bluuebunny/crossref_metadata_2025 huggingface dataset:
Electron energization and thermal to non-thermal energy partition during earth's magnetotail reconnection
Authors: Oka M. , Phan T. D. , Øieroset M. , Turner D. L. , Drake J. F. , Li X. , Fuselier S. A. , Gershman D. J. , Giles B. L. , Ergun R. E. , Torbert R. B. , Wei H. Y. , Strangeway R. J. , Russell C. T. , Burch J. L.
Published: May 2022

Electrons in earth's magnetotail are energized significantly both in the form of heating and in the form of acceleration to non-thermal energies. While magnetic reconnection is considered to play an important role in this energization, it still remains unclear how electrons are energized and how energy is partitioned between thermal and non-thermal components. Here, we show, based on in situ observations by NASA's Magnetospheric Multiscale mission combined with multi-component spectral fitting methods, that the average electron energy ε¯ (or equivalently temperature) is substantially higher when the locally averaged electric field magnitude |E| is also higher. While this result is consistent with the classification of “plasma-sheet” and “tail-lobe” reconnection during which reconnection is considered to occur on closed and open magnetic field lines, respectively, it further suggests that a stochastic Fermi acceleration in 3D, reconnection-driven turbulence is essential for the production and confinement of energetic electrons in the reconnection region. The puzzle is that the non-thermal power-law component can be quite small even when the electric field is large and the bulk population is significantly heated. The fraction of non-thermal electron energies varies from sample to sample between ∼20% and ∼60%, regardless of the electric field magnitude. Interestingly, these values of non-thermal fractions are similar to those obtained for the above-the-looptop hard x-ray coronal sources for solar flares.
Newly designed ignition circuit to improve the ignition reliability of Hall thruster
Authors: Li Jingjing , Li Wenbo , Wei Liqiu , Zhou Liwei , Ji Tianyuan , Jiang Wenjia , Li Tingwan , Li Hong , Tang Jingfeng , He Yongfeng , Ding Yongjie
Published: May 2022

This study proposes a newly designed ignition circuit that does not change the ignition starting parameters of a Hall thruster, reduces the critical ignition voltage, and improves ignition reliability. The complexity and weight of the Hall thruster power supply system are reduced by multiplexing the ignition and discharge power supplies. Under the condition that the design parameters are satisfied, that is, R3+REC2 is much larger than RCC1, the residual energy in the circuit after the cathode breakdown can be fed into the thruster discharge channel to improve the ignition energy supply. The experimental results show that when the anode voltage is 98 V, only nine of the 100 ignition tests are successful using the traditional ignition circuit, whereas the number of successes using the newly designed ignition circuit is as high as 99, which provides a simple solution method for improving the ignition reliability.
Electronic band structure and chemical bonding in trigonal Se and Te
Authors: Orlov V. G. , Sergeev G. S.
Published: May 2022

Herein, the electronic band structure and charge density distribution are theoretically studied in trigonal Se and Te to clarify the uncertainty stemming from the different views on the types of chemical bonding in their crystals and to reconsider the role of valence s- and p-electrons in bonding. The lack of overlapping of the lower and upper bands of valence p-electrons in trigonal Se and the large band separation of valence s- and p-electrons present an opportunity to estimate the contributions of valence s- and p-electrons to the charge densities of two types of bond critical points (BCPs) in trigonal Se. Valence s-electrons and lower p-electrons significantly contribute to the charge density of BCPs of the first type, covalently connecting the nearest neighboring atoms within helical chains. In contrast, the lower and upper valence p-electrons are mainly responsible for the BCPs of the second type linking the neighboring chains in the Se and Te trigonal crystal structures. The nonlocal long-range van der Waals (vdW) correlation functional vdW-DF2, which is important for determining lattice constants, has a minimal effect on BCP parameters, which define the chemical bonding types. The exchange potential of Becke and Johnson modified by Tran and Blaha and the short-range electron–electron correlations considered in the local density approximation correctly reproduce not only the energy bandgap values but also various peculiarities in the electronic band structure of trigonal Se and Te, such as band crossings (Weyl nodes) of the valence p-electrons recently found in trigonal Te via angle-resolved photoemission spectroscopy experiments.
Skew-symmetric hom-algebroids and their representation theory
Authors: Peyghan Esmaeil , Nourmohammadifar Leila
Published: May 2022

In this paper, we introduce skew-symmetric hom-algebroids and linear almost Poisson structures on dual hom-bundles. In addition, we show that these two geometric notions are related to each other and present several interesting examples of them. Moreover, we study the representation theory of skew-symmetric hom-algebroids and their dual spaces. Finally, we give the notion of phase spaces of skew-symmetric algebroids.
Intrinsic ferromagnetic triferroicity in bilayer T′-VTe2
Authors: Zhang Ting , Xu Xilong , Dai Ying , Huang Baibiao , Ma Yandong
Published: May 2022

Multiferroics, which combines two or more ferroic orders, is of significant fundamental and practical importance in condensed-matter physics and materials science. Although multiferroics has been broadly studied for decades, intrinsic triferroicity is rarely explored, especially with ferromagnetic ordering. Here, we propose a general mechanism for realizing intrinsic ferromagnetic triferroicity in two-dimensional van der Waals lattices through interlayer sliding and further demonstrate it in bilayer T′-VTe2. Using first-principles calculations, we reveal that bilayer T′-VTe2 exhibits spontaneous ferromagnetism, ferroelasticity, and ferroelectricity simultaneously, yielding the long-sought intrinsic triferroicity. We further predict that such a system could possess many distinctive physics, for example, the ferroelastic control of magnetization orientation and ferroelectric control of magnetic moment distribution. The explored mechanism and phenomena not only greatly enrich the research on two-dimensional multiferroics but also provide a promising avenue to realize novel quantum device applications.
Photon excitation effect on formation of graphene nanocrystallites during carbon film growth process
Authors: Chen Cheng , Zhang Zhixin , Huang Zhiquan , Jian Nan , Diao Dongfeng
Published: May 2022

In this article, we propose a method to deposit nanocrystallite embedded carbon films by electron cyclotron resonance plasma sputtering with photon irradiation cooperated with electron or Ar+ ion irradiation. We found photon irradiation can enhance the growth of graphene nanocrystallites during carbon film deposition. The energy transfer from the photon to the metastable carbon structure excites the growth of sp2 hybridized graphene nanocrystallites, and photon-excited electrons can be accelerated by the bias and further promote the graphene nanocrystallite growth. Photons are the second quantum medium we found that can be used to deposit nanocrystallite embedded carbon films, and their quantum properties with electric neutrality can help us to further understand the formation of the carbon nanocrystallite structure and may shed light on the quantum fabrication of desired materials.
Coronavirus pleomorphism
Authors: Kanso M. A. , Naime M. , Chaurasia V. , Tontiwattanakul K. , Fried E. , Giacomin A. J.
Published: May 2022

The coronavirus is always idealized as a spherical capsid with radially protruding spikes. However, histologically, in the tissues of infected patients, capsids in cross section are elliptical, and only sometimes spherical [Neuman et al., “Supramolecular architecture of severe acute respiratory syndrome coronavirus revealed by electron cryomicroscopy,” J Virol, 80, 7918 (2006)]. This capsid ellipticity implies that coronaviruses are oblate or prolate or both. We call this diversity of shapes, pleomorphism. Recently, the rotational diffusivity of the spherical coronavirus in suspension was calculated, from first principles, using general rigid bead-rod theory [Kanso et al., “Coronavirus rotational diffusivity,” Phys Fluids 32, 113101 (2020)]. We did so by beading the spherical capsid and then also by replacing each of its bulbous spikes with a single bead. In this paper, we use energy minimization for the spreading of the spikes, charged identically, over the oblate or prolate capsids. We use general rigid bead-rod theory to explore the role of such coronavirus cross-sectional ellipticity on its rotational diffusivity, the transport property around which its cell attachment revolves. We learn that coronavirus ellipticity drastically decreases its rotational diffusivity, be it oblate or prolate.
Elucidation of molecular and physiological mechanisms addressing integrated omic approaches for heavy metal stress tolerance in crops
Authors: Mondal Raju , Kumar Amit , Shabnam Aftab Ahmad , Chaturvedi Ashish K.
Published: May 2022

Recent industrialisation has seen an alarming increase in heavy metal pollution, raising the question of how to sustain food production in the presence of heavy metals. Several reviews have addressed the direct and indirect effects of heavy metals on crop physiological and biochemical processes. However, understanding of the physiological and molecular mechanisms requires integrating omic approaches to explore the target mechanism in general in crops, and those insights are still lacking. To date, most of the information related to omic approaches about heavy metals has been sparse and sporadic. This review, by means of examples, attempts to integrate different available proteomic, transcriptomic and genomic approaches in a nutshell along with underlying physiological and molecular mechanisms occurring in crops. Major identified transcription factors (TFs) (MYBs, WRKYs), transgenes (MT2, Nramp6, GSTU3, CIPK, MYB1 and DRE), up-regulated (CAT, SODs, POD and APX), down-regulated (ATPase subunits, Rubisco subunits and photosystem I (PSI) reaction centre) proteins, and miRNA (miR397, miR398a, miR408, OsmiR601 and miR166) for major heavy metals have been summarised. It provides a mode of action of heavy metals and their fate inside the plant. It also elucidates how these omics approaches facilitate in mitigating heavy metal stress and could help in addressing crop tolerance based on these mechanisms. Identifying donors with the aid of novel omic approaches could be useful for the development of HM tolerant crops, promoting future sustainability in heavy-metal-polluted soil and water resources.
Synaptotagmin-1 is a bidirectional Ca
2+
sensor for neuronal endocytosis
Authors: Chen Yang , Hu Shaoqin , Wu Xuanang , Xie Zhenli , Wang Yuan , Wang Bianbian , Li Xiaopeng , Pei Yingmei , Gu Yuhao , Huang Kai , Huo Jingxiao , Wei Anqi , Bi Cheng , Lu Zhe , Song Qian , Xu Huadong , Kang Xinjiang , Shao Shuli , Long Jiangang , Liu Jiankang , Zhou Zhuan , Huang Rong , Chai Zuying , Wang Changhe
Published: May 2022

Significance

Precise and efficient coupling of endocytosis to exocytosis is critical for neurotransmission. The activity-dependent facilitation of endocytosis has been well established for efficient membrane retrieval; however, whether neural activity clamps endocytosis to avoid excessive membrane retrieval remains debatable with the mechanisms largely unknown. The present work provides compelling evidence that synaptotagmin-1 (Syt1) functions as a primary bidirectional Ca
2+
sensor to promote slow, small-sized clathrin-mediated endocytosis but inhibit the fast, large-sized bulk endocytosis during elevated neural activity, the disruption of which leads to inefficient vesicle recycling under mild stimulation but excessive membrane retrieval following sustained neurotransmission. Thus, Syt1 serves as a fine-tuning Ca
2+
sensor to ensure both efficient and precise coupling of endocytosis to exocytosis in response to different neural activities.
Exploring age-related changes in the realisation of (t)
Authors: Buchstaller Isabelle , Mearns Adam , Auer Anja , Krause-Lerche Anne
Published: May 2022

An understanding of linguistic heterogeneity in older speakers is crucial for the study of language variation and change. To date, intra-speaker malleability in older populations remains under-researched, in varieties of English and more generally. This paper contributes panel data to the question of how aging individuals engage with ongoing changes in the realisation of (t) in the Tyneside region in the North-East of England. We examine the variable ways in which six speakers recorded in their 20s/30s and re-interviewed in their 60s/70s adapt to community-wide change. The finding that some speakers exhibit malleability in their variable realisation of (t) substantiates a life-course perspective over a strict maturational explanation. More specifically, our analysis explores the contribution of long-term (in)stability to lifespan-specific identity construction in the Tyneside area. Our findings support calls for the incorporation of sophisticated statistical methods in combination with social constructivist approaches into panel research on older age populations.
Actitudes de los mallorquines hacia el castellano y el andaluz
Authors: Méndez Guerrero Beatriz
Published: May 2022

Abstracta

Las evaluaciones sociales que hacen los individuos hacia las variedades lingüísticas son objeto de estudio de la
sociolingüística desde hace tiempo y han ganado protagonismo en el siglo veintiuno. Esto es así porque de estas actitudes se
deduce hacia dónde se encaminará la lengua en el futuro. En esta investigación se presentan los resultados de un estudio de
actitudes hacia el castellano y el andaluz a partir de una muestra de 70 jóvenes mallorquines. Siguiendo la metodología del
proyecto PRECAVES XXI, se presentan los resultados sobre el reconocimiento de las variedades, la valoración directa que se hace de
ellas (dimensiones cognitiva y afectiva) y la proximidad que establece el grupo entre su variedad y las variedades castellana y
andaluza. Las principales conclusiones indican que tanto el reconocimiento de las variedades como su valoración es positiva y que
los mallorquines perciben mucha proximidad con el castellano (su variedad propia), pero no con el andaluz.
Too close for comfort? Endomembranes promote missegregation by enclosing lost chromosomes
Authors: Donker Lisa , Godinho Susana A.
Published: May 2022

Correct segregation of chromosomes during mitosis is essential to prevent aneuploidy. In this issue, Ferrandiz et al. (2022. J. Cell Biol.https://doi.org/10.1083/jcb.202203021) show that endomembranes can promote chromosome missegregation by “ensheathing” misaligned chromosomes, preventing their integration into the metaphase plate. Their findings point toward endomembranes as a potential risk factor for aneuploidy.
Comparison of neural basis expansion analysis for interpretable time series (N-BEATS) and recurrent neural networks for heart dysfunction classification
Authors: Puszkarski B , Hryniów K , Sarwas G
Published: May 2022

Objective. The primary purpose of this work is to analyze the ability of N-BEATS architecture for the problem of prediction and classification of electrocardiogram (ECG) signals. To achieve this, performance comparison with various types of other SotA (state-of-the-art) recurrent neural network architectures commonly used for such problems is conducted. Approach. Four architectures (N-BEATS, LSTM, LSTM with peepholes, GRU) were tested for performance and dimension reduction problems for different number of leads (2, 3, 4, 6, 12), both in variants consisting of blended branches, allowing retaining accuracy while reducing the computational capacity needed. The analysis was performed on datasets and using metrics from Challenges in Cardiology (CinC) 2021 competition. Main results. Best results were achieved for LSTM with peepholes, then LSTM, GRU and the worst for N-BEATS (challenge metrics respectively: 0.42, 0.40, 0.39, 0.35; for times: 0.0395 s, 0.0036 s, 0.0027 s, 0.0002 s). Commonly used LSTM outperforms N-BEATS in terms of multi-label classification, data set resilience, and obtained challenge metrics. Still, N-BEATS can obtain acceptable results for 2 lead classification (metric of 0.35 for N-BEATS and 0.38 for other networks) and outperforms other solutions in terms of complexity and speed. Significance. This paper features a novel approach of using the N-BEATS, which was previously used only for forecasting, to classify ECG signals with success. While N-BEATS multi-label classification capacity is lower than LSTM, its speed obtaining results with a reduced number of leads (faster by one to two degrees of magnitude) allows for arrhythmias detection and classification while using off-the-shelf wearable devices (Holter monitors, sport bands, etc).
Design and investigation of a resonant piezoelectric pump with high output pressure using a displacement-amplifying vibrator
Authors: Pan Qiaosheng , Li Yinghao , Diao Weidong , Wang Xiaoliang , Zhang Chi , Liu Shanlin , Li Ruijun
Published: May 2022

A resonant piezoelectric pump using a displacement-amplifying vibrator is proposed in this paper to improve the output pressure of the piezoelectric pump. The piezoelectric pump is composed of a displacement-amplifying vibrator and a pump body. The displacement-amplifying vibrator consists of two amplifiers and two piezoelectric stacks. The pump body comprises a piston shaft, an orifice plate, a valve body, check valves and a runner plate. A clearance exists between the piston shaft and the orifice plate. A groove is designed on the piston shaft, and the pump body is sealed by O-rings. The displacement-amplifying vibrator works in the resonant state, which has a large output amplitude. In this paper, the working principle of the piezoelectric pump is introduced and the influencing factors of output pressure of the piezoelectric pump are theoretically analyzed. The resonant frequency and stiffness of check valves with different thicknesses are simulated and compared, and three displacement amplifiers are designed and simulated. Prototypes of piezoelectric pump are made, and the effect of valve thickness, the diameter of piston shaft, and the displacement-amplifying vibrator is experimentally investigated. The experimental results show that the piezoelectric pump prototype with displacement-amplifying vibrator 3, 10 mm piston shaft and 0.05 mm-thick check valve has the maximum output pressure. Under the driving voltage of 500 Vpp, the maximum output pressure is 4.73 MPa, and the maximum flowrate is 65.7 ml min−1.
Design and characterization of a 3D printed miniature actuator using shape memory alloy wires
Authors: Teymoori Morteza , Kocatürk Özgür
Published: May 2022

Microfluidics has been at the center of attention in chemical and biological sciences over the last decade since it can miniaturize many laboratory-based applications. However, the transition from concept to a practical microfluidic chip is greatly hindered due to the widespread conventional soft lithography techniques which are used for the fabrication of the microfluidic chips. These methods are not time- and cost-efficient. Additive manufacturing technique (i.e. 3D printing) has grown in many research fields. Many conventional microfluidic system component designs have been adapted to the 3D printing manufacturing techniques. Three-dimensional printed active components such as microvalves and micropumps have also been studied, however, almost all the designs depend on an external pneumatic control unit or syringe pumps so far. In this study, we aimed to address the lack of a microfluidic active component with an integrated actuator unit. We used a shape memory alloy as the actuator. In doing so, we employed an innovative batch fabrication method that utilizes 3D printing. The proposed actuator design can produce high work and concurrently isolate the heat source from the fluidic sample which is of utmost importance for biological samples. The results show that the miniature actuator can block high pressure (up to 150 mmHg) silicone channel partially or completely depending on the application requirements. The actuation time can be controlled electronically and reduced to times as low as 100 ms. In conclusion, this design proved to be a promising candidate for the development of flow control components such as microvalves, micropumps, or micromixers.
Improving the mechanical and thermal properties of hemp concrete by treating the hemp hurds with sodium hydroxide solution
Authors: Adam L , Isopescu D N , Maxineasa S G
Published: May 2022

The objectives of the research were to analyse how the treatment with sodium hydroxide solution of hemp stems influences the mechanical and thermal behaviours of concrete when hemp stems are used in the composition of concrete. Tests were performed on hemp concrete samples to evaluate the density and measure the heat transfer coefficient, compressive strength and modulus of elasticity. The activities carried out aimed to identify the influence of the sodium hydroxide solution concentration on the variations of the measured parameters and expressing some conclusions regarding the need to treat the hemp stems before their use in concrete. The need for research is given by the nowadays demand for obtaining eco-sustainable construction materials, in which the possibility of using a material that is considered plant waste becomes an economic resource in a circular economy.
How health influences the way we build
Authors: Cazacu Ch
Published: May 2022

Knowing people’s needs for a healthy life is a fundamental theme for those who design and execute constructions. The environment of a building must combine the most important factors for comfort and health. For a new construction, the hygiene and health of the occupants must become a priority strategy, and needs to be considered early on in the project because it is key to securing a safe construction. How do constructions make us sick and what are the main causes and phenomena, and what consequences do they have on our health are the principal subject from this study. The designer must use materials that are thermally efficient, healthy and comfortable that provides better constructions for the occupants.
Using fibers in construction
Authors: Deaconu O , Chiţonu GC
Published: May 2022

This article is an overview about alternative solutions for reinforced concrete by using different types of fibers. The use of fiber reinforced concrete when is compared to the conventional reinforced concrete solutions. This study has taken in consideration structural performance and the total cost. The use of fibers or dispersed reinforcement also improves some of the characteristics of concrete, such as those related to: cracking, freezing, durability, erosion of ordinary or marine water, wind erosion, permeability, etc. In order to correct to a large extent, the unfavorable characteristics of the reinforced concrete, in the mass of the fresh concrete various types of fibers can be mixed and incorporated in the use of concrete with dispersed reinforcement. As materials often used as fibers, the most commonly are: hooked-end steel (steel fibers), straight polypropylene and straight polyolefin, glass fiber, carbon fiber, aramid fiber, natural hemp fibers, jute, hair, straw, etc.
Tracking control a twin-rotor helicopter used for building measuring with PID-MPC controller
Authors: Guo F
Published: May 2022

In recent years, due to the development of UAV (Unmanned aerial vehicle) technology, UAVs have been used in an increasingly wide range of applications, including the architecture industry. In the field of architecture, the technologies of capturing images of building conditions with UAVs have a huge development, such as architectural planning, remote terrain detection, construction safety supervision and so forth. In general, the applications can be expanded widly, owing to the convenient operation of UAVs for the flyers and that does not require a high degree of precision for the control. However, when it comes to penetration between and within buildings. The lack of flight vision and signal interference often leads to collisions and crashes. Hence, this paper studies how to further optimise the control accuracy of construction measurement UAVs. The aim is to reduce the difficulty of operating the UAV when it faces to interference during architecture measurement. In this paper, a three DOFs two-rotor UAV is selected as the object of study. A mathematical model of the UAV is constructed, which is followed by the designing of an advanced controller based on a PID controller and an MPC (model predictive controller) controller, used for realising offset free reference tracking when changing elevation, pitch and travel angles. The usage of this controller can significantly reduce the cost of control during flight to reduce control bias in the presence of disturbing factors. The application of the controller to UAVs allows for automated and intelligent UAV control.
Verification of elastic wave velocity tomography based on compressive sampling
Authors: Qiao X , Kobayashi Y , Oda K , Nakamura K
Published: May 2022

This paper verifies the compressive sampling(CS)-based elastic wave velocity tomography(EWT) technique. Conventional elastic wave velocity tomography necessitates the quantity of effort and time. Nevertheless, because the central premise of CS algorithm is to recover the original velocity distribution from random measurement subsampling, compressive sampling is adopted at overcoming this challenge. CS algorithm chose fewer paths from entire measurements during the measurement stage. After that, the L1-minimization optimization method adopts to recover the damage area and magnitude in the visualization stage. Because of hugely reduces the measurement workload and a high level of accuracy reconstruction, CS algorithm is more effective in comparison with the conventional algorithms of elastic wave velocity tomography.
Improving the properties of mortars by using recycled paper ash flakes
Authors: Tintisan M L , Siomin A C , Zaharie A , Manea D L
Published: May 2022

This study addresses the need to improve life on earth by finding a way to reintroduce ubiquitous waste back into the system. On a hand, there is the amount of cellulosic waste that can no longer be reintroduced into the paper recycling process. On the other hand, the amount of cement used globally, is growing alarmingly. My study seeks the balance of a mix of these two materials, which would generate desirable effects both from an engineering and ecological point of view. Paper ash, is a material made of particles of various sizes and can play various roles in the composition of mortars. The efficacy of particles up to 0.025 mm in size (powder ash) as a cement substitute and the efficiency of particles in size between 0.025 and 8 mm (flakes) as a pozzolanic additive are demonstrated. The results of the mechanical tests to which the samples were subjected show the possibility of reducing the amount of cement used in standard recipes by adding ash from recycled paper, without compromising the physical and mechanical properties of the mortars. The cement economy can rise up to 20 percent while the mechanical strength increases by 5-10 percent compared to the basic recipe.
Experimental research of main characteristics in a complex multi-layer plate heat exchanger
Authors: Yezhov V S , Semicheva N E , Burtsev A P , Brezhnev A V , Perepelitsa N S
Published: May 2022

The objective of this paper is research of main heat exchange characteristics in a complex multi-layer heat-exchanger with the purpose of determining heat exchanging process intensification dependencies and conditions during utilization of ventilation gas and emission low-grade heat with associated recovery of thermoelectricity.
The network makeup artist (NORMA-2.0): distinguishing annotated groups in a network using innovative layout strategies
Authors: Karatzas Evangelos , Koutrouli Mikaela , Baltoumas Fotis A , Papanikolopoulou Katerina , Bouyioukos Costas , Pavlopoulos Georgios A
Published: May 2022

Motivation

Network biology is a dominant player in today’s multi-omics era. Therefore, the need for visualization tools which can efficiently cope with intra-network heterogeneity emerges.

Results

NORMA-2.0 is a web application which uses efficient layouts to group together areas of interest in a network. In this version, NORMA-2.0 utilizes three different strategies to make such groupings as distinct as possible while it preserves all of the properties from its first version where one can handle multiple networks and annotation files simultaneously.

Availability and implementation

The web resource is available at http://norma.pavlopouloslab.info/. The source code is freely available at https://github.com/PavlopoulosLab/NORMA.
ReadItAndKeep: rapid decontamination of SARS-CoV-2 sequencing reads
Authors: Hunt Martin , Swann Jeremy , Constantinides Bede , Fowler Philip W , Iqbal Zamin
Published: May 2022

Viral sequence data from clinical samples frequently contain contaminating human reads, which must be removed prior to sharing for legal and ethical reasons. To enable host read removal for SARS-CoV-2 sequencing data on low-specification laptops, we developed ReadItAndKeep, a fast lightweight tool for Illumina and nanopore data that only keeps reads matching the SARS-CoV-2 genome. Peak RAM usage is typically below 10 MB, and runtime less than 1 min. We show that by excluding the polyA tail from the viral reference, ReadItAndKeep prevents bleed-through of human reads, whereas mapping to the human genome lets some reads escape. We believe our test approach (including all possible reads from the human genome, human samples from each of the 26 populations in the 1000 genomes data and a diverse set of SARS-CoV-2 genomes) will also be useful for others.

Availability and implementation

ReadItAndKeep is implemented in C++, released under the MIT license, and available from https://github.com/GenomePathogenAnalysisService/read-it-and-keep.

Supplementary information

Supplementary data are available at Bioinformatics online.
Building alternative consensus trees and supertrees usingk-means and Robinson and Foulds distance
Authors: Tahiri Nadia , Fichet Bernard , Makarenkov Vladimir
Published: May 2022

Motivation

Each gene has its own evolutionary history which can substantially differ from evolutionary histories of other genes. For example, some individual genes or operons can be affected by specific horizontal gene transfer or recombination events. Thus, the evolutionary history of each gene should be represented by its own phylogenetic tree which may display different evolutionary patterns from the species tree that accounts for the main patterns of vertical descent. However, the output of traditional consensus tree or supertree inference methods is a unique consensus tree or supertree.

Results

We present a new efficient method for inferring multiple alternative consensus trees and supertrees to best represent the most important evolutionary patterns of a given set of gene phylogenies. We show how an adapted version of the popular k-means clustering algorithm, based on some remarkable properties of the Robinson and Foulds distance, can be used to partition a given set of trees into one (for homogeneous data) or multiple (for heterogeneous data) cluster(s) of trees. Moreover, we adapt the popular Caliński–Harabasz, Silhouette, Ball and Hall, and Gap cluster validity indices to tree clustering with k-means. Special attention is given to the relevant but very challenging problem of inferring alternative supertrees. The use of the Euclidean property of the objective function of the method makes it faster than the existing tree clustering techniques, and thus better suited for analyzing large evolutionary datasets.

Availability and implementation

Our KMeansSuperTreeClustering program along with its C++ source code is available at: https://github.com/TahiriNadia/KMeansSuperTreeClustering.

Supplementary information

Supplementary data are available at Bioinformatics online.
Tau accelerates α-synuclein aggregation and spreading in Parkinson’s disease
Authors: Pan Lina , Li Chunrui , Meng Lanxia , Tian Ye , He Mingyang , Yuan Xin , Zhang Guoxin , Zhang Zhaohui , Xiong Jing , Chen Guiqin , Zhang Zhentao
Published: May 2022

The aggregation and prion-like propagation of α-synuclein are involved in the pathogenesis of Parkinson’s disease. However, the underlying mechanisms regulating the assembly and spreading of α-synuclein fibrils remain poorly understood. Tau co-deposits with α-synuclein in the brains of Parkinson’s disease patients, suggesting a pathological interplay between them.

Here we show that tau interacts with α-synuclein and accelerates its aggregation. Compared with pure α-synuclein fibrils, the tau-modified α-synuclein fibrils show enhanced seeding activity, inducing mitochondrial dysfunction, synaptic impairment and neurotoxicity in vitro. Injection of the tau-modified α-synuclein fibrils into the striatum of mice induces more severe α-synuclein pathology, motor dysfunction and cognitive impairment when compared with the mice injected with pure α-synuclein fibrils. Knockout of tau attenuates the propagation of α-synuclein pathology and Parkinson’s disease-like symptoms both in mice injected with α-syn fibrils and α-syn A53T transgenic mice.

In conclusion, tau facilitates α-synuclein aggregation and propagation in Parkinson’s disease.
Inferring the sequence of brain volume changes in progressive supranuclear palsy using MRI
Authors: Franzmeier Nicolai , Höglinger Günter U.
Published: May 2022

This scientific commentary refers to ‘A data-driven model of brain volume changes in progressive supranuclear palsy’ by Scotton et al. (https://doi.org/10.1093/braincomms/fcac098)
Genetic mechanisms underlying gray matter volume changes in patients with drug-naive first-episode schizophrenia
Authors: Xu Xiaotao , Li Qian , Qian Yinfeng , Cai Huanhuan , Zhang Cun , Zhao Wenming , Zhu Jiajia , Yu Yongqiang
Published: May 2022

Brain structural damage is a typical feature of schizophrenia. Investigating such disease phenotype in patients with drug-naive first-episode schizophrenia (DFSZ) may exclude the confounds of antipsychotics and illness chronicity. However, small sample sizes and marked clinical heterogeneity have precluded definitive identification of gray matter volume (GMV) changes in DFSZ as well as their underlying genetic mechanisms. Here, GMV changes in DFSZ were assessed using a neuroimaging meta-analysis of 19 original studies, including 605 patients and 637 controls. Gene expression data were derived from the Allen Human Brain Atlas and processed with a newly proposed standardized pipeline. Then, we used transcriptome–neuroimaging spatial correlations to identify genes associated with GMV changes in DFSZ, followed by a set of gene functional feature analyses. Meta-analysis revealed consistent GMV reduction in the right superior temporal gyrus, right insula and left inferior temporal gyrus in DFSZ. Moreover, we found that these GMV changes were spatially correlated with expression levels of 1,201 genes, which exhibited a wide range of functional features. Our findings may provide important insights into the genetic mechanisms underlying brain morphological abnormality in schizophrenia.
Radicalising Global IR: Modernity, Capitalism, and the Question of Eurocentrism
Authors: Duzgun Eren
Published: May 2022

Theorising a non-Eurocentric “global international relations” has been a main preoccupation of scholars associated with international political sociology (IPS). In this article, I argue that scholars within the IPS tradition have provided a powerful critique of, but no clear alternative to, Eurocentrism. This is partly attributable to their insufficient problematisation of the historical narratives that propel capitalism backwards into history. By problematising “presentist” conceptions of capitalism, I show that a critical dialogue between IPS and “political Marxism” helps to introduce an alternative foundation for anti-Eurocentrism, which shifts our focus from “capitalist modernity” to “radical modernity”. Radical modernity resists hierarchical colonial ontologies by emphasising the universality of egalitarian social patterns rooted in our common, non-capitalist past. I contend that radical modernity is an enduring legacy that is found universally, transmitted interactively, and revitalised continuously across time and space, hence providing an alternative base on which to theorise and globalise the “international” in a non-Eurocentric way.
NKG2D signaling regulates IL-17A-producing γδT cells in mice to promote cancer progression
Authors: Curio Sophie , Edwards Sarah C , Suzuki Toshiyasu , McGovern Jenny , Triulzi Chiara , Yoshida Nagisa , Jonsson Gustav , Glauner Teresa , Rami Damiano , Wiesheu Robert , Kilbey Anna , Violet Purcell Rachel , Coffelt Seth B , Guerra Nadia
Published: May 2022

γδT cells are unconventional T cells particularly abundant in mucosal tissues that play an important role in tissue surveillance, homeostasis, and cancer. γδT cells recognize stressed cells or cancer cells through the NKG2D receptor to kill these cells and maintain normality. Contrary to the well-established anti-tumor function of these NKG2D-expressing γδT cells, we show here that, in mice, NKG2D regulates a population of pro-tumor γδT cells capable of producing IL-17A. Germline deletion of Klrk1, the gene encoding NKG2D, reduced the frequency of γδT cells in the tumor microenvironment and delayed tumor progression. We further show that blocking NKG2D reduced the capability of γδT cells to produce IL-17A in the pre-metastatic lung and that co-culture of lung T cells with NKG2D ligand-expressing tumor cells specifically increased the frequency of γδT cells. Together, these data support the hypothesis that, in a tumor microenvironment where NKG2D ligands are constitutively expressed, γδT cells accumulate in an NKG2D-dependent manner and drive tumor progression by secreting pro-inflammatory cytokines, such as IL-17A.
A report from the Irish women in cardiology survey, exploring Europe’s largest gender gap in cardiology
Authors: Wong Bethany , Brennan Alice , James Stephanie , Brandon Lisa , Ranganathan Deepti , Dalton Barbra , McDonald Ken , Ward Deirdre
Published: May 2022

Aims

In Ireland, 8% of public cardiology consultants are female; this is the lowest proportion in Europe. We sought to understand perceptions amongst Irish trainees and consultants regarding aspects of working in cardiology in order to identify areas that can be targeted to improve gender equality.

Methods and Results

In September 2021, the Irish Cardiac Society distributed a questionnaire to trainees and consultants in the Republic and Northern Ireland. Ethical approval was obtained from the University College Dublin, Ireland. There were 94 respondents (50% male, 50% consultants) which equates to ∼30% of all trainees and consultants in all Ireland. Although females were more likely to be single, overall, they had additional child-care responsibilities compared with male counterparts. Despite 53% of the respondents preferring to work less than full time, 64% reported a perceived lack of support from their departments. Males were significantly more likely to go into procedural/high radiation sub-specialities. Bullying was reported by 53% of females. Almost 80% of females experienced sexism and 30% reported being overlooked for professional advancement based on their sex. Females also rated their career prospects lower than males. Key challenges for women were: sexism, maternity leave/child-care responsibilities, cardiology as a ‘boys club’ and lack of flexible training. There was interest from both males and females in a mentorship programme and support for women in leadership positions.

Conclusion

Discrimination including sexism, bullying, and equal opportunity for professional advancement are key aspects that need to be addressed to improve gender balance in cardiology within Ireland and Northern Ireland.
Paradoxical prolongation of QT interval during exercise in patients with hypertrophic cardiomyopathy: cellular mechanisms and implications for diastolic function
Authors: Coppini Raffaele , Beltrami Matteo , Doste Ruben , Bueno-Orovio Alfonso , Ferrantini Cecilia , Vitale Giulia , Pioner Josè Manuel , Santini Lorenzo , Argirò Alessia , Berteotti Martina , Mori Fabio , Marchionni Niccolò , Stefàno Pierluigi , Cerbai Elisabetta , Poggesi Corrado , Olivotto Iacopo
Published: May 2022

Aims

Ventricular cardiomyocytes from hypertrophic cardiomyopathy (HCM) patient hearts show prolonged action potential duration (APD), impaired intracellular Ca2+ homeostasis and abnormal electrical response to beta -adrenergic stimulation. We sought to determine whether this behaviour is associated with abnormal changes of repolarization during exercise and worsening of diastolic function, ultimately explaining the intolerance to exercise experienced by some patients without obstruction.

Methods and results

Non-obstructive HCM patients (178) and control subjects (81) underwent standard exercise testing, including exercise echocardiography. Ventricular myocytes were isolated from myocardial samples of 23 HCM and eight non-failing non-hypertrophic surgical patients. The APD shortening in response to high frequencies was maintained in HCM myocytes, while β-adrenergic stimulation unexpectedly prolonged APDs, ultimately leading to a lesser shortening of APDs in response to exercise. In HCM vs. control subjects, we observed a lesser shortening of QT interval at peak exercise (QTc: +27 ± 52 ms in HCM, −4 ± 50 ms in controls, P < 0.0001). In patients showing a marked QTc prolongation (>30 ms), the excessive shortening of the electrical diastolic period was linked with a limited increase of heart-rate and deterioration of diastolic function at peak effort.

Conclusions

Abnormal balance of Ca2+- and K+-currents in HCM cardiomyocytes determines insufficient APD and Ca2+-transient shortening with exercise. In HCM patients, exercise-induced QTc prolongation was associated with impaired diastolic reserve, contributing to the reduced exercise tolerance. Our results support the idea that severe electrical cardiomyocyte abnormalities underlie exercise intolerance in a subgroup of HCM patients without obstruction.
Evaluation of the atrial fibrillation better care pathway in the ENGAGE AF-TIMI 48 trial
Authors: Patel Siddharth M , Palazzolo Michael G , Murphy Sabina A , Antman Elliot M , Braunwald Eugene , Lanz Hans-Joachim , Lip Gregory Y H , Giugliano Robert P , Ruff Christian T
Published: May 2022

Aims

The Atrial fibrillation Better Care (ABC) pathway is endorsed by guidelines to improve care of patients with atrial fibrillation (AF). However, whether the benefit of ABC pathway-concordant care is consistent across anticoagulants remains unclear. We assessed the association between ABC-concordant care and outcomes in this post hoc analysis from the ENGAGE AF-TIMI 48 trial, which was reported prior to the initial description of the ABC pathway.

Methods and results

Patients were retrospectively classified as receiving ABC-concordant care based on optimal anticoagulation, adequate rate control, management of co-morbidities and lifestyle measures. Associations between ABC-concordance and outcomes were assessed with adjustment for components of the CHA2DS2-VASc and HAS-BLED scores. Of 20 926 patients, 7915 (37.8%) satisfied criteria of ABC-concordant care, which was associated with significantly lower incidence of stroke or systemic embolic event [stroke/SEE: hazard ratio (HRadj): 0.54; 95% confidence interval (CI): 0.47–0.63], major bleeding (HRadj 0.66; 95% CI: 0.58–0.75), major adverse cardiac events (HRadj 0.53; 95% CI: 0.48–0.58), primary net clinical outcome (composite of stroke/SEE, major bleeding or death; HRadj 0.61; 95% CI: 0.56–0.65), cardiovascular (CV) hospitalization (HRadj 0.78; 95% CI: 0.74–0.83), CV death (HRadj 0.52; 95% CI: 0.46–0.58), and all-cause mortality (HRadj 0.56; 95% CI: 0.51–0.62), P < 0.001 for each. These associations were qualitatively consistent for both edoxaban and warfarin and across patient subgroups.

Conclusion

Atrial fibrillation Better Care pathway-concordant care is associated with reductions across multiple CV endpoints and all-cause mortality, with benefit in edoxaban- and warfarin-treated patients and across patient subgroups. Increasing implementation of ABC-concordant care may improve clinical outcomes of patients with AF irrespective of anticoagulant.
Antibiotic prescribing for upper respiratory tract infections and acute bronchitis: a longitudinal analysis of general practitioner trainees
Authors: Baillie Emma J , Merlo Gregory , Magin Parker , Tapley Amanda , Mulquiney Katie J , Davis Joshua S , Fielding Alison , Davey Andrew , Holliday Elizabeth , Ball Jean , Spike Neil , FitzGerald Kristen , van Driel Mieke L
Published: May 2022

Background

Most antibiotic prescribing for upper respiratory tract infections (URTIs) and acute bronchitis is inappropriate. Substantive and sustained reductions in prescribing are needed to reduce antibiotic resistance. Prescribing habits develop early in clinicians’ careers. Hence, general practice (GP) trainees are an important group to target.

Objectives

We aimed to establish temporal trends in antibiotic prescribing for URTIs and acute bronchitis/bronchiolitis by Australian GP trainees (registrars).

Methods

A longitudinal analysis, 2010–2019, of the Registrars Clinical Encounters in Training (ReCEnT) dataset. In ReCEnT, registrars record clinical and educational content of 60 consecutive consultations, on 3 occasions, 6 monthly. Analyses were of new diagnoses of URTI and acute bronchitis/bronchiolitis, with the outcome variable a systemic antibiotic being prescribed. The independent variable of interest was year of prescribing (modelled as a continuous variable).

Results

28,372 diagnoses of URTI and 5,289 diagnoses of acute bronchitis/bronchiolitis were recorded by 2,839 registrars. Antibiotic prescribing for URTI decreased from 24% in 2010 to 12% in 2019. Prescribing for acute bronchitis/bronchiolitis decreased from 84% to 72%. “Year” was significantly, negatively associated with antibiotic prescribing for both URTI (odds ratio [OR] 0.90; 95% confidence interval [CI]: 0.88–0.93) and acute bronchitis/bronchiolitis (OR 0.92; 95% CI: 0.88–0.96) on multivariable analysis, with estimates representing the mean annual change.

Conclusions

GP registrars’ prescribing for URTI and acute bronchitis/bronchiolitis declined over the 10-year period. Prescribing for acute bronchitis/bronchiolitis, however, remains higher than recommended benchmarks. Continued education and programme-level antibiotic stewardship interventions are required to further reduce registrars’ antibiotic prescribing for acute bronchitis/bronchiolitis to appropriate levels.