bluuebunny/crossref_metadata_2025 huggingface dataset:
Copper Complexes of Benzoylacetone Bis-Thiosemicarbazones: Metal and Ligand Based Redox Reactivity
Authors: Bilyj Jessica K. , Harmer Jeffrey R. , Bernhardt Paul V.
Published: September 2020

Bis-thiosemicarbazones derived from the β-diketone benzoylacetone (H3banR, R=Me, Et, Ph) are potentially tetradentate N2S2 ligands whose coordination chemistry with copper is reported. In the absence of oxygen and in the presence of base they form anionic CuII complexes of the fully deprotonated ligands [CuII(banR)]–. Upon exposure to atmospheric oxygen they undergo a complex series of reactions leading to two types of products; one a ligand oxidised ketone complex [CuII(banRO)] and the other an unprecedented dimeric di-CuIII complex [(CuIII(banR))2] depending on the R substituent. Time-resolved UV-vis spectroscopy, cyclic voltammetry, spectroelectrochemistry, and electron paramagnetic resonance (EPR) spectroscopy have been used to identify intermediates on the way to stable products formed under both anaerobic and aerobic conditions. It is found that both ligand-centred and Cu-centred oxidation reactions are occurring in parallel leading to this unusually complicated mixture of products.
Underlying beliefs linked to public opinion about gene drive and pest-specific toxin for pest control
Authors: MacDonald Edith A. , Edwards Eric , Balanovic Jovana , Medvecky Fabien
Published: September 2020

Abstract
ContextDeveloping a new tool for wide-scale rat eradication is necessary for significant biodiversity gains. Underlying beliefs linked to public opinion can help guide policy makers to understand public concern and inform an effective discourse.
AimsWe investigated underlying beliefs linked to levels of support for a potentially disruptive tool, gene drive, compared with a traditional stepwise tool, aerial distribution of a new pest-specific toxin.
MethodsUsing the theory of planned behaviour, we surveyed (n=1200) a representative sample of New Zealanders to assess the level of support for the tool related to attitude, normative and control beliefs.
Key resultsAttitude (e.g. gene drive is good/bad and gene drive is risky/safe) and two norms (e.g. people like me and people in my household) were key contributors to level of support for gene drive. Behavioural beliefs (if scientific evidence can prove it works, concern there are unknown consequences, a humane way to rid New Zealand of rats, and gene drive goes against natural way of life) were also significant. For aerial distribution of a new pest-specific toxin, the same attitudes and normative beliefs identified for gene drive also contributed significantly to the model. Four behavioural beliefs, namely, aerial delivery could affect areas outside the target zones, if there is scientific evidence, and it is impossible to make a pest-specific toxin that would not harm our native wildlife were also significant. The impact either tool may have on biodiversity was not significant in either model.
ConclusionsDecision making about both gene drive (a disruptive technology) and aerial distribution of a pest-specific toxin (a stepwise technology) is primarily influenced by attitudes, with a few beliefs also influencing decision making. Novelty of the tool does not affect the underlying beliefs that are influencing levels of support.
ImplicationsPublic engagement that acknowledges and responds to these underlying beliefs, rather than a traditional campaign based on biodiversity and environmental gains, may be more effective at creating a constructive dialogue about if and how these tools should be used, and to avoid replicating the polarised debate about 1080.
The small GTPase MglA together with the TPR domain protein SgmX stimulates type IV pili formation in
M. xanthus
Authors: Potapova Anna , Carreira Luís Antonío Menezes , Søgaard-Andersen Lotte
Published: September 2020

Significance

Many bacteria move across surfaces using type IV pili (T4P). The piliation pattern varies between species; however, the underlying mechanisms governing these patterns remain largely unknown. Here, we demonstrate that in the rod-shaped
Myxococcus xanthus
cells, the unipolar formation of T4P at the leading cell pole is the result of stimulation by the small GTPase MglA together with the effector protein SgmX, while MglB, the cognate MglA GTPase activating protein (GAP) that localizes to the lagging cell pole, blocks this stimulation at the lagging pole due to its GAP activity. During reversals, MglA/SgmX and MglB switch polarity, laying the foundation for T4P formation at the new leading cell pole and inhibition of T4P formation at the former leading cell pole.
Hemolymph protease-5 links the melanization and Toll immune pathways in the tobacco hornworm,
Manduca sexta
Authors: Wang Yang , Yang Fan , Cao Xiaolong , Zou Zhen , Lu Zhiqiang , Kanost Michael R. , Jiang Haobo
Published: September 2020

Significance

Phenoloxidase-catalyzed melanization and Spätzle-triggered Toll signaling are critical innate immune responses of insects that are triggered by specific proteolysis. It has been unclear whether separate protease cascades or an integrated network of serine proteases coordinates these responses. Here we present evidence that hemolymph protease HP5 acts in pathways eliciting activation of both phenoloxidase and Spätzle-1 in
Manduca sexta
. HP5 has a unique specificity by cleaving proHP6 at His
112
, resulting in HP6 activation. CLIP proteases related to HP6 from other insect species, including
Drosophila
Persephone, share this activation site feature with proHP6, and therefore, HP5 orthologs in other species are candidates for key roles in regulating and integrating protease cascade pathways in innate immune responses.
Gold-based therapy: From past to present
Authors: Balfourier Alice , Kolosnjaj-Tabi Jelena , Luciani Nathalie , Carn Florent , Gazeau Florence
Published: September 2020

Despite an abundant literature on gold nanoparticles use for biomedicine, only a few of the gold-based nanodevices are currently tested in clinical trials, and none of them are approved by health agencies. Conversely, ionic gold has been used for decades to treat human rheumatoid arthritis and benefits from 70-y hindsight on medical use. With a view to open up new perspectives in gold nanoparticles research and medical use, we revisit here the literature on therapeutic gold salts. We first summarize the literature on gold salt pharmacokinetics, therapeutic effects, adverse reactions, and the present repurposing of these ancient drugs. Owing to these readings, we evidence the existence of a common metabolism of gold nanoparticles and gold ions and propose to use gold salts as a “shortcut” to assess the long-term effects of gold nanoparticles, such as their fate and toxicity, which remain challenging questions nowadays. Moreover, one of gold salts side effects (i.e., a blue discoloration of the skin exposed to light) leads us to propose a strategy to biosynthesize large gold nanoparticles from gold salts using light irradiation. These hypotheses, which will be further investigated in the near future, open up new avenues in the field of ionic gold and gold nanoparticles-based therapies.
CydDC functions as a cytoplasmic cystine reductase to sensitize
Escherichia coli
to oxidative stress and aminoglycosides
Authors: Mironov Alexander , Seregina Tatyana , Shatalin Konstantin , Nagornykh Maxim , Shakulov Rustem , Nudler Evgeny
Published: September 2020

Significance

The CydDC complex is involved in the assembly of cytochrome
bd
-I, a terminal oxidase of the respiratory chain required for growth under low oxygen conditions. It has been suggested that CydDC shuttles excessive
l
-cysteine from the cytoplasm to the periplasm, thereby maintaining bacterial redox homeostasis. Here, we demonstrate that the principle function of CydDC is in maintaining the reduced state of cytoplasmic
l
-cysteine, as opposed to exporting
l
-cysteine, thereby providing an important connection between sulfur metabolism, oxidative stress, and resistance to antibiotics. In particular, we establish the critical role of cytoplasmic
l
-cysteine in mediating the toxicity of aminoglycosides. Thus, understanding the mechanisms that control the bacterial redox state can lead to more effective strategies to counter bacterial resistance and tolerance.
Timing and structure of the Younger Dryas event and its underlying climate dynamics
Authors: Cheng Hai , Zhang Haiwei , Spötl Christoph , Baker Jonathan , Sinha Ashish , Li Hanying , Bartolomé Miguel , Moreno Ana , Kathayat Gayatri , Zhao Jingyao , Dong Xiyu , Li Youwei , Ning Youfeng , Jia Xue , Zong Baoyun , Ait Brahim Yassine , Pérez-Mejías Carlos , Cai Yanjun , Novello Valdir F. , Cruz Francisco W. , Severinghaus Jeffrey P. , An Zhisheng , Edwards R. Lawrence
Published: September 2020

Significance

The Younger Dryas (YD) was an ∼1,300-y period of extreme climate that dramatically reversed the course of global warming that brought the last Ice Age to a close. Understanding what mechanisms triggered and terminated this event remains enigmatic, but it is fundamental for gaining insights into the inner workings of Earth’s climate system. In this study, we used a combination of well-dated speleothem and ice-core records to pinpoint the timing of its onsets and terminations in various climatic regimes around the world. We show that the YD event occurred first at high northern latitudes and then propagated southward into the tropical monsoon belt through both atmospheric and oceanic processes, ultimately reaching Antarctica before reversing the course to its eventual termination.
Modeling the stability of polygonal patterns of vortices at the poles of Jupiter as revealed by the
Juno
spacecraft
Authors: Li Cheng , Ingersoll Andrew P. , Klipfel Alexandra P. , Brettle Harriet
Published: September 2020

Significance

Like good wine, scientific problems gain significance as they age. Regular patterns of vortices have been studied theoretically and observed in the laboratory since the 19th century, but never before in a planetary atmosphere, with the complicating effects of planetary rotation, spherical geometry, and horizontal convergence and divergence. Instruments on the
Juno
spacecraft have given us the sizes and speeds of the vortices, but a true understanding requires a numerical model that matches the observations and simulates the long-term stability of the patterns. We provide such a model here, but the work is not done. We will make further progress as
Juno
continues its observations of this fascinating phenomenon.
The primary step of biotin synthesis in mycobacteria
Authors: Hu Zhe , Cronan John E.
Published: September 2020

Significance

Biotin is an enzyme cofactor required for growth of mycobacteria, and the
Mycobacterium tuberculosis
biotin synthetic pathway has become a validated target for antitubercular compounds. Current pathway lacks information on synthesis of the pimelate moiety that provides 7 of the 10 biotin carbon atoms. We report the first step in mycobacterial pimelate synthesis parallels the pathway first reported in
Escherichia coli
, in which BioC catalyzed
O
-methylation of a malonyl-acyl carrier protein primer allows entry into fatty acid synthesis. The mycobacterial Tam proteins functionally replace the
E. coli
BioC protein, although these proteins are annotated as performing a different function Moreover,
tam
gene function is required for biotin synthesis by
Mycobacterium smegmatis
and its transcription is repressed by exogenous biotin.
Sexually dimorphic effects of forkhead box a2 (FOXA2) and uterine glands on decidualization and fetoplacental development
Authors: Dhakal Pramod , Kelleher Andrew M. , Behura Susanta K. , Spencer Thomas E.
Published: September 2020

Significance

Uterine glands play a critical role in embryo implantation and pregnancy establishment. Using mouse genetic models, we found that FOXA2-regulated genes in the uterine glands influence development of the decidua, as well as the placenta and fetus in a sex-dependent manner. These findings support the idea that uterine gland dysfunction affects placental and fetal growth with sexually dimorphic impacts on offspring adult health and disease.
AtFLL2, a member of the FLO2 gene family, affects the enlargement of leaves at the vegetative stage and facilitates the regulation of carbon metabolism and flow
Authors: Sato Nonoka , Kihira Miho , Matsushita Ryoko , Kaneko Chihiro , Ishii Yohei , Yin Yong-Gen , Kawachi Naoki , Teramura Hiroshi , Kusano Hiroaki , Shimada Hiroaki
Published: September 2020

Arabidopsis thaliana FLL2, a member of the FLO2 gene family, is expressed specifically in green leaves. The fll2 mutant showed significantly large rosette leaves and reduced the chlorophyll content. The sucrose content was significantly reduced. The glucose content was higher during the vegetative growth stage but decreased during the early reproductive growth stage. The amount of assimilated starch was lower than that in the wild type plant. The expression levels of genes involved in biosynthesis of sucrose and starch were largely altered. These results suggest that, in the fll2 mutant, a small amount of photosynthetic products was used for the biosynthesis of starch, and the products were supplied to promote intracellular growth of the source organs or for transport to the sink organs. These findings suggest that FLL2 is a factor affecting the expression level of genes involved in sugar metabolism, whose mutation caused a change in the assimilated products.

Abbreviations : DAS: days after sowing
Assessing the detectability of a stochastic gravitational wave background with LISA, using an excess of power approach
Authors: Karnesis N , Lilley M , Petiteau A
Published: September 2020

The laser interferometer space antenna will be the first gravitational wave observatory in space. It is scheduled to fly in the early 2030’s. LISA design predicts sensitivity levels that potentially enable the detection a stochastic gravitational wave background signal. This stochastic type of signal is a superposition of signatures from sources that cannot be resolved individually and which are of various types, each one contributing with a different spectral shape. In this work we present a fast methodology to assess the detectability of a stationary, Gaussian, and isotropic stochastic signal in a set of frequency bins, combining information from the available data channels. We derive an analytic expression of the Bayes factor between the instrumental noise-only and the signal plus instrumental noise models, that allows us to compute the detectability bounds of a given signal, as a function of frequency and prior knowledge on the instrumental noise spectrum.
Non-equilibrium chiral domain wall dynamics excited by transverse magnetic field pulses
Authors: Cho Jaehun , Kim Kyoung-Whan , Lee Myoung-Jae , Lee Hyeon-Jun , Kim June-Seo
Published: September 2020

Non-equilibrium domain wall dynamics on a perpendicularly magnetized nanowire manipulated by the transverse magnetic field pulse are numerically investigated. We systematically observe the large displacements of the chiral domain wall and the domain wall tilting angles generated by Dzyaloshinskii–Moriya interaction during the competition between the precession torque and the magnetic damping process. The magnetic-property-dependent domain wall displacements exhibit that the lower magnetic damping constants and Dzyaloshinskii–Moriya energy densities generate the longer transition times and the significant larger domain wall displacements for the non-equilibrium magnetization dynamics. Compare with the spin-polarized-current-driven domain wall dynamics, the transverse magnetic field pulses guarantee faster domain wall movements without Walker breakdown and lower energy consumptions because it is free from the serious Joule heating issue. Finally, we demonstrate successive chiral domain wall displacements, which are necessary to develop multilevel resistive memristors for next-generation artificial intelligent devices based on magnetic domain wall motions.
Observation of photonic spin-momentum locking due to coupling of achiral metamaterials and quantum dots
Authors: Yadav Ravindra Kumar , Liu Wenxiao , Indukuri S R K Chaitanya , Vasista Adarsh B , Kumar G V Pavan , Agarwal Girish S , Basu Jaydeep Kumar
Published: September 2020

Chiral interfaces provide a new platform to execute quantum control of light-matter interactions. One phenomenon which has emerged from engineering such nanophotonic interfaces is spin-momentum locking akin to similar reports in electronic topological materials and phases. While there are reports of spin-momentum locking with combination of chiral emitters and/or chiral metamaterials with directional far field excitation it is not readily observable with both achiral emitters and metamaterials. Here, we report the observation of photonic spin-momentum locking in the form of directional and chiral emission from achiral quantum dots (QDs) evanescently coupled to achiral hyperbolic metamaterials (HMM). Efficient coupling between QDs and the metamaterial leads to emergence of these photonic topological modes which can be detected in the far field. We provide theoretical explanation for the emergence of spin-momentum locking through rigorous modeling based on photon Green’s function where pseudo spin of light arises from coupling of QDs to evanescent modes of HMM.
Crystal structure and phase transition of TlReO4: a combined experimental and theoretical study
Authors: Mondal S , Vaitheeswaran G , Kennedy Brendan J , Chay Clarissa , Injac Sean , Errandonea Daniel
Published: September 2020

The present work describes a density-functional theory (DFT) study of TlReO4 in combination with powder x-ray diffraction experiments as a function of temperature and Raman measurements at ambient temperature. X-ray diffraction measurements reveal three different structures as a function of temperature. A monoclinic structure (space group P21/c) is observed at room temperature while two isostructural tetragonal structures (space group I41/a) are found at low- and high-temperature. In order to complement the experimental results first-principles DFT calculations were performed to compute the structural energy differences. From the total energies it is evident that the monoclinic structure has the lowest total energy when compared to the orthorhombic structure, which was originally proposed to be the structure at room temperature, which agrees with our experiments. The structural and vibrational properties of the low- and room-temperature phase of TlReO4 have been calculated using DFT. Inclusion of van der Waals correction to the standard DFT exchange correlation functional is found to improve the agreement with the observed structural and vibrational properties. The Born effective charge of these phases has also been studied which shows a combination of ionic and covalent nature, resembling metavalent bonding. Calculations of zone-center phonon frequencies lead to the symmetry assignment of previously reported low-temperature Raman modes. We have determined the frequencies of the eight infrared-active, 13 Raman-active and three silent modes of low-temperature TlReO4 along with 105 infrared-active and 108 Raman-active modes for room-temperature TlReO4. Phonons of these two phases of TlReO4 are mainly divided into three regions which are below 150 cm−1 due to vibration of whole crystal, 250 to 400 cm−1 due to wagging, scissoring, rocking and twisting and above 900 cm−1 due to stretching in ReO4 tetrahedron. The strongest infrared peak is associated to the internal asymmetric stretching of ReO4 whereas the strongest Raman peak is associated to the internal symmetric stretching of ReO4. We have also measured the room-temperature Raman spectra of monoclinic TlReO4 identifying up to 28 modes. This Raman spectrum has been interpreted by comparison with the previously reported Raman frequencies of the low-temperature phase and our calculated Raman frequencies of low- and room-temperature phases of TlReO4.
Tunable ferromagnetic ordering in phosphorus adsorbed ReS2 nanosheets
Authors: Li Junfu , Liao Zhongxin , Xia Baorui , Wang Tongtong , Gao Daqiang
Published: September 2020

Layered transition metal dichalcogenides (TMDs) are considered as promising materials for electronic, optoelectronic and spintronic devices due to their outstanding properties. Herein, based on rhenium disulfide (ReS2) nanosheets, we realized the intrinsic room temperature ferromagnetism with the adsorption of P adatoms (P-ReS2). Experiments indicate that the saturation magnetization (Ms
) can be tuned by the P ratios, where the maximum Ms
can reach up to 0.0174 emu g−1. Besides, density functional theory (DFT) calculation results demonstrate that the strong hybridization between Re d and P p orbitals is the main reason of inducing ferromagnetism in P-ReS2 system. This work provides a novel method to engineer the magnetism of TMDs, endowing them with the possibility of spintronic applications.
Magnetic field generation using single-plate targets driven by kJ-ns class laser
Authors: Kumar Deepak , Singh Sushil , Ahmed Hamad , Dudžák Roman , Dostál Jan , Chodukowski Tomasz , Giuffrida Lorenzo , Hadjisolomu Prokopis , Hodge Thomas , Juha Libor , Krouský Eduard , Krůs Miroslav , Li Yuanzhe , Lutoslawski Piotr , De Marco Massimo , Pfeifer Miroslav , Rusiniak Zofia , Skála Jiří , Ullschmeid Jiří , Pisarczyk Tadeusz , Borghesi Marco , Kar Satyabrata
Published: September 2020

Strong magnetic fields of upto 20 T, corresponding to a current of tens of kA were produced in a coil connected to a single-plate of cm2 area irradiated by a kJ-ns laser pulse. The use of such macroscopic plates protects the coil from plasma debris, while maintaining a strong magnetic field for a time-scale much longer than the laser pulse duration. By correlating the measured magnetic field in the coil to the number of electrons emitted from the interaction zone, we deduce that the target capacitance is enhanced by two orders of magnitude because of the plasma sheath in the proximity of the focal spot. The particle-in-cell simulation illustrates the dynamics of sheath potential and current flow through the coil to ground, thus closing the circuit due to the escape of laser-produced hot electrons from the target.
Distribution of inception times in repetitive pulsed discharges in synthetic air
Authors: Mirpour S , Martinez A , Teunissen J , Ebert U , Nijdam S
Published: September 2020

Knowing which processes and species are responsible for discharge inception is important for being able to speed up, delay, or completely avoid it. We study discharge inception in 500 mbar synthetic air by applying 10 ms long 17 kV pulses with a repetition frequency of 2 Hz to a pin-to-plate electrode geometry with a gap length of 6 cm. We record inception times for hundreds of pulses by measuring the time delay between the rising edge of the high-voltage (HV) pulse and the signal from a photo-multiplier tube. Three characteristic time scales for inception are observed: (1) 20 ns, (2) 25 μs, and (3) 125 μs. To investigate the underlying processes, we apply a low-voltage (LV) pulse in between the HV pulses. These LV pulses can speed up or delay discharge inception, and our results suggest that the three time scales correspond to: (1) free electrons or electron detachment from negative ions close to the electrode, (2) a process that liberates electrons from (quasi)-neutrals, and (3) the drift of an elevated density of negative ions to the ionization zone. However, each of these explanations has its caveats, which we discuss. We present a theoretical analysis of the distribution of inception times, and perform particle simulations in the experimental discharge geometry. Some of the observed phenomena can be explained by these approaches, but a surprizing number of open questions remain.
Nylon/Ag fiber sensor for real-time damage monitoring of composites subjected to dynamic loading
Authors: Qureshi Y , Tarfaoui M , Benyahia H , Lafdi K K , Lafdi K
Published: September 2020

In this article, the goal is to monitor the deformation and damage behavior of composites in real-time using a Nylon/Ag fiber sensor when subjected to dynamic loading. Composite samples are integrated with Nylon/Ag fiber sensors at distinct locations and directions between the plies. Then, these samples are experimentally impacted with low-velocity impact using the Taylor Cannon Gun apparatus at three different velocities i.e. 2.5 m s−1, 3 m s−1, and 6.5 m s−1, respectively. These three sets of tests are conducted to determine the detection performance of the Nylon/Ag fiber sensor when the composite sample experiences no damage, some microdamage, and overall breakage. Besides, the fiber sensor placed in each position showed distinct electrical behavior in all three tests and detected the deformation, damage initiation, quantification, identification, and damage propagation. The results confirmed the ability of the fiber sensor to monitor and identify the mechanical deformation during dynamic loading and showed that the sensor can be used as a flexible sensor reinforcement in composites for in-situ monitoring as well.
A dynamic strain-based quench-detection method in an LTS sextupole magnet during excitation and quench
Authors: Gao Peifeng , Guan Mingzhi , Xin Canjie
Published: September 2020

The dynamic strain characteristics and responses of a low-temperature superconducting (LTS) magnet during excitation and a quench are investigated in the present work. For the strain measurements, strain gauges in the form of a half-bridge circuit comprising cryogenic strain gauges and their dummy resistances are embedded directly within the superconducting magnet structure. A wireless high-speed data acquisition system with a resolution of 1 ms is also used to obtain the strain history of the LTS magnet during operation. The dynamic strain induced by thermal or mechanical disturbances is detected promptly and compared with the transport current and temperature signals recorded during a quench. This indicates that the dynamic strain measured in the LTS magnet can capture a quench feature in a timely manner. For a better understanding of the dynamic strain histories in the magnet, the dynamic strain signals are subjected to spectral analysis during the excitation and pre- and post-quench processes. It is shown originally that several spectral peaks on strain measured are always observed at the onset of a quench. Thus, the dynamic strain characteristics and responses provide a evaluation means of superconducting magnet.
Experimental implementation of arbitrary entangled operations
Authors: Hong Seongjin , Park Chang Hoon , Choi Yeon-Ho , Kim Yong-Su , Cho Young-Wook , Oh Kyunghwan , Lim Hyang-Tag
Published: September 2020

Quantum entanglement lies at the heart of quantum mechanics in both fundamental and practical aspects. The entanglement of quantum states has been studied widely both theoretically and experimentally, however, the entanglement of operators has not been studied much experimentally in spite of its importance. Here, we propose a scheme to realize arbitrary entangled operations based on a coherent superposition of local operations with a non-zero probability of failure. Then, we experimentally implement several intriguing two-qubit entangled operations in photonic systems. We also discuss the generalization of our scheme to extend the number of superposed operations and the number of qubits. Due to the simplicity of our scheme, we believe that it can reduce the complexity or required resources of the quantum circuits and provide insights to investigate properties of entangled operations.
Quantum device fine-tuning using unsupervised embedding learning
Authors: van Esbroeck N M , Lennon D T , Moon H , Nguyen V , Vigneau F , Camenzind L C , Yu L , Zumbühl D M , Briggs G A D , Sejdinovic D , Ares N
Published: September 2020

Quantum devices with a large number of gate electrodes allow for precise control of device parameters. This capability is hard to fully exploit due to the complex dependence of these parameters on applied gate voltages. We experimentally demonstrate an algorithm capable of fine-tuning several device parameters at once. The algorithm acquires a measurement and assigns it a score using a variational auto-encoder. Gate voltage settings are set to optimize this score in real-time in an unsupervised fashion. We report fine-tuning times of a double quantum dot device within approximately 40 min.
Emergent pattern formation of active magnetic suspensions in an external field
Authors: Koessel Fabian R , Jabbari-Farouji Sara
Published: September 2020

We study collective self-organization of weakly magnetic active suspensions in a uniform external field by analyzing a mesoscopic continuum model that we have recently developed. Our model is based on a Smoluchowski equation for a particle probability density function in an alignment field coupled to a mean-field description of the flow arising from the activity and the alignment torque. Performing linear stability analysis of the Smoluchowski equation and the resulting orientational moment equations combined with non-linear 3D simulations, we provide a comprehensive picture of instability patterns as a function of strengths of activity and magnetic field. For sufficiently high activity and moderate magnetic field strengths, the competition between the activity-induced flow and external magnetic torque renders a homogeneous polar steady state unstable. As a result, four distinct dynamical patterns of collective motion emerge. The instability patterns for pushers include traveling sheets governed by bend-twist instabilities and dynamical aggregates. For pullers, finite-sized and system spanning pillar-like concentrated regions predominated by splay deformations emerge which migrate in the field direction. Notably, at very strong magnetic fields, we observe a reentrant hydrodynamic stability of the polar steady state.
Cold-hot coupled waves in a flowing magnetized plasma
Authors: Uk Lee Min , Ji Jeong-Young , Yun Gunsu S.
Published: September 2020

Nonlinear coupling of cold and hot waves in a flowing magnetized plasma is analyzed with the Vlasov equation. An analytical solution is obtained for cold waves of a small amplitude (weak flow) and a long wavelength. The distribution function is obtained by integrating the kinetic equation along a perturbed phase-space trajectory for a time-varying plasma flow. The kinetic description presents a generalized dispersion relation that involves resonances depending on cold and hot wave dispersions. Coherent fluid motion leads to radiation peaks in addition to the cyclotron harmonics, where the wavenumber of the cold wave determines the peak frequencies. The peaks appear narrow when the wave propagates perpendicular to the time-averaged flow while they become broad due to the Doppler effect when the wave propagates parallel to the flow. Fully kinetic particle-in-cell simulations corroborate the theoretical predictions. The dispersion relation and resulting wave spectra provide information about plasma parameters and flow properties.
Quantitative analysis of the Schottky interface of reduced graphene oxide Schottky diodes
Authors: Aodah Souad , Bano N , Hussain I , AlSalhi Mohamad S
Published: September 2020

A Schottky contact is greatly vital for electronic devices; therefore, a quantitative analysis of the Schottky interface is important in realizing a high-performance Schottky diode. In this study, we fabricate an r-GO-based Schottky diode and elucidate the charge traps in r-GO by analyzing the current–voltage characteristics. The conduction becomes space charge limited (at high voltage) because of these traps. The trap energy and concentration were calculated as ∼0.20 ± 0.02 eV and 2.11 × 1015 cm−3, respectively. Quantitative information about charge traps will help in the fabrication of high-quality r-GO-based electronic devices. The trap density is the core challenge for the material community; therefore, controlling the traps is essential in improving the performance of r-GO-based electronic devices. We believe that the quantitative analysis of the Schottky interface could be beneficial for the improvement of the charge transport in r-GO-based electronic devices.
The Dark Money Subsidy? Tax Policy and Donations to Section 501(c)(4) Organizations
Authors: Galle Brian
Published: September 2020

This article presents the first empirical examination of giving to §501(c)(4) organizations, which have recently become important players in U.S. politics. Unlike gifts to charity, donations to a 501(c)(4) are not legally deductible. Yet, gifts to c(4) organizations are highly elastic to the after-tax price of charitable giving. At the lower end of the observed tax price range, c(4) giving falls with tax price, consistent with the hypothesis that giving to c(3) and c(4) organizations are substitutes. Over the top quarter of the distribution of tax price, however, gifts to c(4) organizations are negatively correlated with the after-tax price of giving to charity. That is, donors appear to respond as though the deduction subsidized their gift to a c(4). Donor responses to benefits for which they are not eligible may reflect the low salience of legal limitations or deliberate overclaiming. These results imply subsidies for charity can crowd out or in donations to c(4) organizations, with potential implications for U.S. politics. I cannot observe whether donors claim tax deductions for ineligible gifts, so the net results for the Treasury are unclear.
GRaSP: a graph-based residue neighborhood strategy to predict binding sites
Authors: Santana Charles A , Silveira Sabrina de A , Moraes João P A , Izidoro Sandro C , de Melo-Minardi Raquel C , Ribeiro António J M , Tyzack Jonathan D , Borkakoti Neera , Thornton Janet M
Published: September 2020

Motivation

The discovery of protein–ligand-binding sites is a major step for elucidating protein function and for investigating new functional roles. Detecting protein–ligand-binding sites experimentally is time-consuming and expensive. Thus, a variety of in silico methods to detect and predict binding sites was proposed as they can be scalable, fast and present low cost.

Results

We proposed Graph-based Residue neighborhood Strategy to Predict binding sites (GRaSP), a novel residue centric and scalable method to predict ligand-binding site residues. It is based on a supervised learning strategy that models the residue environment as a graph at the atomic level. Results show that GRaSP made compatible or superior predictions when compared with methods described in the literature. GRaSP outperformed six other residue-centric methods, including the one considered as state-of-the-art. Also, our method achieved better results than the method from CAMEO independent assessment. GRaSP ranked second when compared with five state-of-the-art pocket-centric methods, which we consider a significant result, as it was not devised to predict pockets. Finally, our method proved scalable as it took 10–20 s on average to predict the binding site for a protein complex whereas the state-of-the-art residue-centric method takes 2–5 h on average.

Availability and implementation

The source code and datasets are available at https://github.com/charles-abreu/GRaSP.

Supplementary information

Supplementary data are available at Bioinformatics online.
methylclock: a Bioconductor package to estimate DNA methylation age
Authors: Pelegí-Sisó Dolors , de Prado Paula , Ronkainen Justiina , Bustamante Mariona , González Juan R
Published: September 2020

Motivation

Ageing is a biological and psychosocial process related to diseases and mortality. It correlates with changes in DNA methylation (DNAm) in all human tissues. Therefore, epigenetic markers can be used to estimate biological age using DNAm profiling across tissues.

Results

We developed a Bioconductor package that allows computation of several existing DNAm adult/childhood and gestational age clocks. Functions to visualize the DNAm age prediction versus chronological age and the correlation between DNAm clocks are also available as well as other features, such as missing data imputation of cell types’ estimates, that are required for DNAm age clocks.

Availability and implementation

https://github.com/isglobal-brge/methylclock.

Supplementary information

Supplementary data are available at Bioinformatics online.
Bayesian analysis of longitudinal and multidimensional functional data
Authors: Shamshoian John , Şentürk Damla , Jeste Shafali , Telesca Donatello
Published: September 2020

Multi-dimensional functional data arises in numerous modern scientific experimental and observational studies. In this article, we focus on longitudinal functional data, a structured form of multidimensional functional data. Operating within a longitudinal functional framework we aim to capture low dimensional interpretable features. We propose a computationally efficient nonparametric Bayesian method to simultaneously smooth observed data, estimate conditional functional means and functional covariance surfaces. Statistical inference is based on Monte Carlo samples from the posterior measure through adaptive blocked Gibbs sampling. Several operative characteristics associated with the proposed modeling framework are assessed comparatively in a simulated environment. We illustrate the application of our work in two case studies. The first case study involves age-specific fertility collected over time for various countries. The second case study is an implicit learning experiment in children with autism spectrum disorder.
Top–Down Attentional Modulation in Human Frontal Cortex: Differential Engagement during External and Internal Attention
Authors: Kam Julia W Y , Helfrich Randolph F , Solbakk Anne-Kristin , Endestad Tor , Larsson Pål G , Lin Jack J , Knight Robert T
Published: September 2020

Decades of electrophysiological research on top–down control converge on the role of the lateral frontal cortex in facilitating attention to behaviorally relevant external inputs. However, the involvement of frontal cortex in the top–down control of attention directed to the external versus internal environment remains poorly understood. To address this, we recorded intracranial electrocorticography while subjects directed their attention externally to tones and responded to infrequent target tones, or internally to their own thoughts while ignoring the tones. Our analyses focused on frontal and temporal cortices. We first computed the target effect, as indexed by the difference in high frequency activity (70–150 Hz) between target and standard tones. Importantly, we then compared the target effect between external and internal attention, reflecting a top–down attentional effect elicited by task demands, in each region of interest. Both frontal and temporal cortices showed target effects during external and internal attention, suggesting this effect is present irrespective of attention states. However, only the frontal cortex showed an enhanced target effect during external relative to internal attention. These findings provide electrophysiological evidence for top–down attentional modulation in the lateral frontal cortex, revealing preferential engagement with external attention.
DNA Methylation and Immune Cell Markers Demonstrate Evidence of Accelerated Aging in Patients with Chronic Hepatitis B Virus or Hepatitis C Virus, with or without Human Immunodeficienct Virus Co-infection
Authors: Gindin Yevgeniy , Gaggar Anuj , Lok Anna S , Janssen Harry L A , Ferrari Carlo , Subramanian G Mani , Jiang Zhaoshi , Masur Henry , Emmanuel Benjamin , Poonia Bhawna , Kottilil Shyam
Published: September 2020

Background

Several chronic diseases accelerate biological aging. We investigated age acceleration and the association between peripheral blood DNA methylation (DNAm) and immune cell markers in patients chronically infected with the hepatitis B virus (HBV) or the hepatitis C virus (HCV) with and without human immunodeficiency virus (HIV) co-infection.

Methods

Age acceleration was measured as the difference between epigenetic age (Horvath clock) and chronological age. The immune marker model of age acceleration was developed using Elastic Net regression to select both the immune markers and their associated weights in the final linear model.

Results

Patients with chronic HBV (n = 51) had a significantly higher median epigenetic age compared to chronological age (age accelerated) (P < .001). In patients with chronic HCV infection (n = 63), age acceleration was associated with liver fibrosis as assessed by histology (P < .05), or presence of HIV co-infection (P < .05), but not HCV mono-infection. Age acceleration defined by immune markers was concordant with age acceleration by DNA methylation (correlation coefficient = .59 in HBV; P = .0025). One-year treatment of HBV patients with nucleoside therapy was associated with a modest reduction in age acceleration, as measured using the immune marker model (−.65 years, P = .018).

Conclusion

Our findings suggest that patients with chronic viral hepatitis have accelerated epigenetic aging, that immune markers define biological age, and have the potential to assess the effects of therapeutic intervention on age acceleration.
Private Set Operations Over Encrypted Cloud Dataset and Applications
Authors: Rafiee Mojtaba , Khazaei Shahram
Published: September 2020

We introduce the notion of private set operations (PSO) as a symmetric-key primitive in the cloud scenario, where a client securely outsources his dataset to a cloud service provider and later privately issues queries in the form of common set operations. We define a syntax and security notion for PSO and propose a general construction that satisfies it. There are two main ingredients to our PSO scheme: an adjustable join (Adjoin) scheme (MIT-CSAIL-TR-2012-006 (2012) Cryptographic treatment of CryptDB’s adjustable join. http://people.csail.mit.edu/nickolai/papers/popa-join-tr.pdf) and a tuple set (TSet) scheme (Cash, D., Jarecki, S., Jutla, C. S., Krawczyk, H., Rosu, M.-C., and Steiner, M. (2013) Highly-Scalable Searchable Symmetric Encryption With Support for Boolean Queries. 33rd Annual Cryptology Conf., Santa Barbara, CA, August 18–22, pp. 353–373. Springer, Berlin, Heidelberg). We also propose an Adjoin construction that is substantially more efficient (in computation and storage) than the previous ones (Mironov, I., Segev, G., and Shahaf, I. (2017) Strengthening the Security of Encrypted Databases: Non-Transitive Joins. 15th Int. Conf., TCC 2017, Baltimore, MD, USA, November 12–15, pp. 631–661. Springer, Cham) due to the hardness assumption that we rely on, while retaining the same security notion. The proposed PSO scheme can be used to perform join queries on encrypted databases without revealing the duplicate patterns in the unqueried columns, which is inherent to an Adjoin scheme. In addition, we also show that the PSO scheme can be used to perform Boolean search queries on a collection of encrypted documents. We also provide standard security proofs for our constructions and present detailed efficiency evaluation and compare them with well-known previous ones.
A checklist recipe: making species data open and FAIR
Authors: Reyserhove Lien , Desmet Peter , Oldoni Damiano , Adriaens Tim , Strubbe Diederik , Davis Amy J S , Vanderhoeven Sonia , Verloove Filip , Groom Quentin
Published: September 2020

Species checklists are a crucial source of information for research and policy. Unfortunately, many traditional species checklists vary wildly in their content, format, availability and maintenance. The fact that these are not open, findable, accessible, interoperable and reusable (FAIR) severely hampers fast and efficient information flow to policy and decision-making that are required to tackle the current biodiversity crisis. Here, we propose a reproducible, semi-automated workflow to transform traditional checklist data into a FAIR and open species registry. We showcase our workflow by applying it to the publication of the Manual of Alien Plants, a species checklist specifically developed for the Tracking Invasive Alien Species (TrIAS) project. Our approach combines source data management, reproducible data transformation to Darwin Core using R, version control, data documentation and publication to the Global Biodiversity Information Facility (GBIF). This checklist publication workflow is openly available for data holders and applicable to species registries varying in thematic, taxonomic or geographical scope and could serve as an important tool to open up research and strengthen environmental decision-making.
Multimodality imaging in valvular heart disease: how to use state-of-the-art technology in daily practice
Authors: Reid Anna , Blanke Philipp , Bax Jeroen J , Leipsic Jonathon
Published: September 2020

Our understanding of the complexities of valvular heart disease (VHD) has evolved in recent years, primarily because of the increased use of multimodality imaging (MMI). Whilst echocardiography remains the primary imaging technique, the contemporary evaluation of patients with VHD requires comprehensive analysis of the mechanism of valvular dysfunction, accurate quantification of severity, and active exclusion extravalvular consequences. Furthermore, advances in surgical and percutaneous therapies have driven the need for meticulous multimodality imaging to aid in patient and procedural selection. Fundamental decision-making regarding whom, when, and how to treat patients with VHD has become more complex. There has been rapid technological advancement in MMI; many techniques are now available in routine clinical practice, and their integration into has the potential to truly individualize management strategies. This review provides an overview of the current evidence for the use of MMI in VHD, and how various techniques within each modality can be used practically to answer clinical conundrums.
The contribution of employment and working conditions to occupational inequalities in non-communicable diseases in Europe
Authors: McNamara Courtney L , Toch-Marquardt Marlen , Albani Viviana , Eikemo Terje A , Bambra Clare
Published: September 2020

Background

Social inequalities in non-communicable diseases (NCDs) are evident across all European regions. Employment and working conditions are important determinants of NCDs, however, few comparative studies have examined how these conditions contribute to health inequalities. This study therefore examines the association of non-standard employment and poor working conditions with occupational inequalities in multiple NCDs and whether there are differences by gender and across European regions.

Methods

We used cross-sectional data from 20 European countries for women and men aged 25–75 (n = 19 876), from round 7 of the European Social Survey. Data were analyzed for self-rated health (SRH) and 9 NCDs: heart/circulatory problems, high blood pressure, arm/hand pain, breathing problems, diabetes, severe headaches, cancer, obesity and depression. We used logistic regression models, stratified by gender, and adjusted rate ratios to examine whether occupational inequalities in NCDs were reduced after adjusting for non-standard employment and poor working conditions, across European regions.

Results

After adjustment, occupational inequalities were significantly reduced across all regions of Europe. Reductions were particularly large among the lowest occupational group and for poor-SRH, depression and obesity. For these conditions, reductions were in the range of 60–99%.

Conclusions

Employment and working conditions are important determinants of occupational inequalities in NCDs. Labour market regulations should therefore be considered in the formulation of NCD prevention strategies.