bluuebunny/crossref_metadata_2025 huggingface dataset:
Glycomic analysis of host response reveals high mannose as a key mediator of influenza severity
Authors: Heindel Daniel W. , Koppolu Sujeethraj , Zhang Yue , Kasper Brian , Meche Lawrence , Vaiana Christopher A. , Bissel Stephanie J. , Carter Chalise E. , Kelvin Alyson A. , Elaish Mohamed , Lopez-Orozco Joaquin , Zhang Bin , Zhou Bin , Chou Tsui-Wen , Lashua Lauren , Hobman Tom C. , Ross Ted M. , Ghedin Elodie , Mahal Lara K.
Published: October 2020

Significance

Influenza virus infection causes a range of outcomes from mild illness to death. The molecular mechanisms leading to these differential host responses are currently unknown. Herein, we identify the induction of high mannose, a glycan epitope, as a key mediator of severe disease outcome. We propose a mechanism in which activation of the unfolded protein response (UPR) upon influenza virus infection induces cell surface high mannose, which is then recognized by the innate immune lectin MBL2, activating the complement cascade and leading to subsequent inflammation. This work is the first to systematically study host glycomic changes in response to influenza virus infection, identifying high mannose as a key feature of differential host response.
Trapped topoisomerase II initiates formation of de novo duplications via the nonhomologous end-joining pathway in yeast
Authors: Stantial Nicole , Rogojina Anna , Gilbertson Matthew , Sun Yilun , Miles Hannah , Shaltz Samantha , Berger James , Nitiss Karin C. , Jinks-Robertson Sue , Nitiss John L.
Published: October 2020

Significance

Transcription and replication of DNA create topological problems that are resolved by topoisomerases. These enzymes nick DNA strands to allow strand passage and then reseal the broken DNA to restore its integrity. Topoisomerase II (Top2) nicks complementary DNA strands to create double-strand break (DSB) intermediates that can be stabilized by chemotherapeutic drugs and are toxic if not repaired. We identified a mutant form of yeast Top2 that forms stabilized cleavage intermediates in the absence of drugs. Overexpression of the mutant Top2 was associated with a unique mutation signature in which small, unique segments of DNA are duplicated. These de novo duplications required the nonhomologous end-joining pathway of DSB repair, and their Top2 dependence has clinical and evolutionary implications.
p31
comet
promotes homologous recombination by inactivating REV7 through the TRIP13 ATPase
Authors: Sarangi Prabha , Clairmont Connor S. , Galli Lucas D. , Moreau Lisa A. , D’Andrea Alan D.
Published: October 2020

Significance

HORMA domain proteins play integral roles in several cellular processes such as mitosis, meiosis, and DNA repair. Intriguingly, despite their disparate cellular functions, the HORMA proteins MAD2, REV7, and HORMAD1/2 are controlled by a common regulatory circuit involving the ATPase TRIP13. Here, we extend this paradigm, showing that the adaptor protein p31
comet
, known to mediate TRIP13 activity toward MAD2, is also involved in REV7 regulation. Notably, TRIP13 is overexpressed in many cancers, and TRIP13 hyperactivity inactivates the REV7-Shieldin complex, a critical determinant of sensitivity to Poly-ADP-ribose polymerase (PARP) inhibitors, causing resistance to this clinically important class of drugs. In this work, we present evidence that p31
comet
overexpression is also common in cancer and largely mirrors the effects of TRIP13 overexpression.
Identify potent SARS-CoV-2 main protease inhibitors via accelerated free energy perturbation-based virtual screening of existing drugs
Authors: Li Zhe , Li Xin , Huang Yi-You , Wu Yaoxing , Liu Runduo , Zhou Lingli , Lin Yuxi , Wu Deyan , Zhang Lei , Liu Hao , Xu Ximing , Yu Kunqian , Zhang Yuxia , Cui Jun , Zhan Chang-Guo , Wang Xin , Luo Hai-Bin
Published: October 2020

Significance

Drug repurposing effort for treatment of a new disease, such as COVID-19, usually starts from a virtual screening of existing drugs, followed by experimental validation, but the actual hit rate is generally rather low with traditional computational methods. It has been demonstrated that a new virtual screening approach with accelerated free energy perturbation-based absolute binding free energy (FEP-ABFE) predictions can reach an unprecedentedly high hit rate, leading to successful identification of 15 potent inhibitors of SARS-CoV-2 main protease (M
pro
) from 25 computationally selected drugs under a threshold of K
i
= 4 μM. The outcomes of this study are valuable for not only drug repurposing to treat COVID-19 but also demonstrating the promising potential of the FEP-ABFE prediction-based virtual screening approach.
Vimentin filaments drive migratory persistence in polyploidal cancer cells
Authors: Xuan Botai , Ghosh Deepraj , Jiang Joy , Shao Rachelle , Dawson Michelle R.
Published: October 2020

Significance

Polyploidal cells have been shown to correlate with poor patient outcomes in the clinic, as well as with increased chemoresistance and tumorigenicity. They are also implicated in cancer aggression due to their highly migratory phenotype. There is a serious lack of understanding of the underlying biophysical mechanisms that drive their increased migration. Here we address this lack of knowledge and show that vimentin is key to their migratory phenotype, especially in the context of cellular jamming. We also propose a therapeutic avenue that can be adapted in the clinic to mitigate the deleterious effects of these giant cancer cells on patient outcomes.
Human disturbance increases trophic niche overlap in terrestrial carnivore communities
Authors: Manlick Philip J. , Pauli Jonathan N.
Published: October 2020

Significance

Niche theory posits that species must limit overlap in the use of space, time, or resources to minimize competition. However, human disturbances are rapidly altering ecosystems with uncertain consequences for niche partitioning. Dietary niche partitioning is the primary way many species limit interspecific competition, and it is particularly important for carnivores because diet overlap can trigger interference competition and interspecific killing. We used stable isotope analyses to examine carnivore diets across the Great Lakes region in the United States and show that carnivores inhabiting disturbed ecosystems consume more human foods, leading to significant increases in both niche breadth and dietary niche overlap among competing species. These results suggest that carnivores in human-dominated landscapes experience significant interspecific competition and conflict due to the consumption of human food subsidies.
EXO70D isoforms mediate selective autophagic degradation of type-A ARR proteins to regulate cytokinin sensitivity
Authors: Acheampong Atiako Kwame , Shanks Carly , Cheng Chia-Yi , Schaller G. Eric , Dagdas Yasin , Kieber Joseph J.
Published: October 2020

Significance

One of the central regulators of plant growth and development is the phytohormone cytokinin. Likewise, it has become increasingly apparent that autophagy is a critical regulatory process in both plants and animals. Our work provides a mechanistic link between these regulatory processes, demonstrating that autophagy can fine-tune cytokinin perception by modulating the level of the type-A ARRs, which negatively regulate the cellular response to cytokinin. Further, our work sheds light on the mechanism of selective autophagy and on how a particular cargo is targeted for autophagic degradation by a novel autophagy receptor belonging to the EXO70D gene family.
Annually resolved Atlantic sea surface temperature variability over the past 2,900 y
Authors: Lapointe Francois , Bradley Raymond S. , Francus Pierre , Balascio Nicholas L. , Abbott Mark B. , Stoner Joseph S. , St-Onge Guillaume , De Coninck Arnaud , Labarre Thibault
Published: October 2020

Significance

Atlantic multidecadal sea surface temperature variability (AMV) strongly influences the Northern Hemisphere’s climate, including the Arctic. Here using a well-dated annually laminated lake sediment core, we show that the AMV exerts a strong influence on High-Arctic climate during the instrumental period (past ∼150 y) through atmospheric teleconnection. This highly resolved climate archive is then used to produce the first AMV reconstruction spanning the last ∼3 millennia at unprecedented temporal resolution. Our terrestrial record is significantly correlated to several sea surface temperature proxies in the Atlantic, highlighting the reliability of this record as an annual tracer of the AMV. The results show that the current warmth in sea surface temperature is unseen in the context of the past ∼3 millennia.
Physics successfully implements Lagrange multiplier optimization
Authors: Vadlamani Sri Krishna , Xiao Tianyao Patrick , Yablonovitch Eli
Published: October 2020

Significance

All through human civilization, optimization has played a major role, from aerodynamics to airline scheduling, delivery routing, and telecommunications decoding. Optimization is receiving increasing attention, since it is central to today’s artificial intelligence. All of these optimization problems are among the hardest for human or machine to solve. It has been overlooked that physics itself does optimization in the normal evolution of dynamical systems, such as seeking out the minimum energy state. We show that among such physics principles, the idea of minimum power dissipation, also called the Principle of Minimum Entropy Generation, appears to be the most useful, since it can be readily implemented in electrical or optical circuits.
The inner membrane protein YhdP modulates the rate of anterograde phospholipid flow in
Escherichia coli
Authors: Grimm Jacqueline , Shi Handuo , Wang Wei , Mitchell Angela M. , Wingreen Ned S. , Huang Kerwyn Casey , Silhavy Thomas J.
Published: October 2020

Significance

The outer membrane (OM) of Gram-negative bacteria serves as a barrier that protects cells from harmful chemical compounds, including many antibiotics. Understanding how bacteria build this barrier is an important step in engineering strategies to circumvent it. A long-standing mystery in the field is how phospholipids (PLs) are transported from the inner membrane (IM) to the OM. We previously discovered that a mutation in the gene
mlaA
that causes rapid flow of PLs to the OM, eventually resulting in IM rupture. Here, we found that deletion of the gene
yhdP
delayed cell death in the
mlaA
mutant by slowing flow of PLs to the OM. These findings reveal a high-flux diffusive pathway for PL transport in Gram-negative bacteria modulated by YhdP.
The loss of inflection as grammar complication
Authors: Sims-Williams Helen , Enger Hans-Olav
Published: October 2020

The loss of inflectional categories is often thought of as a type of simplification. In this paper we present a survey of phenomena involving the reduction of adjective agreement in Scandinavian, using examples from Norwegian, and discuss their diachronic origins, including a new account of the development of indeclinability in adjectives such askry‘proud’. These examples each involve lexically restricted non-canonical inflection – syncretism, defectiveness, overdifferentiation and periphrasis – in particular paradigm cells or syntactic environments. They show that the loss of inflection does not necessarily simplify grammar, and in some cases, can increase grammatical complexity by adding lexical exceptions to general rules. This excludes simplification as the motivation, even if it is the eventual result. We argue from these historical developments that speakers are liable to analyse idiosyncratic patterns of inflection as lexically specified, even where more general (but perhaps more abstract) alternatives are possible. Thus speakers do not always operate with a maximally elegant, reductionist approach to inflection classes.
Explicitation and cognitive load in simultaneous interpreting
Authors: Gumul Ewa
Published: October 2020

This article investigates the correlation between explicitation and increased cognitive load in simultaneous interpreting by trainee interpreters. It has been hypothesised, on the one hand, that certain explicitating shifts in simultaneous interpreting may be caused by increased cognitive load and they may be performed in an attempt to mask processing problems; and, on the other, that performing explicitating shifts may lead to increased cognitive load and trigger processing problems. The study triangulates product analysis (manual comparison of source and target texts) with process analysis (retrospective protocols of the participants). In the product the correlation between the occurrence of explicitating shifts and increased cognitive load is sought by identifying problem indicators in the form of three types of disfluency: hesitation markers, false starts and anomalous pauses exceeding two seconds (performance measure). Retrospective protocols are analysed in search of reports of explicitating shifts and/or increased cognitive load experienced and/or the cognitive effort expended (subjective measure). The product analysis shows the correlation between explicitating shifts and cognitive load at the level of 31%. The Spearman’s rank-order correlation coefficientr = 0.48 indicates that there is a positive association between these two variables. This finding is further confirmed by 122 retrospective comments of the subjects in the study.
Explicit and implicit activation of gender stereotypes additively impair soccer performance and learning in women
Authors: Cardozo Priscila , Cibeira Leon Flôres , Rigo Luiz Carlos , Chiviacowsky Suzete
Published: October 2020

Studies involving the manipulation of instructions regarding the negative characteristics of a group or comparisons with members of another group (explicit activation of stereotypes) have shown that age, weight, and gender stereotypes can be harmful to motor performance and learning. To date, however, no study has observed whether implicit stereotype threats, such as the sex of the coach or experimenter, can also influence the acquisition of motor skills. In the present study, the individual and combined impact of implicit and explicit influences of gender stereotype on women's soccer performance and learning was examined. In a 2 × 2 design, 60 women were divided into four groups according to the presence or absence of explicit (ES) and implicit (IS) stereotypes: ES/IS, ES, IS, and control. The groups with implicit activation practiced in the presence of a male experimenter. The groups with explicit activation received instructions activating the gender negative stereotype. The control group practiced without stereotype activations. The results showed that both explicit and implicit activation additively impaired soccer performance and learning, with both main effects being significant for practice and retention. The ES/IS group showed lower scores on the task relative to the other groups, while the ES and IS groups showed worse scores compared with the control group. The findings suggest that stigmatised populations may be forced to cope with more than one social identity threat while learning sport motor skills and indicate the importance of further studies testing strategies to minimise the deleterious effects of negative stereotypes.
Novel phospho-switch function of delta-catenin in dendrite development
Authors: Baumert Ryan , Ji Hong , Paulucci-Holthauzen Adriana , Wolfe Aaron , Sagum Cari , Hodgson Louis , Arikkath Jyothi , Chen Xiaojiang , Bedford Mark T. , Waxham M. Neal , McCrea Pierre D.
Published: October 2020

In neurons, dendrites form the major sites of information receipt and integration. It is thus vital that, during development, the dendritic arbor is adequately formed to enable proper neural circuit formation and function. While several known processes shape the arbor, little is known of those that govern dendrite branching versus extension. Here, we report a new mechanism instructing dendrites to branch versus extend. In it, glutamate signaling activates mGluR5 receptors to promote Ckd5-mediated phosphorylation of the C-terminal PDZ-binding motif of delta-catenin. The phosphorylation state of this motif determines delta-catenin’s ability to bind either Pdlim5 or Magi1. Whereas the delta:Pdlim5 complex enhances dendrite branching at the expense of elongation, the delta:Magi1 complex instead promotes lengthening. Our data suggest that these complexes affect dendrite development by differentially regulating the small-GTPase RhoA and actin-associated protein Cortactin. We thus reveal a “phospho-switch” within delta-catenin, subject to a glutamate-mediated signaling pathway, that assists in balancing the branching versus extension of dendrites during neural development.
Inhibition of class I PI3K enhances chaperone-mediated autophagy
Authors: Endicott S. Joseph , Ziemba Zachary J. , Beckmann Logan J. , Boynton Dennis N. , Miller Richard A.
Published: October 2020

Chaperone-mediated autophagy (CMA) is the most selective form of lysosomal proteolysis, where individual peptides, recognized by a consensus motif, are translocated directly across the lysosomal membrane. CMA regulates the abundance of many disease-related proteins, with causative roles in neoplasia, neurodegeneration, hepatosteatosis, and other pathologies relevant to human health and aging. At the lysosomal membrane, CMA is inhibited by Akt-dependent phosphorylation of the CMA regulator GFAP. The INS-PI3K-PDPK1 pathway regulates Akt, but its role in CMA is unclear. Here, we report that inhibition of class I PI3K or PDPK1 activates CMA. In contrast, selective inhibition of class III PI3Ks does not activate CMA. Isolated liver lysosomes from mice treated with either of two orally bioavailable class I PI3K inhibitors, pictilisib or buparlisib, display elevated CMA activity, and decreased phosphorylation of lysosomal GFAP, with no change in macroautophagy. The findings of this study represent an important first step in repurposing class I PI3K inhibitors to modulate CMA in vivo.
Spatial regulation of clathrin-mediated endocytosis through position-dependent site maturation
Authors: Pedersen Ross T.A. , Hassinger Julian E. , Marchando Paul , Drubin David G.
Published: October 2020

During clathrin-mediated endocytosis (CME), over 50 different proteins assemble on the plasma membrane to reshape it into a cargo-laden vesicle. It has long been assumed that cargo triggers local CME site assembly in Saccharomyces cerevisiae based on the discovery that cortical actin patches, which cluster near exocytic sites, are CME sites. Quantitative imaging data reported here lead to a radically different view of which CME steps are regulated and which steps are deterministic. We quantitatively and spatially describe progression through the CME pathway and pinpoint a cargo-sensitive regulatory transition point that governs progression from the initiation phase of CME to the internalization phase. Thus, site maturation, rather than site initiation, accounts for the previously observed polarized distribution of actin patches in this organism. While previous studies suggested that cargo ensures its own internalization by regulating either CME initiation rates or frequency of abortive events, our data instead identify maturation through a checkpoint in the pathway as the cargo-sensitive step.
PD-1 restraint of regulatory T cell suppressive activity is critical for immune tolerance
Authors: Tan Catherine L. , Kuchroo Juhi R. , Sage Peter T. , Liang Dan , Francisco Loise M. , Buck Jessica , Thaker Youg Raj , Zhang Qianxia , McArdel Shannon L. , Juneja Vikram R. , Lee Sun Jung , Lovitch Scott B. , Lian Christine , Murphy George F. , Blazar Bruce R. , Vignali Dario A.A. , Freeman Gordon J. , Sharpe Arlene H.
Published: October 2020

Inhibitory signals through the PD-1 pathway regulate T cell activation, T cell tolerance, and T cell exhaustion. Studies of PD-1 function have focused primarily on effector T cells. Far less is known about PD-1 function in regulatory T (T reg) cells. To study the role of PD-1 in T reg cells, we generated mice that selectively lack PD-1 in T reg cells. PD-1–deficient T reg cells exhibit an activated phenotype and enhanced immunosuppressive function. The in vivo significance of the potent suppressive capacity of PD-1–deficient T reg cells is illustrated by ameliorated experimental autoimmune encephalomyelitis (EAE) and protection from diabetes in nonobese diabetic (NOD) mice lacking PD-1 selectively in T reg cells. We identified reduced signaling through the PI3K–AKT pathway as a mechanism underlying the enhanced suppressive capacity of PD-1–deficient T reg cells. Our findings demonstrate that cell-intrinsic PD-1 restraint of T reg cells is a significant mechanism by which PD-1 inhibitory signals regulate T cell tolerance and autoimmunity.
Qki is an essential regulator of microglial phagocytosis in demyelination
Authors: Ren Jiangong , Dai Congxin , Zhou Xin , Barnes Joseph A. , Chen Xi , Wang Yunfei , Yuan Liang , Shingu Takashi , Heimberger Amy B. , Chen Yiwen , Hu Jian
Published: October 2020

The mechanism underpinning the regulation of microglial phagocytosis in demyelinating diseases is unclear. Here, we showed that the Quaking protein (Qki) in microglia was greatly induced by demyelination in the brains of both mice and humans. Deletion of the Quaking gene (Qk) in microglia severely impaired the clearance of myelin debris. Transcriptomic profiling indicated that depletion of Qki impaired total RNA levels and splicing of the genes involved in phagosome formation and maturation. RNA immunoprecipitation (RIP) confirmed the physical interactions between the Qki protein and the mRNAs of Qki targets that are involved in phagocytosis, indicating that Qki regulates their RNA stability. Both Qki depletion and inhibition of Qki target Cd36 greatly reduced the phagocytic activity of microglia and macrophages. The defective uptake and degradation of myelin debris caused by Qki depletion in microglia resulted in unresolved myelin debris that impaired axon integrity, oligodendrocyte maturation, and subsequent remyelination. Thus, our results demonstrate that Qki is an essential regulator of microglia’s phagocytic activity under demyelinating conditions.
Generalized scalar field cosmologies: a global dynamical systems formulation
Authors: Leon Genly , Franz Silva Felipe Orlando
Published: October 2020

Local and global phase-space descriptions and averaging methods are used to find qualitative features of solutions for the FLRW and the Bianchi I metrics in the context of scalar field cosmologies with arbitrary potentials and arbitrary couplings to matter. The stability of the equilibrium points in a phase-space as well as the dynamics in the regime where the scalar field diverges are studied. Equilibrium points that represent some solutions of cosmological interest such as: several types of scaling solutions, a kinetic dominated solution representing a stiff fluid, a solution dominated by an effective energy density of geometric origin, a quintessence scalar field dominated solution, the vacuum de Sitter solution associated to the minimum of the potential, and a non-interacting matter dominated solution are obtained. All of which reveal a very rich cosmological phenomenology.
The effect of very small ball gaps in Newton’s cradle
Authors: Cross Rod
Published: October 2020

A Newton’s cradle with three steel balls was filmed with a slow motion video camera to examine the collision dynamics. The initial collision with two stationary balls in contact was as expected, with the incident ball bouncing backwards slowly, the middle ball moving forwards slowly and the ball at the far end emerging at a speed slightly less than the incident ball. A short time later, a different outcome was observed when one ball collided with two balls visually in contact. In that case the incident ball came to rest and remained in contact with the middle ball, as if the two balls in contact were actually separated before the collision. The second observation can be explained if the impact force has the form F = kx

n
where n is larger than the n = 1.5 exponent usually used to describe collisions between solid spheres. Alternatively, the result can be explained with an n = 1.5 exponent if there is a very small gap between the balls, not visible on video film. The latter explanation was confirmed by measuring electrical contact between the balls.
Evaluating Bohm’s quantum force in the scattering process by a classical potential
Authors: Santana W S , Cruz C , Lima E , Prudente F V
Published: October 2020

In this work, we show an application of the de Broglie–Bohm quantum theory of motion (QTM) as a powerful tool for evaluating Bohm’s quantum force in the scattering process of a Gaussian wavepacket by a classical Eckart potential. Our results show that in the absence of a classical potential, the system experiences quantum effects arising from an effective force, intrinsically related to the existence of the wavepacket itself. In contrast, in the scattering by the classical potential, it experiences a quantum force effect even in the absence of any classical force, reinforcing the fact that potentials can act without classical force fields. Thus, this application could be useful to introduce QTM, through the discussion of the concept of Bohm’s quantum force, as a classroom working tool instead of merely an alternative interpretation of the quantum theory.
Variation of thermoelectric figure-of-merits for Mg2Si
x
Sn1-x
solid solutions
Authors: Yi Su-in , Yu Choongho
Published: October 2020

Recent advances in figure-of-merit enhancement for thermoelectric materials are mostly based on alloy material systems, which often require specific conditions to obtain the optimal electrical properties by valley convergence simultaneously with the minimized lattice thermal conductivity through maximum phonon-alloy scattering. However these conditions especially stoichiometry are often hard to control because of microstructural heterogeneity or immiscibility during material processing and prolonged use. This could easily foster the valley edge offset, inducing the negligible valley convergence as well as the abating phonon-alloy scattering. Here Mg2Si0.3Sn0.7 pellets with different spatial uniformity were prepared by varying mixing and annealing time. Mg2SixSn1-x solid solutions of a wide alloy range were studied because the susceptible ranges for valley convergence (0.6 < x < 0.8) and phonon-alloy scattering (0.1 < x < 0.9) are dissimilar. The power factor ranged from 4.4 mWm−1 K−2 to 3.2 mWm−1 K−2 at 573 K and effective mass from 1.1 m
0 to 0.8 m
0, and thermal conductivity also varied depending on the degree of homogeneity of Mg2Si0.3Sn0.7 due to the alteration of phonon-alloy scattering, resulting in a large swing of ZT between 1.33 and 0.8 at 673 K. Lastly we found the dependency of single valley effective mass (m*
) on valley edge offset (ΔE
c) where conduction band valley X3 and X1 are broadened with valley convergence (i.e. m
* at ΔE
c = 0 > m
* at ΔE
c ≠ 0), proposing a modification on material parameter B ∼ NV
(ΔE
c)/m*
(ΔE
c), where both valley degeneracy (NV
) and m
* are functions of ΔE
c, on which none of any literature has paid attention so far. Our thorough investigation with an example of Mg2Si0.3Sn0.7 can be utilized for other thermoelectric materials most of which are fundamentally relying on high valley degeneracy and alloying at the base.
Calibration of hydrophones using a frequency domain filter processing method: theory and experiment
Authors: Chen Yi , Yang Liuqing , Zhou Lisheng , Jin Xiaofeng , Jia Guanghui
Published: October 2020

To eliminate the interferences coming from the boundaries of a water tank and extend its low frequency calibration limit, a frequency domain filter processing (FDFP) method is proposed for hydrophone calibration measurements. The frequency domain filter function is designed according to the a priori spatial position of projector and hydrophone pair in a water tank. A simultaneous comparison method is used for calibration, and a wideband pink noise pulse signal is transmitted. After application of the FDFP method, the transfer impedances of projector and hydrophone pairs in a quasi-free-field are obtained, and interferences reflected from the boundaries of the water tank are effectively eliminated. To verify the FDFP method, an experimental system is established for calibration of the free-field sensitivity of a TC 4033 hydrophone. For a non-anechoic water tank of 1.5 m × 0.88 m × 0.90 m, the lowest calibration frequency is extended from 20 kHz to 3.15 kHz, and the calibration result is consistent with the free-field reciprocity calibration result obtained in an anechoic water tank of 50 m × 15 m × 10 m in the frequency range 3.15 kHz to 31.5 kHz.
Metamaterial surface and modified Vivaldi antenna to tune gain of microwave imaging instrument
Authors: Ahmed Aijaz , Kumari Vineeta , Sheoran Gyanendra
Published: October 2020

This work presents the design of a modified Vivaldi antenna, a metamaterial structure and their combined utilization for tuning the gain. Two triangular shaped conducting patches are used to form a (5 mm × 5 mm) unit metamaterial structure, which is used on the Vivaldi antenna to enhance the bandwidth and the gain. The proposed antenna has a −10 dB bandwidth of 17.36 GHz ranging from 3.3 to 21.6 GHz. The absorption capability of the metamaterial structure is observed for multiple polarization angles and the corresponding losses are also measured. The metamaterial surface, made up of periodic arrays of the proposed structure, is further implemented to tune the gain of the antenna, to make an application-independent near-field microwave imaging instrument.
Graphene field effect transistor scaling for ultra-low-noise sensors
Authors: Tran Ngoc Anh Minh , Fakih Ibrahim , Durnan Oliver , Hu Anjun , Aygar Ayse Melis , Napal Ilargi , Centeno Alba , Zurutuza Amaia , Reulet Bertrand , Szkopek Thomas
Published: October 2020

The discovery of the field effect in graphene initiated the development of graphene field effect transistor (FET) sensors, wherein high mobility surface conduction is readily modulated by surface adsorption. For all graphene transistor sensors, low-frequency 1/f noise determines sensor resolution, and the absolute measure of 1/f noise is thus a crucial performance metric for sensor applications. Here we report a simple method for reducing 1/f noise by scaling the active area of graphene FET sensors. We measured 1/f noise in graphene FETs with size 5 μm × 5 μm to 5.12 mm × 5.12 mm, observing more than five orders of magnitude reduction in 1/f noise. We report the lowest normalized graphene 1/f noise parameter observed to date, 5 × 10−13, and we demonstrate a sulfate ion sensor with a record resolution of 1.2 × 10−3 log molar concentration units. Our work highlights the importance of area scaling in graphene FET sensor design, wherein increased channel area improves sensor resolution.
FBP-Net for direct reconstruction of dynamic PET images
Authors: Wang Bo , Liu Huafeng
Published: October 2020

Dynamic positron emission tomography (PET) imaging can provide information about metabolic changes over time, used for kinetic analysis and auxiliary diagnosis. Existing deep learning-based reconstruction methods have too many trainable parameters and poor generalization, and require mass data to train the neural network. However, obtaining large amounts of medical data is expensive and time-consuming. To reduce the need for data and improve the generalization of network, we combined the filtered back-projection (FBP) algorithm with neural network, and proposed FBP-Net which could directly reconstruct PET images from sinograms instead of post-processing the rough reconstruction images obtained by traditional methods. The FBP-Net contained two parts: the FBP part and the denoiser part. The FBP part adaptively learned the frequency filter to realize the transformation from the detector domain to the image domain, and normalized the coarse reconstruction images obtained. The denoiser part merged the information of all time frames to improve the quality of dynamic PET reconstruction images, especially the early time frames. The proposed FBP-Net was performed on simulation and real dataset, and the results were compared with the state-of-art U-net and DeepPET. The results showed that FBP-Net did not tend to overfit the training set and had a stronger generalization.
Coordinate parameterisation and spectral method optimisation for Beltrami field solver in stellarator geometry
Authors: Qu Z S , Pfefferlé D , Hudson S R , Baillod A , Kumar A , Dewar R L , Hole M J
Published: October 2020

The numerical solution of the stepped pressure equilibrium (Hudson et al 2012 Phys. Plasmas
19 112502) requires a fast and robust solver to obtain the Beltrami field in three-dimensional geometry such as stellarators. The spectral method implemented in the stepped pressure equilibrium code (SPEC) is efficient when the domain is a hollow torus, but ill-conditioning of the discretised linear equations occurs in the (solid) toroid due to the artificially singular coordinate parameterisation near the axis. In this work, we propose an improved choice for the reference axis to prevent coordinates surfaces from overlapping. Then, we examine the parity and asymptotics of the magnetic vector potential near the axis and suggest the use of recombined and rescaled Zernike radial basis functions. The maximum relative error in the magnetic field of the Wendelstein 7-X geometry is shown to reach 10−9 at high resolution in a series of convergence tests and benchmarks against the boundary integral equation solver for Taylor states. The new method is also reported to significantly improve the accuracy of multi-volume SPEC calculations. A comparison between free-boundary SPEC and the analytical Dommaschk potential is presented with higher-than-usual Fourier resolution. It is illustrated that we are able to resolve low amplitude current sheets when an interface is placed where there is no flux surface in the analytic solution. This was previously concealed because of insufficient numerical resolution.
A revised comprehensive approach for determining the H2 and D2 rovibrational population from the Fulcher-α emission in low temperature plasmas
Authors: Briefi S , Fantz U
Published: October 2020

The emission of the Fulcher-

α

d

3

Π

u

→

a

3

Σ

g

+

transition is well-known for providing access to the rovibrational population of the hydrogen molecule in low temperature plasmas by means of optical emission spectroscopy. A revised comprehensive approach is developed for the evaluation that omits several simplifying assumptions, which are often made. The rovibrational distribution is directly calculated in the

X

1

Σ

g

+

state considering the typically observed hockey-stick population. The projection into the d
3Π
u
state is performed via vibrationally resolved electron impact excitation cross sections and radiative decay into the

a

3

Σ

g

+

is considered via vibrationally resolved transition probabilities. The obtained steady-state population is fitted to the experimentally measured one via varying the population parameters in the electronic ground state. The impact of this evaluation routine compared to the simplified ones is demonstrated both for H2 and D2 at two experiments: a standard CW low-power laboratory ICP and the pulsed high-power negative ion source plasma of the Linac4 accelerator at CERN. This assessment demonstrates that especially the simplification of measuring only the first five rotational emission lines (i.e. neglecting the rotational hockey-stick distribution) can affect the evaluation results significantly. In the application example, this leads to an overestimation of the gas temperature up to a factor of nine and to an underestimation of the determined intensity of the full Fulcher-α transition (required for applying collisional radiative models) up to a factor of three.
Level anti-crossings of a nitrogen-vacancy center in diamond: decoherence-free subspaces and 3D sensors of microwave magnetic fields
Authors: Rama Koteswara Rao K , Suter Dieter
Published: October 2020

Nitrogen-vacancy (NV) centers in diamond have become an important tool for quantum technologies. All of these applications rely on long coherence times of electron and nuclear spins associated with these centers. Here, we study the energy level anti-crossings of an NV center in diamond coupled to a first-shell 13C nuclear spin in a small static magnetic field. These level anti-crossings (LACs) occur for specific orientations of the static magnetic field due to the strong non-secular components of the Hamiltonian. At these orientations we observe decoherence-free subspaces, where the electron spin coherence times (

T

2

*

) are 5–7 times longer than those at other orientations. Another interesting property at these LACs is that individual transition amplitudes are dominated by a single component of the magnetic dipole moment. Accordingly, this can be used for vector detection of microwave magnetic fields with a single NV center. This is particularly important to precisely control the center using numerical optimal control techniques.
Identifying potential gene biomarkers for Parkinson’s disease through an information entropy based approach
Authors: Monaco A , Pantaleo E , Amoroso N , Bellantuono L , Lombardi A , Tateo A , Tangaro S , Bellotti R
Published: October 2020

Parkinson’s disease (PD) is a chronic, progressive neurodegenerative disease and represents the most common disease of this type, after Alzheimer’s dementia. It is characterized by motor and nonmotor features and by a long prodromal stage that lasts many years. Genetic research has shown that PD is a complex and multisystem disorder. To capture the molecular complexity of this disease we used a complex network approach. We maximized the information entropy of the gene co-expression matrix betweenness to obtain a gene adjacency matrix; then we used a fast greedy algorithm to detect communities. Finally we applied principal component analysis on the detected gene communities, with the ultimate purpose of discriminating between PD patients and healthy controls by means of a random forests classifier. We used a publicly available substantia nigra microarray dataset, GSE20163, from NCBI GEO database, containing gene expression profiles for 10 PD patients and 18 normal controls. With this methodology we identified two gene communities that discriminated between the two groups with mean accuracy of 0.88 ± 0.03 and 0.84 ± 0.03, respectively, and validated our results on an independent microarray experiment. The two gene communities presented a considerable reduction in size, over 100 times, compared to the initial network and were stable within a range of tested parameters. Further research focusing on the restricted number of genes belonging to the selected communities may reveal essential mechanisms responsible for PD at a network level and could contribute to the discovery of new biomarkers for PD.
Rapidity dependence of global polarization in heavy ion collisions *
Authors: Liang Zuo-Tang , Song Jun , Upsal Isaac , Wang Qun , Xu Zhangbu
Published: October 2020

We use a geometric model for hadron polarization in heavy ion collisions with an emphasis on the rapidity dependence. The model is based on the model of Brodsky, Gunion, and Kuhn, as well as the Bjorken scaling model. We make predictions regarding the rapidity dependence of global

polarization in the collision energy range of 7.7-200 GeV by assuming the rapidity dependence of two parameters,

and

. The predictions can be tested by future beam-energy-scan experiments at the Relativistic Heavy Ion Collider of Brookhaven National Lab.
Development of Ar+16 charge exchange recombination spectroscopy measurements at ASDEX Upgrade
Authors: McDermott R.M. , Dux R. , Guzman F. , Pütterich T. , Fischer R. , Kappatou A.
Published: October 2020

Argon is being considered as a radiator for future fusion devices. To support this, experiments in present day devices are needed to assess its effectiveness as a radiator and to study its compatibility with key aspects of reactor operation. For these purposes, accurate measurement of the Ar density in the confined plasma region are required. Charge exchange recombination spectroscopy is capable of providing this information, but requires validated cross-sections to produce accurate density profiles. For typical ASDEX Upgrade plasma parameters Ar+16 is the charge state of the most interest and the ArXVI n = 15–14 was identified as the best target for these measurements. Due to the fine structure splitting, the Ar charge exchange (CX) emission lines are highly asymmetric and detailed modeling is required to extract accurate ion temperatures or rotations. For the evaluation of Ar+16 densities, there are two main sets of CX cross-sections available: the data calculated by Schultz et al (Whyte et al 2010 J. Phys. B At. Mol. Opt. Phys
43 144002, Schultz et al 2010 J. Phys. B At. Mol. Opt. Phys.
43 144002) (ORNL) and by Errea et al (2006 J. Phys. B At. Mol. Opt. Phys.
39 L91) (UAM). These cross-sections differ by over an order of magnitude and have very different energy dependencies. In this work, the validity of these datasets is tested experimentally. The Ar density profiles calculated using the ORNL cross-sections are 10–50× too large while the UAM densities are a factor of 2.73 too small. The UAM data, however, does a much better job at capturing the observed energy dependence. The authors conclude that the CTMC calculations of Errea, which use a hydrogenic distribution to describe the initial target and donor distributions better reproduce the experimental data. However, to produce accurate Ar density profiles, these cross-sections need to be corrected downward and the best profiles are produced with a small correction to the UAM energy dependence.
The role of collisionless trapped electron mode turbulence on removal of helium ash and transport of deuterium-tritium ions
Authors: Guo Weixin , Zhang Mingzhu , Wang Lu , Zhuang Ge
Published: October 2020

Removal of helium ash and the anomalous transport of deuterium (D) and tritium (T) ions driven by collisionless trapped electron mode (CTEM) turbulence in tokamak plasmas with weak magnetic shear are studied. We derive the eigenvalue of CTEM with helium ash, and calculate the quasi-linear turbulent fluxes of helium ash, D and T ions simultaneously. Based on the analytical results, the parametric dependence of CTEM instability as well as the anomalous transport of helium ash and D-T ions is investigated, in order to explore the parameter region that is favorable for expelling more helium ash than D and T ions. It is found that helium ash with higher temperature and steeper density profile plays a role of destabilizing CTEM instability, and has higher transport level than that of T ions. We also find that increasing electron temperature and flattening electron density profile are favorable for exhausting helium ash. Isotopic effects (i.e. increasing the fraction of T ions) enhance the transport of both helium ash and D-T ions. Moreover, the trend of stronger transport level of helium ash than that of D-T ions is enhanced by raising electron temperature and flattening electron density profile as well as isotopic effects. Besides, the diffusivity is much larger than the convection. This indicates that the CTEM turbulence driven helium ash transport is favorable for removing helium ash under the parameter region used in the present paper. The possible relevance of our theoretical results to experimental observations is also discussed.
Simulations of fusion neutron source based on the axially symmetric mirror trap for the thorium hybrid reactor
Authors: Prikhodko V.V. , Arzhannikov A.V.
Published: October 2020

The axially symmetric open mirror trap is considered as a neutron source for the hybrid thorium reactor. Plasma parameters are optimized in order to achieve the maximum neutron yield in the volume surrounded by the subcritical fuel assembly while meeting the stability criteria. For plasma consisting of equal amounts of deuterium and tritium isotopes, in the fuel assembly region, the neutron yield was found to be 0.6 × 1017 n/s at an input power of 20 MW, and it will increase to 2.6 × 1017 n/s if the input power increases two times. In optimal regimes, the plasma parameters were close to those achieved in experiments at the GDT facility.
Efficiency investigation of a negative hydrogen ion beam production with the use of the gasdynamic ECR plasma source
Authors: Lapin R L , Skalyga V A , Izotov I V , Golubev S V , Razin S V , Bokhanov A F , Kazakov M Yu , Shaposhnikov R A , Kiseleva E M , Tarvainen O
Published: October 2020

Negative hydrogen ion sources are of great demand in modern physics as injectors into accelerators and drivers for neutral beam injectors for fusion devices. It has been shown earlier that the use of the gasdynamic ECR discharge provides the opportunity to extract up to 80 mA/cm2 of negative ion current density. We studied experimentally the volumetric negative hydrogen ion production and vacuum ultraviolet emission in a gasdynamic ECR discharge. The high-density plasma was sustained by the pulsed 37 GHz / 100 kW gyrotron radiation in a magnetic configuration consisting of two consecutive simple mirror traps. The future prospects of the volumetric H− source based on the gasdynamic ECR discharge related to the transition from pulsed to continuous operating mode with the use of an improved magnetic confinement system are discussed. Numerical simulation of the negative hydrogen ion beam extraction at the continuous operating mode facility was performed. Optimal configuration of the extraction electrodes and the electron damping magnets was found.
Numerical simulations of nanosecond discharge in gas-dynamic flows
Authors: Ermakov E A , Ivanov I E , Kryukov I A , Mursenkova I V , Znamenskaya I A
Published: October 2020

Numerical simulations were performed of the nanosecond high-voltage breakdown in nitrogen at a voltage of 25–35 kV in the sub-centimeter discharge gaps. The streamer configurations were studied at two constant pressures, as well as at the radially varying pressure, simulating the pressure distribution in the axial region of the vortex “columnar” gas-dynamic flow. In each case, the characteristic parameters and propagation velocities of the primary and secondary streamers were calculated. It was ascertained that the law of pressure change in the radial direction strongly affects the spatial structure of the negative streamer.
Combined thermomechanical and optical simulations of planar-optical polymer waveguides
Authors: Suar Monali , Baran Murat , Günther Axel , Roth Bernhard
Published: October 2020

In this work, we describe a theoretical approach for combined thermal, mechanical and optical simulation and analysis of planar polymer waveguides. We consider a finite element approach for thermal and stress/deformation simulation. Also, a Crank-Nicholson finite difference beam propagation method (CN-BPM) is implemented to perform the optical simulation. The results of the finite element (thermo-mechanical) analysis are coupled with the CN-BPM results to carry out the optical simulation of poly(methyl methacrylate) (PMMA) waveguides as function of temperature. For thermal simulation, a model was designed where a polysilicon microheater was added to the upper cladding of the PMMA waveguides to vary the temperature between 20 °C and 200 °C. Thus, the impact of the induced temperature gradients on the refractive index modulation of the PMMA waveguides and the corresponding change in numerical aperture are obtained. In addition, the temperature gradients influence the beam intensity profiles and the movement of the primary eyes within the optical waveguides, thus, impacting the optical properties. Furthermore, the thermally induced mechanical stress and deformation were calculated for transverse and axial directions. In the next step, validation of the model by systematic experimental studies will be performed. In general, our approach provides a toolbox for more comprehensive multi-physics theoretical analysis of polymer-optical waveguides which, in future, can be extended to more complex and functional structures as required for flexible sensor networks, as example.