bluuebunny/crossref_metadata_2025_split huggingface dataset:
Whole-genome variation of transposable element insertions in a maize diversity panel
Authors: Qiu Yinjie , O’Connor Christine H , Della Coletta Rafael , Renk Jonathan S , Monnahan Patrick J , Noshay Jaclyn M , Liang Zhikai , Gilbert Amanda , Anderson Sarah N , McGaugh Suzanne E , Springer Nathan M , Hirsch Candice N 
Published: July 2021

AbstractIntact transposable elements (TEs) account for 65% of the maize genome and can impact gene function and regulation. Although TEs comprise the majority of the maize genome and affect important phenotypes, genome-wide patterns of TE polymorphisms in maize have only been studied in a handful of maize genotypes, due to the challenging nature of assessing highly repetitive sequences. We implemented a method to use short-read sequencing data from 509 diverse inbred lines to classify the presence/absence of 445,418 nonredundant TEs that were previously annotated in four genome assemblies including B73, Mo17, PH207, and W22. Different orders of TEs (i.e., LTRs, Helitrons, and TIRs) had different frequency distributions within the population. LTRs with lower LTR similarity were generally more frequent in the population than LTRs with higher LTR similarity, though high-frequency insertions with very high LTR similarity were observed. LTR similarity and frequency estimates of nested elements and the outer elements in which they insert revealed that most nesting events occurred very near the timing of the outer element insertion. TEs within genes were at higher frequency than those that were outside of genes and this is particularly true for those not inserted into introns. Many TE insertional polymorphisms observed in this population were tagged by SNP markers. However, there were also 19.9% of the TE polymorphisms that were not well tagged by SNPs (R2 &lt; 0.5) that potentially represent information that has not been well captured in previous SNP-based marker-trait association studies. This study provides a population scale genome-wide assessment of TE variation in maize and provides valuable insight on variation in TEs in maize and factors that contribute to this variation.
The Association Between Longevity-Associated FOXO3 Allele and Heart Disease in Septuagenarians and Octogenarians: The SONIC Study
Authors: Klinpudtan Nonglak , Allsopp Richard C , Kabayama Mai , Godai Kayo , Gondo Yasuyuki , Masui Yukie , Akagi Yuya , Srithumsuk Werayuth , Sugimoto Ken , Akasaka Hiroshi , Takami Yoichi , Takeya Yasushi , Yamamoto Koichi , Ikebe Kazunori , Yasumoto Saori , Ogawa Madoka , Ishizaki Tatsuro , Arai Yasumichi , Rakugi Hiromi , Chen Randi , Willcox Bradley J , Willcox D Craig , Kamide Kei 
Published: July 2021

Abstract
The G allele of FOXO3 gene (single-nucleotide polymorphism; rs2802292) is strongly associated with human longevity. However, knowledge of the effect of FOXO3 in older populations, men or women, with heart disease is limited. This cross-sectional study in Japan included 1836 older adults in the 70- and 80-year-old groups. DNA samples isolated from buffy coat samples of peripheral blood were used to genotype FOXO3 (rs2802292). Self-reports were used to obtain heart disease data according to physician diagnosis. Multiple logistic regression was used to test the association by adjusting for the traditional risk factor of heart disease. The prevalence of heart disease in women FOXO3 G-allele carriers was higher than noncarriers (16.7% vs 11.6%, p = .022). The prevalence of coronary heart disease was lower for FOXO3 G carriers in the 70-year-old group for both sexes (men: 9.3% vs 4.3%, p = .042 and women: 10% vs 9%, p = .079, respectively). The G allele was negatively associated with heart disease after adjusting for diabetes, hypertension, dyslipidemia, and smoking in men (odds ratio [OR] = 0.70, 95% confidence intervals [CIs], 0.49–0.99, p = .046), although the association was weaker after full adjustment. In contrast, women carriers of the FOXO3 G allele showed a positive association with heart disease after total adjustment (OR = 1.49, 95% CI, 1.00–2.21, p = .049). In conclusion, the longevity-associated G allele of FOXO3 was observed to have contrasting associations with heart disease prevalence according to sex in older Japanese. To further confirm this association, a longitudinal study and a large sample size will be required.
Frequency domain spectral element method for modelling poroelastic waves in 3-D anisotropic, heterogeneous and attenuative porous media
Authors: Zhan Weichen , Zhuang Mingwei , Liu Qi Qiang , Shi Linlin , Sun Yuefeng , Liu Qing Huo 
Published: July 2021

SUMMARY
Simulating poroelastic waves in large-scale 3-D problems having porous media coupled with elastic solids and fluids is computationally challenging for traditional methods. It is well established that the spectral element method (SEM) is more effective than the traditional methods like the finite element method (FEM) when dealing with complex geophysical problems, for its high-order accuracy with exponential convergence. However, at present, little research has been done for SEM in the frequency domain, which will be more efficient than the time-domain SEM for narrowband simulations with multiple sources, material dispersion and attenuation. Herein, we systematically develop a SEM in the frequency domain to simulate coupled poroelastic, elastic and acoustic waves in anisotropic (i.e. porosity, permeability and elastic coefficients with anisotropy), heterogeneous, and lossy media. Furthermore, we completely remove the dimension inconsistency between the displacement field and the pressure in porous media to reduce the condition number of the system matrix by around 16 orders of magnitude while maintaining the symmetry of the system matrix. To solve the multiphysics coupling problems, we apply different coupling conditions to different interface types, and use basis functions to discretize the corresponding governing equations. Numerical examples show that the proposed SEM can obtain higher accuracy with much fewer unknowns compared with the FEM and has the capacity to solve the large-scale real coupling problems.
Frequency of occurrence and antimicrobial susceptibility of bacteria isolated from respiratory samples of patients hospitalized with pneumonia in Western Europe, Eastern Europe and the USA: results from the SENTRY Antimicrobial Surveillance Program (2016–19)
Authors: Sader Helio S , Streit Jennifer M , Carvalhaes Cecilia G , Huband Michael D , Shortridge Dee , Mendes Rodrigo E , Castanheira Mariana 
Published: July 2021

Abstract

Background
The SENTRY Antimicrobial Surveillance Program monitors the frequency of occurrence and antimicrobial susceptibility of organisms from various infection types worldwide.

Objectives
To evaluate the SENTRY programme results for organisms isolated from respiratory samples of patients hospitalized with probable pneumonia.

Methods
A total of 28 918 bacterial isolates were consecutively collected (one per patient) in 2016–19 from 121 medical centres located in western Europe (W-EU; n = 7966), eastern Europe (E-EU; n = 3182) and the USA (n = 17 770) and then susceptibility tested by reference broth microdilution methods in a central laboratory.

Results
Gram-negative bacilli (GNB) represented 76.3%, 88.6% and 69.1% of organisms; non-fermentative (NF) GNB accounted for 26.9%, 51.8% and 34.6% of organisms in W-EU, E-EU and USA, respectively. Pseudomonas aeruginosa susceptibility to piperacillin/tazobactam and meropenem was 75.4% and 76.9% in W-EU, 57.4% and 48.3% in E-EU, and 76.1% and 74.8% in the USA, respectively. Only 10.4% of Acinetobacter baumannii isolates from E-EU were meropenem susceptible compared with 45.8% in W-EU and 58.8% in the USA. Overall MRSA rates were 21.4% in W-EU and 28.7% in E-EU. In the USA, MRSA rates decreased from 44.8% in 2016 to 40.1% in 2019. Carbapenem resistance among Enterobacterales decreased continuously in the USA from 3.0% in 2016 to 1.7% in 2019 (2.4% overall) and was higher in E-EU (16.6%) than W-EU (2.2%). Klebsiella pneumoniae susceptibility to meropenem was 91.3%, 72.5% and 95.3% in W-EU, E-EU and the USA, respectively.

Conclusions
Rank order and antimicrobial susceptibility of bacteria isolated from patients with pneumonia widely varied by geography. MDR NF-GNB represented an important cause of pneumonia.
Whole-genome re-sequencing association study on yearling wool traits in Chinese fine-wool sheep
Authors: Zhao Hongchang , Zhu Shaohua , Guo Tingting , Han Mei , Chen Bowen , Qiao Guoyan , Wu Yi , Yuan Chao , Liu Jianbin , Lu Zengkui , Sun Weibo , Wang Tianxiang , Li Fanwen , Zhang Yajun , Hou Fujun , Yue Yaojing , Yang Bohui 
Published: July 2021

AbstractTo investigate single nucleotide polymorphism (SNP) loci associated with yearling wool traits of fine-wool sheep for optimizing marker-assisted selection and dissection of the genetic architecture of wool traits, we conducted a genome-wide association study (GWAS) based on the fixed and random model circulating probability unification (FarmCPU) for yearling staple length (YSL), yearling mean fiber diameter (YFD), yearling greasy fleece weight (YGFW), and yearling clean fleece rate (YCFR) by using the whole-genome re-sequenced data (totaling 577 sheep) from the following four fine-wool sheep breeds in China: Alpine Merino sheep (AMS), Chinese Merino sheep (CMS), Qinghai fine-wool sheep (QHS), and Aohan fine-wool sheep (AHS). A total of 16 SNPs were detected above the genome-wise significant threshold (P = 5.45E-09), and 79 SNPs were located above the suggestive significance threshold (P = 5.00E-07) from the GWAS results. For YFD and YGFW traits, 7 and 9 SNPs reached the genome-wise significance thresholds, whereas 10 and 12 SNPs reached the suggestive significance threshold, respectively. For YSL and YCFR traits, none of the SNPs reached the genome-wise significance thresholds, whereas 57 SNPs exceeded the suggestive significance threshold. We recorded 14 genes located at the region of ±50-kb near the genome-wise significant SNPs and 59 genes located at the region of ±50-kb near the suggestive significant SNPs. Meanwhile, we used the Average Information Restricted Maximum likelihood algorithm (AI-REML) in the “HIBLUP” package to estimate the heritability and variance components of the four desired yearling wool traits. The estimated heritability values (h2) of YSL, YFD, YGFW, and YCFR were 0.6208, 0.7460, 0.6758, and 0.5559, respectively. We noted that the genetic parameters in this study can be used for fine-wool sheep breeding. The newly detected significant SNPs and the newly identified candidate genes in this study would enhance our understanding of yearling wool formation, and significant SNPs can be applied to genome selection in fine-wool sheep breeding.
Oscar Wilde and the Confidence Trick
Authors: Boyiopoulos Kostas 
Published: July 2021

Abstract
Critics have long highlighted the centrality of forgery in Oscar Wilde. This essay focuses instead on the idea of the confidence trick in Wilde’s life and work, with a special focus on ‘The Portrait of Mr. W. H.’. The capstone of the confidence trick is the so-called long con, a type of elaborate deception that resembles an extended theatrical performance. With its properties of narrativity and plot-making, the long con subsumes forgery. Its use in literature points to literature itself as a piece of trickery. Through cultural, biographical and textual analysis, this essay dwells on the various striking ways by which Wilde’s fictions are entangled with reality as they are pervaded by the long con trope. By considering Wilde’s perceived image in his 1882 American tour and his brushing shoulders with famous conmen, the essay first suggests that the confidence trick and dandyism share common ground. It demonstrates that the confidence trick is akin to Wilde’s ‘lying’ and catalytic as an aesthetic performance. The cultural consciousness of the confidence trick is strongly present in such works as An Ideal Husband and The Importance of Being Earnest, which are built around long cons. ‘Mr. W. H.’ features a long con and in targeting the reader operates as one. Paradoxically, because of its open exploration of forgery, the story as a confidence trick in literature is failproof, imperceptible, and so perfect.
Total mass density slopes of early-type galaxies using Jeans dynamical modelling at redshifts 0.29 &lt; z &lt; 0.55
Authors: Derkenne Caro , McDermid Richard M , Poci Adriano , Remus Rhea-Silvia , Jørgensen Inger , Emsellem Eric 
Published: July 2021

ABSTRACT
The change of the total mass density slope, γ, of early-type galaxies through cosmic time is a probe of evolutionary pathways. Hydrodynamical cosmological simulations show that at high redshifts density profiles of early-type galaxies were on average steep (γ ∼ −3). As redshift approaches zero, gas-poor mergers progressively cause the total mass density slope to approach the ‘isothermal’ slope of γ ∼ −2. Simulations therefore predict steep density slopes at high redshifts, with little to no evolution in density slopes below z ∼ 1. Gravitational lensing results in the same redshift range find the opposite, namely a significant trend of shallow density slopes at high redshifts, becoming steeper as redshift approaches zero. Gravitational lensing results indicate a different evolutionary mechanism for early-type galaxies than dry merging, such as continued gas accretion or off-axis mergers. At redshift zero, isothermal solutions are obtained by both simulations and dynamical modelling. This work applies the Jeans dynamical modelling technique to observations of galaxies at intermediate redshifts (0.29 &lt; z &lt; 0.55) in order to derive density slopes to address the tension between observations and simulations. We combine two-dimensional kinematic fields from Multi Unit Spectroscopic Explorer data with Hubble Space Telescope photometry. The density slopes of 90 early-type galaxies from the Frontier Fields project are presented. The total sample has a median of γ = −2.11 ± 0.03  (standard error), in agreement with dynamical modelling studies at redshift zero. The lack of evolution in total density slopes in the past 4–6 Gyr supports a dry merging model for early-type galaxy evolution.
High-resolution spectroscopic follow-up of the most metal-poor candidates from SkyMapper DR1.1
Authors: Yong D , Da Costa G S , Bessell M S , Chiti A , Frebel A , Gao X , Lind K , Mackey A D , Marino A F , Murphy S J , Nordlander T , Asplund M , Casey A R , Kobayashi C , Norris J E , Schmidt B P 
Published: July 2021

ABSTRACT
We present chemical abundances for 21 elements (from Li to Eu) in 150 metal-poor Galactic stars spanning −4.1 &lt; [Fe/H] &lt; −2.1. The targets were selected from the SkyMapper survey and include 90 objects with [Fe/H] ≤ −3 of which some 15 have [Fe/H] ≤ −3.5. When combining the sample with our previous studies, we find that the metallicity distribution function has a power-law slope of Δ(log N)/Δ[Fe/H] = 1.51 ± 0.01 dex per dex over the range −4 ≤ [Fe/H] ≤ −3. With only seven carbon-enhanced metal-poor stars in the sample, we again find that the selection of metal-poor stars based on SkyMapper filters is biased against highly carbon-rich stars for [Fe/H] &gt; −3.5. Of the 20 objects for which we could measure nitrogen, 11 are nitrogen-enhanced metal-poor (NEMP) stars. Within our sample, the high NEMP fraction (55 per cent ± 21 per cent) is compatible with the upper range of predicted values (between 12 per cent and 35 per cent). The chemical abundance ratios [X/Fe] versus [Fe/H] exhibit similar trends to previous studies of metal-poor stars and Galactic chemical evolution models. We report the discovery of nine new r-I stars, four new r-II stars, one of which is the most metal-poor known, nine low-α stars with [α/Fe] ≤ 0.15 as well as one unusual star with [Zn/Fe] = +1.4 and [Sr/Fe] = +1.2 but with normal [Ba/Fe]. Finally, we combine our sample with literature data to provide the most extensive view of the early chemical enrichment of the Milky Way Galaxy.
Non-uniqueness in quasar absorption models and implications for measurements of the fine structure constant
Authors: Lee Chung-Chi , Webb John K , Milaković Dinko , Carswell Robert F 
Published: July 2021

ABSTRACT
High resolution spectra of quasar absorption systems provide the best constraints on temporal or spatial changes of fundamental constants in the early Universe. An important systematic that has never before been quantified concerns model non-uniqueness. The absorption structure is generally complicated, comprising many blended lines. This characteristic means any given system can be fitted equally well by many slightly different models, each having a different value of α, the fine structure constant. We use AI Monte Carlo modelling to quantify non-uniqueness. Extensive supercomputer calculations are reported, revealing new systematic effects that guide future analyses: (i) Whilst higher signal to noise and improved spectral resolution produces a smaller statistical uncertainty for α, model non-uniqueness adds a significant additional uncertainty. (ii) Non-uniqueness depends on the line broadening mechanism used. We show that modelling the spectral data using turbulent line broadening results in far greater non-uniqueness, hence this should no longer be done. Instead, for varying α studies, it is important to use the more physically appropriate compound broadening. (iii) We have studied two absorption systems in detail. Generalising thus requires caution. Nevertheless, if non-uniqueness is present in all or most quasar absorption systems, it seems unavoidable that attempts to determine the existence (or non-existence) of spacetime variations of fundamental constants is best approached using a statistical sample.
Large-scale 21 cm signal predictions at cosmic dawn with calibrated subgrid galaxy formation
Authors: Gillet N J F , Aubert D , Mertens F G , Ocvirk P 
Published: July 2021

ABSTRACT
The process of heating and reionization of the Universe at high redshifts links small-scale structures/galaxy formation and large-scale intergalactic medium (IGM) properties. Even if the first one is difficult to observe, an observation window is opening on the second one, with the promising development of current and future radio telescopes. They will permit to observe the 21 cm brightness temperature global signal and fluctuations. The need for large-scale simulations is therefore strong to understand the properties of the IGM that will be observed. However, at the same time, the urge to resolve the structures responsible for those processes is important. We introduce in this study a simulation framework of the cosmic dawn and reionization, based on hydrodynamics and radiative transfer code and a simple subgrid galaxy formation process for 1 Mpc-resolution simulations. Here, this model is calibrated on the state-of-the-art simulation CoDaII. This scheme permits us to follow consistently dark matter, hydrodynamics, and radiative transfer evolution on large scales, while the subgrid model deals with the galaxy formation scale, in particular, taking into account the different feedback on the star formation. We process the simulation to produce a simulated 21 cm signal as close as possible to the observations.
A systematic study of photoionized emission and warm absorption signatures of the NLS1 Mrk 335
Authors: Liu H , Parker M L , Jiang J , Kara E , Bambi Cosimo , Grupe D , Komossa S 
Published: July 2021

ABSTRACT
We present an analysis of all the archival high-resolution spectra of the narrow-line Seyfert 1 galaxy Mrk 335 obtained with Reflection Grating Spectrometer (RGS) onboard XMM–Newton. The spectra show rich emission and absorption features in low and intermediate flux intervals. We model the emission lines with the pion_xs grid and try to find any possible correlation between the properties of the emitting gas and the source flux. Current data do not allow detailed trace of the response of the line emitting gas to the X-ray flux of Mrk 335, but the flux of the X-ray lines is significantly less variable than the X-ray continuum. We also find that the warm absorber’s properties are not correlated with the flux variability. From the latest XMM–Newton observation in 2019 December, we find that the photoionized emission and distant reflection components have not responded to the flux drop of Mrk 335 from 2018 July. However, the possible existence of partial covering absorber in the 2018–2019 low state of Mrk 335 makes it difficult to constrain the scale of the emitting gas using this lack of response.
A Chinese hamster transcription start site atlas that enables targeted editing of CHO cells
Authors: Shamie Isaac , Duttke Sascha H , Karottki Karen J la Cour , Han Claudia Z , Hansen Anders H , Hefzi Hooman , Xiong Kai , Li Shangzhong , Roth Samuel J , Tao Jenhan , Lee Gyun Min , Glass Christopher K , Kildegaard Helene Faustrup , Benner Christopher , Lewis Nathan E 
Published: July 2021

AbstractChinese hamster ovary (CHO) cells are widely used for producing biopharmaceuticals, and engineering gene expression in CHO is key to improving drug quality and affordability. However, engineering gene expression or activating silent genes requires accurate annotation of the underlying regulatory elements and transcription start sites (TSSs). Unfortunately, most TSSs in the published Chinese hamster genome sequence were computationally predicted and are frequently inaccurate. Here, we use nascent transcription start site sequencing methods to revise TSS annotations for 15 308 Chinese hamster genes and 3034 non-coding RNAs based on experimental data from CHO-K1 cells and 10 hamster tissues. We further capture tens of thousands of putative transcribed enhancer regions with this method. Our revised TSSs improves upon the RefSeq annotation by revealing core sequence features of gene regulation such as the TATA box and the Initiator and, as exemplified by targeting the glycosyltransferase gene Mgat3, facilitate activating silent genes by CRISPRa. Together, we envision our revised annotation and data will provide a rich resource for the CHO community, improve genome engineering efforts and aid comparative and evolutionary studies.
In vivoandin vitrohuman gene essentiality estimations capture contrasting functional constraints
Authors: Caldu-Primo Jose Luis , Verduzco-Martínez Jorge Armando , Alvarez-Buylla Elena R , Davila-Velderrain Jose 
Published: July 2021

AbstractGene essentiality estimation is a popular empirical approach to link genotypes to phenotypes. In humans, essentiality is estimated based on loss-of-function (LoF) mutation intolerance, either from population exome sequencing (in vivo) data or CRISPR-based in vitro perturbation experiments. Both approaches identify genes presumed to have detrimental consequences on the organism upon mutation. Are these genes constrained by having key cellular/organismal roles? Do in vivo and in vitro estimations equally recover these constraints? Insights into these questions have important implications in generalizing observations from cell models and interpreting disease risk genes. To empirically address these questions, we integrate genome-scale datasets and compare structural, functional and evolutionary features of essential genes versus genes with extremely high mutational tolerance. We found that essentiality estimates do recover functional constraints. However, the organismal or cellular context of estimation leads to functionally contrasting properties underlying the constraint. Our results suggest that depletion of LoF mutations in human populations effectively captures organismal-level functional constraints not experimentally accessible through CRISPR-based screens. Finally, we identify a set of genes (OrgEssential), which are mutationally intolerant in vivo but highly tolerant in vitro. These genes drive observed functional constraint differences and have an unexpected preference for nervous system expression.