bluuebunny/crossref_metadata_2025_split huggingface dataset:
Continuous chromosome-scale haplotypes assembled from a single interspecies F1 hybrid of yak and cattle
Authors: Rice Edward S , Koren Sergey , Rhie Arang , Heaton Michael P , Kalbfleisch Theodore S , Hardy Timothy , Hackett Peter H , Bickhart Derek M , Rosen Benjamin D , Ley Brian Vander , Maurer Nicholas W , Green Richard E , Phillippy Adam M , Petersen Jessica L , Smith Timothy P L 
Published: April 2020

Abstract

Background
The development of trio binning as an approach for assembling diploid genomes has enabled the creation of fully haplotype-resolved reference genomes. Unlike other methods of assembly for diploid genomes, this approach is enhanced, rather than hindered, by the heterozygosity of the individual sequenced. To maximize heterozygosity and simultaneously assemble reference genomes for 2 species, we applied trio binning to an interspecies F1 hybrid of yak (Bos grunniens) and cattle (Bos taurus), 2 species that diverged nearly 5 million years ago. The genomes of both of these species are composed of acrocentric autosomes.

Results
We produced the most continuous haplotype-resolved assemblies for a diploid animal yet reported. Both the maternal (yak) and paternal (cattle) assemblies have the largest 2 chromosomes in single haplotigs, and more than one-third of the autosomes similarly lack gaps. The maximum length haplotig produced was 153 Mb without any scaffolding or gap-filling steps and represents the longest haplotig reported for any species. The assemblies are also more complete and accurate than those reported for most other vertebrates, with 97% of mammalian universal single-copy orthologs present.

Conclusions
The high heterozygosity inherent to interspecies crosses maximizes the effectiveness of the trio binning method. The interspecies trio binning approach we describe is likely to provide the highest-quality assemblies for any pair of species that can interbreed to produce hybrid offspring that develop to sufficient cell numbers for DNA extraction.
Exact and approximate reflection/transmission responses from a layer containing vertical fractures
Authors: Jin Song , Stovas Alexey 
Published: April 2020

SUMMARYAnalyses of vertical fractures are of great interest in characterizing the fluid flow and minimum in situ stress direction in reservoirs. Long-wavelength equivalent orthorhombic (ORT) media typically characterize the anisotropy induced by a set of vertical parallel fractures or two sets of vertical and mutually orthogonal fractures embedded into a transversely isotropic medium with a vertical symmetry axis (VTI). Reflection and transmission (R/T) responses quantify wave amplitude variations in 1-D media and help to reveal the model property enclosing the heterogeneity. Conventionally, the R/T responses are analysed for an interface bounded by two half-spaces. However, for a plane wave travelling through a subsurface layer, the wave scattering effects at the top and bottom of the layer interact with each other. For a continuous infinite ORT space cut in two halves along the horizontal symmetry plane, we focus on the plane wave R/T responses from an ORT layer that is placed between the two halves, where the azimuths of the vertical symmetry plane in the layer and in the upper and lower half-spaces are identical. The R/T coefficient modelling method can be found in many publications for the ORT layer with an arbitrary finite thickness. We decompose the exact R/T coefficients into series expansions that correspond to different orders of intrabed multiples in the ORT layer. Under the weak-contrast assumption for the ORT half-spaces and the ORT layer, we use the anisotropic background medium to obtain the first-order R/T coefficient approximations and second-order reflectivity approximations. There is no constraint for the middle layer thickness in the obtained first-order reflectivity approximations. In the proposed first-order transmissivity approximations and second-order reflectivity approximations, the layer thickness is assumed to be thin to obtain appropriate approximations for a few wave modes. The isotropic background medium is also considered for weakly anisotropic models to obtain simpler approximations that facilitate parametric analyses. For the ORT layer with its thickness much smaller than the propagating wave's wavelength, the influences of the layer thickness on R/T coefficients can be inspected conveniently from the derived approximations. Particularly, the R/T coefficients are analysed for the model which would be a homogeneous VTI medium, if the vertical parallel fractures were absent from the middle layer. Numerical tests demonstrate that the proposed R/T coefficient approximations perform well for the thin ORT layer. The approximation accuracy decreases when the thin layer thickness increases.
Protein–protein interaction network with machine learning models and multiomics data reveal potential neurodegenerative disease-related proteins
Authors: Yu Xinjian , Lai Siqi , Chen Hongjun , Chen Ming 
Published: April 2020

AbstractResearch of protein–protein interaction in several model organisms is accumulating since the development of high-throughput experimental technologies and computational methods. The protein–protein interaction network (PPIN) is able to examine biological processes in a systematic manner and has already been used to predict potential disease-related proteins or drug targets. Based on the topological characteristics of the PPIN, we investigated the application of the random forest classification algorithm to predict proteins that may cause neurodegenerative disease, a set of pathological changes featured by protein malfunction. By integrating multiomics data, we further showed the validity of our machine learning model and narrowed down the prediction results to several hub proteins that play essential roles in the PPIN. The novel insights into neurodegeneration pathogenesis brought by this computational study can indicate promising directions for future experimental research.
Impaired mitochondrial–endoplasmic reticulum interaction and mitophagy in Miro1-mutant neurons in Parkinson’s disease
Authors: Berenguer-Escuder Clara , Grossmann Dajana , Antony Paul , Arena Giuseppe , Wasner Kobi , Massart François , Jarazo Javier , Walter Jonas , Schwamborn Jens C , Grünewald Anne , Krüger Rejko 
Published: April 2020

Abstract
Mitochondrial Rho GTPase 1 (Miro1) protein is a well-known adaptor for mitochondrial transport and also regulates mitochondrial quality control and function. Furthermore, Miro1 was associated with mitochondrial-endoplasmic reticulum (ER) contact sites (MERCs), which are key regulators of cellular calcium homeostasis and the initiation of autophagy. Impairments of these mechanisms were linked to neurodegeneration in Parkinson’s disease (PD). We recently revealed that PD fibroblasts harboring Miro1 mutations displayed dysregulations in MERC organization and abundance, affecting mitochondrial homeostasis and clearance. We hypothesize that mutant Miro1 impairs the function of MERCs and mitochondrial dynamics, altering neuronal homeostasis and integrity in PD. PD skin fibroblasts harboring the Miro1-R272Q mutation were differentiated into patient-derived neurons. Live-cell imaging and immunocytochemistry were used to study mitophagy and the organization and function of MERCs. Markers of autophagy or mitochondrial function were assessed by western blotting. Quantification of organelle juxtapositions revealed an increased number of MERCs in patient-derived neurons. Live-cell imaging results showed alterations of mitochondrial dynamics and increased sensitivity to calcium stress, as well as reduced mitochondrial clearance. Finally, western blot analysis indicated a blockage of the autophagy flux in Miro1-mutant neurons. Miro1-mutant neurons display altered ER-mitochondrial tethering compared with control neurons. This alteration likely interferes with proper MERC function, contributing to a defective autophagic flux and cytosolic calcium handling capacity. Moreover, mutant Miro1 affects mitochondrial dynamics in neurons, which may result in disrupted mitochondrial turnover and altered mitochondrial movement.
Lipid storage patterns in marine copepods: environmental, ecological, and intrinsic drivers
Authors: Cavallo Alessandro , Peck Lloyd S 
Published: April 2020

AbstractSeasonality of food supply is a major driver of physiological and ecological adaptations of marine zooplankton. High-latitude marine copepods accumulate lipids for maintenance and reproductive maturation during the food-depleted winter period. The relationship between latitude and lipid storage in copepods is well established, but it is influenced by many factors, such as trophic position, sex, and depth distribution. In this study, the influence of latitude and collection depth, trophic level, sex, and the presence or absence of dormancy on the relative amount and composition of lipids stored was assessed by analysing published data. Our analyses confirmed higher lipid contents (expressed as % dry weight) in high-latitude species, and in deep-dwelling tropical copepods compared to shallow-living ones. Contrary to our original hypothesis, carnivorous and herbivorous copepods had similar lipid levels. Copepod species that undergo dormancy had higher levels of wax ester and were more common at polar and temperate latitudes. Lastly, adult male and female copepods did not significantly differ in the amount of lipids they store, suggesting that the portion of male reproductive investment, which may depend on lipid stores, has been underestimated. Taken together, these results both confirm some previously reported trends and refute others.
Genomic Epidemiology of Invasive Methicillin-Resistant Staphylococcus aureus Infections Among Hospitalized Individuals in Ontario, Canada
Authors: Guthrie Jennifer L , Teatero Sarah , Hirai Sotaro , Fortuna Alex , Rosen Daniel , Mallo Gustavo V , Campbell Jennifer , Pelude Linda , Golding George , Simor Andrew E , Patel Samir N , McGeer Allison , Fittipaldi Nahuel ,   Ontario CNISP Hospital Investigators, Delport Johan , Evans Gerald , Hota Susy , Katz Kevin , Lemieux Camille , Mertz Dominik , Science Michelle , Thampi Nisha 
Published: April 2020

Abstract

Background
Prevention and control of methicillin-resistant Staphylococcus aureus (MRSA) infections remain challenging. In-depth surveillance integrating patient and isolate data can provide evidence to better inform infection control and public health practice.

Methods
We analyzed MRSA cases diagnosed in 2010 (n = 212) and 2016 (n = 214) by hospitals in Ontario, Canada. Case-level clinical and demographic data were integrated with isolate characteristics, including antimicrobial resistance (AMR), classic genotyping, and whole-genome sequencing results.

Results
Community-associated MRSA (epidemiologically defined) increased significantly from 23.6% in 2010 to 43.0% in 2016 (P &lt; .001). The MRSA population structure changed over time, with a 1.5× increase in clonal complex (CC)8 strains and a concomitant decrease in CC5. The clonal shift was reflected in AMR patterns, with a decrease in erythromycin (86.7% to 78.4%, P = .036) and clindamycin resistance (84.3% to 47.9%, P &lt; .001) and a &gt;2-fold increase in fusidic acid resistance (9.0% to 22.5%, P &lt; .001). Isolates within both CC5 and CC8 were relatively genetically diverse. We identified 6 small genomic clusters—3 potentially related to transmission in healthcare settings.

Conclusions
Community-associated MRSA is increasing among hospitalized individuals in Ontario. Clonal shifting from CC5 to CC8 has impacted AMR. We identified a relatively high genetic diversity and limited genomic clustering within these dominant CCs.
Nonalcoholic Fatty Liver Disease and the Development of Metabolic Comorbid Conditions in Patients With Human Immunodeficiency Virus Infection
Authors: Krahn Thomas , Martel Myriam , Sapir-Pichhadze Ruth , Kronfli Nadine , Falutz Julian , Guaraldi Giovanni , Lebouche Bertrand , Klein Marina B , Wong Philip , Deschenes Marc , Ghali Peter , Sebastiani Giada 
Published: April 2020

Abstract

Background
Cardiovascular and liver disease are main causes of death in people with human immunodeficiency virus (HIV) (PWH). In HIV-uninfected patients, nonalcoholic fatty liver disease (NAFLD) is associated with incident metabolic complications. We investigated the effect of NAFLD on development of metabolic comorbid conditions in PWH.

Methods
We included PWH undergoing a screening program for NAFLD using transient elastography. NAFLD was defined as a controlled attenuation parameter ≥248 dB/m with exclusion of other liver diseases. Incident diabetes, hypertension, dyslipidemia, and chronic kidney disease were investigated using survival analysis and Cox proportional hazards.

Results
The study included 485 HIV-monoinfected patients. During a median follow-up of 40.1 months (interquartile range, 26.5–50.7 months), patients with NAFLD had higher incidences of diabetes (4.74 [95% confidence interval, 3.09–7.27] vs 0.87 [.42–1.83] per 100 person-years) and dyslipidemia (8.16 [5.42–12.27] vs 3.99 [2.67–5.95] per 100 person-years) than those without NAFLD. With multivariable analysis, NAFLD was an independent predictor of diabetes (adjusted hazard ratio, 5.13; 95% confidence interval, 2.14–12.31) and dyslipidemia (2.35; 1.34–4.14) development.

Conclusions
HIV-monoinfected patients with NAFLD are at higher risk of incident diabetes and dyslipidemia. Early referral strategies and timely management of metabolic risk may improve outcomes.
A Simple and Sensitive Dispersive Micro-Solid-Phase Extraction Coupled with High-Performance Liquid Chromatography for Quantification of Honokiol and Magnolol in Complex Matrices
Authors: Chu Chu , Li Jing , Wang Shan , Weng Lvnan , Jiang Luyi , Zhang Huan , Liu Caijing , Yan Jizhong 
Published: April 2020

AbstractBackgroundHonokiol and magnolol were considered as markers for the analysis of Cortex Magnoliae Officinalis, its related Chinese Patent Medicines and their metabolites. However, the determination of these two analytes in a water-soluble sample is difficult and therefore requires a more efficient method.ObjectiveTo develop a sensitive method for the determination of honokiol and magnolol in a water-soluble sample for better quality control of Cortex Magnoliae Officinalis and its related Chinese Patent Medicines.MethodIn this work, a combination of dispersive micro-solid-phase extraction (DMSPE) and high-performance liquid chromatography (HPLC) has been developed for simultaneous preconcentration and determination of honokiol and magnolol in complex bio-samples. Several experimental factors affecting the extraction efficiency were optimized by single factor test.ResultsUnder the optimized extraction conditions, the proposed method exhibited good linearity of not less than 0.9998, satisfactory precision with relative standard deviation of less than 1.3%, and acceptable mean recoveries of 97.3% and 101.5% for honokiol and magnolol, respectively. Furthermore, the method exhibits extremely high sensitivity with detection limits of 0.0097 and 0.0231 ng/mL, which is even more sensitive than those methods developed by MS.ConclusionsThe method established in this study is fast, economic, accurate, easy to operate, and importantly well suited to the extraction and analysis of honokiol and magnolol in a real complex sample matrix.
Crystal structure of adenylate kinase from an extremophilic archaeon Aeropyrum pernix with ATP and AMP
Authors: Shibanuma Yoshinori , Nemoto Naoki , Yamamoto Norifumi , Sampei Gen-Ichi , Kawai Gota 
Published: April 2020

AbstractThe crystal structure of an adenylate kinase from an extremophilic archaeon Aeropyrum pernix was determined in complex with full ligands, ATP-Mg2+ and AMP, at a resolution of 2.0 Å. The protein forms a trimer as found for other adenylate kinases from archaea. Interestingly, the reacting three atoms, two phosphorus and one oxygen atoms, were located almost in line, supporting the SN2 nucleophilic substitution reaction mechanism. Based on the crystal structure obtained, the reaction coordinate was estimated by the quantum mechanics calculations combined with molecular dynamics. It was found that the reaction undergoes two energy barriers; the steps for breaking the bond between the oxygen and γ-phosphorus atoms of ATP to produce a phosphoryl fragment and creating the bond between the phosphoryl fragment and the oxygen atom of the β-phosphate group of ADP. The reaction coordinate analysis also suggested the role of amino-acid residues for the catalysis of adenylate kinase.
NGTS J214358.5−380102 – NGTS discovery of the most eccentric known eclipsing M-dwarf binary system
Authors: Acton Jack S , Goad Michael R , Raynard Liam , Casewell Sarah L , Jackman James A G , Alexander Richard D , Anderson David R , Bayliss Daniel , Bryant Edward M , Burleigh Matthew R , Belardi Claudia , Cooke Benjamin F , Eigmüller Philipp , Gill Samuel , Jenkins James S , Lendl Monika , Louden Tom , McCormac James , Moyano Maximiliano , Nielsen Louise D , Tilbrook Rosanna H , Udry Stéphane , Watson Christopher A , West Richard G , Wheatley Peter J , Vines Jose I 
Published: April 2020

ABSTRACT
We present the discovery of NGTS J214358.5–380102, an eccentric M-dwarf binary discovered by the Next-Generation Transit Survey (NGTS). The system period of 7.618 d is greater than many known eclipsing M-dwarf binary systems. Its orbital eccentricity of $0.323^{+0.0014}_{-0.0037}$ is large relative to the period and semimajor axis of the binary. Global modelling of photometry and radial velocities indicates stellar masses of MA = $0.426 ^{+0.0056}_{-0.0049}$ M⊙, MB = $0.455 ^{+0.0058}_{-0.0052}$ M⊙ and stellar radii RA = $0.461 ^{+0.038}_{-0.025}$ R⊙, RB = $0.411 ^{+0.027}_{-0.039}$ R⊙, respectively. Comparisons with stellar models for low-mass stars show that one star is consistent with model predictions whereas the other is substantially oversized. Spectral analysis of the system suggests a primary of spectral type M3V, consistent with both modelled masses and radii, and with spectral energy distribution fitting of NGTS photometry. As the most eccentric eclipsing M-dwarf binary known, NGTS J214358.5–380102 provides an interesting insight into the strength of tidal effects in the circularization of stellar orbits.
The dynamics of the γ Vel cluster and nearby Vela OB2 association
Authors: Armstrong Joseph J , Wright Nicholas J , Jeffries R D , Jackson R J 
Published: April 2020

ABSTRACT
The kinematics of low-mass stars in nearby OB associations can provide clues about their origins and evolution. Combining the precise positions, proper motions, and parallaxes given in the second Gaia Data Release with radial-velocity measurements obtained with the Hermes spectrograph at the Anglo-Australian Telescope, we have an opportunity to study in detail the kinematics of low-mass stars belonging to the nearby γ Vel cluster and the Vela OB2 association it is projected against. The presence of lithium is used to confirm the youth of our targets. We separate our sample into the cluster and association populations based on the Gaia-ESO Survey membership probabilities their parallaxes, and kinematics. We find strong evidence for expansion in the OB association population with at least 4σ significance along all three axes, though the expansion is notably anisotropic. We discuss these results in the context of cluster and association dispersal theories.
First cosmology results using type Ia supernovae from the Dark Energy Survey: the effect of host galaxy properties on supernova luminosity
Authors: Smith M , Sullivan M , Wiseman P , Kessler R , Scolnic D , Brout D , D’Andrea C B , Davis T M , Foley R J , Frohmaier C , Galbany L , Gupta R R , Gutiérrez C P , Hinton S R , Kelsey L , Lidman C , Macaulay E , Möller A , Nichol R C , Nugent P , Palmese A , Pursiainen M , Sako M , Swann E , Thomas R C , Tucker B E , Vincenzi M , Carollo D , Lewis G F , Sommer N E , Abbott T M C , Aguena M , Allam S , Avila S , Bertin E , Bhargava S , Brooks D , Buckley-Geer E , Burke D L , Carnero Rosell A , Carrasco Kind M , Costanzi M , da Costa L N , De Vicente J , Desai S , Diehl H T , Doel P , Eifler T F , Everett S , Flaugher B , Fosalba P , Frieman J , García-Bellido J , Gaztanaga E , Glazebrook K , Gruen D , Gruendl R A , Gschwend J , Gutierrez G , Hartley W G , Hollowood D L , Honscheid K , James D J , Krause E , Kuehn K , Kuropatkin N , Lima M , MacCrann N , Maia M A G , Marshall J L , Martini P , Melchior P , Menanteau F , Miquel R , Paz-Chinchón F , Plazas A A , Romer A K , Roodman A , Rykoff E S , Sanchez E , Scarpine V , Schubnell M , Serrano S , Sevilla-Noarbe I , Suchyta E , Swanson M E C , Tarle G , Thomas D , Tucker D L , Varga T N , Walker A R ,   (DES Collaboration)
Published: April 2020

ABSTRACT
We present improved photometric measurements for the host galaxies of 206 spectroscopically confirmed type Ia supernovae discovered by the Dark Energy Survey Supernova Program (DES-SN) and used in the first DES-SN cosmological analysis. For the DES-SN sample, when considering a 5D (z, x1, c, α, β) bias correction, we find evidence of a Hubble residual ‘mass step’, where SNe Ia in high-mass galaxies (&gt;1010M⊙) are intrinsically more luminous (after correction) than their low-mass counterparts by $\gamma =0.040\pm 0.019$ mag. This value is larger by 0.031 mag than the value found in the first DES-SN cosmological analysis. This difference is due to a combination of updated photometric measurements and improved star formation histories and is not from host-galaxy misidentification. When using a 1D (redshift-only) bias correction the inferred mass step is larger, with $\gamma =0.066\pm 0.020$ mag. The 1D−5D γ difference for DES-SN is $0.026\pm 0.009$ mag. We show that this difference is due to a strong correlation between host galaxy stellar mass and the x1 component of the 5D distance-bias correction. Including an intrinsic correlation between the observed properties of SNe Ia, stretch and colour, and stellar mass in simulated SN Ia samples, we show that a 5D fit recovers γ with −9 mmag bias compared to a +2 mmag bias for a 1D fit. This difference can explain part of the discrepancy seen in the data. Improvements in modelling correlations between galaxy properties and SN is necessary to ensure unbiased precision estimates of the dark energy equation of state as we enter the era of LSST.
The observed velocity distribution of young pulsars – II. Analysis of complete PSRπ
Authors: Igoshev Andrei P 
Published: April 2020

ABSTRACT
Understanding the natal kicks, or birth velocities, of neutron stars is essential for understanding the evolution of massive binaries and double neutron star formation. We use maximum likelihood methods as published in Verbunt et al. to analyse a new large data set of parallaxes and proper motions measured by Deller et al. This sample is roughly three times larger than number of measurements available before. For both the complete sample and its younger part (spin-down ages τ &lt; 3 Myr), we find that a bimodal Maxwellian distribution describes the measured parallaxes and proper motions better than a single Maxwellian with probability of 99.3 and 95.0 per cent, respectively. The bimodal Maxwellian distribution has three parameters: fraction of low-velocity pulsars and distribution parameters σ1 and σ2 for low- and high-velocity modes. For a complete sample, these parameters are as follows: $42_{-15}^{+17}$ per cent, $\sigma _1=128_{-18}^{+22}$ km s−1, and σ2 = 298 ± 28 km s−1. For younger pulsars, which are assumed to represent the natal kick, these parameters are as follows: $20_{-10}^{+11}$ per cent, $\sigma _1=56_{-15}^{+25}$ km s−1, and σ2 = 336 ± 45 km s−1. In the young population, 5 ± 3 per cent of pulsars have velocities less than 60 km s−1. We perform multiple Monte Carlo tests for the method taking into account realistic observational selection. We find that the method reliably estimates all parameters of the natal kick distribution. Results of the velocity analysis are weakly sensitive to the exact values of scale lengths of the Galactic pulsar distribution.