and DR5 were observed leading to differences in conformation and structural dynamics of the multi-domain RXR–RAR DNA complexes. These results reveal that the topological organization of the RAR binding element confer regulatory information by modulating the overall topology and structural dynamics of the RXR–RAR heterodimers.
Decrease of respiratory diseases in one social children welfare institute in Shanxi Province during COVID-19
Authors: B Liu , QF Han , WP Liang , XY Shi , JJ Wei 
Published: August 2020

Abstract

Background
To assess the impact of disinfection measures on the incidence of common diseases in children welfare institute during the epidemic of Corona Virus Disease 2019 (COVID-19), and provide a basis for the daily disinfection management of children welfare institute.

Methods
This study surveyed and analyzed common diseases among children under the age of 14 in one social children welfare institute in Shanxi Province from January to May in 2018–2020 by the year-on-year method.

Results
The prevalence rate of respiratory diseases in 2020 was a significantly negative growth compared with 2018 and 2019. There was no obvious pattern of changes in digestive diseases group.

Conclusion
In view of the above anti-epidemic measures, it indicates that the children gathering institutions should strengthen effective personal protection and public health management to reduce infectious disease among children.
Stress hyperglycaemia is associated with poor functional outcomes in patients with acute ischaemic stroke after intravenous thrombolysis
Authors: Ngiam J N , Cheong C W S , Leow A S T , Wei Y -T , Thet J K X , Lee I Y S , Sia C -H , Tan B Y Q , Khoo C -M , Sharma V K , Yeo L L L 
Published: August 2020

Summary

Background
Transient hyperglycaemia in the context of illness with or without known diabetes has been termed as ‘stress hyperglycaemia’. Stress hyperglycaemia can result in poor functional outcomes in patients with acute ischaemic stroke (AIS) who underwent mechanical thrombectomy. We investigated the association between stress hyperglycaemia and clinical outcomes in AIS patients undergoing intravenous thrombolysis (IVT).

Methods
We examined 666 consecutive patients with AIS who underwent IVT from 2006 to 2018. All patients had a glycated haemoglobin level (HbA1c) and fasting venous blood glucose measured within 24 h of admission. Stress hyperglycaemia ratio (SHR) was defined as the ratio of the fasting glucose to the HbA1c. Univariate and multivariate analyses were employed to identify predictors of poor functional outcomes (modified Rankin Scale 3–6 at 3 months) after IVT.

Results
Three-hundred and sixty-one patients (54.2%) had good functional outcomes. These patients tended to be younger (60.7 ± 12.7 vs. 70 ± 14.4 years, P &lt; 0.001), male (70.7% vs. 51.5%, P &lt; 0.001), had lower prevalence of atrial fibrillation (13.0% vs. 20.7%, P = 0.008) and lower SHR (0.88 ± 0.20 vs. 0.99 ± 26, P &lt; 0.001). Patients with high SHR (≥0.97) were slightly older than those with low SHR (&lt;0.97) and were more likely to have diabetes mellitus. On multivariate analysis, higher SHR was independently associated with poor functional outcomes (adjusted odds ratio 3.85, 95% confidence interval 1.59–9.09, P = 0.003).

Conclusion
SHR appears to be an important predictor of functional outcomes in patients with AIS undergoing IVT. This may have important implications on the role of glycaemic control in the acute management of ischaemic stroke.
Incidence, risk factors and validation of the RABBIT score for serious infections in a cohort of 1557 patients with rheumatoid arthritis
Authors: Thomas Konstantinos , Lazarini Argyro , Kaltsonoudis Evripidis , Voulgari Paraskevi V , Drosos Alexandros A , Repa Argyro , Sali Ainour Molla Ismail , Sidiropoulos Prodromos , Tsatsani Panagiota , Gazi Sousana , Evangelia Argyriou , Boki Kyriaki A , Katsimbri Pelagia , Boumpas Dimitrios , Fragkiadaki Kalliopi , Tektonidou Maria G , Sfikakis Petros P , Karagianni Konstantina , Sakkas Lazaros I , Grika Eleftheria P , Vlachoyiannopoulos Panagiotis G , Evangelatos Gerasimos , Iliopoulos Alexios , Dimitroulas Theodoros , Garyfallos Alexandros , Melissaropoulos Konstantinos , Georgiou Panagiotis , Areti Maria , Georganas Constantinos , Vounotrypidis Periklis , Georgiopoulos Georgios , Kitas George D , Vassilopoulos Dimitrios 
Published: August 2020

Abstract

Objectives
Predicting serious infections (SI) in patients with rheumatoid arthritis (RA) is crucial for the implementation of appropriate preventive measures. Here we aimed to identify risk factors for SI and to validate the RA Observation of Biologic Therapy (RABBIT) risk score in real-life settings.

Methods
A multi-centre, prospective, RA cohort study in Greece. Demographics, disease characteristics, treatments and comorbidities were documented at first evaluation and one year later. The incidence of SI was recorded and compared with the expected SI rate using the RABBIT risk score.

Results
A total of 1557 RA patients were included. During follow-up, 38 SI were recorded [incidence rate ratio (IRR): 2.3/100 patient-years]. Patients who developed SI had longer disease duration, higher HAQ at first evaluation and were more likely to have a history of previous SI, chronic lung disease, cardiovascular disease and chronic kidney disease. By multivariate analysis, longer disease duration (IRR: 1.05; 95% CI: 1.005, 1.1), history of previous SI (IRR: 4.15; 95% CI: 1.7, 10.1), diabetes (IRR: 2.55; 95% CI: 1.06, 6.14), chronic lung disease (IRR: 3.14; 95% CI: 1.35, 7.27) and daily prednisolone dose ≥10 mg (IRR: 4.77; 95% CI: 1.47, 15.5) were independent risk factors for SI. Using the RABBIT risk score in 1359 patients, the expected SI incidence rate was 1.71/100 patient-years, not different from the observed (1.91/100 patient-years; P = 0.97).

Conclusion
In this large real-life, prospective study of RA patients, the incidence of SI was 2.3/100 patient-years. Longer disease duration, history of previous SI, comorbidities and high glucocorticoid dose were independently associated with SI. The RABBIT score accurately predicted SI in our cohort.
The Effects of Erratic Ratings on Placebo Response and Signal Detection in the Roche Bitopertin Phase 3 Negative Symptom Studies—A Post Hoc Analysis
Authors: Umbricht Daniel , Kott Alan , Daniel David G 
Published: August 2020

Abstract

Objective
In the current post hoc analyses, we assessed the impact of erratic ratings, a marker of questionable measurement quality, on placebo and drug response and drug-placebo separation in schizophrenia negative symptom trials.

Methods
Data were obtained from three phase 3, multi-center, 24-week, randomized, double-blind, placebo-controlled trials with bitopertin in the treatment of negative symptoms of schizophrenia. Erratic ratings were operationally defined as at least one occurrence of at least a 20% change in negative symptom factor score in the opposite direction at consecutive visits. The effect of erratic ratings on placebo and drug response and drug-placebo separation was assessed by the protocol on a subject and site-level using a mixed model repeated measures analysis.

Results
Placebo response was significantly increased in the presence of erratic ratings, both at the subject and site levels. Treatment response in the presence of erratic ratings was mixed and inconsistent across doses and protocols. In most cases removing data generated by subjects and sites with erratic ratings resulted in a numerical increase of drug-placebo difference favoring treatment. Additionally, in this post hoc analysis, 10 mg of bitopertin separated statistically significantly from placebo at the end of study in one of the protocols.

Discussion
Erratic rating patterns appear to be consistently associated with increased response to placebo and a mixed response to treatment in the bitopertin negative symptoms trials and to have degraded drug-placebo separation. As a quality indicator, they may flag the need for enhanced quality control of affected sites in clinical trials.
Fiber degrading enzymes increased monosaccharides release and fermentation in corn distillers dried grains with solubles and wheat middlings steeped without or with protease
Authors: Rho Youngji , Patterson Rob , Joye Iris , Martinez Mario , Squires E James , Kiarie Elijah G 
Published: August 2020

Abstract
Treating fibrous feed ingredients with exogenous feed enzymes may improve their utilization in monogastric animals. An in vitro study was conducted to determine the effects of steeping corn distillers dried grains with solubles (DDGS) or wheat middlings (WM) with exogenous feed enzymes. Four treatments were arranged as follows: 1) co-product steeped with water (CON), 2) CON plus 0.5-g fiber degrading enzymes (FDE), 3) CON plus 0.5-g protease (PRO), and 4) CON plus 0.5-g FDE and 0.5 g PRO (FDEPRO). The FDE contained about 62,000, 37,000, and 8,000 U/g of xylanase, cellulase, and β-glucanase, respectively, whereas activities in PRO amounted to 2,500,000, 1,300,000, and 800,000 U/g of acid, alkaline, and neutral proteases, respectively. Briefly, 50 g of DDGS or WM samples (n = 8) were mixed with 500-mL water with or without enzymes and steeped for 0 to 72 h at 37 °C with continuous agitation. The pH, concentration of monosaccharides, and organic acids in the supernatant and apparent disappearance (AD) of fiber in solids were measured at 0, 12, 24, 48, and 72 h. There was treatment and time interaction (P &lt; 0.005) on monosaccharides concentration. At 12 h, arabinose and glucose concentrations were similar (P &gt; 0.05) between FDE and FDEPRO but higher (P = 0.002) than for CON in DDGS. For WM, FDE, and FDEPRO had higher (P &lt; 0.001) xylose concentration than CON and PRO, whereas glucose concentration was higher (P &lt; 0.001) for enzymes than CON at 12 h. However, FDEPRO had higher (P &lt; 0.001) xylose concentration than CON, whereas xylose concentration for FDE and PRO was intermediate at 24 h. There was an interaction (P &lt; 0.05) between treatment and time effect on lactic acid concentration in DDGS and WM (P &lt; 0.005), and acetic acid concentration in WM (P &lt; 0.001). In general, monosaccharide concentration was higher between 12 and 24 h and decreased after 48 h, whereas the pH decreased, and concentration of organic acids increased continuously over time (P &lt; 0.05). The AD of NDF and ADF in DDGS was greater (P = 0.001) for FDE and FDEPRO than CON and PRO at 72 h. In WM, enzymes increased (P = 0.007) AD of NDF relative to CON at 72 h. Nonetheless, greater (P &lt; 0.05) AD of fiber was observed between 48 and 72 h. In conclusion, although there were differences in responses among co-products, fiber degrading enzymes increased release of fermentable monosaccharides from co-products at 12 to 24 h of steeping and these effects were not extended with the addition of protease.
Hydraulic traits of Neotropical canopy liana and tree species across a broad range of wood density: implications for predicting drought mortality with models
Authors: De Guzman Mark E , Acosta-Rangel Aleyda , Winter Klaus , Meinzer Frederick C , Bonal Damien , Santiago Louis S 
Published: August 2020

AbstractWood density (WD) is often used as a proxy for hydraulic traits such as vulnerability to drought-induced xylem cavitation and maximum water transport capacity, with dense-wooded species generally being more resistant to drought-induced xylem cavitation, having lower rates of maximum water transport and lower sapwood capacitance than light-wooded species. However, relationships between WD and the hydraulic traits that they aim to predict have not been well established in tropical forests, where modeling is necessary to predict drought responses for a high diversity of unmeasured species. We evaluated WD and relationships with stem xylem vulnerability by measuring cavitation curves, sapwood water release curves and minimum seasonal water potential (Ψmin) on upper canopy branches of six tree species and three liana species from a single wet tropical forest site in Panama. The objective was to better understand coordination and trade-offs among hydraulic traits and the potential utility of these relationships for modeling purposes. We found that parameters from sapwood water release curves such as capacitance, saturated water content and sapwood turgor loss point (Ψtlp,x) were related to WD, whereas stem vulnerability curve parameters were not. However, the water potential corresponding to 50% loss of hydraulic conductivity (P50) was related to Ψtlp,x and sapwood osmotic potential at full turgor (πo,x). Furthermore, species with lower Ψmin showed lower P50, Ψtlp,x and πo,x suggesting greater drought resistance. Our results indicate that WD is a good easy-to-measure proxy for some traits related to drought resistance, but not others. The ability of hydraulic traits such as P50 and Ψtlp,x to predict mortality must be carefully examined if WD values are to be used to predict drought responses in species without detailed physiological measurements.
Salinity has little effect on photosynthetic and respiratory responses to seasonal temperature changes in black mangrove (Avicennia germinans) seedlings
Authors: Aspinwall Michael J , Faciane Martina , Harris Kylie , O’Toole Madison , Neece Amy , Jerome Vrinda , Colón Mateo , Chieppa Jeff , Feller Ilka C 
Published: August 2020

Abstract
Temperature and salinity are important regulators of mangrove range limits and productivity, but the physiological responses of mangroves to the interactive effects of temperature and salinity remain uncertain. We tested the hypothesis that salinity alters photosynthetic responses to seasonal changes in temperature and vapor pressure deficit (D), as well as thermal acclimation _of leaf respiration in black mangrove (Avicennia germinans). To test this hypothesis, we grew seedlings of A. germinans in an outdoor experiment for ~ 12 months under four treatments spanning 0 to 55 ppt porewater salinity. We repeatedly measured seedling growth and in situ rates of leaf net photosynthesis (Asat) and stomatal conductance to water vapor (gs) at prevailing leaf temperatures, along with estimated rates of Rubisco carboxylation (Vcmax) and electron transport for RuBP regeneration (Jmax), and measured rates of leaf respiration at 25 °C (Rarea25). We developed empirical models describing the seasonal response of leaf gas exchange and photosynthetic capacity to leaf temperature and D, and the response of Rarea25 to changes in mean daily air temperature. We tested the effect of salinity on model parameters. Over time, salinity had weak or inconsistent effects on Asat, gs and Rarea25. Salinity also had little effect on the biochemical parameters of photosynthesis (Vcmax, Jmax) and individual measurements of Asat, gs, Vcmax and Jmax showed a similar response to seasonal changes in temperature and D across all salinity treatments. Individual measurements of Rarea25 showed a similar inverse relationship with mean daily air temperature across all salinity treatments. We conclude that photosynthetic responses to seasonal changes in temperature and D, as well as seasonal temperature acclimation of leaf R, are largely consistent across a range of salinities in A. germinans. These results might simplify predictions of photosynthetic and respiratory responses to temperature in young mangroves.