bluuebunny/crossref_metadata_2025 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

Intact 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 < 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

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

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

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

To 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

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 < z < 0.55
Authors: Derkenne Caro , McDermid Richard M , Poci Adriano , Remus Rhea-Silvia , Jørgensen Inger , Emsellem Eric
Published: July 2021

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 < z < 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

We present chemical abundances for 21 elements (from Li to Eu) in 150 metal-poor Galactic stars spanning −4.1 < [Fe/H] < −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] > −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

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

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

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

Chinese 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

Gene 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.
Multispecies coalescent and its applications to infer species phylogenies and cross-species gene flow
Authors: Jiao Xiyun , Flouri Tomáš , Yang Ziheng
Published: July 2021

Multispecies coalescent (MSC) is the extension of the single-population coalescent model to multiple species. It integrates the phylogenetic process of species divergences and the population genetic process of coalescent, and provides a powerful framework for a number of inference problems using genomic sequence data from multiple species, including estimation of species divergence times and population sizes, estimation of species trees accommodating discordant gene trees, inference of cross-species gene flow and species delimitation. In this review, we introduce the major features of the MSC model, discuss full-likelihood and heuristic methods of species tree estimation and summarize recent methodological advances in inference of cross-species gene flow. We discuss the statistical and computational challenges in the field and research directions where breakthroughs may be likely in the next few years.
Highest-resolution rotation curve of the inner Milky Way proving the galactic shock wave
Authors: Sofue Yoshiaki
Published: July 2021

We present a rotation curve (RC) of the inner Galaxy of the first quadrant at 10° ≤ l ≤ 50° (R = 1.3–6.2 kpc) with the highest spatial (2 pc) and velocity (1.3 km s−1) resolutions. We used 12CO(J = 1–0)-line survey data observed with the Nobeyama 45 m telescope at an effective angular resolution of 20″ (originally 15″), and applied the tangent–velocity method to the longitude–velocity diagrams by employing the Gaussian deconvolution of the individual CO-line profiles. A number of RC bumps, or local variation of rotation velocity, with velocity amplitudes ∼±9 km s−1 and radial scale length ∼0.5–1 kpc are superposed on the mean rotation velocity. The prominent velocity bump and corresponding density variation around R ∼ 4 kpc in the tangential direction of the Scutum arm (4 kpc molecular arm) is naturally explained by an ordinary galactic shock wave in a spiral arm with small pitch angle, not necessarily requiring a bar-induced strong shock.
Subnational Politics and Redistribution in a Federal System: Determinants of Progressive Social Spending in Brazilian States
Authors: Dunn Claire
Published: July 2021

What role do subnational governments play in shaping a country’s redistributive efforts? Existing literature suggests that federalism can be a hindrance to redistribution. Such negative effects may be particularly true of Latin America’s federations due to high levels of regional inequality and malapportioned political institutions. However, in order to fully understand redistribution in federal systems in Latin America, we need to examine not only how subnational governments affect centralized redistributive efforts, but also what efforts these subnational governments are making themselves. In this article, I contribute to our understanding of subnational social spending in Latin America’s largest federation, Brazil. My results suggest that, in Brazil, state governments are constrained actors, but they do pursue different levels of redistributive social spending with higher levels being more likely under left parties.
The well-being and the will of the people amid COVID-19
Authors: Rosales Renniel Jayson Jacinto , Adia Crizlene Magpantay , Miral Kiara Cristine Macuha
Published: July 2021

The well-being and the will of the Filipino people are now to be considered. With many people gathering and having leisure time, the well-being of the people is being balanced now. The spiritual, mental and social well-being of the people are being satisfied but with the consequence of putting our safety at stake because of the seemingly unending threat of the COVID-19 pandemic in the Philippines. We know that we want a normal life, but it seems too much for the people to stay at home while seeing other countries enjoy a post-pandemic life.
Enemies of the future? Questioning the regimes of promising in emerging science and technology
Authors: Robinson Douglas K R , Audétat Marc , Joly Pierre-Benoit , Van Lente Harro
Published: July 2021

This editorial introduces the basic idea and content of the special section ‘Enemies of the future? Questioning the regimes of promising in emerging science and technology’. It sheds light on how visions and stories of technological futures are being produced and, in combination, have stabilized into ‘regimes of promising’ that shape emerging technoscientific domains and guide research, innovation, and governance within these domains. The special section zooms in to particular illustrative instances that reveal the dynamics of the dominant regime of promising and also reveal how they are breaking down and in some cases being replaced by alternatives. The purpose of this special section is to show the importance of regimes of promising for research and innovation policy and to stimulate further discussions on alternative regimes of promising and their ramifications.
Effects of grain adaptation programs and antimicrobial feed additives on performance and nutrient digestibility of Bos indicus cattle fed whole shelled corn
Authors: Mobiglia Andrea M , Camilo Fernando R , Couto Victor R M , Castro Flavio G F , Drouillard James S , Gouvêa Vinícius N , Fernandes Juliano J R
Published: July 2021

Two experiments were conducted to evaluate the effects of feed additives [monensin (MON); 30 mg/kg of dry matter (DM), and virginiamycin (VM); 25 mg/kg DM] and grain adaptation programs [adding roughage (ROU; sugarcane bagasse) or not (NO-ROU) during the 20-d adaptation period] on performance, carcass characteristics, and nutrient digestibility of Bos indicus cattle fed finishing diets containing 85% whole shelled corn and 15% of a pelleted protein-mineral-vitamin supplement. In Exp.1, 105 Nellore bulls [initial body weight (BW) = 368 ± 25 kg] were used in a complete randomized block design with a 2 × 2 factorial arrangement of treatments, consisting of two feed additives (MON and VM) associated with two adaptation programs (ROU or NO-ROU during the 20-d adaptation period). Effects of feed additives × adaptation programs were not detected (P ≥ 0.13). Feed additives did not affect dry matter intake (DMI), average daily gain (ADG), and feed efficiency (G:F) during the 20-d adaptation period (P ≥ 0.35). During the total feeding period (105 d), feeding MON decreased DMI (P ≤ 0.03) compared to VM. Adding sugarcane bagasse to finishing diets during the 20-d adaptation period (ROU) increased ADG (P = 0.05) and G:F (P = 0.03), and tended to increase BW (P = 0.09) compared to NO-ROU. In Exp. 2, 10 ruminally cannulated Nellore steers (BW = 268 ± 38 kg) were used in a completely randomized design to evaluate the effects of the two feed additives used in the Exp. 1 (MON and VM; 5 steers/treatment) on DMI, total apparent digestibility of nutrients, and ruminal fermentation characteristics. No differences in DMI, total tract apparent digestibility of nutrients, and ruminal fermentation characteristics were observed between MON and VM (P ≥ 0.32). An effect of sampling day (P < 0.001) was observed for ruminal pH, which was greater on day 0 compared to day 7, 14, and 21 of the experimental period (P ≤ 0.05). In summary, supplementing monensin and virginiamycin for finishing Nellore bulls fed whole shelled corn diets, resulted in similar growth performance and carcass characteristics. Including sugarcane bagasse to adapt finishing bulls to no-roughage diets containing whole shelled corn is an alternative to increase growth performance.
Knowledge on prevention, diagnosis and treatment of snakebite envenoming among doctors in snakebite-dense regions in Sri Lanka
Authors: Darshani Saumya , Gnanathasan Ariaranee , Arambepola Carukshi , Chang Thashi
Published: July 2021

Background

Sri Lanka is one of the highest envenoming reporting countries globally with >80 000 snakebites per year. Among other factors, knowledge of snakebite among doctors predominantly determines patient outcomes.

Methods

Using a pretested 72-item self-administered questionnaire, we assessed knowledge on identifying common snake species, signs of envenoming and management of venomous snakebites among 280 doctors working in eight state hospitals in regions where snakebite prevalence is highest in Sri Lanka.

Results

Visually, 92.1% correctly identified a cobra and 74.3% identified a Russell's viper, but only 30% could identify a hump-nosed viper (HNV). Syndromic identification of snakes was best for the krait (71.8%) followed by the cobra (59.6%), but poor for the HNV (30%). The median knowledge scores of pictorial and syndromic snake identification, indoor preventive measures and indications of antivenom were <75% of the maximum score. Apart from 62.5% who expected the victim to bring the snake along to the hospital, most doctors selected the correct options of pre-hospital care. The duration of work experience did not influence the competency of syndromic identification. Utilisation of local guidelines was associated with better knowledge in antivenom usage (odds ratio 2.22 [95% confidence interval 1.04 to 5.36]; p=0.03).

Conclusions

Specific deficiencies of core knowledge in snakebite management exist among doctors working in snakebite prevalent regions.
DNA barcoding and coalescent-based delimitation of endosymbiotic clevelandellid ciliates (Ciliophora: Clevelandellida): a shift to molecular taxonomy in the inventory of ciliate diversity in panesthiine cockroaches
Authors: Pecina Lukáš , Vďačný Peter
Published: July 2021

Phylogenetically distinct lineages may be hidden behind identical or highly similar morphologies. The phenomenon of morphological crypticity has been recently detected in symbiotic ciliates of the family Clevelandellidae, as multivariate and Fourier shape analyses failed to distinguish genetically distinct taxa. To address the question of species boundaries, the phylogenetic information contained in the rDNA cistron of clevelandellid ciliates, which had been isolated from the digestive tract of blaberid cockroaches, was studied using a multifaceted statistical approach. Multigene phylogenies revealed that the genus Clevelandella is paraphyletic containing members of the genus Paraclevelandia. To resolve the paraphyly of Clevelandella, two new genera, Anteclevelandella gen. nov. and Rhynchoclevelandella gen. nov., are proposed based on morphological synapomorphies and shared molecular characters. Multigene analyses and Bayesian species delimitation supported the existence of 13 distinct species within the family Clevelandellidae, eight of which represent new taxa. Moreover, two new Nyctotherus species were recognized within the clade that is sister to the Clevelandellidae. According to the present distance and network analyses, the first two domains of the 28S rRNA gene showed much higher power for species discrimination than the 18S rRNA gene and ITS region. Therefore, the former molecular marker was proposed to be a suitable group-specific barcode for the family Clevelandellidae.
Sensitivity of Venturia carpophila from China to Five Fungicides and Characterization of Carbendazim-Resistant Isolates
Authors: Zhou Yang , Fan Fei , Chaisiri Chingchai , Zhu Yi-Ting , Zhao Yang , Luo Meng-Ke , Li Xi-Cheng , Yin Liang-Fen , Yin Wei-Xiao , Luo Chao-Xi
Published: July 2021

Peach scab is a fungal disease caused by Venturia carpophila that can significantly reduce peach yield and quality. Fungicide application is the main control measure for peach scab worldwide. To better understand the fungicide-resistance status and devise suitable management strategies, the sensitivity of 135 single-spore V. carpophila isolates to the commonly used fungicides carbendazim, iprodione, propiconazole, azoxystrobin, and boscalid were determined using a microtiter plate test method. Results showed that the mean effective concentrations to cause inhibitions by 50% (EC50) of tested isolates to iprodione, propiconazole, azoxystrobin, and boscalid were 16.287, 0.165, 0.570, and 0.136 µg/ml, respectively. The EC50 values of V. carpophila isolates to four fungicides displayed unimodal frequency distributions, indicating no resistance occurred to these fungicides. On the contrary, bimodal frequency distribution was observed for carbendazim, indicating that V. carpophila developed resistance to carbendazim. Resistance was widely detected from all 14 provinces studied. Molecular analysis showed that the point mutation E198K of the TUB2 gene determined high resistance, whereas E198G conferred moderate resistance. Moderate and high resistances were stable, and the resistant isolates did not show significant fitness penalties. On the contrary, some resistant isolates showed better competitiveness under certain stresses. This is the first report to detect the sensitivity of V. carpophila to fungicides, which enables future monitoring of fungicide resistance and provides basic information to allow the design of suitable peach scab management strategies.
Influence of Spatial Planting Arrangement of Winter Rye Cover Crop on Corn Seedling Disease and Corn Productivity
Authors: Kurtz Sarah M. , Acharya Jyotsna , Kaspar Thomas C. , Robertson Alison E.
Published: July 2021

Despite numerous environmental benefits associated with cover crop (CC) use, some farmers are reluctant to include CCs in their production systems because of reported yield declines in corn. There are numerous potential reasons for this yield decline, including seedling disease. A winter rye CC can serve as a “green bridge” for corn seedling pathogens. We hypothesized that proximity of corn seedling roots to decaying rye CC roots contributes to corn seeding disease. An experimental field plot and an on-farm study were conducted over 2 years to evaluate growth, development, and disease severity of corn seedlings planted at various distances from decaying winter rye CC plants. The experimental field plot study was conducted in a no-till corn–soybean rotation with five replications of a winter rye CC treatment seeded as (i) no-CC control, (ii) broadcast, (iii) 19-cm drilled rows, and (iv) 76-cm drilled rows. The on-farm study was no-till corn–soybean rotation with four replications of a winter rye CC seeded as 38-cm drilled rows, 76-cm drilled rows, and no-CC control. The corn was planted on 76-cm rows shortly after rye was terminated. With multiple seeding arrangements of winter rye, corn was planted at different distances from winter rye. Corn radicle root rot severity and incidence, shoot height, shoot dry weight, corn height and chlorophyll at VT (tasseling), ear parameters, and yield were collected. Soil samples were taken in the corn row and the interrow at winter rye termination, corn planting, and corn growth stage V3 (three leaves with fully developed collars) to estimate the abundance of Pythium clade B members present in soil samples. Our results showed that increased distance between winter rye residue and corn reduced seedling disease and Pythium clade B populations in the radicles and soil and increased shoot dry weight, leaf chlorophyll, plant height, and yield. This suggests that physically distancing the corn crop from the winter rye CC is one way to reduce the negative effects of a winter rye CC on corn.
Effect of Planting into a Green Winter Cereal Rye Cover Crop on Growth and Development, Seedling Disease, and Yield of Corn
Authors: Acharya J. , Moorman T. B. , Kaspar T. C. , Lenssen A. W. , Gailans S. , Robertson A. E.
Published: July 2021

Terminating winter cereal rye (Secale cereale L.) cover crops ≥10 days before planting (DBP) corn is recommended to minimize seedling disease and potential yield loss. In Iowa, cold temperatures and frequent precipitation can prevent farmers from following that recommendation and sometimes force them to plant corn while the rye plants are still green, referred to as “planting green” (PG). A field trial was established to evaluate the effect of rye termination shortly before or after corn planting on growth, seedling root disease, and yield of corn. A rye cover crop was terminated 17 and 3 DBP and 6 and 12 days after planting (DAP) corn; corn planted following no rye was included as a control. Rye biomass, C/N ratio, and N accumulation increased when terminated 6 or 12 DAP corn compared with rye terminated 17 or 3 DBP corn. Corn seedlings were taller from the PG treatments. More radicle root rot was observed when rye was terminated 3 DBP, 6 DAP, and 12 DAP corn than for the 17 DBP treatment and the no-rye control. Generally, greater Pythium clade B populations were detected on radicles and seminal roots of corn from the PG treatments. Corn populations, ears, or barren plants were not affected by the treatments. In both years, the no-rye control had the greatest corn yield and the 12 DAP treatment had the lowest yield. Our results suggest that PG increased corn seedling root disease and contributed to reduced corn yield.
First Report of Leaf Spot Caused by Septoria villarsiae on Nymphoides peltata in the United States
Authors: De Souza Monique , Singh Raghuwinder , Harms Nathan E. , McPhedran John , Smart Alicyn N.
Published: July 2021

Nymphoides peltata, commonly known as yellow floating heart, is a freshwater aquatic plant with floating leaves. It is a highly invasive aquatic weed that has been introduced into several countries, including Ireland, New Zealand, Sweden, and the United States. In September 2019, N. peltata plants exhibiting leaf spots were collected from a private pond near Buxton, York County, Maine. Leaf spots were present on a majority of plants, and pycnidia were observed in the center of the spots. Individual pycnidia were aseptically transferred to 1/4-strength potato dextrose agar. Dark gray to black slow-growing colonies were observed between 7 and 14 days. Based on the morphological characteristics, the fungus was identified as Septoria sp. Translation elongation factor 1-alpha gene was amplified, and a 570-bp sequence resulted in 100 and 99.74% homology with Septoria villarsiae strains CBS565.88 and CBS514.78 isolated from N. peltata in the Netherlands, respectively. Previously, S. villarsiae has been reported on Limnanthemum nymphoides from India and on N. peltata from Korea, Poland, Romania, and the Netherlands. To our knowledge, this is the first report of leaf spot caused by S. villarsiae on N. peltata in the United States.
Personalized Positive End-Expiratory Pressure and Tidal Volume in Acute Respiratory Distress Syndrome: Bedside Physiology-Based Approach
Authors: Mauri Tommaso
Published: July 2021

OBJECTIVES:

Positive end-expiratory pressure and tidal volume may have a key role for the outcome of patients with acute respiratory distress syndrome. The variety of acute respiratory distress syndrome phenotypes implies personalization of those settings. To guide personalized positive end-expiratory pressure and tidal volume, physicians need to have an in-depth understanding of the physiologic effects and bedside methods to measure the extent of these effects. In the present article, a step-by-step physiologic approach to select personalized positive end-expiratory pressure and tidal volume at the bedside is described.

DATA SOURCES:

The present review is a critical reanalysis of the traditional and latest literature on the topic.

STUDY SELECTION:

Relevant clinical and physiologic studies on positive end-expiratory pressure and tidal volume setting were reviewed.

DATA EXTRACTION:

Reappraisal of the available physiologic and clinical data.

DATA SYNTHESIS:

Positive end-expiratory pressure is aimed at stabilizing alveolar recruitment, thus reducing the risk of volutrauma and atelectrauma. Bedside assessment of the potential for lung recruitment is a preliminary step to recognize patients who benefit from higher positive end-expiratory pressure level. In patients with higher potential for lung recruitment, positive end-expiratory pressure could be selected by physiology-based methods balancing recruitment and overdistension. In patients with lower potential for lung recruitment or in shock, positive end-expiratory pressure could be maintained in the 5–8 cm H2O range. Tidal volume induces alveolar recruitment and improves gas exchange. After setting personalized positive end-expiratory pressure, tidal volume could be based on lung inflation (collapsed lung size) respecting safety thresholds of static and dynamic lung stress. Positive end-expiratory pressure and tidal volume could be kept stable for some hours in order to allow early recognition of changes in the clinical course of acute respiratory distress syndrome but also frequently reassessed to avoid crossing of safety thresholds.

CONCLUSIONS:

The setting of personalized positive end-expiratory pressure and tidal volume based on sound physiologic bedside measures may represent an effective strategy for treating acute respiratory distress syndrome patients.
Cardiopulmonary Exercise Testing in Critically Ill Coronavirus Disease 2019 Survivors: Evidence of a Sustained Exercise Intolerance and Hypermetabolism
Authors: Joris Maurice , Minguet Pauline , Colson Camille , Joris Jean , Fadeur Marjorie , Minguet Gregory , Guiot Julien , Misset Benoit , Rousseau Anne-Françoise
Published: July 2021

OBJECTIVES:

To investigate exercise capacity at 3 and 6 months after a prolonged ICU stay.

DESIGN:

Observational monocentric study.

SETTING:

A post-ICU follow-up clinic in a tertiary university hospital in Liège, Belgium.

PATIENTS:

Patients surviving an ICU stay greater than or equal to 7 days for a severe coronavirus disease 2019 pneumonia and attending our post-ICU follow-up clinic.

MEASUREMENTS AND MAIN RESULTS:

Cardiopulmonary and metabolic variables provided by a cardiopulmonary exercise testing on a cycle ergometer were collected at rest, at peak exercise, and during recovery. Fourteen patients (10 males, 59 yr [52–62 yr], all obese with body mass index > 27 kg/m2) were included after a hospital stay of 40 days (35–53 d). At rest, respiratory quotient was abnormally high at both 3 and 6 months (0.9 [0.83–0.96] and 0.94 [0.86–0.97], respectively). Oxygen uptake was also abnormally increased at 3 months (8.24 mL/min/kg [5.38–10.54 mL/min/kg]) but significantly decreased at 6 months (p = 0.013). At 3 months, at the maximum workload (67% [55–89%] of predicted workload), oxygen uptake peaked at 81% (64–104%) of predicted maximum oxygen uptake, with oxygen pulse and heart rate reaching respectively 110% (76–140%) and 71% (64–81%) of predicted maximum values. Ventilatory equivalent for carbon dioxide remains within normal ranges. The 50% decrease in oxygen uptake after maximum effort was delayed, at 130 seconds (115–142 s). Recovery was incomplete with a persistent anaerobic metabolism. At 6 months, no significant improvement was observed, excepting an increase in heart rate reaching 79% (72–95%) (p = 0.008).

CONCLUSIONS:

Prolonged reduced exercise capacity was observed up to 6 months in critically ill coronavirus disease 2019 survivors. This disability did not result from residual pulmonary or cardiac dysfunction but rather from a metabolic disorder characterized by a sustained hypermetabolism and an impaired oxygen utilization.
New sign of anterior zonular dehiscence
Authors: Rossiter-Thornton Michael , Lau Oliver C.F. , Azar Domit A.
Published: July 2021

A new anterior capsule sign was encountered at the time of phacoemulsification surgery in an eye that had previously sustained blunt trauma. A combination of traumatic dehiscence of the anterior zonular fibers, dehiscence between the lens and capsular epithelium, and recumbency at the time of surgery is posited to be the cause of the appearance. To the authors' knowledge, this is the first reported instance of this sign.