bluuebunny/crossref_metadata_2025 huggingface dataset:
Heterogeneous nucleation of YBCO via fluorine based MOD process: thermodynamic and kinetic approach
Authors: Pinto V , Celentano G , Tomellini M
Published: August 2020

The nucleation of YBa2Cu3O7−δ (YBCO) film deposited via metal organic decomposition (MOD) approach is a complex process that has a key role in YBCO film crystalline orientation and, consequently, superconducting properties. Up to now, several studies have been carried out to clarify this step in the fluorine based MOD route which employs only or partially metals trifluoroacetate for the precursor solution preparation. However, these previous works provided only qualitative indications, whereas a quantitative theoretical investigation seems to be still lacking.

In this paper, the free energy for critical nucleus formation of fluorine based MOD YBCO has been determined according to the classical nucleation theory. The volume contribution to the free energy is computed using thermodynamic data on (Y, Ba, Cu, O) systems available from the literature. The free energy barrier for nucleation depends upon nucleus orientation, via the work of adhesion and surface energies of vacuum/nucleus interfaces. The model is applied to describe heterogeneous nucleation of YBCO on (001) SrTiO3 single crystal and provides quantitative information on nucleation barriers as a function of temperature and both precursor and gas phase compositions. Through a kinetic approach, the energy barriers are further employed to estimate the fraction of c-oriented nuclei as a function of temperature and water partial pressure.

Comparison with experimental data from literature lends support to the proposed computations. Therefore, the results shown in this work may be useful in designing the YBCO deposition process in order to obtain films with superior superconducting properties avoiding expensive and time-consuming experimental optimizations.
Superconductivity of lanthanum hydride synthesized using AlH3 as a hydrogen source
Authors: Sakata Masafumi , Einaga Mari , Dezhong Meng , Sato Toyoto , Orimo Shin-ichi , Shimizu Katsuya
Published: August 2020

Hydrogen-rich compounds show high-

T

c

superconductivity related to dense hydrogen under extremely high pressure (above 100 GPa). A recent investigation to search for high-

T

c

superconductive hydrides has advanced a synthesis technique using infrared laser heating of a hydrogen source material under conditions of extremely high pressure and temperature. In order to find a suitable synthesis route for high-

T

c

superconductive hydrides, the selection of a hydrogen source material has to be considered. In this study, the synthesis of hydrogen-rich lanthanum hydrides (LaH
x
) was performed using aluminium trihydride (AlH3) as the hydrogen source. Simple lanthanum on AlH3 was pressurized at 150 GPa and heated by infrared laser irradiation. After the laser heating, superconductivity at

T

c

∼ 70 K was observed at 170 GPa. This indicates that LaH
x
(x

<

10) was synthesized using AlH3 as the hydrogen source under conditions of extremely high pressure.
Improved bone regeneration using collagen-coated biphasic calcium phosphate with high porosity in a rabbit calvarial model
Authors: Seo Seung-Jun , Kim Yong-Gun
Published: August 2020

Many growth factors have been paired with synthetic bone grafts to accelerate the healing process in vivo. Collagen has been particularly examined as a mediator of the enhancement of bone regeneration. This study investigated the new bone formation potential of micro–macroporous biphasic calcium phosphate (m-BCP), high porosity biphasic calcium phosphate (p-BCP), and collagen-coated p-BCP (cp-BCP) using a rabbit calvarial defect model. At 2 or 8 weeks after surgery, bone tissue was collected. The three-dimensional analysis of new bone formation using synchrotron radiation micro-computed tomography and histological study were conducted. The new bone formation values observed at 2 and 8 weeks in the negative control, m-BCP, p-BCP, and cp-BCP groups were 11.21 ± 1.36 mm3, 21.75 ± 1.18 mm3, 24.59 ± 1.26 mm3, and 29.54 ± 2.72 mm3, respectively, and 18.34 ± 3.99 mm3, 32.27 ± 3.78 mm3, 43.12 ± 1.61 mm3, and 58.20 ± 3.84 mm3, respectively. New bone formation was greatest in the cp-BCP group, while the amount of new bone at 8 weeks was higher than at 2 weeks in each group. The use of cp-BCP to enhance new bone formation during the healing period could improve bone regeneration.
STED controlled photobleaching for sub-diffractional optical nanopatterning
Authors: Murtezi Eljesa , Puthukodan Sujitha , Buchegger Bianca , Jacak Jaroslaw , Klar Thomas A
Published: August 2020

Laser-assisted protein adsorption by photobleaching (LAPAP) is a versatile tool to nanopattern proteins on the micrometer scale. Sub-micron patterning is, however, difficult due to diffraction. We show that, similar to stimulated emission depletion (STED) microscopy, a depleting beam can effectively suppress LAPAP and hence is apt to locally control LAPAP in order to write sub-diffractional lines of proteins. Specifically, we attach biotinylated Atto 390 to glass substrates and incubate with Alexa 555 labeled streptavidin. The Alexa 555 is subsequently imaged with STED nanoscopy. The method is currently limited by diffusion of the biotinylated Atto 390 molecules.
An assessment of the structural resolution of various fingerprints commonly used in machine learning
Authors: Parsaeifard Behnam , Sankar De Deb , Christensen Anders S , Faber Felix A , Kocer Emir , De Sandip , Behler Jörg , Anatole von Lilienfeld O , Goedecker Stefan
Published: August 2020

Atomic environment fingerprints are widely used in computational materials science, from machine learning potentials to the quantification of similarities between atomic configurations. Many approaches to the construction of such fingerprints, also called structural descriptors, have been proposed. In this work, we compare the performance of fingerprints based on the overlap matrix, the smooth overlap of atomic positions, Behler–Parrinello atom-centered symmetry functions, modified Behler–Parrinello symmetry functions used in the ANI-1ccx potential and the Faber–Christensen–Huang–Lilienfeld fingerprint under various aspects. We study their ability to resolve differences in local environments and in particular examine whether there are certain atomic movements that leave the fingerprints exactly or nearly invariant. For this purpose, we introduce a sensitivity matrix whose eigenvalues quantify the effect of atomic displacement modes on the fingerprint. Further, we check whether these displacements correlate with the variation of localized physical quantities such as forces. Finally, we extend our examination to the correlation between molecular fingerprints obtained from the atomic fingerprints and global quantities of entire molecules.
Fast reconstruction of single-shot wide-angle diffraction images through deep learning
Authors: Stielow T , Schmidt R , Peltz C , Fennel T , Scheel S
Published: August 2020

Single-shot x-ray imaging of short-lived nanostructures such as clusters and nanoparticles near a phase transition or non-crystalizing objects such as large proteins and viruses is currently the most elegant method for characterizing their structure. Using hard x-ray radiation provides scattering images that encode two-dimensional projections, which can be combined to identify the full three-dimensional object structure from multiple identical samples. Wide-angle scattering using XUV or soft x-rays, despite yielding lower resolution, provides three-dimensional structural information in a single shot and has opened routes towards the characterization of non-reproducible objects in the gas phase. The retrieval of the structural information contained in wide-angle scattering images is highly non-trivial, and currently no efficient rigorous algorithm is known. Here we show that deep learning networks, trained with simulated scattering data, allow for fast and accurate reconstruction of shape and orientation of nanoparticles from experimental images. The gain in speed compared to conventional retrieval techniques opens the route for automated structure reconstruction algorithms capable of real-time discrimination and pre-identification of nanostructures in scattering experiments with high repetition rate—thus representing the enabling technology for fast femtosecond nanocrystallography.
Regulation of sugar metabolism genes in the nitrogen-dependent susceptibility of tomato stems toBotrytis cinerea
Authors: Lacrampe Nathalie , Lopez-Lauri Félicie , Lugan Raphaël , Colombié Sophie , Olivares Jérôme , Nicot Philippe C , Lecompte François
Published: August 2020

Background and Aims

The main soluble sugars are important components of plant defence against pathogens, but the underlying mechanisms are unclear. Upon infection by Botrytis cinerea, the activation of several sugar transporters, from both plant and fungus, illustrates the struggle for carbon resources. In sink tissues, the metabolic use of the sugars mobilized in the synthesis of defence compounds or antifungal barriers is not fully understood.

Methods

In this study, the nitrogen-dependent variation of tomato stem susceptibility to B. cinerea was used to examine, before and throughout the course of infection, the transcriptional activity of enzymes involved in sugar metabolism. Under different nitrate nutrition regimes, the expression of genes that encode the enzymes of sugar metabolism (invertases, sucrose synthases, hexokinases, fructokinases and phosphofructokinases) was determined and sugar contents were measured before inoculation and in asymptomatic tissues surrounding the lesions after inoculation.

Key Results

At high nitrogen availability, decreased susceptibility was associated with the overexpression of several genes 2 d after inoculation: sucrose synthases Sl-SUS1 and Sl-SUS3, cell wall invertases Sl-LIN5 to Sl-LIN9 and some fructokinase and phosphofructokinase genes. By contrast, increased susceptibility corresponded to the early repression of several genes that encode cell wall invertase and sucrose synthase. The course of sugar contents was coherent with gene expression.

Conclusions

The activation of specific genes that encode sucrose synthase is required for enhanced defence. Since the overexpression of fructokinase is also associated with reduced susceptibility, it can be hypothesized that supplementary sucrose cleavage by sucrose synthases is dedicated to the production of cell wall components from UDP-glucose, or to the additional implication of fructose in the synthesis of antimicrobial compounds, or both.
A review of computational strategies for denoising and imputation of single-cell transcriptomic data
Authors: Patruno Lucrezia , Maspero Davide , Craighero Francesco , Angaroni Fabrizio , Antoniotti Marco , Graudenzi Alex
Published: August 2020

Motivation

The advancements of single-cell sequencing methods have paved the way for the characterization of cellular states at unprecedented resolution, revolutionizing the investigation on complex biological systems. Yet, single-cell sequencing experiments are hindered by several technical issues, which cause output data to be noisy, impacting the reliability of downstream analyses. Therefore, a growing number of data science methods has been proposed to recover lost or corrupted information from single-cell sequencing data. To date, however, no quantitative benchmarks have been proposed to evaluate such methods.

Results

We present a comprehensive analysis of the state-of-the-art computational approaches for denoising and imputation of single-cell transcriptomic data, comparing their performance in different experimental scenarios. In detail, we compared 19 denoising and imputation methods, on both simulated and real-world datasets, with respect to several performance metrics related to imputation of dropout events, recovery of true expression profiles, characterization of cell similarity, identification of differentially expressed genes and computation time. The effectiveness and scalability of all methods were assessed with regard to distinct sequencing protocols, sample size and different levels of biological variability and technical noise. As a result, we identify a subset of versatile approaches exhibiting solid performances on most tests and show that certain algorithmic families prove effective on specific tasks but inefficient on others. Finally, most methods appear to benefit from the introduction of appropriate assumptions on noise distribution of biological processes.
The role of landscape history in the distribution and conservation of threatened flora in the Southwest Australian Floristic Region
Authors: Gosper Carl R , Coates David J , Hopper Stephen D , Byrne Margaret , Yates Colin J
Published: August 2020

The flora of the Southwest Australian Floristic Region (SWAFR) is characterized by remarkable richness, endemism, spatial turnover and numbers of threatened taxa. Increasingly, evolutionary history is recognized as contributing to SWAFR biogeographical patterns, culminating in the theory of old, climatically buffered, infertile landscapes (OCBILs) [and their counterpoint: young, often disturbed, fertile landscapes (YODFELs)]. For the SWAFR, we: (1) developed a spatially explicit distribution of OCBILs and YODFELs; (2) analysed the spatial distribution of Threatened and Priority (Data Deficient) flora; and (3) tested the hypotheses that Threatened and Priority flora will be most strongly represented in OCBILs and will have small geographical ranges. We found that OCBILs and YODFELs dominated spatially distinct portions of the SWAFR. Threatened and Priority flora were not uniformly or randomly distributed and were more strongly characterized by narrow-range endemics than the non-Threatened flora. The occurrence of Threatened and Priority flora was positively correlated with the age of surface exposure of landscape features and unique geological features of limited extent (if not YODFELs). The concentration of Threatened flora in OCBILs provides the opportunity to improve conservation management through investigations of how plant traits favoured by evolution in OCBILs might increase or decrease the susceptibility of the flora to anthropogenic threats.
A review of the fossil record of caecilians (Lissamphibia: Gymnophionomorpha) with comments on its use to calibrate molecular timetrees
Authors: Santos Rodolfo Otávio , Laurin Michel , Zaher Hussam
Published: August 2020

Gymnophiona, popularly known as caecilians, the most poorly known major taxon of extant amphibians, are elongate and limbless tetrapods, with compact ossified skulls and reduced eyes, mainly adapted to fossorial life as adults. Caecilians are poorly represented in the fossil record, but despite the scarcity of fossil specimens described (only four named taxa, in addition to indeterminate fragmentary material), their fossils play a key role in our knowledge of the origin and evolution of Lissamphibia, as well as contribute directly to a better understanding of the phylogeny, taxonomy and biogeography of extant gymnophionan taxa. These records are scattered throughout geological time (from the Jurassic to the sub-Recent) and space (North and South America and Africa). Here, we revisit the caecilian fossil record, providing a brief description of all known extinct taxa described so far, along with general remarks about their impact on systematics, time range, and geographical distribution of the clade, as well as prospects for future research. Possible calibration constraints based on the caecilian fossil record are provided.
Systematic Error for Extraction of Controlled Substances from Plant/Fungal Materials
Authors: Nagy Júlia , Veress Tibor
Published: August 2020

The aim of this work was to investigate the applicability of a mathematical model developed for the description of supercritical fluid extraction (SFE) of cannabinoids from marijuana and hashish for liquid extraction of other substances. The mentioned model is applicable for dynamic SFE whose implementation is analogous to liquid–solid extraction in quasi-counter current mode. According to this model, quasi-counter current liquid–solid extractions were designed by calculation of component transport constants for extractions of psilocin from hallucinogenic mushroom, mescaline from hallucinogenic cactus, harmine from tropical lyan and salvinorin A from hallucinogenic sage. The mentioned model was found to be suitable for the determination of extraction time needed to reach a predefined extraction recovery for quasi-counter current liquid–solid extractions, as well, which allows the elimination of systematic error caused by the non-extracted part. The calculated component transport constants predict the expectable velocity of the extraction, i.e., the higher the component transport constant is, the higher the extraction velocity is. For mushrooms, it could be stated that preliminary treatment of mushrooms with liquid nitrogen significantly increases the extractability of psilocin.
Audiences’ Communicative Agency in a Datafied Age: Interpretative, Relational and Increasingly Prospective
Authors: Ytre-Arne Brita , Das Ranjana
Published: August 2020

This article develops a conceptualization of audience agency in the face of datafication. We consider how people, as audiences and users of media and technologies, face transforming communicative conditions, and how these conditions challenge the power potentials of audiences in processes of communication—that is, their communicative agency. To develop our conceptualization, we unpack the concept of audiences’ communicative agency by examining its foundations in communication scholarship, in reception theory and sociology, arguing that agency is understood as interpretative and relational, and applied to make important normative assessments. We further draw on emerging scholarship on encounters with data in the everyday to discuss how audience agency is now challenged by datafication, arguing that communicative agency is increasingly prospective in a datafied age. Thereby, we provide a theoretical conceptualization for further analysis of audiences in transforming communicative conditions.
Clarifications of the Russian Supreme Court on General Aspects of Intellectual Property Protection: A Summary
Authors: Kapyrina Natalia
Published: August 2020

Since April 2019, Russian intellectual property law has been enriched by an interpretative Resolution of the highest judicial instance, the Plenary Session of the Supreme Court, which performs, among other prerogatives, the task to ensure the correct and uniform application of law.** The last time a judicial instrument of an equivalent scale was adopted was in 2009 (the Joint Resolution No. 5/29 of 26 March 2009 of the Plenary Sessions of the Supreme Court and of the Supreme Arbitration Court ‘On certain issues arising in connection with the enactment of Part Four of the CCRF’). Back then a significant number of issues deriving from the introduction in 2006 of Part Four of the Civil Code (dedicated to Intellectual Property) were identified, solved and converted into guidance for courts and other legal professionals. Now, subsequent revisions of the legislation, primarily aimed at its ‘modernisation’, as well as the adoption of other modifying instruments (such as the Ruling of the Constitutional Court n° 28-P of 13 December 2016), pushed by a growing IP practice and disparate case law, have provided a fertile ground for this new supreme judicial effort. The outcome is generous – useful to those wishing to acquire a global overview of Russian IP law. It slightly resembles a Prévert’s inventory, as many issues are touched upon with a varying depth, length and degree of sophistication. Although some observers have deplored the avoidance of this or that issue, the document is comprehensive and lengthy (182 paragraphs), and generally lauded by the Russian IP community.1
Deep learning methods applied to electronic monitoring data: automated catch event detection for longline fishing
Authors: Qiao Maoying , Wang Dadong , Tuck Geoffrey N , Little L Richard , Punt Andre E , Gerner Mike
Published: August 2020

Electronic monitoring (EM) systems have become functional and cost-effective tools for the conservation and sustainable harvesting of marine resources. EM is an alternative to on-board observers, which produces video segments that can subsequently be reviewed by analysts. It is currently used in a range of fisheries. There are two major challenges to the widespread adoption of EM. One is the large storage requirement for the video footage recorded and the other is the long time required by analysts to review the video footage. We propose an automated catch event detection framework to address these challenges. Our solution, based on deep learning techniques, automatically extracts video segments of catch events, which substantially reduces storage space and review time by analysts. Here, we demonstrate the framework using video footage from three longline fishing trips. The system recalled nearly 100% of the catch events across all trips.
Community-level consumption of antibiotics according to the AWaRe (Access, Watch, Reserve) classification in rural Vietnam
Authors: Nguyen Nam Vinh , Do Nga Thi Thuy , Nguyen Chuc Thi Kim , Tran Toan Khanh , Ho Phuc Dang , Nguyen Hanh Hong , Vu Huong Thi Lan , Wertheim Heiman F L , van Doorn H Rogier , Lewycka Sonia
Published: August 2020

Objectives

To review community-level consumption of antibiotics in rural Vietnam, according to the WHO Access, Watch, Reserve (AWaRe) classification of 2019, and identify factors associated with the choice of these antibiotics.

Methods

In this cross-sectional study, data on antibiotic purchases were collected through a customer exit survey of 20 community antibiotic suppliers in Ba Vi District, Hanoi, between September 2017 and July 2018. Antibiotic consumption was estimated through the number of antibiotic encounters, the number of DDDs supplied and the number of treatment days (DOTs) with antibiotics, and analysed according to the AWaRe classification. The factors associated with watch-group antibiotic supply were identified through multivariable logistic regression analysis.

Results

In total, there were 1342 antibiotic encounters, with access-group antibiotics supplied in 792 encounters (59.0%), watch-group antibiotics supplied in 527 encounters (39.3%) and not-recommended antibiotics supplied in 23 encounters (1.7%). No reserve-group antibiotics were supplied. In children, the consumption of watch-group antibiotics dominated in all three measures (54.8% of encounters, 53.0% of DOTs and 53.6% of DDDs). Factors associated with a higher likelihood of watch-group antibiotic supply were: private pharmacy (OR, 4.23; 95% CI, 2.8–6.38; P < 0.001), non-prescription antibiotic sale (OR, 2.62; 95% CI, 1.78–3.87; P < 0.001) and children (OR, 2.56; 95% CI, 1.84–3.55; P < 0.001).

Conclusions

High consumption of watch-group antibiotics was observed, especially for use in children. The frequent supply of watch-group antibiotics at private pharmacies reconfirms the need for implementing pharmacy-targeted interventions in Vietnam.
Serum and Urine Protein Electrophoresis and Serum-Free Light Chain Assays in the Diagnosis and Monitoring of Monoclonal Gammopathies
Authors: Singh Gurmukh
Published: August 2020

Background

Laboratory methods for diagnosis and monitoring of monoclonal gammopathies have evolved to include serum and urine protein electrophoresis, immunofixation electrophoresis, capillary zone electrophoresis, and immunosubtraction, serum-free light chain assay, mass spectrometry, and newly described QUIET.

Content

This review presents a critical appraisal of the test methods and reporting practices for the findings generated by the tests for monoclonal gammopathies. Recommendations for desirable practices to optimize test selection and provide value-added reports are presented. The shortcomings of the serum-free light chain assay are highlighted, and new assays for measuring monoclonal serum free light chains are addressed.

The various assays for screening, diagnosis, and monitoring of monoclonal gammopathies should be used in an algorithmic approach to avoid unnecessary testing. Reporting of the test results should be tailored to the clinical context of each individual patient to add value. Caution is urged in the interpretation of results of serum-free light chain assay, kappa/lambda ratio, and myeloma defining conditions. The distortions in serum-free light chain assay and development of oligoclonal bands in patients‘ status post hematopoietic stem cell transplants is emphasized and the need to note the location of original monoclonal Ig is stressed. The need for developing criteria that consider the differences in the biology of kappa and lambda light chain associated lesions is stressed. A new method of measuring monoclonal serum-free light chains is introduced. Reference is also made to a newly defined entity of light chain predominant intact immunoglobulin monoclonal gammopathy. The utility of urine testing in the diagnosis and monitoring of light chain only lesions is emphasized.
Incorporating Magnetic Resonance Imaging and Biomarkers in Active Surveillance Protocols - Results From the Prospective Stockholm3 Active Surveillance Trial (STHLM3AS)
Authors: Olsson Henrik , Nordström Tobias , Jäderling Fredrik , Egevad Lars , Vigneswaran Hari T , Annerstedt Magnus , Grönberg Henrik , Eklund Martin , Lantz Anna
Published: August 2020

Background

Active surveillance (AS) for men with low-risk prostate cancer (PC) can lead to patient morbidity and healthcare overutilization. The aim of this study was to evaluate an AS protocol using the Stockholm3 test and magnetic resonance imaging (MRI) to reduce biopsy intensity.

Methods

We conducted a prospective multicenter study of 280 invited men from a contemporary screening study (STHLM3), with Gleason Score (GS) 3 + 3 PC on a current AS protocol. Patients underwent prostate-MRI and blood sampling for analysis of the Stockholm3 test including protein biomarkers, genetic variants, and clinical variables to predict risk of GS ≥3 + 4 PC followed by systematic biopsies and targeted biopsies (for Prostate Imaging Reporting and Data System version 2 ≥3 lesions) in all men. Primary outcomes were reclassification to GS ≥3 + 4 PC and clinically significant PC (csPCa), including unfavorable intermediate risk PC or higher based on National Comprehensive Cancer Network guidelines.

Results

Adding MRI-targeted biopsies to systematic biopsies increased sensitivity of GS ≥3 + 4 PC compared with systematic biopsies alone (relative sensitivity [RS] = 1.52, 95% confidence interval [CI] = 1.28 to 1.85). Performing biopsies in only MRI positive increased sensitivity of GS ≥3 + 4 PC (RS = 1.30, 95% CI = 1.04 to 1.67) and reduced number of biopsy procedures by 49.3% while missing 7.2% GS ≥3 + 4 PC and 1.4% csPCa. Excluding men with negative Stockholm3 test reduced the number of MRI investigations at follow-up by 22.5% and biopsies by 56.8% while missing 6.9% GS ≥3 + 4 PC and 1.3% csPCa.

Conclusion

Including MRI and targeted/systematic biopsies in the follow-up for men on AS increased sensitivity of PC reclassification. Incorporation of risk prediction models including biomarkers may reduce the need for MRI use in men with low-risk PC.
A case report of a unique aorto-bifemoral graft infection and its treatment
Authors: Uslu Hatim Yahya , Kurt Halil
Published: August 2020

In this study, we report a unique case of aorto-bifemoral graft infection, which developed in a 47-year-old male patient after endovascular aortic aneurysmal repair (EVAR) and extra anatomic axillo-femoral bypass. The patient had previously been treated by EVAR for an infrarenal abdominal aortic aneurysm. Earlier, the EVAR was blocked by a thrombosis and treated with an extra-anatomic axillo femoral bypass, which then became occluded. The patient was then treated with an aorto-bifemoral bypass using a Dacron Y graft. A few months later, he was referred to our cardiovascular center with high body temperature, weight loss, inability to stand and walk, and very serious sepsis. A computed abdominal tomography scan revealed that a part of the graft proximal to the bifurcation had totally eroded into the proximal jejunum. We treated this patient with multiple surgeries, antibiotic administrations and hypochlorous acid irrigation without graft excision, which carries a high morbidity and mortality risks.
On-sky results for adaptive optics control with data-driven models on low-order modes
Authors: Sinquin Baptiste , Prengère Léonard , Kulcsár Caroline , Raynaud Henri-François , Gendron Eric , Osborn James , Basden Alastair , Conan Jean-Marc , Bharmal Nazim , Bardou Lisa , Staykov Lazar , Morris Tim , Buey Tristan , Chemla Fanny , Cohen Matthieu
Published: August 2020

Dedicated tip–tilt loops are commonly implemented on adaptive optics (AO) systems. In addition, a number of recent high-performance systems feature tip–tilt controllers that are more efficient than the integral action controller. In this context, linear–quadratic–Gaussian (LQG) tip–tilt regulators based on stochastic models identified from AO telemetry have demonstrated their capacity to effectively compensate for the cumulated effects of atmospheric disturbance, windshake and vibrations. These tip–tilt LQG regulators can also be periodically retuned during AO operations, thus allowing to track changes in the disturbances’ temporal dynamics. This paper investigates the potential benefit of extending the number of low-order modes to be controlled using models identified from AO telemetry. The global stochastic dynamical model of a chosen number of turbulent low-order modes is identified through data-driven modelling from wavefront sensor measurements. The remaining higher modes are modelled using priors with autoregressive models of order 2. The loop is then globally controlled using the optimal LQG regulator build from all these models. Our control strategy allows for combining a dedicated tip–tilt loop with a deformable mirror that corrects for the remaining low-order modes and for the higher orders altogether, without resorting to mode decoupling. Performance results are obtained through evaluation of the Strehl ratio computed on H-band images from the scientific camera, or in replay mode using on-sky AO telemetry recorded in 2019 July on the CANARY instrument.
The fates of merging supermassive black holes and a proposal for a new class of X-ray sources
Authors: Zivancev Charles , Ostriker Jeremiah , Küpper Andreas H W
Published: August 2020

We perform N-body simulations on some of the most massive galaxies extracted from a cosmological simulation of hierarchical structure formation with total masses in the range 1012 M⊙ < Mtot < 3 × 1013 M⊙ from 4 ≥ z ≥ 0. After galactic mergers, we track the dynamical evolution of the infalling black holes (BHs) around their host’s central BHs (CBHs). From 11 different simulations, we find that, of the 86 infalling BHs with masses >104 M⊙, 36 merge with their host’s CBH, 13 are ejected from their host galaxy, and 37 are still orbiting at z = 0. Across all galaxies, 33 BHs are kicked to a higher orbit after close interactions with the CBH binary or multiple, after which only one of them merged with their hosts. These orbiting BHs should be detectable by their anomalous (not low-mass X-ray binary) spectra. The X-ray luminosities of the orbiting massive BHs at z = 0 are in the range $10^{28}-10^{43}\, \mathrm{erg}~\mathrm{s}^{-1}$, with a currently undetectable median value of $10^{33}\, \mathrm{erg}~\mathrm{s}^{-1}$. However, the most luminous ∼5 per cent should be detectable by existing X-ray facilities.
The clustering of the SDSS-IV extended baryon oscillation spectroscopic survey DR16 luminous red galaxy and emission-line galaxy samples: cosmic distance and structure growth measurements using multiple tracers in configuration space
Authors: Wang Yuting , Zhao Gong-Bo , Zhao Cheng , Philcox Oliver H E , Alam Shadab , Tamone Amélie , de Mattia Arnaud , Ross Ashley J , Raichoor Anand , Burtin Etienne , Paviot Romain , de la Torre Sylvain , Percival Will J , Dawson Kyle S , Gil-Marín Héctor , Bautista Julian E , Hou Jiamin , Koyama Kazuya , Peacock John A , Ruhlmann-Kleider Vanina , Bourboux Hélion du Mas des , Chuang Chia-Hsun , Comparat Johan , Escoffier Stephanie , Kneib Jean-Paul , Mueller Eva-Maria , Newman Jeffrey A , Rossi Graziano , Shafieloo Arman , Schneider Donald P
Published: August 2020

We perform a multitracer analysis using the complete Sloan Digital Sky Survey IV (SDSS-IV) extended Baryon Oscillation Spectroscopic Survey (eBOSS) DR16 luminous red galaxy (LRG) and the DR16 emission-line galaxy (ELG) samples in the configuration space, and successfully detect a cross-correlation between the two samples, and find the growth rate to be fσ8=0.342 ± 0.085 (∼25 per cent accuracy) from the cross-sample alone. We perform a joint measurement of the baryonic acoustic oscillation (BAO) and redshift space distortion (RSD) parameters at a single effective redshift of zeff = 0.77, using the autocorrelation and cross-correlation functions of the LRG and ELG samples, and find that the comoving angular diameter distance DM(zeff)/rd = 18.85 ± 0.38, the Hubble distance DH(zeff)/rd = 19.64 ± 0.57, and fσ8(zeff) = 0.432 ± 0.038, which is consistent with a ΛCDM model at $68{\ \rm per\ cent}$ CL. Compared to the single-tracer analysis on the LRG sample, the Figure of Merit of α⊥, α∥, andfσ8 is improved by a factor of 1.11 in our multitracer analysis, and in particular, the statistical uncertainty of fσ8 is reduced by $11.6{\ \rm per\ cent}$.
The Milky Way’s rotation curve with superfluid dark matter
Authors: Hossenfelder S , Mistele T
Published: August 2020

Recent studies have shown that dark matter with a superfluid phase in which phonons mediate a long-distance force gives rise to the phenomenologically well-established regularities of Modified Newtonian Dynamics (mond). Superfluid dark matter, therefore, has emerged as a promising explanation for astrophysical observations by combining the benefits of both particle dark matter and mond, or its relativistic completions, respectively. We here investigate whether superfluid dark matter can reproduce the observed Milky Way rotation curve for $R \lt 25\, \rm {kpc}$ and are able to answer this question in the affirmative. Our analysis demonstrates that superfluid dark matter fits the data well with parameters in reasonable ranges. The most notable difference between superfluid dark matter and mond is that superfluid dark matter requires about $20{{\ \rm per\ cent}}$ less total baryonic mass (with a suitable interpolation function). The total baryonic mass is then $5.96 \times 10^{10}\, \mathrm{ M}_\odot$, of which $1.03 \times 10^{10}\, \mathrm{ M}_\odot$ are from the bulge, $3.95 \times 10^{10}\, \mathrm{ M}_\odot$ are from the stellar disc, and $0.98 \times 10^{10}\, \mathrm{ M}_\odot$ are from the gas disc. Our analysis further allows us to estimate the radius of the Milky Way’s superfluid core (concretely, the so-called nfw and thermal radii) and the total mass of dark matter in both the superfluid and the normal phase. By varying the boundary conditions of the superfluid to give virial masses $M_{200}^{\rm {DM}}$ in the range of $0.5\!-\!3.0 \times 10^{12}\, \mathrm{ M}_\odot$, we find that the Navarro, Frenk, and White (nfw) radius RNFW varies between $65$ and $73\, \rm {kpc}$, while the thermal radius RT varies between about $67$ and $105\, \rm {kpc}$. This is the first such treatment of a non-spherically symmetric system in superfluid dark matter.
Rapid, robust plasmid verification by de novo assembly of short sequencing reads
Authors: Gallegos Jenna E , Rogers Mark F , Cialek Charlotte A , Peccoud Jean
Published: August 2020

Plasmids are a foundational tool for basic and applied research across all subfields of biology. Increasingly, researchers in synthetic biology are relying on and developing massive libraries of plasmids as vectors for directed evolution, combinatorial gene circuit tests, and for CRISPR multiplexing. Verification of plasmid sequences following synthesis is a crucial quality control step that creates a bottleneck in plasmid fabrication workflows. Crucially, researchers often elect to forego the cumbersome verification step, potentially leading to reproducibility and—depending on the application—security issues. In order to facilitate plasmid verification to improve the quality and reproducibility of life science research, we developed a fast, simple, and open source pipeline for assembly and verification of plasmid sequences from Illumina reads. We demonstrate that our pipeline, which relies on de novo assembly, can also be used to detect contaminating sequences in plasmid samples. In addition to presenting our pipeline, we discuss the role for verification and quality control in the increasingly complex life science workflows ushered in by synthetic biology.
Test–Retest Instability of Temporal Summation and Conditioned Pain Modulation Measures in Older Adults
Authors: Naugle Kelly Marie , Ohlman Thomas , Wind Brandon , Miller Leah
Published: August 2020

Objective

The temporal stability (test–retest reliability) of temporal summation of pain (TS) and conditioned pain modulation (CPM) has yet to be established in healthy older adults. The purpose of this study was to compare the temporal stability of TS and CPM in healthy older and younger adults and to investigate factors that might influence TS and CPM stability.

Methods

In a test–retest study, 40 healthy older adults and 30 healthy younger adults completed two sessions of quantitative sensory testing within a two-week period that included TS of heat pain, TS of mechanical pain, and CPM with pressure pain thresholds and suprathreshold heat pain as test stimuli and a cold water immersion as a conditioning stimulus. Participants also completed self-report measures of situational catastrophizing, anxiety, clinical pain, and physical activity. Absolute and relative stability were examined for each variable. Bivariate correlations examined the associations of age, clinical, behavioral, and psychological variables with the intra-individual stability of TS and CPM.

Results

The results revealed moderate to excellent stability for the TS measures and poor to moderate stability for CPM. The results also revealed significant age differences for two of the TS measures and CPM, with younger adults having greater stability compared with older adults. Additionally, the magnitude and stability of psychological factors were correlated with stability of TS.

Conclusions

These findings suggest that TS and CPM may be more reliable in younger compared with older adults. Furthermore, psychological states may be an important factor influencing the stability of TS in healthy adults.
The cut-off values for the intima–media complex thickness assessed by colour Doppler sonography in seven cranial and aortic arch arteries
Authors: Ješe Rok , Rotar Žiga , Tomšič Matija , Hočevar Alojzija
Published: August 2020

Objectives

Colour Doppler sonography (CDS) is becoming ever more important in the diagnosis of GCA. Data on cut-off values for intima–media complex thickness (IMT) that can be used in clinical practice to distinguish between normal and inflamed arteries are limited. We aimed to derive potential cut-off values for IMT of seven preselected arteries by comparing IMT between GCA patients and a control group.

Methods

We performed CDS of the preselected temporal, facial, occipital, carotid, vertebral, subclavian and axillary arteries in consecutive newly diagnosed GCA patients between October 2013 and September 2019. A ‘halo’ with positive compression sign was considered a positive finding. We measured the maximum IMT in the preselected arteries and compared it with the maximum IMT of the control group.

Results

We were able to demonstrate a halo sign in at least one of the examined arteries of 244/248 (98.4%) GCA patients. Temporal arteries were the most commonly affected vessels, involved in 192 (77.4%) patients. We found extracranial large vessel involvement in 87 (35.1%) patients. The following cut-off values showed high levels of diagnostic accuracy: ≥0.4 mm for temporal, facial and occipital arteries, ≥0.7 mm for vertebral arteries, and ≥1 mm for carotid, subclavian and axillary arteries.

Conclusion

The involvement of a large array of arteries is easily and commonly detected by CDS and provides a high diagnostic yield in patients with suspected GCA. Proposed IMT cut-off values might further improve the diagnostic utility of CDS in these patients.
Systemic overexpression of interleukin-22 induces the negative immune-regulator SOCS3 and potently reduces experimental arthritis in mice
Authors: Aarts Joyce , Roeleveld Debbie M , Helsen Monique M , Walgreen Birgitte , Vitters Elly L , Kolls Jay , van de Loo Fons A , van Lent Peter L , van der Kraan Peter M , Koenders Marije I
Published: August 2020

Objective

High levels of IL-22 are present in serum and synovial fluid of patients with RA. As both pro- and anti-inflammatory roles for IL-22 have been described in studies using animal models of RA, its exact function in arthritis remains poorly defined. With this study we aimed to further unravel the mechanism by which IL-22 exerts its effects and to decipher its therapeutic potential by overexpression of IL-22 either locally or systemically during experimental arthritis.

Methods

CIA was induced in DBA-1 mice by immunization and booster injection with type II collagen (col II). Before arthritis onset, IL-22 was overexpressed either locally by intra-articular injection or systemically by i.v. injection using an adenoviral vector and clinical arthritis was scored for a period of 10 days. Subsequently, joints were isolated for histological analysis of arthritis severity and mRNA and protein expression of various inflammatory mediators was determined in the synovium, spleen and serum.

Results

Local IL-22 overexpression did not alter arthritis pathology, whereas systemic overexpression of IL-22 potently reduced disease incidence, severity and pathology during CIA. Mice systemically overexpressing IL-22 showed strongly reduced serum cytokine levels of TNF-α and macrophage inflammatory protein 1α that correlated significantly with the enhanced expression of the negative immune regulator SOCS3 in the spleen.

Conclusion

With this study, we revealed clear anti-inflammatory effects of systemic IL-22 overexpression during CIA. Additionally, we are the first to show that the protective effect of systemic IL-22 during experimental arthritis is likely orchestrated via upregulation of the negative regulator SOCS3.
Socioeconomic Inequality in Children’s Achievement from Infancy to Adolescence: The Case of Germany
Authors: Skopek Jan , Passaretta Giampiero
Published: August 2020

When in children’s lives do gaps by family socioeconomic status (SES) in cognitive skills emerge, how large are they before children enter school, and how do they develop over schooling? We study the evolution of achievement gaps by parental education from birth to adolescence in Germany. We exploit data from fifty-seven tests taken from the age of seven months to sixteen years by the National Educational Panel Study. Because Germany has one of the most stratified education systems in the Western World, we hypothesized that achievement gaps will grow particularly during tracked secondary schooling. However, our findings show that SES gaps emerge and expand long before children enter school and then remain stable throughout their school careers. Because gaps stop growing, we tentatively conclude that schooling decreases inequality in learning by family SES.
Astrocytic Regulation of Synchronous Bursting in Cortical Cultures: From Local to Global
Authors: Kumar Ravi , Huang Yu-Ting , Chen Chun-Chung , Tzeng Shun-Fen , Chan Chi-Keung
Published: August 2020

Synchronous bursting (SB) is ubiquitous in neuronal networks and independent of network structure. Although it is known to be driven by glutamatergic neurotransmissions, its underlying mechanism remains unclear. Recent studies show that local glutamate recycle by astrocytes affects nearby neuronal activities, which indicate that the local dynamics might also be the origin of SBs in networks. We investigated the effects of local glutamate dynamics on SBs in both cultures developed on multielectrode array (MEA) systems and a tripartite synapse simulation. Local glutamate uptake by astrocytes was altered by pharmacological targeting of GLT-1 glutamate transporters, whereas neuronal firing activities and synaptic glutamate level was simultaneously monitored with MEA and astrocyte-specific glutamate sensors (intensity-based glutamate-sensing fluorescent reporter), respectively. Global SB properties were significantly altered on targeting GLT-1. Detailed simulation of a network with astrocytic glutamate uptake and recycle mechanisms, conforming with the experimental observations, shows that astrocytes function as a slow negative feedback to neuronal activities in the network. SB in the network can be realized as an alternation between positive and negative feedback in the neurons and astrocytes, respectively. An understanding of glutamate trafficking dynamics is of general application to explain how astrocyte malfunction can result in pathological seizure-like phenomena in neuronal systems.
Left ventricular mass reduction and hypertrophy regression following renal artery revascularization: a meta-analysis
Authors: Cuspidi Cesare , Tadic Marijana , Sala Carla , Quarti-Trevano Fosca , Gherbesi Elisa , Mancia Giuseppe , Grassi Guido
Published: August 2020

Aim:

Few echocardiographic studies have focused on regression of left ventricular hypertrophy (LVH) in patients with renal artery stenosis after revascularization, with inconsistent results. We performed a systematic meta-analysis of these studies in order to offer a comprehensive information on this topic.

Methods:

The PubMed, OVID-MEDLINE, and Cochrane library databases were analyzed to search English-language articles published from 1 January 1990 up to 31 March 2020. Studies were identified by crossing the following terms: ‘renal artery stenosis’, ‘renovascular hypertension’, ‘fibromuscular dysplasia’, ‘renal artery stenting’, ‘renal artery surgery’ with ‘cardiac damage’, ‘hypertensive heart disease’ ‘left ventricular mass’, ‘left ventricular hypertrophy’, ‘echocardiography’.

Results:

A total of 726 hypertensive patients with renal artery stenosis (mean age 61 years, 64% men, 98% treated, 10% with fibromuscular dysplasia) were included in 13 studies. Baseline and postintervention pooled mean LVM values were 220 ± 15 and 203 ± 19 g, respectively (SMD −0.24 ± 0.06, CI −0.37 to −0.21, P<0.0001); corresponding values for LV mass index were 129.0 ± 6 and 115 ± 7 g/m2, respectively (SMD −0.28 ± 0.04, CI −0.36 to 0.21, P < 0.0001). Renal revascularization was associated with a 40% lower risk of LVH. This trend was accompanied by a reduction in the number of antihypertensive drugs (SMD −0.27 ± 0.04, CI −0.37 to 0.17, P < 0.0001).

Conclusion:

The present meta-analysis suggests that renal artery revascularization added to antihypertensive therapy promotes a favourable effect on LV structure, as reflected by a significant decrease in absolute and indexed LV mass index as well by a lower risk of LVH. Limitations include: high prevalence of modest renal artery stenosis (≥50%); small sample of fibromuscular dysplasia; lack of randomized design of most studies.