bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sirtuin 5 promotes arterial thrombosis by blunting the fibrinolytic system
Authors: Liberale Luca , Akhmedov Alexander , Vlachogiannis Nikolaos I , Bonetti Nicole R , Nageswaran Vanasa , Miranda Melroy X , Puspitasari Yustina M , Schwarz Lena , Costantino Sarah , Paneni Francesco , Beer Jürg H , Ruschitzka Frank , Montecucco Fabrizio , Lüscher Thomas F , Stamatelopoulos Kimon , Stellos Konstantinos , Camici Giovanni G 
Published: September 2020

Abstract

Aims
Arterial thrombosis as a result of plaque rupture or erosion is a key event in acute cardiovascular events. Sirtuin 5 (SIRT5) belongs to the lifespan-regulating sirtuin superfamily and has been implicated in acute ischaemic stroke and cardiac hypertrophy. This project aims at investigating the role of SIRT5 in arterial thrombus formation.

Methods and results
Sirt5 transgenic (Sirt5Tg/0) and knock-out (Sirt5−/−) mice underwent photochemically induced carotid endothelial injury to trigger arterial thrombosis. Primary human aortic endothelial cells (HAECs) were treated with SIRT5 silencing-RNA (si-SIRT5) as well as peripheral blood mononuclear cells from acute coronary syndrome (ACS) patients and non-ACS controls (case–control study, total n = 171) were used to increase the translational relevance of our data. Compared to wild-type controls, Sirt5Tg/0 mice displayed accelerated arterial thrombus formation following endothelial-specific damage. Conversely, in Sirt5−/− mice, arterial thrombosis was blunted. Platelet function was unaltered, as assessed by ex vivo collagen-induced aggregometry. Similarly, activation of the coagulation cascade as assessed by vascular and plasma tissue factor (TF) and TF pathway inhibitor expression was unaltered. Increased thrombus embolization episodes and circulating D-dimer levels suggested augmented activation of the fibrinolytic system in Sirt5−/− mice. Accordingly, Sirt5−/− mice showed reduced plasma and vascular expression of the fibrinolysis inhibitor plasminogen activator inhibitor (PAI)-1. In HAECs, SIRT5-silencing inhibited PAI-1 gene and protein expression in response to TNF-α. This effect was mediated by increased AMPK activation and reduced phosphorylation of the MAP kinase ERK 1/2, but not JNK and p38 as shown both in vivo and in vitro. Lastly, both PAI-1 and SIRT5 gene expressions are increased in ACS patients compared to non-ACS controls after adjustment for cardiovascular risk factors, while PAI-1 expression increased across tertiles of SIRT5.

Conclusion
SIRT5 promotes arterial thrombosis by modulating fibrinolysis through endothelial PAI-1 expression. Hence, SIRT5 may be an interesting therapeutic target in the context of atherothrombotic events.
Wealth in Spain 1900–2017 A Country of Two Lands
Authors: Blanco Miguel Artola , Bauluz Luis , Martínez-Toledano Clara 
Published: September 2020

AbstractThis study reconstructs Spain’s national wealth from 1900 to 2017. By combining new sources with existing accounts, we estimate the wealth of both private and government sectors and use a new asset-specific decomposition of the long-run accumulation of wealth. We find that, during the twentieth century, the national wealth-to-income ratio remained within a relatively narrow range—between 400% and 600%—until the housing boom of the early 2000s led to an unprecedented rise to 800% in 2007. Our results highlight the importance of land, housing capital gains and international capital flows as key elements of wealth accumulation.
Bacteriophages as drivers of bacterial virulence and their potential for biotechnological exploitation
Authors: Schroven Kaat , Aertsen Abram , Lavigne Rob 
Published: September 2020

ABSTRACTBacteria-infecting viruses (phages) and their hosts maintain an ancient and complex relationship. Bacterial predation by lytic phages drives an ongoing phage-host arms race, whereas temperate phages initiate mutualistic relationships with their hosts upon lysogenization as prophages. In human pathogens, these prophages impact bacterial virulence in distinct ways: by secretion of phage-encoded toxins, modulation of the bacterial envelope, mediation of bacterial infectivity and the control of bacterial cell regulation. This review builds the argument that virulence-influencing prophages hold extensive, unexplored potential for biotechnology. More specifically, it highlights the development potential of novel therapies against infectious diseases, to address the current antibiotic resistance crisis. First, designer bacteriophages may serve to deliver genes encoding cargo proteins which repress bacterial virulence. Secondly, one may develop small molecules mimicking phage-derived proteins targeting central regulators of bacterial virulence. Thirdly, bacteria equipped with phage-derived synthetic circuits which modulate key virulence factors could serve as vaccine candidates to prevent bacterial infections. The development and exploitation of such antibacterial strategies will depend on the discovery of other prophage-derived, virulence control mechanisms and, more generally, on the dissection of the mutualistic relationship between temperate phages and bacteria, as well as on continuing developments in the synthetic biology field.
Incentives or restrictions: policy choices in farmers’ chemical fertilizer reduction and substitution behaviors
Authors: Yang Yurong , Li Zhaoliang , Zhang Yan 
Published: September 2020

AbstractBased on 804 samples of farmers in Hubei Province, a typical major grain-producing area in China, this study empirically analyzed the effects of two different policy tools, i.e. economic incentives (subsidies) and order enforcements (regulatory restrictions), as well as the effects of their interaction, on farmers’ chemical fertilizer reduction and substitution behaviors. Samples were grouped according to the degree of concurrent employment to analyze the effects on different groups. The results show that (1) the influences of these policies on the behaviors were significantly positive; (2) after constructing the interactive variables of the policies, the influence of the order enforcement policy was no longer significant, but the influence of the interaction was significantly positive; (3) the low-degree concurrent employment farmers were more likely to be affected by the order enforcement policy, whereas the high-degree ones were more affected by the economic incentive policy; and (4) the behaviors of the low-degree ones were strongly affected by family management characteristics, whereas the high-degree ones were more affected by the farmers’ individual characteristics.
LC–QTOF-MS Presumptive Identification of Synthetic Cannabinoids without Reference Chromatographic Retention/Mass Spectral Information. II. Evaluation of a Computational Approach for Predicting and Identifying Unknown High-Resolution Product Ion Mass Spectra
Authors: Polettini Aldo E , Kutzler Johannes , Sauer Christoph , Guber Susanne , Schultis Wolfgang 
Published: September 2020

AbstractDespite liquid chromatography–high-resolution tandem mass spectrometry (MS2) enables untargeted acquisition, data processing in toxicological screenings is almost invariably performed in targeted mode. We developed a computational approach based on open source chemometrics software that, starting from a suspected synthetic cannabinoid (SC) determined formula, searches for isomers in different new psychoactive substances web databases, predicts retention time (RT) and high-resolution MS2 spectrum, and compares them with the unknown providing a rank-ordered candidates list. R was applied on 105 SC measured data to develop and validate a multiple linear regression quantitative structure–activity relationship model predicting RT. Competitive Fragmentation Modeling for Metabolite Identification (CFM-ID) freeware was used to predict/compare spectra with Jaccard similarity index. Data-dependent acquisition was performed with an Agilent Infinity 1290 LC-6550 iFunnel Q-TOF MS with ZORBAX Eclipse-Plus C18 (100 × 2.1 mm2/1.8 µm) in water/acetonitrile/ammonium formate gradient. Ability of the combined RT/MS2 prediction to identify unknowns was evaluated on SC standards (with leave-one-out from the RT model) and on unexpected SC encountered in real cases. RT prediction reduced the number of isomers retrieved from a group of new psychoactive substances web databases to one-third (2,792 ± 3,358→845 ± 983) and differentiated between SC isomers when spectra were not selective (4F-MDMB-BUTINACA, 4F-MDMB-BUTINACA 2ʹ-indazole isomer) or unavailable (4CN-Cumyl-B7AICA, 4CN-Cumyl-BUTINACA). When comparing 30/40 eV measured spectra of 99 SC against RT-selected, CFM-ID predicted spectra of isomers, the right candidate ranked 1st on median and 4th on average; 54% and 88% of times the right match ranked 1st or within the first 5 matches, respectively. To our knowledge, this is the first case of extensive chemometrics application to toxicological screening. In most cases, presumptive identification (being based on computation, it requires further information for confirmation) of unexpected SC was achieved without reference measured information. This method is currently the closest possible to true unbiased/untargeted screening. The bottleneck of the method is the processing time required to predict mass spectra (ca. 30–35 s/compound using a 64-bit 2.50-GHz Intel® Core™ i5-7200U CPU). However, strategies can be implemented to reduce prediction processing time.
The Fact-Law Distinction: Strategic Factfinding and Lawmaking in a Judicial Hierarchy
Authors: Shahshahani Sepehr 
Published: September 2020

Abstract
A fundamental but understudied procedural institution of American law is that appellate courts defer more to trial courts’ findings of fact than to their conclusions of law. I formally model this procedural institution, showing how trial courts use factfinding to achieve their preferred outcome and how appellate courts craft rules in anticipation of trial courts’ strategic factfinding. Trial courts do not always report facts truthfully. Appellate courts do not commit to consistent rules, but consistent rules may emerge in equilibrium, creating a misleading appearance of judicial commitment to legal consistency. Preference divergence between trial and appellate courts has a nonmonotonic effect on factfinding. Fact deference can explain suboptimal rulemaking and reversals even when there is no uncertainty about the likelihood of review or the reviewing court’s ideal rule. The model is also useful in understanding why the institution of fact deference persists. Applications to policing and other domains are discussed. (JEL K40, K41, D02)
The disintegrating old open cluster Czernik 3
Authors: Sharma Saurabh , Ghosh Arpan , Ojha D K , Pandey R , Sinha T , Pandey A K , Ghosh S K , Panwar N , Pandey S B 
Published: September 2020

ABSTRACT
We have performed a detailed analysis of the Czernik 3 (Cz3) open cluster by using deep near-infrared photometry taken with TIRCAM2 on the 3.6 m Devasthal optical telescope along with the recently available high-quality proper motion data from the Gaia DR2 and deep photometric data from Pan-STARRS1. The cluster has a highly elongated morphology with fractal distribution of stars. The core and cluster radii of the cluster are estimated as 0.5 and 1.2 pc, respectively. We have identified 45 stars as cluster members using the Gaia proper motion data. The distance and age of the cluster are found to be 3.5 ± 0.9 kpc and $0.9^{+0.3}_{-0.1}$ Gyr, respectively. The slope of the mass function `Γ′ in the cluster region, in the mass range ∼0.95 &lt;M/M⊙ &lt; 2.2, is found to be −1.01 ± 0.43. The cluster shows the signatures of mass segregation and is dynamically relaxed (dynamical age = 10 Myr). This along with its small size, big tidal radius, low density/large separation of stars, and elongated and distorted morphology indicates that the Cz3 is a loosely bound disintegrating cluster under the influence of external tidal interactions.
Turbulent, pinned superfluids in neutron stars and pulsar glitch recoveries
Authors: Haskell B , Antonopoulou D , Barenghi C 
Published: September 2020

ABSTRACT
Pulsar glitches offer an insight into the dynamics of superfluids in the high-density interior of a neutron star. To model these phenomena, however, one needs to have an understanding of the dynamics of a turbulent array of superfluid vortices moving through a pinning lattice. In this paper, we develop a theoretical approach to describe vortex-mediated mutual friction in a pinned, turbulent and rotating superfluid. Our model is then applied to the study of the post-glitch rotational evolution in the Vela pulsar and in PSR J0537-6910. We show that in both cases a turbulent model fits the evolution of the spin frequency derivative better than a laminar one. We also predict that the second derivative of the frequency after a glitch should be correlated with the waiting time since the previous glitch, which we find to be consistent with observational data for these pulsars. The main conclusion of this paper is that in the post-glitch rotational evolution of these two pulsars we are most likely observing the response to the glitch of a pinned turbulent region of the star (possibly the crust) and not the laminar response of a regular straight vortex array.
CasCollect: targeted assembly of CRISPR-associated operons from high-throughput sequencing data
Authors: Podlevsky Joshua D , Hudson Corey M , Timlin Jerilyn A , Williams Kelly P 
Published: September 2020

Abstract
CRISPR arrays and CRISPR-associated (Cas) proteins comprise a widespread adaptive immune system in bacteria and archaea. These systems function as a defense against exogenous parasitic mobile genetic elements that include bacteriophages, plasmids and foreign nucleic acids. With the continuous spread of antibiotic resistance, knowledge of pathogen susceptibility to bacteriophage therapy is becoming more critical. Additionally, gene-editing applications would benefit from the discovery of new cas genes with favorable properties. While next-generation sequencing has produced staggering quantities of data, transitioning from raw sequencing reads to the identification of CRISPR/Cas systems has remained challenging. This is especially true for metagenomic data, which has the highest potential for identifying novel cas genes. We report a comprehensive computational pipeline, CasCollect, for the targeted assembly and annotation of cas genes and CRISPR arrays—even isolated arrays—from raw sequencing reads. Benchmarking our targeted assembly pipeline demonstrates significantly improved timing by almost two orders of magnitude compared with conventional assembly and annotation, while retaining the ability to detect CRISPR arrays and cas genes. CasCollect is a highly versatile pipeline and can be used for targeted assembly of any specialty gene set, reconfigurable for user provided Hidden Markov Models and/or reference nucleotide sequences.
Read trimming is not required for mapping and quantification of RNA-seq reads at the gene level
Authors: Liao Yang , Shi Wei 
Published: September 2020

Abstract
RNA sequencing (RNA-seq) is currently the standard method for genome-wide expression profiling. RNA-seq reads often need to be mapped to a reference genome before read counts can be produced for genes. Read trimming methods have been developed to assist read mapping by removing adapter sequences and low-sequencing-quality bases. It is however unclear what is the impact of read trimming on the quantification of RNA-seq data, an important task in RNA-seq data analysis. In this study, we used a benchmark RNA-seq dataset and simulation data to assess the impact of read trimming on mapping and quantification of RNA-seq reads. We found that adapter sequences can be effectively removed by read aligner via ’soft-clipping’ and that many low-sequencing-quality bases, which would be removed by read trimming tools, were rescued by the aligner. Accuracy of gene expression quantification from using untrimmed reads was found to be comparable to or slightly better than that from using trimmed reads, based on Pearson correlation with reverse transcriptase-polymerase chain reaction data and simulation truth. Total data analysis time was reduced by up to an order of magnitude when read trimming was not performed. Our study suggests that read trimming is a redundant process in the quantification of RNA-seq expression data.
Association of Early Nasopharyngeal Immune Markers With COVID-19 Clinical Outcome: Predictive Value of CCL2/MCP-1
Authors: Sierra Beatriz , Pérez Ana B , Aguirre Eglis , Bracho Claudia , Valdés Odalys , Jimenez Narciso , Baldoquin Waldemar , Gonzalez Guelsys , Ortega Lilia M , Montalvo Maria C , Resik Sonia , Alvarez Delmis , Guzmán Maria G 
Published: September 2020

Abstract
Early recognition of severe forms of coronavirus disease 2019 (COVID-19) is essential for an opportune and effective intervention, reducing life-risking complications. An altered inflammatory immune response seems to be associated with COVID-19’s pathogenesis and progression to severity. Here we demonstrate the utility of early nasopharyngeal swab samples for detection of the early expression of immune markers and the potential value of CCL2/MCP-1 in predicting disease outcome.
Perceptions of Kinesiophobia in Relation to Physical Activity and Exercise After Myocardial Infarction: A Qualitative Study
Authors: Bäck Maria , Caldenius Victoria , Svensson Leif , Lundberg Mari 
Published: September 2020

Abstract

Objective
Physical activity and exercise are central components in rehabilitation after a myocardial infarction. Kinesiophobia (fear of movement) is a well-known barrier for a good rehabilitation outcome in these patients; however, there is a lack of studies focusing on the patient perspective. The aim of this study was to explore patients’ perceptions of kinesiophobia in relation to physical activity and exercise 2 to 3 months after an acute myocardial infarction.

Methods
This qualitative study design used individual semi-structured interviews. Face-to-face interviews were conducted with 21 patients post-myocardial infarction who were screened for kinesiophobia (≥32 on the Tampa Scale for Kinesiophobia Heart). The interviews were transcribed and analyzed according to an inductive content analysis.

Results
An overarching theme was defined as “coping with fear of movement after a myocardial infarction—a dynamic process over time” comprising 2 subthemes and explaining how coping with kinesiophobia runs in parallel processes integrating the patient’s internal process and a contextual external process. The 2 processes are described in a total of 8 categories. The internal process was an iterative process governed by a combination of factors: ambivalence, hypervigilance, insecurity about progression, and avoidance behavior. The external process contains the categories of relatives’ anxiety, prerequisites for feeling safe, information, and the exercise-based cardiac rehabilitation program.

Conclusion
Coping with fear of movement after a myocardial infarction is a dynamic process that requires internal and external support. To further improve cardiac rehabilitation programs, person-centered strategies that support the process of each person—as well as new treatment strategies to reduce kinesiophobia—need to be elaborated.

Impact
Patients with a myocardial infarction were found to be ambivalent about how they expressed their fear of movement; therefore, it is crucial for physical therapists to acknowledge signs of fear by listening carefully to the patient’s full story in addition to using adequate self-reports and tests of physical fitness. These results will inform the design, development, and evaluation of new treatment strategies, with the overall aim of reducing kinesiophobia and increasing physical activity and participation in exercise-based cardiac rehabilitation.
Elaboration of a new synovial predictive score of septic origin for acute arthritis on the native joint (RESAS)
Authors: Coiffier Guillaume , Berthoud Olivia , Albert Jean David , Robin François , Goussault Claire , Gougeon-Jolivet Anne , Bendavid Claude , Guggenbuhl Pascal 
Published: September 2020

Abstract

Objective
To establish a new predictive score for the diagnosis of septic arthritis (SA) according to different synovial fluid (SF) variables.

Methods
First, we analysed the different clinical, biological and SF variables associated with the diagnosis of SA (according to the Newman’s criteria) in a monocentric cohort of acute arthritis (&lt;30 days) (n = 233) (SYNOLACTATE cohort). A new score predictive of SA (RESAS) was created using the independent discriminant variables after multivariate analysis. A value was attributed to each variable of the score according to the weighting based on their likelihood ratio for the diagnosis of SA. RESAS performance was then tested on the first cohort (internal validation) and then checked on a second independent cohort (n = 70) (external validation).

Results
After multivariate analysis, four independent variables of the SF were included for RESAS: (i) purulent SF or white blood cells count ≥70 000/mm3; (ii) absence/presence of crystals; (iii) lactate; and (iv) glucose synovial level. RESAS ranged between −4 and +13 points. The performance of RESAS to predicted SA was excellent with area under the curve (AUC)=0.928 (0.877–0.980) in internal validation and AUC=0.986 (0.962–1.00) in external validation. For a RESAS threshold ≥+4, SA was diagnosed with Se=56.0% (0.371–0.733), Sp=98.1% (0.952–0.993), LR+=29.1 (10.4–81.6) in the first cohort and with Se=91.7% (0.646–0.985), Sp=98.3% (0.909–0.997), LR+=53.2 (7.56–373) in the second cohort.

Conclusion
RESAS is a new composite score of four SF variables with excellent performance to predicted SA in acute arthritis population.