bluuebunny/crossref_metadata_2025_split huggingface dataset:
Can soluble urokinase plasminogen receptor predict outcomes after cardiac surgery?
Authors: Schultz-Swarthfigure Chase T , McCall Philip , Docking Robert , Galley Helen F , Shelley Benjamin 
Published: September 2020

Abstract

OBJECTIVES
Soluble urokinase plasminogen activator receptor (suPAR) is a biomarker that has been implicated in several cardiac pathologies and has been shown to be elevated in critically ill populations. We measured plasma suPAR in a cohort of cardiac surgical patients to evaluate its ability to predict prolonged intensive care unit (ICU) and hospital length of stay and development of complications following surgery. We compared suPAR against EuroSCORE II and C-reactive protein (CRP).

METHODS
Ninety patients undergoing cardiac surgery were recruited with samples taken preoperatively and on postoperative days 1, 2 and 3. suPAR was measured using enzyme-linked immunosorbent assay. Area under the receiver operator curve (AUROC) was used to test predictive capability of suPAR. Comparison was made with EuroSCORE II and CRP.

RESULTS
suPAR increased over time (P &lt; 0.001) with higher levels in patients requiring prolonged ICU and hospital stay, and prolonged ventilation (P &lt; 0.05). suPAR was predictive for prolonged ICU and hospital stay, and prolonged ventilation at all time points (AUROC 0.66–0.74). Interestingly, this association was also observed preoperatively, with preoperative suPAR predicting prolonged ICU (AUROC 0.66), and hospital stay (AUROC 0.67) and prolonged ventilation (AUROC 0.74). The predictive value of preoperative suPAR compared favourably to EuroSCORE II and CRP.

CONCLUSIONS
suPAR increases following cardiac surgery and levels are higher in those who require prolonged ICU stay, prolonged hospital stay and prolonged ventilation. Preoperative suPAR compares favourably to EuroSCORE II and CRP in the prediction of these outcomes. suPAR could be a useful biomarker in predicting outcome following cardiac surgery, helping inform clinical decision-making.

Clinical registration
West of Scotland Research Ethics Committee Reference: 12/WS/0179 (AM01).
Evidence for familial clustering in breast cancer age of onset
Authors: Von Holle Ann , O’Brien Katie M , Sandler Dale P , Weinberg Clarice R 
Published: September 2020

Abstract

Background
Familial clustering of age at onset would have implications for both personalized screening and aetiology, but has not been studied for breast cancer.

Methods
We prospectively studied a cohort of 23 145 sisters to explore whether their breast cancer risk changed near the age at diagnosis of a previously affected older sister. Using an age-time-dependent variable in a Cox regression model, we estimated hazard ratios for breast cancer when participants were near their sister’s diagnosis age, relative to similarly aged women whose sister was diagnosed at a very different age. To rule out a correlation driven by young-onset familial cancer, we separately investigated women who had enrolled at age 50 or older.

Results
Of the 23 145 women, 1412 developed breast cancer during follow-up (median 9.5 years). The estimated hazard ratio was 1.80 (95% confidence interval: 1.18, 2.74) at their sister’s age at diagnosis, suggesting a substantial increase in risk compared with women of the same age but whose sister was diagnosed at a very different age. Restriction to women who enrolled at or after age 50 produced similar results.

Conclusions
This familial clustering suggests that there may be important genetic and/or early environmental risk factors that influence the timing of breast cancer, even when onset is late in life. Personalized screening might need to account for the age at which a sister was earlier diagnosed with breast cancer.
A mathematical model of asynchronous data flow in parallel computers*
Authors: Barnard Richard C , Huang Kai , Hauck Cory 
Published: September 2020

AbstractWe present a simplified model of data flow on processors in a high-performance computing framework involving computations necessitating inter-processor communications. From this ordinary differential model, we take its asymptotic limit, resulting in a model which treats the computer as a continuum of processors and data flow as an Eulerian fluid governed by a conservation law. We derive a Hamilton–Jacobi equation associated with this conservation law for which the existence and uniqueness of solutions can be proven. We then present the results of numerical experiments for both discrete and continuum models; these show a qualitative agreement between the two and the effect of variations in the computing environment’s processing capabilities on the progress of the modelled computation.
Bridging theOtherSide of the Gap: Teaching “Practical Theory” to Future Practitioners
Authors: Blankshain Jessica D , Cooper David A , Gvosdev Nikolas K 
Published: September 2020

AbstractMuch has been written about the need to “bridge the gap” between the academic study of international relations—particularly policy-oriented subfields such as foreign policy analysis and security studies—and the needs of policymakers. This important agenda largely focuses on encouraging academics to produce more policy-relevant, accessible research. While such efforts are indispensable, they neglect another important piece of the equation: teaching future policymakers how to translate theory into practice. The bridge needs to be a two-way street. Scholars add value for policy because their work is grounded in theory, offering analytical structure to make sense of a complex world. But applying theory to policy is unlikely to resonate with practitioners who do not have the basic conceptual literacy to grasp why theory-informed research is relevant to their own hands-on concerns. We therefore propose a teaching approach we term “practical theory,” geared specifically for professionally oriented students. Drawing on our own experience in teaching, developing curriculum, and writing for students in professional master's degree programs, we recommend instructors: choose theories and frameworks that are most likely to be useful in practice, update these theories for the times as needed, reconsider nomenclature and banish unnecessary academic jargon, and apply theory early and often.
The changing epidemiology of carbapenemase-producingKlebsiella pneumoniaein Italy: toward polyclonal evolution with emergence of high-risk lineages
Authors: Di Pilato Vincenzo , Errico Giulia , Monaco Monica , Giani Tommaso , Del Grosso Maria , Antonelli Alberto , David Sophia , Lindh Erika , Camilli Romina , Aanensen David M , Rossolini Gian Maria , Pantosti Annalisa ,   the AR-ISS Laboratory Study Group on carbapenemase-producing Klebsiella pneumoniae, Manso E , Pedna M F , Mungiguerra M , Moscati Presidio Ospedaliero G , Mosca A , Vailati F , Aschbacher R , Imbriani A , Sartore P , di Cittadella Ospedale Civile , Giraldi C , di Cosenza Azienda Ospedaliera , Piana F , Pecile P , Careggi Ospedale , De Nittis R , Pini B , Manzoni Ospedale A , Mirri P , Bianchi E , Restelli A , Morelli D , Tumori Istituto , Catania M R , Barbaro A , Bernaschi P , Parisi G , Gualdi P , Dusi P A , Bona R , Paolo Ospedale S , D’Andrea M M , Cavallo R , Lanzafame P , Sartor A , Grandesso S , Milano F 
Published: September 2020

AbstractBackgroundPrevious studies showed that the epidemic of carbapenem-resistant Klebsiella pneumoniae (CR-KP) observed in Italy since 2010 was sustained mostly by strains of clonal group (CG) 258 producing KPC-type carbapenemases. In the framework of the National Antibiotic-Resistance Surveillance (AR-ISS), a countrywide survey was conducted in 2016 to explore the evolution of the phenotypic and genotypic characteristics of CR-KP isolates.MethodsFrom March to July 2016, hospital laboratories participating in AR-ISS were requested to provide consecutive, non-duplicated CR-KP (meropenem and/or imipenem MIC &gt;1 mg/L) from invasive infections. Antibiotic susceptibility was determined according to EUCAST recommendations. A WGS approach was adopted to characterize the isolates by investigating phylogeny, resistome and virulome.ResultsTwenty-four laboratories provided 157 CR-KP isolates, of which 156 were confirmed as K. pneumoniae sensu stricto by WGS and found to carry at least one carbapenemase-encoding gene, corresponding in most cases (96.1%) to blaKPC. MLST- and SNP-based phylogeny revealed that 87.8% of the isolates clustered in four major lineages: CG258 (47.4%), with ST512 as the most common clone, CG307 (19.9%), ST101 (15.4%) and ST395 (5.1%). A close association was identified between lineages and antibiotic resistance phenotypes and genotypes, virulence traits and capsular types. Colistin resistance, mainly associated with mgrB mutations, was common in all major lineages except ST395.ConclusionsThis WGS-based survey showed that, although CG258 remained the most common CR-KP lineage in Italy, a polyclonal population has emerged with the spread of the new high-risk lineages CG307, ST101 and ST395, while KPC remained the most common carbapenemase.
Different processes for translating expressive versus informative texts? A computer-assisted study of professionals’ English–Chinese translation
Authors: Zheng Jianwei , Fan Wenjun 
Published: September 2020

AbstractThis article explores the differences of translation processes for expressive and informative texts by professional translators primarily by triangulating pausing and revision data retrieved by Keystroke logging experiment and rational report thereof via questionnaire survey and interview. The article discovers that in terms of temporal distribution, the drafting of informative text accounts for a larger proportion of time, while orientation and checking accounts for a smaller proportion compared with those of expressive texts. At orientation interval, translators come to fully understand the source expressive text at the very beginning, while generally conducting syntactic analysis of and re-sequencing the semantic component of source text in target language in translating informative text. At drafting interval, structural modification frequency word rate (MWR) in translating the expressive text is larger than that in translating the informative texts, while spelling and lexical MWRs of both texts are similar. At checking interval, both texts hardly see any structural modification, but lexical MWR for the former is much bigger than that for the latter. These data, along with pausing and revision rational report, suggest the priority of familiarity with standardized grammar and expertise in specialized field for translating informative text, and the importance of embedded reading and writing training for translating expressive text.
From solar-like to mira stars: a unifying description of stellar pulsators in the presence of stochastic noise
Authors: Cunha M S , Avelino P P , Chaplin W J 
Published: September 2020

ABSTRACTWe discuss and characterize the power spectral density properties of a model aimed at describing pulsations in stars from the main-sequence to the asymptotic giant branch. We show that the predicted limit of the power spectral density for a pulsation mode in the presence of stochastic noise is always well approximated by a Lorentzian function. While in stars predominantly stochastically driven the width of the Lorentzian is defined by the mode lifetime, in stars where the driving is predominately coherent the width is defined by the amplitude of the stochastic perturbations. In stars where both drivings are comparable, the width is defined by both these parameters and is smaller than that expected from pure stochastic driving. We illustrate our model through numerical simulations and propose a well-defined classification of stars into predominantly stochastic (solar-like) and predominately coherent (classic) pulsators. We apply the model to the study of the Mira variable U Per, and the semiregular variable L2 Pup and, following our classification, conclude that they are both classical pulsators. Our model provides a natural explanation for the change in behaviour of the pulsation amplitude-period relation noted in several earlier works. Moreover, our study of L2 Pup enables us to test the scaling relation between the mode line width and effective temperature, confirming that an exponential scaling reproduces well the data all the way from the main sequence to the asymptotic giant branch, down to temperatures about 1000 K below what has been tested in previous studies.
H i scale height in spiral galaxies
Authors: Patra Narendra Nath 
Published: September 2020

ABSTRACT
We model the galactic discs of seven nearby large spiral galaxies as three-component systems consist of stars, molecular gas, and atomic gas in vertical hydrostatic equilibrium. We set up the corresponding joint Poisson–Boltzmann equation and solve it numerically to estimate the 3D distribution of H i in these galaxies. While solving the Poisson–Boltzmann equation, we do not consider a constant H i velocity dispersion (σHI); rather, we develop an iterative method to self-consistently estimate the σHI profile in a galaxy by using the observed second-moment profile of the H i spectral cube. Using the density solutions, we determine the H i vertical scale height in our galaxies. We find that the H i discs flare in a linear fashion as a function of radius. H i scale height in our galaxies is found to vary between a few hundred parsecs at the centre to ∼1–2 kpc at the outskirts. We estimate the axial ratio of the H i discs in our sample galaxies and find a median ratio of 0.1, which is much lower than what is found for dwarf galaxies, indicating much thinner H i discs in spiral galaxies. Very low axial ratios in three of our sample galaxies (NGC 5055, NGC 6946, and NGC 7331) suggest them to be potential superthin galaxies. Using the H i distribution and the H i hole sizes in NGC 6946, we find that most of the H i holes in this galaxy are broken out into the circumgalactic medium and this breaking out is more effective in the inner radii as compared to the outer radii.
Wide-field study of the peculiar globular cluster system hosted by the field lenticular NGC 1172
Authors: Ennis Ana Inés , Caso Juan Pablo , Bassino Lilia P , Salinas Ricardo , Gómez Matías 
Published: September 2020

ABSTRACT
We present a wide-field study of the globular cluster system (GCS) of the field lenticular galaxy NGC 1172, based on observations from Gemini Multi-Object Spectrograph/Gemini (optical), FourStar/Magellan (NIR), and archival data from ACS/Hubble Space Telescope (optical). This analysis covers the full extension of the GCS, and results in a value of specific frequency (SN = 8.6 ± 1.5) peculiarly high for an intermediate-mass galaxy in a low-density environment such as this one. We find that the GCS appears to be bimodal, although the colour distribution is narrow and does not allow for an accurate separation of the subpopulations. However, the combination of optical and NIR filters allows us to obtain an estimation of the metallicity distribution based on the photometry, which supports bimodality. We conclude that the presence of a large fraction of metal-poor globular clusters (GCs) and the high specific frequency point to NGC 1172 having accreted a significant amount of GCs from low-mass satellites in the past.
Tensorial solution of the Poisson equation and the dark matter amount and distribution of UGC 8490 and UGC 9753
Authors: Repetto P 
Published: September 2020

ABSTRACT
In the first part of this article we expand three fundamental aspects of the methodology connected to the determination of a relation among the spatial density and the gravitational potential that can be specialized to distinct mass density agglomerations. As a consequence, we obtain general relations for the diagonal entries of a square symmetric matrix without zeros, we provide an expression of the gravitational potential, suitable, to represent several different mass density configurations, and we determine relations for the semi-axes of a triaxial spheroidal mass distribution, as a function of the spheroid mass density, volume density, and radius. In the second part of this paper, we employ the tools developed in the first part, to analyse the mass density content and the inner and global structure of the dark matter haloes of UGC 8490 and UGC 9753, through the fits to the dark matter rotation curves of the two galaxies, assuming a triaxial spheroidal dark matter mass configuration. We employ the Navarro Frenk and White, Burkert, DiCintio, Einasto and Stadel dark matter models, and we obtain that both a cored Burkert and cuspy DiCintio and Navarro Frenk and White inward dark matter distributions could represent equally well the observed data, furthermore we determine an oblate spheroidal dark matter mass density configuration for UGC 8490 and UGC 9753. The latter outcome is confirmed by the estimation of the gravitational torques exerted by the dark matter halo of each analysed galaxy, on the corresponding baryonic components.
The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes
Authors: Seaver Samuel M D , Liu Filipe , Zhang Qizhi , Jeffryes James , Faria José P , Edirisinghe Janaka N , Mundy Michael , Chia Nicholas , Noor Elad , Beber Moritz E , Best Aaron A , DeJongh Matthew , Kimbrel Jeffrey A , D’haeseleer Patrik , McCorkle Sean R , Bolton Jay R , Pearson Erik , Canon Shane , Wood-Charlson Elisha M , Cottingham Robert W , Arkin Adam P , Henry Christopher S 
Published: September 2020

AbstractFor over 10 years, ModelSEED has been a primary resource for the construction of draft genome-scale metabolic models based on annotated microbial or plant genomes. Now being released, the biochemistry database serves as the foundation of biochemical data underlying ModelSEED and KBase. The biochemistry database embodies several properties that, taken together, distinguish it from other published biochemistry resources by: (i) including compartmentalization, transport reactions, charged molecules and proton balancing on reactions; (ii) being extensible by the user community, with all data stored in GitHub; and (iii) design as a biochemical ‘Rosetta Stone’ to facilitate comparison and integration of annotations from many different tools and databases. The database was constructed by combining chemical data from many resources, applying standard transformations, identifying redundancies and computing thermodynamic properties. The ModelSEED biochemistry is continually tested using flux balance analysis to ensure the biochemical network is modeling-ready and capable of simulating diverse phenotypes. Ontologies can be designed to aid in comparing and reconciling metabolic reconstructions that differ in how they represent various metabolic pathways. ModelSEED now includes 33,978 compounds and 36,645 reactions, available as a set of extensible files on GitHub, and available to search at https://modelseed.org/biochem and KBase.
Label-free profiling of DNA aptamer-small molecule binding using T5 exonuclease
Authors: Alkhamis Obtin , Yang Weijuan , Farhana Rifat , Yu Haixiang , Xiao Yi 
Published: September 2020

AbstractIn vitro aptamer isolation methods can yield hundreds of potential candidates, but selecting the optimal aptamer for a given application is challenging and laborious. Existing aptamer characterization methods either entail low-throughput analysis with sophisticated instrumentation, or offer the potential for higher throughput at the cost of providing a relatively increased risk of false-positive or -negative results. Here, we describe a novel method for accurately and sensitively evaluating the binding between DNA aptamers and small-molecule ligands in a high-throughput format without any aptamer engineering or labeling requirements. This approach is based on our new finding that ligand binding inhibits aptamer digestion by T5 exonuclease, where the extent of this inhibition correlates closely with the strength of aptamer-ligand binding. Our assay enables accurate and efficient screening of the ligand-binding profiles of individual aptamers, as well as the identification of the best target binders from a batch of aptamer candidates, independent of the ligands in question or the aptamer sequence and structure. We demonstrate the general applicability of this assay with a total of 106 aptamer-ligand pairs and validate these results with a gold-standard method. We expect that our assay can be readily expanded to characterize small-molecule-binding aptamers in an automated, high-throughput fashion.
StreptomeDB 3.0: an updated compendium of streptomycetes natural products
Authors: Moumbock Aurélien F A , Gao Mingjie , Qaseem Ammar , Li Jianyu , Kirchner Pascal A , Ndingkokhar Bakoh , Bekono Boris D , Simoben Conrad V , Babiaka Smith B , Malange Yvette I , Sauter Florian , Zierep Paul , Ntie-Kang Fidele , Günther Stefan 
Published: September 2020

Abstract
Antimicrobial resistance is an emerging global health threat necessitating the rapid development of novel antimicrobials. Remarkably, the vast majority of currently available antibiotics are natural products (NPs) isolated from streptomycetes, soil-dwelling bacteria of the genus Streptomyces. However, there is still a huge reservoir of streptomycetes NPs which remains pharmaceutically untapped and a compendium thereof could serve as a source of inspiration for the rational design of novel antibiotics. Initially released in 2012, StreptomeDB (http://www.pharmbioinf.uni-freiburg.de/streptomedb) is the first and only public online database that enables the interactive phylogenetic exploration of streptomycetes and their isolated or mutasynthesized NPs. In this third release, there are substantial improvements over its forerunners, especially in terms of data content. For instance, about 2500 unique NPs were newly annotated through manual curation of about 1300 PubMed-indexed articles, published in the last five years since the second release. To increase interoperability, StreptomeDB entries were hyperlinked to several spectral, (bio)chemical and chemical vendor databases, and also to a genome-based NP prediction server. Moreover, predicted pharmacokinetic and toxicity profiles were added. Lastly, some recent real-world use cases of StreptomeDB are highlighted, to illustrate its applicability in life sciences.
Effectiveness of Invasive Techniques in Patients with Fibromyalgia: Systematic Review and Meta-Analysis
Authors: Sarmiento-Hernández Isabel , Pérez-Marín María de los Ángeles , Nunez-Nagy Susana , Pecos-Martín Daniel , Gallego-Izquierdo Tomás , Sosa-Reina M Dolores 
Published: September 2020

Abstract

Objective
To attain a synthesis of the evidence on the effectiveness of invasive techniques in patients with fibromyalgia, through systematic review and meta-analysis and by assessing the methodological quality of the studies considered.

Methods
A systematic review and meta-analysis were carried out as defined in the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement. The bibliographic research was carried out in the PEDro, Cochrane, PubMed, Science Direct, Web of Science, Google Academics, Dialnet, and Scielo databases from September through December of 2018.

Results
Results show that invasive techniques produce a significant decrease in the pain, the impact of fibromyalgia and in the pain pressure threshold (standardized mean difference [95% confidence interval]: -0.94 [-1.44, -0.44], P of global effect= 0.0002; -0.99 [-1.69, -0.29], P of global effect= 0.006; and 0.31 [0.02, 0.61], P of global effect = 0.04, respectively). Lastly, a significant increase was observed in the quality-of-life variable after intervention (0.84 [0.30, 1.38], P of global effect = 0.002).

Conclusions
Invasive techniques are considered effective for pain relief, as well as for producing a short-term increase in the pain pressure threshold, an improvement in quality of life, and a decrease in the impact of fibromyalgia.