Miracle-dz/UniFAR-FTUs huggingface dataset:
Atrial fibrillation, progression of coronary atherosclerosis and myocardial infarction

Background Despite atrial fibrillation representing an established risk factor for stroke, the association between atrial fibrillation and both progression of coronary atherosclerosis and major adverse cardiovascular events is not well characterized. We assessed the serial measures of coronary atheroma burden and cardiovascular outcomes in patients with and without atrial fibrillation. Methods Data were analyzed from nine clinical trials involving 4966 patients with coronary artery disease undergoing serial intravascular ultrasonography at 18–24 month intervals to assess changes in percent atheroma volume (PAV). Using a propensity weighted analysis, and following adjustment for baseline variables, patients with (n = 190) or without (n = 4776) atrial fibrillation were compared with regard to coronary plaque volume and major adverse cardiovascular events (death, myocardial infarction, and stroke). Results Atrial fibrillation patients demonstrated lower baseline PAV (36.0 ± 8.9 vs. 38.1 ± 8.9%, p = 0.002) and less PAV progression (–0.07 ± 0.34 vs. + 0.23 ± 0.34%, p = 0.001) compared with the non-atrial fibrillation group. Multivariable analysis revealed atrial fibrillation to independently predict both myocardial infarction [HR, 2.41 (1.74,3.35), p<0.001] 2.41 (1.74, 3.35), p < 0.00) and major adverse cardiovascular events [HR, 2.2, (1.66, 2.92), p<0.001] 2.20 (1.66, 2.92), p < 0.001]. Kaplan–Meier analysis showed that atrial fibrillation compared with non-atrial fibrillation patients had a significantly higher two-year cumulative incidence of overall major adverse cardiovascular events (4.4 vs. 2.0%, log-rank p = 0.02) and myocardial infarction (3.3 vs. 1.5%, log-rank p = 0.05). Conclusions The presence of atrial fibrillation independently associates with a heightened risk of myocardial infarction despite a lower baseline burden and progression rate of coronary atheroma. Further studies are necessary to define the pathogenesis of myocardial infarction in the setting of atrial fibrillation.
Differences between measured and reported volatile organic compound emissions from oil sands facilities in Alberta, Canada

Significance Validation of volatile organic compound (VOC) emission reports, especially from large industrial facilities, is rarely attempted. Given uncertainties in emission reports, their evaluation and validation will build confidence in emission inventories. It is shown that a top-down approach can provide measurement-based emission rates for such emission validation. Comparisons with emission reports from Alberta oil sands surface mining facilities revealed significant differences in VOC emissions between top-down emissions rates and reports. Comparison with VOC species emission reports using currently accepted estimation methods indicates that emissions were underestimated in the reports for most species. This exercise shows that improvements in the accuracy and completeness of emissions estimates from complex facilities would enhance their application to assessing the impacts of such emissions. Large-scale oil production from oil sands deposits in Alberta, Canada has raised concerns about environmental impacts, such as the magnitude of air pollution emissions. This paper reports compound emission rates (E) for 69–89 nonbiogenic volatile organic compounds (VOCs) for each of four surface mining facilities, determined with a top-down approach using aircraft measurements in the summer of 2013. The aggregate emission rate (aE) of the nonbiogenic VOCs ranged from 50 ± 14 to 70 ± 22 t/d depending on the facility. In comparison, equivalent VOC emission rates reported to the Canadian National Pollutant Release Inventory (NPRI) using accepted estimation methods were lower than the aE values by factors of 2.0 ± 0.6, 3.1 ± 1.1, 4.5 ± 1.5, and 4.1 ± 1.6 for the four facilities, indicating underestimation in the reported VOC emissions. For 11 of the combined 93 VOC species reported by all four facilities, the reported emission rate and E were similar; but for the other 82 species, the reported emission rate was lower than E. The median ratio of E to that reported for all species by a facility ranged from 4.5 to 375 depending on the facility. Moreover, between 9 and 53 VOCs, for which there are existing reporting requirements to the NPRI, were not included in the facility emission reports. The comparisons between the emission reports and measurement-based emission rates indicate that improvements to VOC emission estimation methods would enhance the accuracy and completeness of emission estimates and their applicability to environmental impact assessments of oil sands developments.
RADIATION-INDUCED OPTICAL EFFECTS IN CHALCOGENIDE SEMICONDUCTOR GLASSES

A variety of methodological resolutions suitable to identify unambiguously radiation-induced effects in chalcogenide glassy semiconductors is analyzed in details. The radiation-optical effects in chalcogenide glasses are comprehensively considered as resulting from both intrinsic and impurity-related redistribution of covalent chemical bonds known as destruction-polymerization transformations. Two types of experimental measuring protocols are utilized to study the radiation-induced effects within ex-situ direct or in-situ backward chronology, the latter being more adequate for correct testing of competitive inputs from both channels of destruction-polymerization transformations. A critical assessment is given on misleading speculations of some authors ignoring intrinsic radiation-structural transformations in glassy As 2 S 3 in view of accompanying oxidation and thermally-induced physical-ageing processes. In final, the As 2 S 3 glass is nominated to be the best model object among a wide group of chalcogenide glassy semiconductors revealing the highest sensitivity to radiation-induced metastability.
Machine Learning vs. Rules and Out-of-the-Box vs. Retrained: An Evaluation of Open-Source Bibliographic Reference and Citation Parsers

Bibliographic reference parsing refers to extracting machine-readable metadata, such as the names of the authors, the title, or journal name, from bibliographic reference strings. Many approaches to this problem have been proposed so far, including regular expressions, knowledge bases and supervised machine learning. Many open source reference parsers based on various algorithms are also available. In this paper, we apply, evaluate and compare ten reference parsing tools in a specific business use case. The tools are Anystyle-Parser, Biblio, CERMINE, Citation, Citation-Parser, GROBID, ParsCit, PDFSSA4MET, Reference Tagger and Science Parse, and we compare them in both their out-of-the-box versions and versions tuned to the project-specific data. According to our evaluation, the best performing out-of-the-box tool is GROBID (F1 0.89), followed by CERMINE (F1 0.83) and ParsCit (F1 0.75). We also found that even though machine learning-based tools and tools based on rules or regular expressions achieve on average similar precision (0.77 for ML-based tools vs. 0.76 for non-ML-based tools), applying machine learning-based tools results in a recall three times higher than in the case of non-ML-based tools (0.66 vs. 0.22). Our study also confirms that tuning the models to the task-specific data results in the increase in the quality. The retrained versions of reference parsers are in all cases better than their out-of-the-box counterparts; for GROBID F1 increased by 3% (0.92 vs. 0.89), for CERMINE by 11% (0.92 vs. 0.83), and for ParsCit by 16% (0.87 vs. 0.75).
Effect of Grain Size and Residual Strain on the Dynamic Transformation of Austenite under Plate Rolling Conditions

When austenite is deformed within the austenite phase field, that is, above the equilibrium transformation temperature Ae3, it partially transforms dynamically into ferrite. Here, rough rolling simulations are conducted at 1100 °C on an X70 steel to study the influence of grain size and residual strain on this type of transformation. Three simulated roughing passes are applied with pass strains of 0.4 at a strain rate of 1.0 s−1. The resulting stress–strain curves are recorded and analyzed. The volume fractions of ferrite and martensite (prior austenite) are determined on quenched samples by means of metallographic techniques. It is observed that dynamic transformation took place during the first roughing pass and that the volume fraction of transformed ferrite increases with the cumulative strain. Both the critical strain to the onset of dynamic transformation as well as the grain size decrease with pass number.
Quaternary Ammonium and Phosphonium Ionic Liquids in Chemical and Environmental Engineering

Quaternary ammonium salts (quats) are an economically advantageous class of industrial compounds. They have surface-active properties, possess anti-microbial activity and are known to be bioactive (Boethling & Lynch, 1992; Juergensen et al., 2000). Contrary, reports regarding low melting tetraalkylphosphonium salts were relatively rare in the literature during the last decades (Bradaric et al., 2003). Although ILs based on quaternary ammonium cations have been known and produced for years, and also numerous phosphonium based ILs have been produced even in ton-scale, these groups of ionic liquids have been more or less “neglected” in the literature comparing to their imidazolium or pyridinium based counterparts. However, during the last decade significant work has been done, pointing out the advantages and broad application spectrum of these types of ionic liquids. Their improved thermal and chemical stability in comparison to e.g. pyridinium and imidazolium based ILs, their unique miscibility behaviour and solvating properties advances their use in specific applications (Rogers et al., 2002; Plechkova & Seddon, 2007; Chowdhury et al., 2007; Wasserscheid & Welton, 2008). Several ILs based on these classes of cations are already commercially available and have been successfully applied as phase-transfer catalysts, solvents, lubricants, gas capture agents, coating materials, or chemical sensors (Bradaric et al., 2003; Weng et al., 2006; Pernak et al., 2006; Yuan et al., 2007; Fraser & MacFarlane, 2009; Werner et al., 2010). Tricaprylylmethylammonium chloride (trade name Aliquat® 336), produced in ton-scale by Henkel, is nowadays widely used as metal extraction agent, phase transfer catalyst, surfactant, or antistatic agent. In contrast, trihexyl(tetradecyl)phosphonium chloride (trade name Cyphos® IL 101) was developed by Cytec Industries as a thermally stable phase transfer catalyst (Bradaric et al., 2003). Due to the relatively simple preparation route, Cyphos® IL 101 is produced in ton-scale and therefore represents a fairly cheap IL. Hence, due to their commercial availability and low prices, both Aliquat® 336 and Cyphos® IL 101 can be used themselves or represent favorable precursors for a series of ionic liquids. The goal of this chapter is to give some insight into the fascinating and fast-growing field of
Review article: Sepsis in the emergency department – Part 2: Investigations and monitoring

Sepsis is characterised by organ dysfunction resulting from infection, with no reliable single objective test and current diagnosis based on clinical features and results of investigations. In the ED, investigations may be conducted to diagnose infection as the cause of the presenting illness, identify the source, distinguish sepsis from uncomplicated infection (i.e. without organ dysfunction) and/ or risk stratification. Appropriate sample collection for microbiological testing remains key for subsequent confirmation of diagnosis and rationalisation of antimicrobials. Routine laboratory investigations such as creatinine, bilirubin, platelet count and lactate are now critical elements in the diagnosis of sepsis and septic shock. With no biomarker sufficiently validated to rule out bacterial infection in the ED, there remains substantial interest in biomarkers representing various pathogenic pathways. New technologies for screening multiple genes and proteins are identifying unique network ‘signatures’ of clinical interest. Other future directions include rapid detection of bacterial DNA in blood, genes for antibiotic resistance and EMR‐based computational biomarkers that collate multiple information sources. Reliable, cost‐effective tests, validated in the ED to promptly and accurately identify sepsis, and to guide initial antibiotic choices, are important goals of current research efforts.
Mothers Care More, But Fathers Decide: Educating Parents about Child Health in Uganda.

Research on intrahousehold decision-making generally finds that fathers have more bargaining power than mothers, but mothers put more weight on children's well-being. This suggests a tradeoff when targeting policies to improve child health: fathers have more power to change household behavior in ways that improve child health, but mothers might have a stronger desire to do so. This paper compares health classes in Uganda that enrolled either mothers or fathers. We find that educating mothers leads to greater adoption of health-promoting behaviors by the household. In addition, educating one parent leads to positive spillovers on the other spouse's health behaviors.
Superconductivity and non-Fermi liquid behavior near a nematic quantum critical point

Significance It has been conjectured that many properties of highly correlated materials, including high-temperature superconductivity, may arise from proximity to a metallic quantum critical point. However, the nature of quantum critical phenomena in metals is incompletely understood. Using numerically exact quantum Monte Carlo methods, we simulated a model that can be tuned through a metallic quantum critical point and observed behaviors that are strikingly reminiscent of experiments. Among these phenomena are high-temperature superconductivity, non-Fermi liquid behavior of the electron Green function, and “bad metal” behavior of the electrical conductivity. Using determinantal quantum Monte Carlo, we compute the properties of a lattice model with spin 12 itinerant electrons tuned through a quantum phase transition to an Ising nematic phase. The nematic fluctuations induce superconductivity with a broad dome in the superconducting Tc enclosing the nematic quantum critical point. For temperatures above Tc, we see strikingly non-Fermi liquid behavior, including a “nodal–antinodal dichotomy” reminiscent of that seen in several transition metal oxides. In addition, the critical fluctuations have a strong effect on the low-frequency optical conductivity, resulting in behavior consistent with “bad metal” phenomenology.
Inflammation, Immune Activation, Immunosenescence, and Hormonal Biomarkers in the Frailty-Related Phenotype of Men with or at Risk for HIV

Background The extent to which inflammation, immune activation/immunosenescence, and hormonal abnormalities are driven by HIV or frailty is not clear. Methods HIV-infected frail men (n=155) were matched to non-frail, HIV-infected (n=141) and HIV-uninfected (n=150) men by age, calendar year, and antiretroviral therapy (ART) use (HIV only). Frailty was defined by ≥3 frailty-related phenotype criteria (weight loss, exhaustion, low activity, slowness) at ≥2 visits, or at 1 visit with ≥1 criteria at ≥2 visits. IL-6, hs-CRP, sTNFR-1 and 2, DHEA-S, free testosterone, HOMA-IR, IGF-1, and %CD4+CD28-, %CD8+CD28-, %CD4+CD38+DR+, %CD8+CD38+DR+ T-cells were measured. Log-linear regressions were adjusted for a priori selected covariates to determine differences by frailty and HIV status. Results In multivariate analyses adjusted for covariates, among HIV-infected men, frailty was associated with higher IL-6 and hs-CRP and lower free testosterone and DHEA. In contrast, HIV infection but not frailty was associated with significantly greater immune senescence (% CD4+28- or CD8+28- T-cells) and immune activation (% CD4+CD38+HLA-DR+ and CD8+CD38+HLA-DR+). Conclusions Frailty among HIV-infected men was associated with increased inflammation and lower hormone levels, independent of co-morbid conditions. Interventions targeting these pathways should be evaluated to determine the impact on prevention or reversal of frailty among HIV-infected men.
Structural variants caused by Alu insertions are associated with risks for many human diseases

Significance Repetitive sequences comprise a large portion of the genome and are often thought of as “junk DNA. ” They are a significant source of genetic variation, particularly Alu elements. Their functional consequence is frequently dismissed. Here, we test the hypothesis that Alu polymorphisms contribute to phenotypic differences between individuals. We identified an enrichment of Alu polymorphisms in regions of the genome associated with human disease risk. Further, we find 44 instances where the trait-associated SNP is a surrogate for presence or absence of an Alu insertion. This finding indicates that the Alu may be the variant effecting disease risk, an intriguing possibility given its size and regulatory potential. This work emphasizes the importance of considering repeat polymorphisms in functional variant analysis. Interspersed repeat sequences comprise much of our DNA, although their functional effects are poorly understood. The most commonly occurring repeat is the Alu short interspersed element. New Alu insertions occur in human populations, and have been responsible for several instances of genetic disease. In this study, we sought to determine if there are instances of polymorphic Alu insertion variants that function in a common variant, common disease paradigm. We cataloged 809 polymorphic Alu elements mapping to 1,159 loci implicated in disease risk by genome-wide association study (GWAS) (P < 10−8). We found that Alu insertion variants occur disproportionately at GWAS loci (P = 0.013). Moreover, we identified 44 of these Alu elements in linkage disequilibrium (r2 > 0.7) with the trait-associated SNP. This figure represents a >20-fold increase in the number of polymorphic Alu elements associated with human phenotypes. This work provides a broader perspective on how structural variants in repetitive DNAs may contribute to human disease.
Nucleoside Diphosphate Kinase-3 (NME3) Enhances TLR5-Induced NFκB Activation

Bacterial flagellin is a potent activator of NFκB signaling, inflammation, and host innate immunity, and recent data indicate that flagellin represents a novel antitumor ligand acting through toll-like receptor 5 (TLR5) and the NFκB pathway to induce host immunity and aid in the clearance of tumor xenografts. To identify innate signaling components of TLR5 responsible for these antitumor effects, a loss-of-function high-throughput screen was employed utilizing carcinoma cells expressing a dynamic NFκB bioluminescent reporter stimulated by Salmonella typhimurium expressing flagellin. A live cell screen of a siRNA library targeting 691 known and predicted human kinases to identify novel tumor cell modulators of TLR5-induced NFκB activation uncovered several interesting positive and negative candidate regulators not previously recognized, including nucleoside diphosphate kinase 3 (NME3), characterized as an enhancer of signaling responses to flagellin. Targeted knockdown and overexpression assays confirmed the regulatory contribution of NME3 to TLR5-mediated NFκB signaling, mechanistically downstream of MyD88. Furthermore, Kaplan–Meier survival analysis showed that NME3 expression correlated highly with TLR5 expression in breast, lung, ovarian, and gastric cancers, and furthermore, high-level expression of NME3 increased overall survival for patients with breast, lung, and ovarian cancer, but the opposite in gastric cancer. Together, these data identify a previously unrecognized proinflammatory role for NME3 in signaling downstream of TLR5 that may potentiate cancer immunotherapies. Implications: Proinflammatory signaling mediated by innate immunity engagement of flagellin-activated TLR5 in tumor cells results in antitumor effects through NME3 kinase, a positive downstream regulator of flagellin-mediated NFκB signaling, enhancing survival for several human cancers. Mol Cancer Res; 16(6); 986–99. ©2018 AACR.
Photophysical properties of benzanthrone derivatives: effect of substituent, solvent polarity and hydrogen bonding

Benzanthrone derivatives are potential fluorescent probes for various chemical and biological environments. A mechanistic understanding of their photophysical properties is pivotal for designing an efficient fluorescence sensor based on the benzanthrone framework. In this study, we report on the effect of chemical substitution on the photophysical properties of two benzanthrone derivatives, namely, 3-( N ′-methyl)-piperazino-7 H -benzo[de]anthracen-7-one [Me-PBA] and 3-( N ′-phenyl)-piperazino-7 H -benzo[de]anthracen-7-one [Ph-PBA] in different solvents and solvent mixtures of varying polarities and proticities. Both benzanthrone derivatives show interesting solvent-dependent photophysical properties. Although both derivatives exhibit strong intramolecular charge transfer (ICT) characteristics in the excited state, the extent of the charge transfer is significantly influenced by the nature of the chemical substitution. Modulation of photophysical parameters as a function of solvent properties led us to propose that ICT is affected by solvent polarity and hydrogen bonding. From the viscosity effect, it is revealed that the weaker emission of Ph-PBA compared to Me-PBA in polar solvents is primarily due to the non-radiative torsional motion of the phenyl group in the former derivative. In protic solvents, intermolecular hydrogen bonding imparts strong non-radiative deactivation to both derivatives, thus rendering a weak fluorescence yield.
Positive Urgency and Emotional Reactivity: Evidence for Altered Responding to Positive Stimuli

Positive urgency, defined as a tendency to become impulsive during positive affective states, has gained support as a form of impulsivity that is particularly important for understanding psychopathology. Despite this, little is known about the emotional mechanisms and correlates of this form of impulsivity. We hypothesized that positive urgency would be related to greater emotional reactivity in response to a positive film clip. Seventy-five undergraduates watched a positive film clip, and a multimodal assessment of emotion was conducted, including subjective emotional experience, physiological activation (i.e., heart rate, respiratory sinus arrhythmia, skin conductance), and facial emotional behavior (i.e., objectively coded using the Facial Action Coding System). Positive urgency was not significantly related to greater positive emotional reactivity but rather a more complex array of emotions expressed in facial behavior, as indexed by similar levels of positive yet greater levels of negative behavior. These findings show that positive urgency may be linked to altered emotionality, but does not appear related to heightened positive emotional reactivity. Potential implications for functional outcomes are discussed.