bluuebunny/crossref_metadata_2025 huggingface dataset:
Periodic offset boosting for attractor self-reproducing
Authors: Li Chunbiao , Jiang Yicheng , Wang Ran , Liu Zuohua
Published: November 2021

The special regime of multistability of attractor self-reproducing is deeply decoded based on the conception of offset boosting in this letter. Attractor self-reproducing is essentially originated from periodic initial condition-triggered offset boosting. Typically, a trigonometric function is applied for attractor self-reproducing. The position, size, and clone frequency determine the selected periodic function. Specifically, in-depth investigation on three elements of sinusoidal quantity is taken into account and then a universal law of attractor self-reproducing is built: the original position of an attractor determines the initial phase and the size of attractor sets the amplitude, while the reproducing interval between two attractors determines the frequency of the trigonometric function. It is found that the product of amplitude and frequency is a constant determined by the reproducing periodic function. The positive and negative switching of the slope in sinusoidal function also leads to the waste of phase space since in general there is no attractor reproduced at the region with negative slope except that new polarity balance is reconstructed paying back the attractor with conditional symmetry. Three-element-oriented offset boosting makes attractor self-reproducing more designable, achievable, and adjustable, which brings great convenience to engineering applications.
Electrically controllable zero-energy states in Rashba oxide heterostructure with in-plane magnetic field cooling
Authors: Ma Haijiao Harsan , Gan Xin , Li Lei , Zhang Yuguo , Zhang Yue-ying , Hui Yu-peng , Zhou Jianhui , Zhong Zhicheng , Zhang Jincheng , Hao Yue
Published: November 2021

Zero-energy states in tunnel spectra, an important manifestation of topological superconductivity, have been the focus of the field of topological phases of matter. However, experimentally creating and controlling the zero-energy states is difficult, e.g., it requires a large magnetic field in the case of topological superconductivity. Here, we report on an effective approach to generate controllable zero-energy states in the superconducting Rashba oxide heterostructure by in-plane magnetic field cooling. A pronounced zero-bias conductance peak emerging below a threshold magnetic field down to zero after in-plane magnetic field cooling of a Rashba perovskite oxide heterostructure connecting to an s-wave superconductor. We further demonstrate the high tunability of the zero-energy states between a zero-bias conductance peak and a zero-bias conductance valley by electrical gating at a zero magnetic field. Our theoretical analysis indicates that the in-plane magnetic field or magnetization could lead to finite center-of-mass momentum pairing that supports topological zero-energy states in the Rashba system and provides an opportunity to manipulate topological zero-energy states through gating.
Higher-order ferromagnetic resonances in periodic arrays of synthetic-antiferromagnet nanodisks
Authors: Borynskyi V. Yu. , Polishchuk D. M. , Melnyk A. K. , Kravets A. F. , Tovstolytkin A. I. , Korenivski V.
Published: November 2021

We investigate spin dynamics in nanodisk arrays of synthetic-antiferromagnets (SAF) made of Py/NiCu/Py trilayers, where the NiCu spacer undergoes a Curie transition at about 200 K. The observed ferromagnetic resonance spectra have three distinct resonance modes at room temperature, which are fully recreated in our micromagnetic simulations, showing also how the intra-SAF asymmetry can be used to create and control the higher-order resonances in the structure. Below the Curie temperature of the spacer, the system effectively transitions into a single-layer nanodisk array with only two resonance modes. Our results show how multilayering of nanoarrays can add tunable GHz functionality relevant for such rapidly developing fields as magnetic metamaterials, magnonic crystals, arrays of spin-torque oscillators, and neuromorphic junctions.
Topological, nonreciprocal, and multiresonant slow light beyond the time-bandwidth limit
Authors: Tsakmakidis Kosmas L. , Baskourelos Konstantinos , Stefański Tomasz
Published: November 2021

Topologically protected transport has recently emerged as an effective means to address a recurring problem hampering the field of slow light for the past two decades: its keen sensitivity to disorders and structural imperfections. With it, there has been renewed interest in efforts to overcome the delay-time-bandwidth limitation usually characterizing slow-light devices, on occasion thought to be a fundamental limit. What exactly is this limit, and what does it imply? Can it be overcome? If yes, how could topological slow light help, and in what systems? What applications might be expected by overcoming the limit? Our Perspective here attempts addressing these and other related questions while pointing to important new functionalities both for classical and quantum devices that overcoming the limit can enable.
Accelerating molecular property calculations with semiempirical preconditioning
Authors: Zhou Zehao , Parker Shane M.
Published: November 2021

Computing ab initio molecular linear response properties, e.g., electronic excitation energies and transition dipole moments, requires the solution of large eigenvalue problems or large systems of equations. These large eigenvalue problems or large systems of equations are commonly solved iteratively using Krylov space algorithms, such as the Davidson algorithm for eigenvalue problems. A critical ingredient in Krylov space algorithms is the preconditioner, which is used to generate optimal update vectors in each iteration. We propose to use semiempirical approximations as preconditioners to accelerate the calculation of ab initio properties. The crucial advantage to improving the preconditioner is that the converged result is unchanged, so there is no trade-off between accuracy and speedup. We demonstrate our approach by accelerating the calculation of electronic excitation energies and electric polarizabilities from linear response time-dependent density functional theory using the simplified time-dependent density functional theory semiempirical model. For excitation energies, the semiempirical preconditioner reduces the number of iterations on average by 37% and up to 70%. The semiempirical preconditioner reduces the number of iterations for computing the polarizability by 15% on average and up to 33%. Moreover, we show that the preconditioner can be further improved by tuning the empirical parameters that define the semiempirical model, leading to an additional reduction in the number of iterations by about 20%. Our approach bridges the gap between semiempirical models and ab initio methods and charts a path toward combining the speed of semiempirical models with the accuracy of ab initio methods.
Accurate energies of transition metal atoms, ions, and monoxides using selected configuration interaction and density-based basis-set corrections
Authors: Yao Yuan , Giner Emmanuel , Anderson Tyler A. , Toulouse Julien , Umrigar C. J.
Published: November 2021

The semistochastic heat-bath configuration interaction method is a selected configuration interaction plus perturbation theory method that has provided near-full configuration interaction (FCI) levels of accuracy for many systems with both single- and multi-reference character. However, obtaining accurate energies in the complete basis-set limit is hindered by the slow convergence of the FCI energy with respect to basis size. Here, we show that the recently developed basis-set correction method based on range-separated density functional theory can be used to significantly speed up basis-set convergence in SHCI calculations. In particular, we study two such schemes that differ in the functional used and apply them to transition metal atoms and monoxides to obtain total, ionization, and dissociation energies well converged to the complete-basis-set limit within chemical accuracy.
Inverse spin Hall voltage enhancement in cascaded Py/Ta micro-array
Authors: Huang Fei , Peng Bin , Zhang Zhuoyue , Zhang Wanli , Zhang Wenxu
Published: November 2021

Microwave power harvesting is one of the promising ways to solve energy problems in the future. Improving the power harvesting ability is the central work in this area. The inverse spin Hall effect (ISHE) in ferromagnetic (FM) and nonmagnetic (NM) metallic bilayers can be utilized to convert microwave power to direct current, which may be one of the candidates of microwave power harvesting. In this work, a FM/NM microstrip array is proposed to enhance the ISHE signal, while the spin rectification effect signal in the FM layer is suppressed. This enhancement is equivalent to connecting the power sources in series, namely, the ISHE voltage is proportional to the number of the FM/NM microstrips. Our work fertilizes the spintronics and shows the possibility to use ISHE in microwave power transfer and harvesting.
Phylogenetic placement of the spider genus
Authors: Jordán Juan Pablo , Domínguez-Trujillo Mariela , Cisneros-Heredia Diego F.
Published: November 2021

The genus Taczanowskia Keyserling, 1879 is one of the rarest groups of spiders in the orb-weaving family Araneidae, with only five species described and 17 specimens cited in publications. Our study provides new insights into the evolutionary relationships and diversity of Taczanowskia. Using morphological data, we tested the evolutionary relationships of the genus within the family Araneidae and propose the first phylogenetic hypothesis depicting the relationships among species of Taczanowskia. Our results place Taczanowskia as sister to Mastophora Holmberg, 1876, and confirm the monophyly of Taczanowskia. We describe the first species of Taczanowskia from Ecuador, collected at a Waorani community on the River Curaray basin, Amazonian lowlands of Ecuador. The new species can be easily diagnosed from all other species of Taczanowskia by having two tubercles in the opisthosoma; a distinct patchy dark–light colouration pattern with dark spots concentrated towards the anterior margin and on the lateral tips; small bundles of white setae forming a reticulum across the dorsal part of the opisthosoma, and the first two femora thick but lacking teeth on the margin. ZooBank registration: urn:lsid:zoobank.org:pub:46B8C1F7-A474-4DC3-90BC-940F84AC099D
The fate of urea
Authors: Nguyen Dai H. , Grace Peter R. , Rowlings David W. , Biala Johannes , Scheer Clemens
Published: November 2021

Context Organic amendments (OAs) from agricultural and non-agricultural industries provide an alternative source of nitrogen (N) and other nutrients for crop production, especially with increasing costs of synthetic fertilisers. Aims This study examined the fate of urea in combination with OA in the form of raw mill mud, composted mill mud and high N compost in a maize field experiment on a sandy loam soil in a rain-fed subtropical environment. Methods OAs (346 kg N ha−1) were incorporated at sowing with 15N labelled urea (200 kg N ha−1) applied 28 days later, including a no OA control. Key results Grain yield, aboveground biomass and roots were not significantly different across all treatments, averaging 8.1, 17.4 and 1.3 t ha−1 at harvest. Total N uptake was 249.1 kg N ha−1 (on average) with fertiliser, native soil N and OAs sources accounting for 49.5, 44 and 6.5% of the total N uptake respectively. There was no significant difference in N fertiliser recovery between the OA treatments and the unamended control, with 61.7 and 3.7% of the applied N recovered in the plant and soil (to 100 cm), respectively, at harvest. Nitrogen fertiliser losses were equivalent to 33.6% of the applied N and were attributed to N leaching after extensive rainfall events late in the growing season. Conclusions OAs with high mineral and/or organic N content at time of application can supply significant amounts of plant available N but high levels of soil mineral N at sowing may hinder their full potential. Implications Reducing N loss and cost, and improving overall soil fertility by replacing synthetic N fertilisers with OAs may contribute to more environmentally sustainable crop production.
Comparing information diffusion mechanisms by matching on cascade size
Authors: Juul Jonas L. , Ugander Johan
Published: November 2021

Significance

Do different types of information spread differently online? In recent years, studies have sought answers to such questions by comparing statistical properties of network paths taken by different kinds of content diffusing online. Here, we demonstrate the importance of controlling for correlations between properties being compared. In particular, we show that previously reported structural differences between diffusion paths of false and true news on Twitter disappear when comparing only cascades of the same size; differences between diffusion paths of images, videos, news, and petitions persist. Paired with a theoretical analysis of diffusion processes, our results suggest that, in order to limit the spread of false news, it may be enough to focus on reducing the mean “infectiousness” of the information.
COVID-19 within families amplifies the prosociality gap between adolescents of high and low socioeconomic status
Authors: Terrier Camille , Chen Daniel L. , Sutter Matthias
Published: November 2021

Significance

Noncognitive skills are important for lifetime outcomes. Here, we study how COVID-19 infections affect the prosociality—one key noncognitive skill with important relations to labor market outcomes—of French high school students. We put a major focus on the question whether COVID-19 has a differential effect on students from low or high socioeconomic status (SES). While it is known by now that COVID-19 has had more negative health and economic effects on people with low SES, the effects on noncognitive skills have not been studied so far. We find that COVID-19 within families amplifies the gap in prosociality between adolescents of high and low SES.
Microstructure and morphology of Si crystals grown in pure Si and Al–Si melts
Authors: Toropova L V , Alexandrov D V , Rettenmayr M , Liu D
Published: November 2021

Microstructure of Al-40 wt%Si samples solidified in electromagnetic levitation furnace is studied at high melt undercooling. Primary Si with feathery and dendritic structures is observed. As this takes place, single Si crystals either contain secondary dendrite arms or represent faceted structures. Our experiments show that at a certain undercooling, there exists the microstructural transition zone of faceted to non-faceted growth. Also, we analyze the shape of dendritic crystals solidifying from liquid Si as well as from hypereutectic Al–Si melts at high growth undercoolings. The shapes of dendrite tips grown at undercoolings >100 K along the surface of levitated Al-40 wt%Si droplets are compared with pure Si dendrite tips from the literature. The dendrite tips are digitized and superimposed with theoretical shape function recently derived by stitching the Ivantsov and Brener solutions. We show that experimental and theoretical dendrite tips are in good agreement for Si and Al–Si samples.
Production and characterization of biocompatible nanoﬁbrous scaffolds made of β-sitosterol loaded polyvinyl alcohol/tragacanth gum composites
Authors: Albukhaty Salim , Al-Karagoly Hassan , Allafchian Ali Reza , Jalali Seyed Amir Hossein , Al-Kelabi Thair , Muhannad Mustafa
Published: November 2021

Electrospun polyvinyl alcohol (PVA) and tragacanth gum (TG) were used to develop nanofibrous scaffolds containing poorly water-soluble β-Sitosterol (β-S). Different concentrations and ratios of the polymeric composite including β-S (10% w v−1) in PVA (8% w v−1) combined with TG (0.5 and 1% w v−1) were prepared and electrospun. The synthesis method includes four electrospinning parameters of solution concentration, feeding rate, voltage, and distance of the collector to the tip of the needle, which are independently optimized to achieve uniform nanofibers with a desirable mean diameter for cell culture. The collected nanofibers were characterized by SEM, FTIR, and XRD measurements. A contact angle measurement described the hydrophilicity of the scaffold. MTT test was carried out on the obtained nanofibers containing L929 normal fibroblast cells. The mechanical strength, porosity, and deterioration of the scaffolds were well discussed. The mean nanofiber diameters ranged from 63 ± 20 nm to 97 ± 46 nm. The nanofibers loaded with β-S were freely soluble in water and displayed a remarkable biocompatible nature. The cultured cells illustrated sheet-like stretched growth morphology and penetrated the nanofibrous pores of the PVA/β-S/TG scaffolds. The dissolution was related to submicron-level recrystallization of β-S with sufficient conditions for culturing L929 cells. It was concluded that electrospinning is a promising technique for poorly water-soluble β-S formulations that could be used in biomedical applications.
Propagation-invariant vortex Airy beam whose singular point follows its main lobe
Authors: Suzuki Masato , Yamane Keisaku , Omatsu Takashige , Morita Ryuji
Published: November 2021

We propose and demonstrate a novel vortex Airy beam which is a superposition of an Airy beam and its laterally sheared beam with a π/2 phase shift. This new-type of vortex Airy beam exhibits stable propagation dynamics, wherein its singular point closely follows its main lobe, unlike conventional vortex Airy beams. Notably, the orbital angular mode purity of this new vortex Airy beam is up to 10% better than that of a conventional vortex Airy beam. We anticipate that this new type of vortex Airy beam, which combines the characteristics of an optical vortex and a diffraction-free Airy beam, will facilitate new directions in applications such as microscopy, material processing and nonlinear optics.
Helium injection plasmas in FTU
Authors: Mazzotta C. , Pucella G. , Giovannozzi E. , Marinucci M. , the FTU Team
Published: November 2021

In order to extend observations on the increase of electron density peaking in neon doped plasmas, already reported in FTU Mazzotta et al (2015 Nucl. Fusion
55 073027), some sessions have been performed by injecting helium gas on the L-mode plasmas during the last two experimental campaigns. This favorable scenario, which can fall within so called ‘highly radiative’ or ‘plasma detachment’ themes, is investigated in this paper. The description of the impact of the helium injection on plasma behavior, by varying plasma parameters and shape, is exposed, especially with respect to the density peaking and edge conditioning. It has been recorded that, not only the total amount of puffed helium, but also the injection rate intervenes in triggering a particle inflow. Finally, by using VUV spectroscopy measurements, a model to estimate concentrations of impurities is outlined here for the first time, in this way the helium amount is deduced.
Private Takings of Land for Urban Redevelopment: A Tale of Two Cities
Authors: Low Kelvin F K , Wan Wai Yee , Chan Alwin
Published: November 2021

In 1999, both Hong Kong and Singapore brought into force legislation that permitted a supermajority of apartment owners within a building development that met certain statutory criteria to force a minority of dissenters to sell the development as a whole. Both territories did so because, as land-scarce cities, it was considered that the redevelopment of aging buildings was an urgent imperative. In so doing, although they claimed to be following other jurisdictions, both Hong Kong and Singapore broke new ground in pioneering the private takings of land among common law jurisdictions. These developments have proven controversial in both territories, although the controversies have differed because of differences in implementation and historical background in both cities, despite their shared past as British colonies in Asia. This Article compares the two regimes to each other as well as to a more mature regime permitting private takings of shares in mergers and acquisitions law to highlight the lessons to be learned in order to prevent abuse.
Infantile SOD1 deficiency syndrome caused by a homozygous SOD1 variant with absence of enzyme activity
Authors: Ezer Shlomit , Daana Muhannad , Park Julien H , Yanovsky-Dagan Shira , Nordström Ulrika , Basal Adily , Edvardson Simon , Saada Ann , Otto Markus , Meiner Vardiella , Marklund Stefan L , Andersen Peter Munch , Harel Tamar
Published: November 2021

Pathogenic variants in SOD1, encoding superoxide dismutase 1, are responsible for about 20% of all familial amyotrophic lateral sclerosis cases, through a gain-of-function mechanism. Recently, two reports showed that a specific homozygous SOD1 loss-of-function variant is associated with an infantile progressive motor-neurological syndrome.

Exome sequencing followed by molecular studies, including cDNA analysis, SOD1 protein levels and enzymatic activity, and plasma neurofilament light chain levels, were undertaken in an infant with severe global developmental delay, axial hypotonia and limb spasticity.

We identified a homozygous 3-bp in-frame deletion in SOD1. cDNA analysis predicted the loss of a single valine residue from a tandem pair (p.Val119/Val120) in the wild-type protein, yet expression levels and splicing were preserved. Analysis of SOD1 activity and protein levels in erythrocyte lysates showed essentially no enzymatic activity and undetectable SOD1 protein in the child, whereas the parents had ∼50% protein expression and activity relative to controls. Neurofilament light chain levels in plasma were elevated, implying ongoing axonal injury and neurodegeneration.

Thus, we provide confirmatory evidence of a second biallelic variant in an infant with a severe neurological syndrome and suggest that the in-frame deletion causes instability and subsequent degeneration of SOD1. We highlight the importance of the valine residues at positions V119-120, and suggest possible implications for future therapeutics research.
Ventricular fibrillation arrest due to Brugada syndrome in a coronavirus disease 2019 patient with negative procainamide challenge: a case report
Authors: Zou Guangchen , Khanna Mukul , Zahid Saliha , Dengle Samir , Matta Bhavna , Zaheer Haris , Farrell Matthew , Stein Russell
Published: November 2021

Background

Pharmacologic challenge test is often used to diagnose Brugada syndrome (BrS) when spontaneous electrocardiograms (ECG) do not show type I Brugada pattern but reported sensitivity varies. The role of the exercise stress test in diagnosing Brugada syndrome is not well-established.

Case summary

A patient had a type I Brugada pattern ECG during the recovery phase of exercise stress test but had a negative procainamide challenge test. He had a loop recorder implanted and later survived a ventricular fibrillation (VF) arrest provoked by coronavirus disease 2019 (COVID-19). Electrocardiogram on arrival showed type 1 Brugada pattern. He was discharged after implantable cardioverter-defibrillator implantation. He later underwent genetic testing and was found to be heterozygous for c.844C>G (p.Arg282Gly) mutation in the SCN5A gene.

Discussion

Type 1 Brugada pattern ECG may be unmasked by ST-segment augmentation during recovery from exercise. Exercise stress test may play a role in the diagnosis of Brugada syndrome when suspicion for Brugada syndrome remains after a negative procainamide challenge test or if the patient has exercise-related symptoms. COVID-19 can unmask BrS and trigger a VF cardiac arrest.
Identification of histone H2B as a potential receptor for Mycoplasma genitalium protein of adhesion
Authors: Liao Yating , Deng Xiangying , Peng Kailan , Dai Pei , Luo Dan , Liu Peng , Chen Liesong , Li Xia , Ye Youyuan , Zeng Yanhua
Published: November 2021

Mycoplasma genitalium, the smallest prokaryotic microorganism capable of independent replication, is increasingly recognized as a sexually transmitted pathogen. M. genitalium protein of adhesion (MgPa) plays a pivotal role in the process of M. genitalium adhesion to host cells. We previously identified cyclophilin A as a cellular receptor of MgPa using the virus overlay protein binding assay (VOPBA) together with liquid chromatography-mass spectrometry (LC-MS). In the current study, we have evaluated H2B as an alternative cellular receptor for MgPa since H2B was assigned the second higher score as a potential binding partner of MgPa in the VOPBA and LC-MS screen. It was found that recombinant MgPa specifically bind to H2B both in the SV-HUC-1 cell membrane and in form of a recombinant protein. H2B was detected throughout the SV-HUC-1 cells, including the cytoplasmic membrane, cytosol and nucleus. Importantly, H2B partially inhibited the adhesion of M. genitalium to SV-HUC-1 cells. Finally, H2B was both co-precipitated with recombinant MgPa and co-localized with M. genitalium and recombinant MgPa in SV-HUC-1 cells. The above observations suggest that H2B may act as a potential cellular receptor of MgPa for mediating M. genitalium adhesion to host cells.
Theoretical prediction of elastic modulus at different states and squirt-flow-related attenuation: extension of Cracks-Pores Effective Medium model
Authors: Zhao Liming , Yin Hanjun , Chen Tongjun , Tang Genyang , Sun Chao , Zhang Mingjin , Zhu Ningjun , Li Fanjia
Published: November 2021

Squirt flow plays an essential role in elastic modulus dispersion and attenuation for fluid-saturated cracked porous rocks. The Mavko–Jizba model and relevant modified models can describe the squirt flow well based on the related elastic moduli, such as dry/drained bulk modulus. However, when these elastic moduli are challenging to attain, it is impossible to model the squirt-flow-related elastic moduli and attenuations with the models. On the other hand, the effective medium theory (EMT) model can estimate these elastic moduli, but cannot predict the undrained/relaxed and partially relaxed saturated elastic moduli and the squirt-flow-related attenuations. This paper extended an EMT model—Cracks–Pores Effective Medium (CPEM) model—to cover the undrained/relaxed and partially relaxed states following the elastic–viscoelastic correspondence principle. The proposed model [i.e. frequency-dependent CPEM (CPEMF) model] can thus estimate the elastic moduli over the different states (dry/drained, undrained/relaxed, partially relaxed and unrelaxed) and associated attenuations. It agrees well with the prediction of the modified Mavko–Jizba–Gurevich model (MJGZ-HF) at unrelaxed state and is precisely consistent with the prediction of Gassmann at undrained/relaxed state. Also, it analytically shows good consistency with the modified Mavko–Jizba–Gurevich model (MJGZ-MF) at partially relaxed state. The numerical simulations of CPEM/CPEMF models and MJGZ-HF/MJGZ-MF models show good agreement at the different states. Furthermore, we interpreted the experimental data on a basaltic sample and a sandstone sample with the CPEM/CPEMF models. The CPEMF model's predictions of elastic modulus at different states and associated modulus dispersion/attenuation are in good agreement with the corresponding measured ones, suggesting that the proposed CPEMF model can efficiently predict the elastic moduli at different states (dry/drained, undrained/relaxed, partially relaxed and unrelaxed) and quantify the squirt-flow-related elastic modulus dispersion and attenuation among different states well.
Judicialización de medicamentos huérfanos en Brasil: la justiciabilidad de un objeto políticamente “no palatable”Judicialization of orphan drugs in Brazil: the justiciability of a politically unpalatable issue
Authors: Cardoso João Vitor
Published: November 2021

Occasionally, elected officials invite the judiciary to resolve those particularly challenging problems for which there are no solutions or that they would rather not address. The access to orphan drugs in Brazil is a problem of such type. With the aim of illustrating how the judicial enforcement of social rights can favor vulnerable groups, this article deploys original data through a case study on the most prominently judicialized orphan drug in Brazil, reliant on quantitative as well as qualitative primary sources. Thus, it advances a twofold argument. First, when the exercise of a social right is associated with a politically unpalatable controversy, meaning one that does not foster enough political interest in a solution, despite embodying a pressing policy problem, elected officials are less likely to address it. Second, the expansion of judicial power would be defensible against the backdrop of an issue of such type. The empirical analysis yields new insights into normative debates concerning social rights judicial enforcement. When politically disadvantaged groups learn to use the constitutional framework to advance their interests by presenting rights claims, in the long term it can generate information about the scope of a legislative inertia, give a voice to silenced actors, and reallocate resources to care for urgent needs of minoritarian groups.
Identification of multiple transfer units and novel subtypes of tmexCD-toprJ gene clusters in clinical carbapenem-resistant Enterobacter cloacae and Klebsiella oxytoca
Authors: Sun Shijun , Wang Qi , Jin Longyang , Guo Yifan , Yin Yuyao , Wang Ruobing , Bi Lei , Zhang Renfei , Han Yungang , Wang Hui
Published: November 2021

Objectives

Tigecycline is a last-resort antibiotic used to treat lethal infections caused by carbapenem-resistant Enterobacterales; however, plasmid-borne tigecycline resistance tmexCD-toprJ gene clusters can confer tigecycline resistance. The aim of the study was to identify novel subtypes and the spread of tmexCD-toprJ.

Methods

Five non-duplicate isolates of different species, carrying tmexCD-toprJ gene clusters or novel subtypes, were isolated from patients across China between November 2018 and June 2019. WGS was performed using Illumina and Nanopore platforms. A phylogenetic tree was constructed using a dataset of 77 sequences carrying the tmexCD-toprJ gene clusters, 72 of which were downloaded from NCBI with a blastn identity cut-off of 95%.

Results

We detected six different transfer units and two novel subtypes (tmexC1D1.2-toprJ1 and tmexC2D2.2-toprJ2) of the tmexCD-toprJ gene clusters. Among the six transfer units, three were mediated by IS26, while the rest were presumably mediated by Tn5393, hypothetical integrases (xerD-hp clusters-umuC-integrases-tnfxB2-tmexC2D2-toprJ2-umuC) and hypothetical units (hp-hp-hp-tnfxB2-tmexC2D2.2-toprJ2-ΔTn5393-Tn6292). Moreover, two tmexCD-toprJ-like gene clusters co-located on the same plasmid with blaNDM in five isolates. Phylogenetic analysis revealed that tmexCD-toprJ gene clusters may have originated in Pseudomonas spp., being mainly distributed in Pseudomonas spp. and Klebsiella spp. (64/77). Most tmexCD-toprJ gene clusters in Enterobacterales were located on plasmids, indicating that the gene clusters have a high inter-species transfer risk after transfer to Enterobacterales.

Conclusions

In summary, to the best of our knowledge, this is the first report of tmexCD-toprJ gene clusters being isolated from Enterobacter cloacae and Klebsiella oxytoca, revealing that these multiple transfer units should be further studied because of their clinical significance.
Mitigation of Biotin Interference in Manual and Automated Immunoassays by Preconjugating Biotinylated Antibodies to the Streptavidin Surface as an Alternative to Biotin Depletion
Authors: Nelson Heather A , La’ulu Sonia L , Lu Jun , Doyle Kelly
Published: November 2021

Background

Streptavidin-to-biotin binding is one of the strongest noncovalent interactions in nature and incorporated into many immunoassays. Biotin-streptavidin coupling assays are susceptible to interference from free biotin in patient specimens, which may falsely decrease or increase results. To prevent biotin interference, we evaluated a method to preconjugate biotinylated antibodies to the assay’s streptavidin solid surface before adding patient specimen and compared this technique to a biotin depletion protocol.

Methods

Biotin interference in 3 manual ELISAs and 2 automated immunoassays was established. Mitigation of biotin interference by preincubation was evaluated in each assay by adding biotinylated antibody to the streptavidin-coated surface before adding biotin- or PBS-spiked serum. Lastly, the preincubation method was compared to a biotin-depletion protocol to compare the effectiveness of mitigating biotin interference.

Results

In the presence of 400 µg/L biotin, analyte detection was reduced to 10% to 15% of total in the ELISA assays and to 15.2% in the automated sandwich (thyroglobulin) immunoassay. In the automated competitive (free thyroxine) immunoassay, biotin caused an increased detection of 551.6%. Preconjugation of the biotinylated capture antibody to the streptavidin surface in the ELISA assays resulted in 84% to 99% activity recovery, compared to 84% to 97% by a biotin depletion protocol. Similarly, automated sandwich and competitive immunoassays obtained 97.1% and 116.5% recovery by preconjugation, compared to 95.6% and 100.3% by the depletion method, respectively.

Conclusion

This study demonstrates how assay redesign to include preconjugation of biotinylated capture antibody to streptavidin is an effective alternative to biotin-depletion methods to mitigate biotin interference.
Topology optimization of irregular flow domain by parametric level set method in unstructured mesh
Authors: Li Jiajing , Gao Liang , Ye Mengli , Li Hao , Li Lizhou
Published: November 2021

In this study, we present a novel method for the topology optimization of the irregular flow domain using a parametric level set method (PLSM). Some improvement was applied on the CS-RBFs (radial basis functions with compact support)-based PLSM to make it suitable for nonuniform mesh, expanding the range field of engineering application of the PLSM. The optimization problem is solved by a gradient-based algorithm with Stokes equations as state constraints, and the objective is set to minimize the power dissipation subject to the volume constraint of flow channels. A PLSM is introduced to avoid the direct solving of the Hamilton–Jacobi partial differential equation, which can have the potential to break through the restriction of relying on structured meshes because no finite difference scheme is required. Then, a self-adaption support radius approach is presented to allow the parametric level set to be evolved on the nonuniformed mesh, which can expand the application of the PLSM to more complicated engineering problems with irregular geometric shapes. A volume integration scheme is applied during the design sensitivity analysis to calculate the shape derivatives, allowing the nucleation of new holes. Numerical examples in two and three dimensions are provided to demonstrate the effectiveness of the proposed method.
Accountability for Human Rights: Applying Business and Human Rights Instruments to Non-Governmental Organizations
Authors: Carolei Domenico , Bernaz Nadia
Published: November 2021

Often seen as selfless champions of human rights, non-governmental organizations are vulnerable to attacks from unscrupulous states, which makes NGO regulation and accountability for human rights a sensitive issue. Yet, like all organizations, NGOs can have negative human rights impacts. States and international organizations have developed business and human rights (BHR) instruments that apply to corporations but there is no equivalent for NGOs. This article assesses the extent to which BHR standards may be relevant to enhance NGO accountability for human rights. It argues that these instruments, although not designed with NGOs in mind, are relevant to their operations and provide an attractive and moderate avenue to enhance NGO accountability. Ultimately, it shows that applying BHR instruments to NGOs could strengthen these instruments.
Applications of deep learning in electron microscopy
Authors: Treder Kevin P , Huang Chen , Kim Judy S , Kirkland Angus I
Published: November 2021

We review the growing use of machine learning in electron microscopy (EM) driven in part by the availability of fast detectors operating at kiloHertz frame rates leading to large data sets that cannot be processed using manually implemented algorithms. We summarize the various network architectures and error metrics that have been applied to a range of EM-related problems including denoising and inpainting. We then provide a review of the application of these in both physical and life sciences, highlighting how conventional networks and training data have been specifically modified for EM.
Gas infall and radial transport in cosmological simulations of milky way-mass discs
Authors: Trapp Cameron W , Kereš Dušan , Chan Tsang Keung , Escala Ivanna , Hummels Cameron , Hopkins Philip F , Faucher-Giguère Claude-André , Murray Norman , Quataert Eliot , Wetzel Andrew
Published: November 2021

Observations indicate that a continuous supply of gas is needed to maintain observed star formation rates in large, discy galaxies. To fuel star formation, gas must reach the inner regions of such galaxies. Despite its crucial importance for galaxy evolution, how and where gas joins galaxies is poorly constrained observationally and rarely explored in fully cosmological simulations. To investigate gas accretion in the vicinity of galaxies at low redshift, we analyse the FIRE-2 cosmological zoom-in simulations for 4 Milky Way mass galaxies (Mhalo ∼ 1012M⊙), focusing on simulations with cosmic ray physics. We find that at z ∼ 0, gas approaches the disc with angular momentum similar to the gaseous disc edge and low radial velocities, piling-up near the edge and settling into full rotational support. Accreting gas moves predominately parallel to the disc and joins largely in the outskirts. Immediately prior to joining the disc, trajectories briefly become more vertical on average. Within the disc, gas motion is complex, being dominated by spiral arm induced oscillations and feedback. However, time and azimuthal averages show slow net radial infall with transport speeds of 1–3 km s−1 and net mass fluxes through the disc of ∼M⊙ yr−1, comparable to the galaxies’ star formation rates and decreasing towards galactic centre as gas is sunk into star formation. These rates are slightly higher in simulations without cosmic rays (1–7 km s−1, ∼4–5 M⊙ yr−1). We find overall consistency of our results with observational constraints and discuss prospects of future observations of gas flows in and around galaxies.
Milky Way total mass derived by rotation curve and globular cluster kinematics from Gaia EDR3
Authors: Wang Jianling , Hammer Francois , Yang Yanbin
Published: November 2021

Using action-based distribution function for the dynamical model of the Milky Way (MW) we have estimated its total mass and its density profile. Constraints are coming from the globular cluster proper motions from Gaia EDR3, from the rotation curve based on Gaia DR2 data, and from the vertical force data. We use Bayesian Markov chain Monte Carlo method to explore the parameters, for which the globular cluster distribution function and the Galactic potential are fully constrained. Numerical simulations are used to study the uncertainties on the potential constraint if considering a possible massive Large Magellanic Cloud (LMC). We found that a massive LMC (1.5 × 1011 M⊙) will affect the MW mass measurement at large radius, which includes both the MW and the LMC. We also use the FIRE2 Latte cosmological hydrodynamic simulations to make mock data set from an MW-like galaxy that includes many unrelaxed substructures. We test the effect of these unrelaxed substructures on the final results, and found that the measured rotation curve fluctuated around input value within 5 per cent. By keeping a large freedom in choosing a priori mass profile for both baryonic and dark matter leads a total mass of the MW that ranges from $5.36_{-0.68}^{+0.81}\times 10^{11}$ M⊙ to $7.84_{-1.97}^{+3.08} \times 10^{11}$ M⊙. This includes the contribution of a putative massive LMC and significantly narrows the MW total mass range published earlier. Such total mass leads to dark matter density at solar position of $0.34_{-0.02}^{+0.02}$ GeV cm−3.
Besca, a single-cell transcriptomics analysis toolkit to accelerate translational research
Authors: Mädler Sophia Clara , Julien-Laferriere Alice , Wyss Luis , Phan Miroslav , Sonrel Anthony , Kang Albert S W , Ulrich Eric , Schmucki Roland , Zhang Jitao David , Ebeling Martin , Badi Laura , Kam-Thong Tony , Schwalie Petra C , Hatje Klas
Published: November 2021

Single-cell RNA sequencing (scRNA-seq) revolutionized our understanding of disease biology. The promise it presents to also transform translational research requires highly standardized and robust software workflows. Here, we present the toolkit Besca, which streamlines scRNA-seq analyses and their use to deconvolute bulk RNA-seq data according to current best practices. Beyond a standard workflow covering quality control, filtering, and clustering, two complementary Besca modules, utilizing hierarchical cell signatures and supervised machine learning, automate cell annotation and provide harmonized nomenclatures. Subsequently, the gene expression profiles can be employed to estimate cell type proportions in bulk transcriptomics data. Using multiple, diverse scRNA-seq datasets, some stemming from highly heterogeneous tumor tissue, we show how Besca aids acceleration, interoperability, reusability and interpretability of scRNA-seq data analyses, meeting crucial demands in translational research and beyond.
Risk of hydroxychloroquine retinopathy in the community
Authors: Dabit Jesse Y , Hocaoglu Mehmet , Moder Kevin G , Barkmeier Andrew J , Smith Wendy M , O’Byrne Thomas J , Crowson Cynthia S , Duarte-García Alí
Published: November 2021

Objectives

We aimed to estimate the risk of HCQ retinopathy and its risk factors among incident users in the community.

Methods

Using the Rochester Epidemiology Project, a record-linkage system, a cohort of incident users of HCQ was identified from 27 counties in the American upper Midwest. HCQ retinopathy was defined based on characteristic paracentral automated 10-2 visual field (10-2 AVF) defects and parafoveal retinal photoreceptor layer changes on spectral domain optical coherence tomography. Cumulative incidence rates were estimated adjusting for competing risk of death. Risk factors for HCQ retinopathy were examined using Cox models.

Results

The study included 634 incident HCQ users (mean age at initial HCQ use was 53.7 years, 79% females, 91% white). Most common indications for HCQ were RA (57%) and SLE (19%). The average follow-up length was 7.6 years. Eleven patients developed HCQ retinopathy (91% females, 91% white). The majority used HCQ for RA (91%). The cumulative incidence rate at year 5 was 0%, which increased to 3.9% (95% CI 2.0, 7.4) by 10 years. Taking an HCQ dose ≥5 mg/kg was associated with a hazard ratio (HR) of 3.59 (95% CI 1.09, 11.84) compared with lower doses. There was a 48% increase [HR 1.48 (95% CI 1.03, 2.14)] in the risk of HCQ retinopathy for each 100 g of HCQ cumulative dose.

Conclusion

The risk of HCQ retinopathy at 10 years of use is lower compared with previous prevalence-based estimations. A dose ≥5 mg/kg was associated with higher HCQ retinopathy risk.
Diffuse Optical Tomography Using fNIRS Signals Measured from the Skull Surface of the Macaque Monkey
Authors: Hayashi Ryusuke , Yamashita Okito , Yamada Toru , Kawaguchi Hiroshi , Higo Noriyuki
Published: November 2021

Diffuse optical tomography (DOT), as a functional near-infrared spectroscopy (fNIRS) technique, can estimate three-dimensional (3D) images of the functional hemodynamic response in brain volume from measured optical signals. In this study, we applied DOT algorithms to the fNIRS data recorded from the surface of macaque monkeys’ skulls when the animals performed food retrieval tasks using either the left- or right-hand under head-free conditions. The hemodynamic response images, reconstructed by DOT with a high sampling rate and fine voxel size, demonstrated significant activations at the upper limb regions of the primary motor area in the central sulcus and premotor, and parietal areas contralateral to the hands used in the tasks. The results were also reliable in terms of consistency across different recording dates. Time-series analyses of each brain area revealed preceding activity of premotor area to primary motor area consistent with previous physiological studies. Therefore, the fNIRS–DOT protocol demonstrated in this study provides reliable 3D functional brain images over a period of days under head-free conditions for region-of-interest–based time-series analysis.
Transepithelial Diluted Alcohol and Iontophoresis-Assisted Corneal Crosslinking for Progressive Keratoconus in Adults: 4-Year Clinical Results
Authors: Bilgihan Kamil , Uysal Betul Seher , Özmen Mehmet Cüneyt , Eskalen Oguzcan , Gurelik Gokhan
Published: November 2021

Purpose:

The aim of this study was to compare the 4-year clinical outcomes of transepithelial diluted alcohol and iontophoresis-assisted corneal crosslinking (DAI-CXL) and standard corneal crosslinking (S-CXL) in adults with progressive keratoconus.

Methods:

This retrospective study included 36 eyes of 36 keratoconic patients who underwent DAI-CXL (n = 18) or S-CXL (n = 18). Best spectacle-corrected visual acuity (BSCVA) and corneal topography parameters were analyzed at baseline and at 1, 2, 3, and 4 years of follow-up. Corneal demarcation line depth (DLD) at 1 month was measured, and the relation of DLD with corneal thickness (DL%) was assessed.

Results:

BSCVA improved significantly only in S-CXL (P = 0.01). A significant decrease in maximum keratometry and mean keratometry occurred at 4 years in both groups (all P < 0.05), and these changes were similar in both groups (all P > 0.05). There was a significant reduction in the thinnest corneal thickness in S-CXL (P = 0.01); however, the mean thinnest corneal thickness in DAI-CXL remained stable (P = 0.094). Higher-order aberrations and coma aberration decreased significantly in both groups at 4 years (all P < 0.05), with a higher decrease in S-CXL (all P < 0.05). Spherical aberration showed a significant reduction only in S-CXL (P = 0.005). In contrast to the similar mean DLD in both groups, DL% in DAI-CXL was significantly greater than that in S-CXL (P = 0.032). There were no correlations between the improvement in BSCVA, maximum keratometry, mean keratometry, higher-order aberrations, and the mean DLD and DL% (all P > 0.05).

Conclusions:

DAI-CXL was as effective as S-CXL in arresting the progression of keratoconus and showed similar clinical results to S-CXL at the 4-year follow-up.