bluuebunny/crossref_metadata_2025_split huggingface dataset:
Apixaban for treatment of intracardiac thrombosis in children with congenital heart disease
Authors: Esch Jesse J , Hellinger Amy , Friedman Kevin G , VanderPluym Christina J 
Published: February 2020

Abstract
Apixaban is well studied in adults; paediatric data are extremely limited. We describe 3 children (age 2–6 years, weight 13–17 kg) with congenital heart disease who developed intracardiac thrombosis, and in whom typical treatments had failed (in 1) or were considered impractical (in 2). All were treated with apixaban 2.5 mg orally twice daily with complete (in 2) or partial (in 1) thrombus resolution and no clinical bleeding events.
Developmental population pharmacokinetics–pharmacodynamics and dosing optimization of cefoperazone in children
Authors: Shi Hai-Yan , Wang Kai , Wang Rong-Hua , Wu Yue-E , Tang Bo-Hao , Li Xue , Du Bin , Kan Min , Zheng Yi , Xu Bao-Ping , Shen A-Dong , Su Le-Qun , Jacqz-Aigrain Evelyne , Huang Xin , Zhao Wei 
Published: February 2020

AbstractObjectivesTo evaluate the population pharmacokinetics of cefoperazone in children and establish an evidence-based dosing regimen using a developmental pharmacokinetic–pharmacodynamic approach in order to optimize cefoperazone treatment.MethodsA model-based, open-label, opportunistic-sampling pharmacokinetic study was conducted in China. Blood samples from 99 cefoperazone-treated children were collected and quantified by HPLC/MS. NONMEM software was used for population pharmacokinetic–pharmacodynamic analysis. This study was registered at ClinicalTrials.gov (NCT03113344).ResultsA two-compartment model with first-order elimination agreed well with the experimental data. Covariate analysis showed that current body weight had a significant effect on the pharmacokinetics of cefoperazone. Monte Carlo simulation showed that for bacteria for which cefoperazone has an MIC of 0.5 mg/L, 78.1% of hypothetical children treated with ‘40 mg/kg/day, q8h, IV drip 3 h’ would reach the pharmacodynamic target. For bacteria for which cefoperazone has an MIC of 8 mg/L, 88.4% of hypothetical children treated with 80 mg/kg/day (continuous infusion) would reach the treatment goal. A 160 mg/kg/day (continuous infusion) regimen can cover bacteria for which cefoperazone has an MIC of 16 mg/L. Nevertheless, even if using the maximum reported dose of 160 mg/kg/day (continuous infusion), the ratio of hypothetical children reaching the treatment target was only 9.9% for bacteria for which cefoperazone has an MIC of 32 mg/L.ConclusionsFor cefoperazone, population pharmacokinetics were evaluated in children and an appropriate dosing regimen was developed based on developmental pharmacokinetics–pharmacodynamics. The dose indicated in the instructions (20–160 mg/kg/day) can basically cover the clinically common bacteria for which cefoperazone has an MIC of ≤16 mg/L. However, for bacteria for which the MIC is &gt;16 mg/L, cefoperazone is not a preferred choice.
Identification of gp120 polymorphisms in HIV-1 B subtype potentially associated with resistance to fostemsavir
Authors: Bouba Yagai , Berno Giulia , Fabeni Lavinia , Carioti Luca , Salpini Romina , Aquaro Stefano , Svicher Valentina , Perno Carlo Federico , Ceccherini-Silberstein Francesca , Santoro Maria Mercedes 
Published: February 2020

AbstractObjectivesWe evaluated natural resistance to the new antiretroviral fostemsavir and its potential association with other HIV-1 gp120 polymorphisms.MethodsA total of 1997 HIV-1 B subtype gp120 sequences from the Los Alamos HIV Database were analysed for mutation prevalence at fostemsavir resistance-associated positions and potential association with other gp120 polymorphisms. The role of each fostemsavir resistance-related position and the correlated gp120 mutations, both in protein stability and in reducing the binding affinity between antibody and/or T cell lymphocyte epitopes and the MHC molecules, was estimated.ResultsThe prevalence of fostemsavir resistance mutations was as follows: L116Q (0.05%), S375H/M/T (0.55%/1.35%/17.73%, the latter being far less relevant in determining resistance), M426L (7.56%), M434I (4.21%) and M475I (1.65%). Additionally, the M426R polymorphism had a prevalence of 16.32%. A significantly higher prevalence in X4 viruses versus R5 viruses was found only for S375M (0.69% versus 3.93%, P = 0.009) and S375T (16.60% versus 22.11%, P = 0.030). Some fostemsavirv resistance positions positively and significantly correlated with specific gp120 polymorphisms: S375T with I371V; S375M with L134W, I154V and I323T; M475I with K322A; and M426R with G167N, K192T and S195N. The topology of the dendrogram suggested the existence of three distinct clusters (bootstrap ≥0.98) involving these fostemsavir resistance mutations and gp120 polymorphisms. Interestingly, all clustered mutations are localized in class I/II-restricted T cell/antibody epitopes, suggesting a potential role in immune HIV escape.ConclusionsA low prevalence of known fostemsavir resistance mutations was found in the HIV-1 B subtype. The detection of novel HIV-1 gp120 polymorphisms potentially relevant for fostemsavir resistance deserves new in-depth in vitro investigations.
A system uptake analysis and GUIDES checklist evaluation of the Electronic Asthma Management System: A point-of-care computerized clinical decision support system
Authors: Lam Shin Cheung Jeffrey , Paolucci Natalie , Price Courtney , Sykes Jenna , Gupta Samir ,   for the Canadian Respiratory Research Network
Published: February 2020

Abstract

Objective
Computerized clinical decision support systems (CCDSSs) promise improvements in care quality; however, uptake is often suboptimal. We sought to characterize system use, its predictors, and user feedback for the Electronic Asthma Management System (eAMS)—an electronic medical record system–integrated, point-of-care CCDSS for asthma—and applied the GUIDES checklist as a framework to identify areas for improvement.

Materials and Methods
The eAMS was tested in a 1-year prospective cohort study across 3 Ontario primary care sites. We recorded system usage by clinicians and patient characteristics through system logs and chart reviews. We created multivariable models to identify predictors of (1) CCDSS opening and (2) creation of a self-management asthma action plan (AAP) (final CCDSS step). Electronic questionnaires captured user feedback.

Results
Over 1 year, 490 asthma patients saw 121 clinicians. The CCDSS was opened in 205 of 1033 (19.8%) visits and an AAP created in 121 of 1033 (11.7%) visits. Multivariable predictors of opening the CCDSS and producing an AAP included clinic site, having physician-diagnosed asthma, and presenting with an asthma- or respiratory-related complaint. The system usability scale score was 66.3 ± 16.5 (maximum 100). Reported usage barriers included time and system accessibility.

Discussion
The eAMS was used in a minority of asthma patient visits. Varying workflows and cultures across clinics, physician beliefs regarding asthma diagnosis, and relevance of the clinical complaint influenced uptake.

Conclusions
Considering our findings in the context of the GUIDES checklist helped to identify improvements to drive uptake and provides lessons relevant to CCDSS design across diseases.
Determination of Arsenic in Seafood by Electrothermal Atomic Absorption Spectrometry after Microwave Digestion: NMKL Collaborative Study
Authors: Julshamn Kaare , Thorlacius Arngriimur , Lea Per ,   Collaborators:, Barland Kjetil , Eidem Kari , Gjerstad Karl Olav , Grønningen Dag , Larsen Erik H , Lierhagen Syverin , Liukkonen-Lilja Helena , Lind Birger 
Published: February 2020

Abstract
Eight laboratories participated in an interlaboratory method performance (collaborative) study of a method for the determination of arsenic in foodstuffs of marine origin by electrothermal atomic absorption spectrometry after wet digestion using a microwave oven technique. The study was preceded by a practice round of familiarization samples. The method was tested on 8 materials (cod roe, krill, blue mussel, saithe, scampi, cod fillet, shrimp, and cod extract) ranging in As content from 2 to 75 mg/kg. The materials were sent to participants in the study as blind duplicates, and the participants were asked to perform single determinations on each sample. Repeatability relative standard deviations (RSDr) for As ranged from 6.8 to 17.4%. Reproducibility relative standard deviations (RSDR) ranged from 7.6 to 24%. The highest RSDR value was found for the sample with the highest concentration of As.
Intra- and interobserver reliability for predicting hip preservation versus hip arthroplasty utilizing plain radiographs with comparison of surgeon specialization
Authors: Schultz Kyle , Osborne Jeff , Nelson Karen , Potini Vishnu , Chen Chaoyang , Aljuni Andrew , Bedi Asheesh , Bookout James , Yusaf Michael , Bishai Shariff K 
Published: February 2020

Abstract
Surgeon subspecialty training and practice landscape are formative in diagnostic evaluation and treatment recommendations. Varying recommendations can have substantial impact on patients’ care pathways and outcomes. We investigated intra- and interobserver reliability of treatment predictions for total hip arthroplasty (THA) between surgeons performing arthroplasty and/or arthroscopic hip preservation surgery. Anterior–posterior (AP) hip radiographs cropped to include the lateral sourcil, medial sourcil and foveal region of 53 patients with Tönnis Grade 0–3 were evaluated by five surgeons (two performing arthroplasty, two performing arthroscopic hip preservation and one performing both interventions). Surgeons predicted THA versus no THA as the treatment for each image. Predictions were repeated three times with image order randomized, and intra- and interobserver reliability were calculated. Surgeons were blinded to patient characteristics and clinical information. Interobserver reliability was 0.452 whereas intraobserver reliability ranged from 0.270 to 0.690. Arthroscopic hip preservation surgeons were more likely to predict THA (36.9%) than arthroplasty surgeons (32.7%), P = 0.041. Intra- and interobserver reliabilities of surgeons predicting THA versus no THA based on an AP hip radiograph were average at best. Arthroscopic hip preservation surgeons were more likely to predict THA than arthroplasty surgeons. Subjective surgeon interpretation can lead to variability in recommendations to patients; potentially complicating care pathways.
Plot-level rapid screening for photosynthetic parameters using proximal hyperspectral imaging
Authors: Meacham-Hensold Katherine , Fu Peng , Wu Jin , Serbin Shawn , Montes Christopher M , Ainsworth Elizabeth , Guan Kaiyu , Dracup Evan , Pederson Taylor , Driever Steven , Bernacchi Carl 
Published: February 2020

Abstract
Photosynthesis is currently measured using time-laborious and/or destructive methods which slows research and breeding efforts to identify crop germplasm with higher photosynthetic capacities. We present a plot-level screening tool for quantification of photosynthetic parameters and pigment contents that utilizes hyperspectral reflectance from sunlit leaf pixels collected from a plot (~2 m×2 m) in &lt;1 min. Using field-grown Nicotiana tabacum with genetically altered photosynthetic pathways over two growing seasons (2017 and 2018), we built predictive models for eight photosynthetic parameters and pigment traits. Using partial least squares regression (PLSR) analysis of plot-level sunlit vegetative reflectance pixels from a single visible near infra-red (VNIR) (400–900 nm) hyperspectral camera, we predict maximum carboxylation rate of Rubisco (Vc,max, R2=0.79) maximum electron transport rate in given conditions (J1800, R2=0.59), maximal light-saturated photosynthesis (Pmax, R2=0.54), chlorophyll content (R2=0.87), the Chl a/b ratio (R2=0.63), carbon content (R2=0.47), and nitrogen content (R2=0.49). Model predictions did not improve when using two cameras spanning 400–1800 nm, suggesting a robust, widely applicable and more ‘cost-effective’ pipeline requiring only a single VNIR camera. The analysis pipeline and methods can be used in any cropping system with modified species-specific PLSR analysis to offer a high-throughput field phenotyping screening for germplasm with improved photosynthetic performance in field trials.
Multiple conclusion linear logic: cut elimination and more
Authors: Eades III Harley , de Paiva Valeria 
Published: February 2020

Abstract
Full intuitionistic linear logic (FILL) was first introduced by Hyland and de Paiva, and went against current beliefs that it was not possible to incorporate all of the linear connectives, e.g. tensor, par and implication, into an intuitionistic linear logic. Bierman showed that their formalization of FILL did not enjoy cut elimination as such, but Bellin proposed a small change to the definition of FILL regaining cut elimination and using proof nets. In this note we adopt Bellin’s proposed change and give a direct proof of cut elimination for the sequent calculus. Then we show that a categorical model of FILL in the basic dialectica category is also a linear/non-linear model of Benton and a full tensor model of Melliès’ and Tabareau’s tensorial logic. We give a double-negation translation of linear logic into FILL that explicitly uses par in addition to tensor. Lastly, we introduce a new library to be used in the proof assistant Agda for proving properties of dialectica categories.
Resolving the excess of long GRB’s at low redshift in the Swift era
Authors: Le Truong , Ratke Cecilia , Mehta Vedant 
Published: February 2020

ABSTRACT
Utilizing more than 100 long gamma-ray bursts (LGRBs) in the Swift-Ryan-2012 sample that includes the observed redshifts and jet angles, Le & Mehta performed a timely study of the rate density of LGRBs with an assumed broken power-law GRB spectrum and obtained a GRB-burst-rate functional form that gives acceptable fits to the pre-Swift and Swift redshift, and jet angle distributions. The results indicated an excess of LGRBs at redshift below z ∼ 2 in the Swift sample. In this work, we are investigating if the excess is caused by the cosmological Hubble constant H0, the gamma-ray energy released ${\cal E}_{*\gamma }$, the low- and high-energy indices (α, β) of the Band function, the minimum and maximum jet angles θj, min and θj, max, or that the excess is due to a bias in the Swift-Ryan-2012 sample. Our analyses indicate that none of the above physical parameters resolved the excess problem, but suggesting that the Swift-Ryan-2012 sample is biased with possible afterglow selection effect. The following model physical parameter values provide the best fit to the Swift-Ryan-2012 and pre-Swift samples: the Hubble constant $H_0 = 72 \, {\rm km s^{-1} Mpc^{-1}}$, the energy released ${\cal E}_{*\gamma }\sim 4.47 \times 10^{51}$ erg, the energy indices α ∼ 0.9 and β ∼ −2.13, the jet angles of θj, max ∼ 0.8 rad, and θj, min ∼ 0.065 and ∼0.04 rad for pre-Swift and Swift, respectively, s ∼ −1.55 the jet angle power-law index, and a GRB formation rate that is similar to the Hopkins & Beacom observed star formation history and as extended by Li. Using the Swift Gamma-Ray Burst Host Galaxy Legacy Survey (SHOALS) Swift-Perley LGRB sample and applying the same physical parameter values as above, however, our model provides consistent results with this data set and indicating no excess of LGRBs at any redshift.
Metabolic profile of in vitro derived human embryos is not affected by the mode of fertilization
Authors: Leary Christine , Sturmey Roger G 
Published: February 2020

Abstract
The pattern of metabolism by early embryos in vitro has been linked to a range of phenotypes, including viability. However, the extent to which metabolic function of embryos is modified by specific methods used during ART has yet to be fully described. This study has sought to determine if the mode of fertilization used to create embryos affects subsequent embryo metabolism of substrates. A metabolic profile, including consumption of key substrates and the endogenous triglyceride content of individual IVF and ICSI supernumerary embryos, was assessed and compared. Embryo development and quality was also recorded. All embryos were donated at a single clinical IVF center, on Day 5, from 36 patients aged 18–38 years, The data revealed that consumption of glucose and pyruvate, and production of lactate, did not differ between embryos created by IVF or ICSI. Similarly, the mode of insemination did not impact on the triglyceride content of embryos. However, ICSI-derived embryos displayed a more active turnover of amino acids (P = 0.023), compared to IVF embryos. The specific amino acids produced in higher quantities from ICSI compared to IVF embryos were aspartate (P = 0.016), asparagine (P = 0.04), histidine (P = 0.021) and threonine (P = 0.009) while leucine consumption was significantly lower (P = 0.04). However, importantly neither individual nor collective differences in amino acid metabolism were apparent for sibling oocytes subjected to either mode of fertilization. Embryo morphology (the number of top grade embryos) and development (proportion reaching the blastocyst stage) were comparable in patients undergoing IVF and ICSI. In conclusion, the microinjection of spermatozoa into oocytes does not appear to have an impact on subsequent metabolism and viability. Observed differences in amino acid metabolism may be attributed to male factor infertility of the patients rather than the ICSI procedure per se.
RNase II binds to RNase E and modulates its endoribonucleolytic activity in the cyanobacterium Anabaena PCC 7120
Authors: Zhou Cong , Zhang Juyuan , Hu Xinyu , Li Changchang , Wang Li , Huang Qiaoyun , Chen Wenli 
Published: February 2020

AbstractIn Escherichia coli, the endoribonuclease E (RNase E) can recruit several other ribonucleases and regulatory proteins via its noncatalytic domain to form an RNA degradosome that controls cellular RNA turnover. Similar RNA degradation complexes have been found in other bacteria; however, their compositions are varied among different bacterial species. In cyanobacteria, only the exoribonuclease PNPase was shown to bind to the noncatalytic domain of RNase E. Here, we showed that Alr1240, a member of the RNB family of exoribonucleases, could be co-isolated with RNase E from the lysate of the cyanobacterium Anabaena PCC 7120. Enzymatic analysis revealed that Alr1240 is an exoribonuclease II (RNase II), as it only degrades non-structured single-stranded RNA substrates. In contrast to known RNase E-interacting ribonucleases, which bind to the noncatalytic domain of RNase E, the Anabaena RNase II was shown to associate with the catalytic domain of RNase E. Using a strain in which RNase E and RNase II were tagged in situ with GFP and BFP, respectively, we showed that RNase E and RNase II form a compact complex in vivo by a fluorescence resonance energy transfer (FRET) assay. RNase E activity on several synthetic substrates was boosted in the presence of RNase II, suggesting that the activity of RNase E could be regulated by RNase II-RNase E interaction. To our knowledge, Anabaena RNase II is an unusual ribonuclease that interacts with the catalytic domain of RNase E, and it may represent a new type of RNA degradosome and a novel mechanism for regulating the activity of the RNA degradosome. As Anabaena RNase E interacts with RNase II and PNPase via different regions, it is very likely that the three ribonucleases form a large complex and cooperatively regulate RNA metabolism in the cell.
S3norm: simultaneous normalization of sequencing depth and signal-to-noise ratio in epigenomic data
Authors: Xiang Guanjue , Keller Cheryl A , Giardine Belinda , An Lin , Li Qunhua , Zhang Yu , Hardison Ross C 
Published: February 2020

AbstractQuantitative comparison of epigenomic data across multiple cell types or experimental conditions is a promising way to understand the biological functions of epigenetic modifications. However, differences in sequencing depth and signal-to-noise ratios in the data from different experiments can hinder our ability to identify real biological variation from raw epigenomic data. Proper normalization is required prior to data analysis to gain meaningful insights. Most existing methods for data normalization standardize signals by rescaling either background regions or peak regions, assuming that the same scale factor is applicable to both background and peak regions. While such methods adjust for differences in sequencing depths, they do not address differences in the signal-to-noise ratios across different experiments. We developed a new data normalization method, called S3norm, that normalizes the sequencing depths and signal-to-noise ratios across different data sets simultaneously by a monotonic nonlinear transformation. We show empirically that the epigenomic data normalized by our method, compared to existing methods, can better capture real biological variation, such as impact on gene expression regulation.
Anisotropic alignments of hierarchical Li2SiO3/TiO2 @nano-C anode//LiMnPO4@nano-C cathode architectures for full-cell lithium-ion battery
Authors: Khalifa Hesham , El-Safty Sherif A , Reda Abdullah , Shenashen Mohamed A , Eid Alaa I 
Published: February 2020

AbstractWe report on low-cost fabrication and high-energy density of full-cell lithium-ion battery (LIB) models. Super-hierarchical electrode architectures of Li2SiO3/TiO2@nano-carbon anode (LSO.TO@nano-C) and high-voltage olivine LiMnPO4@nano-carbon cathode (LMPO@nano-C) are designed for half- and full-system LIB-CR2032 coin cell models. On the basis of primary architecture-power-driven LIB geometrics, the structure keys including three-dimensional (3D) modeling superhierarchy, multiscale micro/nano architectures and anisotropic surface heterogeneity affect the buildup design of anode/cathode LIB electrodes. Such hierarchical electrode surface topologies enable continuous in-/out-flow rates and fast transport pathways of Li+-ions during charge/discharge cycles. The stacked layer configurations of pouch LIB-types lead to excellent charge/discharge rate, and energy density of 237.6 Wh kg−1. As the most promising LIB-configurations, the high specific energy density of hierarchical pouch battery systems may improve energy storage for long-driving range of electric vehicles. Indeed, the anisotropic alignments of hierarchical electrode architectures in the large-scale LIBs provide proof of excellent capacity storage and outstanding durability and cyclability. The full-system LIB-CR2032 coin cell models maintain high specific capacity of ∼89.8% within a long-term life period of 2000 cycles, and average Coulombic efficiency of 99.8% at 1C rate for future configuration of LIB manufacturing and commercialization challenges.