bluuebunny/crossref_metadata_2025_split huggingface dataset:
Performing parentage analysis for polysomic inheritances based on allelic phenotypes
Authors: Huang Kang , Huber Gwendolyn , Ritland Kermit , Dunn Derek W , Li Baoguo 
Published: February 2021

AbstractPolyploidy poses several problems for parentage analysis. We present a new polysomic inheritance model for parentage analysis based on genotypes or allelic phenotypes to solve these problems. The effects of five factors are simultaneously accommodated in this model: (1) double-reduction, (2) null alleles, (3) negative amplification, (4) genotyping errors and (5) self-fertilization. To solve genotyping ambiguity (unknown allele dosage), we developed a new method to establish the likelihood formulas for allelic phenotype data and to simultaneously include the effects of our five chosen factors. We then evaluated and compared the performance of our new method with three established methods by using both simulated data and empirical data from the cultivated blueberry (Vaccinium corymbosum). We also developed and compared the performance of two additional estimators to estimate the genotyping error rate and the sample rate. We make our new methods freely available in the software package polygene, at http://github.com/huangkang1987/polygene.
Joint ambient noise autocorrelation and receiver function analysis of the Moho
Authors: Mroczek Stefan , Tilmann Frederik 
Published: February 2021

SUMMARYIn the field of seismic interferometry, cross-correlations are used to extract Green’s function from ambient noise data. By applying a single station variation of the method, using autocorrelations, we are in principle able to retrieve zero-offset reflections in a stratified Earth. These reflections are valuable as they do not require an active seismic source and, being zero-offset, are better constrained in space than passive earthquake based measurements. However, studies that target Moho signals with ambient noise autocorrelations often give ambiguous results with unclear Moho reflections. Using a modified processing scheme and phase-weighted stacking, we determine the Moho P-wave reflection time from vertical autocorrelation traces for a test station with a known simple crustal structure (HYB in Hyderabad, India). However, in spite of the simplicity of the structure, the autocorrelation traces show several phases not related to direct reflections. Although we are able to match some of these additional phases in a qualitative way with synthetic modelling, their presence makes it hard to identify the reflection phases without prior knowledge. This prior knowledge can be provided by receiver functions. Receiver functions (arising from mode conversions) are sensitive to the same boundaries as autocorrelations, so should have a high degree of comparability and opportunity for combined analysis but in themselves are not able to independently resolve VP, VS and Moho depth. Using the timing suggested by the receiver functions as a guide, we observe the Moho S-wave reflection on the horizontal autocorrelation of the north component but not on the east component. The timing of the S reflection is consistent with the timing of the PpSs–PsPs receiver function multiple, which also depends only on the S velocity and Moho depth. Finally, we combine P receiver functions and autocorrelations from HYB in a depth–velocity stacking scheme that gives us independent estimates for VP, VS and Moho depth. These are found to be in good agreement with several studies that also supplement receiver functions to obtain unique crustal parameters. By applying the autocorrelation method to a portion of the EASI transect crossing the Bohemian Massif in central Europe, we find approximate consistency with Moho depths determined from receiver functions and spatial coherence between stations, thereby demonstrating that the method is also applicable for temporary deployments. Although application of the autocorrelation method requires great care in phase identification, it has the potential to resolve both average crustal P and S velocities alongside Moho depth in conjunction with receiver functions.
A retrospective ‘real-world’ cohort study of azole therapeutic drug monitoring and evolution of antifungal resistance in cystic fibrosis
Authors: Di Paolo M , Hewitt L , Nwankwo E , Ni M , Vidal-Diaz A , Fisher M C , Armstrong-James D , Shah A 
Published: February 2021

Abstract

Background
Individuals with cystic fibrosis (CF) have an increased susceptibility to fungal infection/allergy, with triazoles often used as first-line therapy. Therapeutic drug monitoring (TDM) is essential due to significant pharmacokinetic variability and the recent emergence of triazole resistance worldwide.

Objectives
In this retrospective study we analysed the ‘real-world’ TDM of azole therapy in a large CF cohort, risk factors for subtherapeutic dosing, and the emergence of azole resistance.

Methods
All adults with CF on azole therapy in a large single UK centre were included. Clinical demographics, TDM and microbiology were analysed over a 2 year study period (2015–17) with multivariate logistic regression used to identify risk factors for subtherapeutic dosing.

Results
91 adults were treated with azole medication during the study period. A high prevalence of chronic subtherapeutic azole dosing was seen with voriconazole (60.8%) and itraconazole capsule (59.6%) use, representing significant risk factors for subtherapeutic levels. Rapid emergence of azole resistance was additionally seen over the follow-up period with a 21.4% probability of CF patients developing a resistant fungal isolate after 2 years. No significant relationship was found however between subtherapeutic azole dosing and azole resistance emergence.

Conclusions
Our study demonstrates a high prevalence of subtherapeutic azole levels in CF adults with increased risk using itraconazole capsules and voriconazole therapy. We show rapid emergence of azole resistance highlighting the need for effective antifungal stewardship. Further large longitudinal studies are needed to understand the effects of antifungal resistance on outcome in CF and the implications of subtherapeutic dosing on resistance evolution.
Antimicrobial stewardship of antiseptics that are pertinent to wounds: the need for a united approach
Authors: Maillard Jean-Yves , Kampf Günter , Cooper Rose 
Published: February 2021

AbstractLong before the nature of infection was recognized, or the significance of biofilms in delayed healing was understood, antimicrobial agents were being used in wound care. In the last 70 years, antibiotics have provided an effective means to control wound infection, but the continued emergence of antibiotic-resistant strains and the documented antibiotic tolerance of biofilms has reduced their effectiveness. A range of wound dressings containing an antimicrobial (antibiotic or non-antibiotic compound) has been developed. Whereas standardized methods for determining the efficacy of non-antibiotic antimicrobials in bacterial suspension tests were developed in the early twentieth century, standardized ways of evaluating the efficacy of antimicrobial dressings against microbial suspensions and biofilms are not available. Resistance to non-antibiotic antimicrobials and cross-resistance with antibiotics has been reported, but consensus on breakpoints is absent and surveillance is impossible. Antimicrobial stewardship is therefore in jeopardy. This review highlights these difficulties and in particular the efficacy of current non-antibiotic antimicrobials used in dressings, their efficacy, and the challenges of translating in vitro efficacy data to the efficacy of dressings in patients. This review calls for a unified approach to developing standardized methods of evaluating antimicrobial dressings that will provide an improved basis for practitioners to make informed choices in wound care.
Clinical data sharing improves quality measurement and patient safety
Authors: D’Amore John D , McCrary Laura K , Denson Jody , Li Chun , Vitale Christopher J , Tokachichu Priyaranjan , Sittig Dean F , McCoy Allison B , Wright Adam 
Published: February 2021

AbstractObjectiveAccurate and robust quality measurement is critical to the future of value-based care. Having incomplete information when calculating quality measures can cause inaccuracies in reported patient outcomes. This research examines how quality calculations vary when using data from an individual electronic health record (EHR) and longitudinal data from a health information exchange (HIE) operating as a multisource registry for quality measurement.Materials and MethodsData were sampled from 53 healthcare organizations in 2018. Organizations represented both ambulatory care practices and health systems participating in the state of Kansas HIE. Fourteen ambulatory quality measures for 5300 patients were calculated using the data from an individual EHR source and contrasted to calculations when HIE data were added to locally recorded data.ResultsA total of 79% of patients received care at more than 1 facility during the 2018 calendar year. A total of 12 994 applicable quality measure calculations were compared using data from the originating organization vs longitudinal data from the HIE. A total of 15% of all quality measure calculations changed (P &lt; .001) when including HIE data sources, affecting 19% of patients. Changes in quality measure calculations were observed across measures and organizations.DiscussionThese results demonstrate that quality measures calculated using single-site EHR data may be limited by incomplete information. Effective data sharing significantly changes quality calculations, which affect healthcare payments, patient safety, and care quality.ConclusionsFederal, state, and commercial programs that use quality measurement as part of reimbursement could promote more accurate and representative quality measurement through methods that increase clinical data sharing.
Effects of administering exogenous bovine somatotropin to beef heifers during the first trimester on conceptus development as well as steroid- and eicosanoid-metabolizing enzymes
Authors: Sanford Carla D , Owen Megan P T , Oosthuizen Nicola , Fontes Pedro L P , Vonnahme Kimberly A , Nelson Megan , Reyaz Arshi , Lemley Caleb O , DiLorenzo Nicolas , Cliff Lamb Graham 
Published: February 2021

Abstract
The aim of this study was to evaluate the effect of bovine somatotropin (bST) on fetal and placental development during the first third of gestation in beef heifers. Angus heifers (n = 97) were randomly assigned to either receive a 500-mg injection of bST (BST) biweekly on days 0, 15, 29, 43, and 57 of gestation or not receive bST (CTL) throughout the experiment. Body weight (BW) was assessed on days −9, −3, 0, 15, 22, 29, 43, 50, 57, 64, and 77, while blood samples were collected on days 0, 22, 50, and 64. Pregnancy status was determined via transrectal ultrasonography on days 29 and 64. A subset of pregnant heifers (BST, n = 7; CTL, n = 5) were harvested on day 84, and complete gravid reproductive tracts and liver tissue were collected for analysis. Cytochrome P450 1A (CYP1A), 2C (CYP2C), 3A (CYP3A), and uridine 5′-diphospho-glucuronosyltransferase (UGT) activities were determined. Mean change in BW and average daily gain of heifers between fixed-time artificial insemination (day 0) and day 77 did not differ between treatments (P ≥ 0.05). Mean concentrations of insulin-like growth factor 1 (IGF-1) were greater (P &lt; 0.001) in BST (347 ± 27.7 ng/mL) compared with CTL (135 ± 32.8 ng/mL) heifers. Mean placental weight, fetal membrane weight, uterine weight, and ovarian and corpus luteum (CL) weights, as well as fetal morphometric data, did not differ (P ≥ 0.05) between treatments. However, BST heifers had greater (P = 0.03) quantities of combined fetal fluid compared with CTL (521.6 ± 22.9 vs. 429.6 ± 27.14 g, respectively). Tendencies were observed for BST heifers to have reproductive tracts with fewer placentomes (P = 0.08) and fetuses with greater umbilical diameters (P = 0.09) compared with CTL. The activity of CYP1A did not differ (P ≥ 0.05) within the maternal and fetal liver, caruncle, cotyledon, or CL tissue samples between treatments. Furthermore, CYP3A activity was only observed in maternal liver samples and was not different between treatments (P ≥ 0.05). Interestingly, CYP2C activity was greater (P = 0.01) in the liver of BST vs. CTL heifers, and UGT activity was greater (P = 0.02) in the CL from BST heifers compared with CTL. In conclusion, the administration of bST during the first third of gestation increased plasma concentrations of IGF-1, which resulted in an increase in fetal fluid, decrease in placentome number, and greater umbilical diameter, but failed to alter fetal development.
Economic and environmental assessments of combined genetics and nutrition optimization strategies to improve the efficiency of sustainable pork production
Authors: Soleimani Tara , Hermesch Susanne , Gilbert Hélène 
Published: February 2021

Abstract
We evaluated the economic and environmental impacts of strategies that incorporated selection for pig feed efficiency and dietary optimization based on a single or multiple objectives tailored to meet the population nutritional requirements, with the goal to optimize sustainable farm feed efficiency. The economic and environmental features of the strategy were evaluated using life cycle assessment (LCA) and bio-economic models. An individual trait-based LCA model was applied to evaluate global warming potential, terrestrial acidification potential, freshwater eutrophication potential (EP), and land occupation of the combined genetics and nutrition optimization to produce 1 kg of live pig weighing 120 kg at the farm gate. A parametric individual trait-based bio-economic model was developed and applied to determine the cost breakdown, revenue, and profit to be gained from a 120-kg live pig at the farm gate. Data from two genetic lines with contrasted levels of feed efficiency were used to apply the combined genetics and nutrition optimization: accounting for the average nutritional requirements for each line, the individual pig responses to diets formulated for least cost, least environmental impacts, or minimum combination of costs and environmental impacts objectives were predicted with INRAPorc. Significant differences in the environmental impacts (P &lt; 0.0001) and profit (P &lt; 0.05) between lines predicted with the same reference diet showed that selection for feed efficiency (residual feed intake) in pigs improves pig production sustainability. When pig responses were simulated with their line-optimized diets, except for EP, all the line environmental impacts were lower (P &lt; 0.05) than with the reference diet. The high correlations of feed conversion ratio with the environmental impacts (&gt; 0.82) and the profit (&lt; −0.88) in both lines underlined the importance of feed efficiency as a lever for the sustainability of pig production systems. Implementing combined genetics and nutrition optimization, the inherent profit and environmental differences between the genetic lines were predicted to be reduced from 23.4% with the reference diet to 7.6% with the diet optimized jointly for economic and environmental objectives (joint diet). Consequently, for increased pig sustainability, diet optimization for sustainability objectives should be applied to cover the specific nutritional requirements arising in the herd from the pigs genetic level.
Validating the effectiveness of alternative euthanasia techniques using penetrating captive bolt guns in mature swine (Sus scrofa domesticus)
Authors: Kramer Scott A , Wagner Brooklyn K , Robles Ivelisse , Moeller Steve J , Bowman Andrew S , Kieffer Justin D , Arruda Andréia Gonçalves , Cressman Michael D , Pairis-Garcia Monique D 
Published: February 2021

AbstractEuthanasia of mature swine is challenging. Temporal and behind-the-ear locations are two sites that have been identified as alternatives to the more commonly used frontal placement. In stage one, the effectiveness of two penetrating captive bolt gun styles (cylinder or pistol) was evaluated using frontal, temporal, and behind-the-ear placement in anesthetized mature swine (n = 36; weight: 267 ± 41 kg). For stage one, when evaluating treatment efficacy by sex, the cylinder-style equipment was 100% effective in achieving death when applied to all cranial locations (frontal, temporal, and behind-the-ear) for sows; however, the pistol-style equipment was only 100% effective when applied at the behind-the-ear location for sows. For boars, the cylinder-style equipment was 100% effective when applied to the frontal and behind-the-ear location, but the pistol-style equipment was not effective for any cranial location in boars. Therefore, the pistol–frontal, pistol–temporal, pistol–behind-the-ear, and cylinder–temporal were not included for boars, and pistol–frontal and pistol–temporal were not included for sows in stage two. In stage two, commercial, mixed-breed, mature swine (n = 42; weight: 292 +/− 56 kg) were randomly assigned to one of four treatments based on the inclusion criteria described in stage one. A three-point traumatic brain injury (TBI) score (0 = normal; 1 = some abnormalities; 2 = grossly abnormal, unrecognizable) was used to evaluate six neuroanatomical structures (cerebral cortex, cerebellum, hypothalamus, thalamus, pons, and brain stem), and the presence of hemorrhage was also noted. All treatments were 100% effective in stage two. A significant interaction between gun style and placement was determined on predicting total TBI as the cylinder style produced a higher total TBI score compared with the pistol type of the magnitude of +2.8 (P &lt; 0.01). The cylinder style tended to produce a greater TBI score than the pistol in the temporal location (+1.2; P = 0.08). No difference was noted for TBI score behind-the-ear between the cylinder- and pistol-style gun (P &gt; 0.05). TBI tended to be less in boars compared with sows (−0.6; P = 0.08). Hemorrhage was observed in frontal, parietal, occipital, and temporal lobes. This study demonstrated that the cylinder-style captive bolt gun more effectively resulted in brain trauma and death compared with a pistol-style gun and the behind-the-ear and temporal placement showed promise as an alternative placement site for euthanizing mature pigs on-farm.
Frozen in the dark: interplay of night-time activity of xanthophyll cycle, xylem attributes, and desiccation tolerance in fern resistance to winter
Authors: Fernández-Marín Beatriz , Arzac Miren Irati , López-Pozo Marina , Laza José Manuel , Roach Thomas , Stegner Matthias , Neuner Gilbert , García-Plazaola José I 
Published: February 2021

Abstract
While most ferns avoid freezing as they have a tropical distribution or shed their fronds, wintergreen species in temperate and boreoalpine ecosystems have to deal with sub-zero temperatures. Increasing evidence has revealed overlapping mechanisms of desiccation and freezing tolerance in angiosperms, but the physiological mechanisms behind freezing tolerance in ferns are far from clear. We evaluated photochemical and hydraulic parameters in five wintergreen fern species differing in their ability to tolerate desiccation. We assessed frond freezing tolerance, ice nucleation temperature and propagation pattern, and xylem anatomical traits. Dynamics of photochemical performance and xanthophyll cycle were evaluated during freeze–thaw events under controlled conditions and, in selected species, in the field. Only desiccation-tolerant species, which possessed a greater fraction of narrow tracheids (&lt;18 μm) than sensitive species, tolerated freezing. Frond freezing occurred in the field at –3.4 ± 0.9 °C (SD) irrespective of freezing tolerance, freezable water content, or tracheid properties. Even in complete darkness, maximal photochemical efficiency of photosystem II was down-regulated concomitantly with zeaxanthin accumulation in response to freezing. This was reversible upon re-warming only in tolerant species. Our results suggest that adaptation for freezing tolerance is associated with desiccation tolerance through complementary xylem properties (which may prevent risk of irreversible cavitation) and effective photoprotection mechanisms. The latter includes de-epoxidation of xanthophylls in darkness, a process evidenced for the first time directly in the field.
A temperature regime that disrupts clock-controlled starch mobilization induces transient carbohydrate starvation, resulting in compact growth
Authors: van Hoogdalem Mark , Shapulatov Umidjon , Sergeeva Lidiya , Busscher-Lange Jacqueline , Schreuder Mariëlle , Jamar Diaan , van der Krol Alexander R 
Published: February 2021

Abstract
In nature, plants are usually subjected to a light/temperature regime of warm days and cold nights (referred to as +DIF). Compared with growth under +DIF, Arabidopsis plants show compact growth under the same photoperiod, but with an inverse temperature regime (cold days and warm nights: –DIF). Here we show that –DIF differentially affects the phase and amplitude of core clock gene expression. Under –DIF, the phase of the morning clock gene CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) is delayed, similar to that of plants grown on low sucrose. Indeed, under –DIF, carbohydrate (CHO) starvation marker genes are specifically up-regulated at the end of the night (EN) in Arabidopsis rosettes. However, only in inner rosette tissue (small sink leaves and petioles of older leaves) are sucrose levels lower under –DIF compared with under +DIF, suggesting that sucrose in source leaf blades is not sensed for CHO status and that sucrose transport from source to sink may be impaired at EN. CHO starvation under –DIF correlated with increased starch breakdown during the night and decreased starch accumulation during the day. Moreover, we demonstrate that different ways of inducing CHO starvation all link to reduced growth of sink leaves. Practical implications for control of plant growth in horticulture are discussed.
Characterizing outflows in the Cygnus X region
Authors: Deb Soumen , Kothes Roland , Rosolowsky Erik 
Published: February 2021

ABSTRACT
In this paper, we perform an analysis of 13 outflows in the Cygnus X star-forming region. We use the James Clerk Maxwell Telescope observations of 13CO(3–2) and C18O(3–2) molecular emission lines combined with archival 12CO(3–2) data. Using these new observations, we measure the mechanical properties of the outflows, and identify the associated protostars, finding their properties consistent with previous surveys of outflows throughout the Milky Way. Finally, we develop and test a method to measure the same properties using the existing 12CO(3–2) line data alone, finding the properties agree to within a factor of 2.