bluuebunny/crossref_metadata_2025 huggingface dataset:
An insight into the flexible drive mechanism in short cylinder ultrasonic piezoelectric vibrator
Authors: Wen Zhiyi , He Qing , Qiao Guanyao
Published: May 2020

In this study, a resonant type piezoelectric vibrator for driving a flexible body is proposed and its driving principle is discussed. The flexible body driven in this article is rigid in the longitudinal direction and flexible in the transverse direction, such as in metal straps and metal wires. The exciting signals used in the piezoelectric transducer in the horizontal and vertical directions are both sinusoidal signals, possessing a phase shift of π/2. Two third-order orthogonal bending in-plane modes of the same frequency were effectively excited, and an elliptic motion formed on the end plane of the vibrator toothed structure. A flexible body was then effectively driven by friction under a certain amount of tension. The proposed vibrator was designed using the finite element method, and the flexible drive models were established, while the output force in the contact friction was analyzed. The vibration characteristics of the vibrator were tested in order to obtain the resonance frequencies and responses. An experimental system was then established to test the mechanical output characteristics. The results demonstrate that the difference in thickness, tension force, and surface roughness between the flexible bodies confer great influence on driving. With a thickness of 0.01 mm, 0.02 mm, and 0.03 mm, the flexible metal strap velocity was found to be 24 mm/s, 43.64 mm/s, and 10.43 mm/s under the corresponding proper tension, smooth surface, and voltage of 200Vp-p, respectively.
Photonic Doppler velocimetry of ohmically exploded aluminum surfaces
Authors: Hutchinson T. M. , Awe T. J. , Bauer B. S. , Dolan D. H. , Pillars J. R. , Hutsel B. T. , Yu E. P. , Klemmer A. W. , Kreher S. E.
Published: May 2020

Photonic Doppler Velocimetry (PDV) was used to investigate the exploding surface of coated metal driven by lineal current density increasing at 3×1015 A/m/s. Aluminum-6061 rods were coated with three thicknesses (5, 17, and 41 μm) of Parylene-N and driven to 850 kA in approximately 100 ns, with the metal thicker than the skin depth. According to PDV, the metal surface melts at 85±13 T and expands with a constant acceleration. Then, at a surface magnetic field of 140–180 T, the metal acceleration begins to increase in time. Later, plasma forms on, and is correlated with PDV signal loss from, uncoated aluminum rods, 5-μm-coated rods, and 17-μm-coated rods, while no evidence suggests that plasma forms on 41-μm-coated metal.
Plasmono-atomic interactions on a fiber tip
Authors: Chan Eng Aik , Adamo Giorgio , Aljunid Syed Abdullah , Ducloy Martial , Zheludev Nikolay , Wilkowski David
Published: May 2020

Light–atom interaction can be engineered by interfacing atoms with various specially designed media, and optical fibers are convenient platforms for realization of compact interfaces. Here, we show that an optical fiber sensor bearing a plasmonic metasurface at its tip can be used to detect modifications of the Doppler-free hyperfine atomic spectra induced by coupling between atomic and plasmonic excitations. We observed the inversion of the phase modulation reflectivity spectra of Cesium vapor in the presence of the metamaterial. This work paves the way for future compact hybrid atomic devices with a cleaved tip as a substrate platform to host various two-dimensional materials.
Analyticity of a restricted formality
Authors: Arnal Didier , Chaabouni Mouna , Hfaiedh Mabrouka
Published: May 2020

The Kontsevich formality can be viewed as a non-linear map F from the L∞ algebra of poly-vector fields on Rd to the space of poly-differential operators. The space of the half-homogenous poly-vector fields is a sub-L∞ algebra. We prove here that the restriction of F to this subspace is weakly analytic.
Vibrational overtone excitation of D2 in a molecular beam with a high-energy, narrow-bandwidth, nanosecond optical parametric oscillator/amplifier
Authors: Wang Yufeng , Wang Wei , Xie Yurun , Wang Tao , Dai Dongxu , Xiao Chunlei , Yang Xueming
Published: May 2020

We have built a high-energy, narrow-bandwidth, nanosecond light source for efficient preparation of vibrationally excited molecules in a molecular beam. It consists of an injection-seeded optical parametric oscillator and two optical parametric amplifiers. Pumped by the second harmonic of a commercial injection-seeded Nd:YAG laser, it can generate pulse energies up to 377 mJ at 655 nm with a bandwidth smaller than 200 MHz. Its stability is excellent, with a standard deviation of pulse energy of 5.2 mJ and a wavelength stability of 0.001 cm−1. We demonstrated this light source in a crossed-molecular-beam experiment of the H + D2 (v = 2, j = 0) → HD + D reaction, in which it was used for overtone excitation of D2 molecules from (v = 0, j = 0) to (v = 2, j = 0) with an overall excitation efficiency of 2.5%.
The electron number density measurement from needle-to-cylinder gas discharge source in helium at atmospheric pressure
Authors: Jovović Jovica
Published: May 2020

The optical emission spectroscopic methods are applied for the characterization of a newly constructed needle-to-cylinder atmospheric pressure gas discharge source operating in helium. The discharge source comprises stainless steel cathode and graphite anode. The focus of this study is on electron number density Ne measurement employing a dedicated fitting procedure on asymmetric He I 447.2 nm and He I 492.2 nm lines emitted during pulsed and DC voltage regime. In the pulsed regime, Ne = (0.55–0.75) × 1015 cm−3, while during DC voltage excitation, Ne = (1.3–1.7) × 1015 cm−3 was measured. The reliable gas temperature Tg measurement was performed using a Boltzmann plot technique on N2(C3Πu–B3Πg) R2 branch lines. The Tg jump from 780 K to 1720 K is observed when switching from DC to pulsed regime. In both regimes, the increase in current caused the increase in Tg. The gas discharge interaction with water drops located on the anode surface was investigated as well. During the water drop treatment, intensive Fe I originating from cathode material were detected. The tentative explanation is that iron-oxide layers are formed on the cathode surface during the plasma–water interaction with subsequent decomposition in plasma. This feature opens the possibility for analytical application on conductive, liquid samples.
Non-contact, non-destructive mapping of thermal diffusivity and surface acoustic wave speed using transient grating spectroscopy
Authors: Reza Abdallah , Dennett Cody A. , Short Michael P. , Waite John , Zayachuk Yevhen , Magazzeni Christopher M. , Hills Simon , Hofmann Felix
Published: May 2020

We present new developments of the laser-induced transient grating spectroscopy (TGS) technique that enable the measurement of large area 2D maps of thermal diffusivity and surface acoustic wave speed. Additional capabilities include targeted measurements and the ability to accommodate samples with increased surface roughness. These new capabilities are demonstrated by recording large TGS maps of deuterium implanted tungsten, linear friction welded aerospace alloys, and high entropy alloys with a range of grain sizes. The results illustrate the ability to view the grain microstructure in elastically anisotropic samples and to detect anomalies in samples, for example, due to irradiation and previous measurements. They also point to the possibility of using TGS to quantify grain size at the surface of polycrystalline materials.
Wake excitation by a powerful microwave pulse and its evolution in a plasma-filled waveguide
Authors: Cao Y. , Bliokh Y. P. , Leopold J. G. , Li A. , Leibovitch G. , Krasik Ya. E.
Published: May 2020

We present the results of an experimental, theoretical, and numerical study of short and long time wake, produced by a 0.6 ns, 0.5 GW, 9.6 GHz high power microwave (HPM) pulse propagating in a plasma-filled cylindrical waveguide. The perturbation of the plasma density caused by the ponderomotive force prevents not only the pulse from spreading due to dispersion, but also leads to pulse compression. The high power pulse leaves far behind it a long lived positively-charged plasma whose electrons oscillate in the Coulomb potential well and ionize the background neutral gas over several tens to hundreds of nanoseconds. This leads to long time light emission observed in the experiment. The density of this newly created plasma can exceed many-folds its initial value. The theoretical model shows that as a result of the wake excitation by the propagating HPM pulse, fast electrons are ejected and collected on the waveguide wall. These high energy electrons, pulse compression, and long time light emission are evidence of the wake formation. The results of the experiment, the analytical model, and the numerical simulations are in good agreement.
Tracking the dynamics of power sources and sinks during the martensitic transformation of a Cu–Al–Ni single crystal
Authors: Ianniciello Lucia , Romanini Michela , Mañosa Lluís , Planes Antoni , Engelbrecht Kurt , Vives Eduard
Published: May 2020

We have tracked the dynamics of the martensitic transformation in a Cu–Al–Ni single crystal by means of acoustic emission and infrared imaging techniques. A Fourier equation-based post-processing of temperature maps has enabled us to reveal the inhomogeneous and discontinuous character of heat power sources and sinks during the transition. A good correlation between the dynamics of thermal and mechanical energy release has been evidenced. It has also been shown that the merging of martensitic interfaces results in an enhanced heat absorption.
Path integral molecular dynamics for fermions: Alleviating the sign problem with the Bogoliubov inequality
Authors: Hirshberg Barak , Invernizzi Michele , Parrinello Michele
Published: May 2020

We present a method for performing path integral molecular dynamics (PIMD) simulations for fermions and address its sign problem. PIMD simulations are widely used for studying many-body quantum systems at thermal equilibrium. However, they assume that the particles are distinguishable and neglect bosonic and fermionic exchange effects. Interacting fermions play a key role in many chemical and physical systems, such as electrons in quantum dots and ultracold trapped atoms. A direct sampling of the fermionic partition function is impossible using PIMD since its integrand is not positive definite. We show that PIMD simulations for fermions are feasible by employing our recently developed method for bosonic PIMD and reweighting the results to obtain fermionic expectation values. The approach is tested against path integral Monte Carlo (PIMC) simulations for up to seven electrons in a two-dimensional quantum dot for a range of interaction strengths. However, like PIMC, the method suffers from the sign problem at low temperatures. We propose a simple approach for alleviating it by simulating an auxiliary system with a larger average sign and obtaining an upper bound to the energy of the original system using the Bogoliubov inequality. This allows fermions to be studied at temperatures lower than would otherwise have been feasible using PIMD, as demonstrated in the case of a three-electron quantum dot. Our results extend the boundaries of PIMD simulations of fermions and will hopefully stimulate the development of new approaches for tackling the sign problem.
Amplification of probiotic bacteria in the skin microbiome to combat Staphylococcus aureus infection
Authors: Huang Tristan Yusho , Herr Deron Raymond , Huang Chun-Ming , Jiang Yong
Published: May 2020

Staphylococcus aureus (S. aureus) is a Gram-positive bacterium. When pathogenic S. aureus colonises onto a skin wound or diabetic ulcer, it can cause a serious infection and lead to amputation or death. The current solutions (e.g. antibiotics and probiotics) are not sufficient enough to be a cure for this infection. To worsen the situation, the S. aureus bacteria continue to develop greater resistance towards antibiotics and are becoming more commonplace. An effective solution is to amplify the activity of probiotic bacteria in the skin microbiome by using selective fermentation initiators (SFIs) to induce fermentation. Our data demonstrated that the numbers of Cutibacterium acnes (C. acnes) and Staphylococcus epidermidis (S. epidermidis), two major bacteria in skin microbiome, on human skin did not vary significantly over the span of seven days. This stimulates probiotic bacteria such as S. epidermidis to produce sufficient short-chain fatty acids (SCFAs) to suppress the growth of S. aureus. The development of this new cure to S. aureus may reduce hospitalisation greatly as S. aureus accounts for the hospitalisation of more than five thousand people per year. Besides antibiotic, probiotics and bacteriophages, SFIs may become novel agents for treatment of infection.
Modelling suppression difficulty: current and future applications
Authors: Rodríguez y Silva Francisco , O'Connor Christopher D. , Thompson Matthew P. , Molina Martínez Juan Ramón , Calkin David E.
Published: May 2020

Improving decision processes and the informational basis upon which decisions are made in pursuit of safer and more effective fire response have become key priorities of the fire research community. One area of emphasis is bridging the gap between fire researchers and managers through development of application-focused, operationally relevant decision support tools. In this paper we focus on a family of such tools designed to characterise the difficulty of suppression operations by weighing suppression challenges against suppression opportunities. These tools integrate potential fire behaviour, vegetation cover types, topography, road and trail networks, existing fuel breaks and fireline production potential to map the operational effort necessary for fire suppression. We include case studies from two large fires in the USA and Spain to demonstrate model updates and improvements intended to better capture extreme fire behaviour and present results demonstrating successful fire containment where suppression difficulty index (SDI) values were low and containment only after a moderation of fire weather where SDI values were high. A basic aim of this work is reducing the uncertainty and increasing the efficiency of suppression operations through assessment of landscape conditions and incorporation of expert knowledge into planning.
The maleness of larger angiosperm flowers
Authors: Paterno Gustavo Brant , Silveira Carina Lima , Kollmann Johannes , Westoby Mark , Fonseca Carlos Roberto
Published: May 2020

Flower biomass varies widely across the angiosperms. Each plant species invests a given amount of biomass to construct its sex organs. A comparative understanding of how this limited resource is partitioned among primary (male and female structures) and secondary (petals and sepals) sexual organs on hermaphrodite species can shed light on general evolutionary processes behind flower evolution. Here, we use allometries relating different flower biomass components across species to test the existence of broad allocation patterns across the angiosperms. Based on a global dataset with flower biomass spanning five orders of magnitude, we show that heavier angiosperm flowers tend to be male-biased and invest strongly in petals to promote pollen export, while lighter flowers tend to be female-biased and invest more in sepals to insure their own seed set. This result demonstrates that larger flowers are not simple carbon copies of small ones, indicating that sexual selection via male–male competition is an important driver of flower biomass evolution and sex allocation strategies across angiosperms.
Targeted inhibition of thrombin attenuates murine neonatal necrotizing enterocolitis
Authors: Namachivayam Kopperuncholan , MohanKumar Krishnan , Shores Darla R. , Jain Sunil K. , Fundora Jennifer , Everett Allen D. , He Ling , Pan Hua , Wickline Samuel A. , Maheshwari Akhil
Published: May 2020

Significance

Necrotizing enterocolitis (NEC) is an inflammatory bowel necrosis of premature infants and is a leading cause of death in these patients. It is an orphan disease with no specific treatment. In this study, we investigated the mechanisms of NEC-related thrombocytopenia, a characteristic feature of this disease. We tested the hypothesis that platelet activation and depletion occur during NEC once mucosal disruption is well established and is secondary to bacterial translocation across the damaged mucosa. Surprisingly, platelet activation turned out to be an early thrombin-mediated pathogenetic event during NEC-like injury. We show that a targeted nanomedicine approach to inhibit thrombin can attenuate NEC-like injury. If confirmed in clinical studies, this would be a specific treatment for NEC.
Exemplar learning reveals the representational origins of expert category perception
Authors: Collins Elliot , Behrmann Marlene
Published: May 2020

Irrespective of whether one has substantial perceptual expertise for a class of stimuli, an observer invariably encounters novel exemplars from this class. To understand how novel exemplars are represented, we examined the extent to which previous experience with a category constrains the acquisition and nature of representation of subsequent exemplars from that category. Participants completed a perceptual training paradigm with either novel other-race faces (category of experience) or novel computer-generated objects (YUFOs) that included pairwise similarity ratings at the beginning, middle, and end of training, and a 20-d visual search training task on a subset of category exemplars. Analyses of pairwise similarity ratings revealed multiple dissociations between the representational spaces for those learning faces and those learning YUFOs. First, representational distance changes were more selective for faces than YUFOs; trained faces exhibited greater magnitude in representational distance change relative to untrained faces, whereas this trained–untrained distance change was much smaller for YUFOs. Second, there was a difference in where the representational distance changes were observed; for faces, representations that were closer together before training exhibited a greater distance change relative to those that were farther apart before training. For YUFOs, however, the distance changes occurred more uniformly across representational space. Last, there was a decrease in dimensionality of the representational space after training on YUFOs, but not after training on faces. Together, these findings demonstrate how previous category experience governs representational patterns of exemplar learning as well as the underlying dimensionality of the representational space.
Agricultural intensification and the evolution of host specialism in the enteric pathogen
Campylobacter jejuni
Authors: Mourkas Evangelos , Taylor Aidan J. , Méric Guillaume , Bayliss Sion C. , Pascoe Ben , Mageiros Leonardos , Calland Jessica K. , Hitchings Matthew D. , Ridley Anne , Vidal Ana , Forbes Ken J. , Strachan Norval J. C. , Parker Craig T. , Parkhill Julian , Jolley Keith A. , Cody Alison J. , Maiden Martin C. J. , Kelly David J. , Sheppard Samuel K.
Published: May 2020

Modern agriculture has dramatically changed the distribution of animal species on Earth. Changes to host ecology have a major impact on the microbiota, potentially increasing the risk of zoonotic pathogens being transmitted to humans, but the impact of intensive livestock production on host-associated bacteria has rarely been studied. Here, we use large isolate collections and comparative genomics techniques, linked to phenotype studies, to understand the timescale and genomic adaptations associated with the proliferation of the most common food-born bacterial pathogen (
Campylobacter jejuni
) in the most prolific agricultural mammal (cattle). Our findings reveal the emergence of cattle specialist
C. jejuni
lineages from a background of host generalist strains that coincided with the dramatic rise in cattle numbers in the 20th century. Cattle adaptation was associated with horizontal gene transfer and significant gene gain and loss. This may be related to differences in host diet, anatomy, and physiology, leading to the proliferation of globally disseminated cattle specialists of major public health importance. This work highlights how genomic plasticity can allow important zoonotic pathogens to exploit altered niches in the face of anthropogenic change and provides information for mitigating some of the risks posed by modern agricultural systems.
A myosin-7B–dependent endocytosis pathway mediates cellular entry of α-synuclein fibrils and polycation-bearing cargos
Authors: Zhang Qi , Xu Yue , Lee Juhyung , Jarnik Michal , Wu Xufeng , Bonifacino Juan S. , Shen Jingshi , Ye Yihong
Published: May 2020

Significance

Direct cell-to-cell spreading of misfolded protein aggregates, such as α-synuclein fibrils (α-Syn), is a pathological hallmark associated with the progression of many neurodegenerative diseases, but it is unclear how mammalian cells take up large protein aggregates to initiate this prion-like protein transmission process. Here we define the endocytosis mechanism of α-Syn preformed fibrils (PFFs) using a combination of genetic, biochemical, and live-cell imaging techniques. Our study shows that α-Syn PFFs enter cells following an entry pathway that is specifically tailored for cargos bearing positive charges. These cargos bind to heparan sulfate proteoglycans on the cell surface via charge–charge interactions, which enable cargo internalization by a previously unknown endocytosis mechanism that requires forces generated by myosin-7B and actin filaments.
Structural basis for divergent and convergent evolution of catalytic machineries in plant aromatic amino acid decarboxylase proteins
Authors: Torrens-Spence Michael P. , Chiang Ying-Chih , Smith Tyler , Vicent Maria A. , Wang Yi , Weng Jing-Ke
Published: May 2020

Radiation of the plant pyridoxal 5′-phosphate (PLP)-dependent aromaticl-amino acid decarboxylase (AAAD) family has yielded an array of paralogous enzymes exhibiting divergent substrate preferences and catalytic mechanisms. Plant AAADs catalyze either the decarboxylation or decarboxylation-dependent oxidative deamination of aromaticl-amino acids to produce aromatic monoamines or aromatic acetaldehydes, respectively. These compounds serve as key precursors for the biosynthesis of several important classes of plant natural products, including indole alkaloids, benzylisoquinoline alkaloids, hydroxycinnamic acid amides, phenylacetaldehyde-derived floral volatiles, and tyrosol derivatives. Here, we present the crystal structures of four functionally distinct plant AAAD paralogs. Through structural and functional analyses, we identify variable structural features of the substrate-binding pocket that underlie the divergent evolution of substrate selectivity toward indole, phenyl, or hydroxyphenyl amino acids in plant AAADs. Moreover, we describe two mechanistic classes of independently arising mutations in AAAD paralogs leading to the convergent evolution of the derived aldehyde synthase activity. Applying knowledge learned from this study, we successfully engineered a shortened benzylisoquinoline alkaloid pathway to produce (S)-norcoclaurine in yeast. This work highlights the pliability of the AAAD fold that allows change of substrate selectivity and access to alternative catalytic mechanisms with only a few mutations.
Electronic nematicity in Sr
2
RuO
4
Authors: Wu Jie , Nair Hari P. , Bollinger Anthony T. , He Xi , Robinson Ian , Schreiber Nathaniel J. , Shen Kyle M. , Schlom Darrell G. , Božović Ivan
Published: May 2020

Significance

We have synthesized high-quality thin films of the unconventional superconductor Sr
2
RuO
4
on various substrates using molecular-beam epitaxy. We have measured the angle-resolved transverse resistivity (ARTR), a sensitive indicator of electronic anisotropy. The ARTR signal, heralding the electronic nematicity or a large nematic susceptibility, is present and substantial already at room temperature and grows by an order of magnitude upon cooling down to 4 K. In Sr
2
RuO
4,
an unconventional superconducting state emerges out of an unconventional metallic state.
Direct observation of helicase–topoisomerase coupling within reverse gyrase
Authors: Yang Xi , Garnier Florence , Débat Hélène , Strick Terence R. , Nadal Marc
Published: May 2020

Significance

Collaboration between RecQ helicase and type IA topoisomerase has been found in organisms representing all levels of complexity, including the well-known BLM helicase–Top3α combination found in humans and capable of dissolving DNA double-Holliday junctions. Uniquely, hyperthermophiles have fused these functional units into a chimeric enzyme known as reverse gyrase (RG), which is capable of positively supercoiling DNA using ATP hydrolysis. Single-molecule experimentation allows us to observe at single-molecule resolution the helicase–topoisomerase coupling in RG that leads to the catalytic transitions that make up a complete ATP cycle. Subunit collaboration in RG serves as an entry point to fully understanding the universal cooperation between RecQ and Top IA.
Mechanism of water extraction from gypsum rock by desert colonizing microorganisms
Authors: Huang Wei , Ertekin Emine , Wang Taifeng , Cruz Luz , Dailey Micah , DiRuggiero Jocelyne , Kisailus David
Published: May 2020

Significance

This research provides an in-depth analysis of how microorganisms are able to survive in the world’s driest non-polar place, the Atacama Desert, Chile. We show that these organisms extract water from gypsum rocks in this desert, enabling these colonizing microorganisms to sustain life in this extreme environment. We believe the results in this work could not only shed light on how microorganisms can obtain water under severe xeric conditions, but also provide insights into potential life in even more extreme environments, such as Mars, as well as offer strategies for advanced water storage methods.
Five enzymes of the Arg/N-degron pathway form a targeting complex: The concept of superchanneling
Authors: Oh Jang-Hyun , Hyun Ju-Yeon , Chen Shun-Jia , Varshavsky Alexander
Published: May 2020

Significance

The Arg/N-degron pathway targets proteins for degradation by recognizing their N-terminal residues. In the present study, we used in vivo and in vitro binding assays to identify specific multienzyme targeting complexes of the Arg/N-degron pathway in yeast (Saccharomyces cerevisiae) and human cells. These targeting complexes contain N-terminal amidases, an arginyltransferase, and specific ubiquitin ligases of the Arg/N-degron pathway. Enzymes or assemblies of enzymes that catalyze sequential reactions have been observed to exhibit substrate channeling, in which a reaction intermediate can be transferred between active sites of interacting enzymes without release of intermediate to the bulk solution. It remains to be determined whether targeting complexes discovered in the present work function to enable substrate channeling.
Encoding inception in the domain of psych verbs in Polish
Authors: Biały Adam
Published: May 2020

The chapter argues that Polish psych verbs are simple eventualities denoting states in both their imperfective and perfective forms. It is argued that the perfectivising prefixes deriving perfective psych verbs belong to the category of superlexical prefixes in the typology of among others, Romanova (2004) and Svenonius (2004) and function to delimit the temporal dimension of the (stative) event, generating inceptive (or inchoative) state. The perfective forms are argued to be simple events, which do not assert change of state. In this respect, Polish OE psych verbs differ from their English and German counterparts, which have been analysed as achievements in the literature (e.g., van Voorst, 1992; Rothmayr, 2009).
Initiators, states and passives in Spanish psych verbs
Authors: Fábregas Antonio , Marín Rafael
Published: May 2020

The goal here is twofold: the first one is to point out the existence of at least two classes of Object Experiencer psychological verbs (henceforth, OEPV) in Spanish with respect to their passive behavior, casting doubt on Landau (2010), who proposes that passivization of OEPVs correlates with the availability of pseudo-passives in a language. The second one is to argue that passives of OEPVs match the aspectual and argumental properties of verbs in such a way that the verbs which do not satisfy the condition that passives must involve events in Spanish must build those events through a repetitive, pluractional interpretation.
The Proverbial Wisdom of a Georgian Language Island in Iran
Authors: Shurgaia Tea
Published: May 2020

The Georgian language island in Iran is not yet on the radar of international scholars. Studies by Georgian scholars have mostly focused on linguistic, ethnologic and historic issues concerning the Georgian community living in Isfahan province; no paremiological approach has been undertaken. This article is based on the analysis of Fereydani proverbs recorded from 1968 to 2014. Study reveals that the proverbs used by the Georgians of the Fereydan region in their mother tongue are: proverbs translated from Persian; proverbs of Georgian origin and proverbs existing in both Persian and Georgian paremiological funds. Archaic Georgian vocabulary preserved in proverbs is also considered. This paper highlights the need for a deeper paremiological approach to the proverbs of the Fereydani Georgians.
Numbing the perception of stigma: system justification decreases psychological distress by reducing perceived stigma among gay men and lesbians (Adormeciendo la percepción del estigma: la justificación del sistema disminuye el malestar psicológico mediante la reducción del estigma percibido entre gays y lesbianas)
Authors: Bahamondes Joaquín , Gómez Fabiola , Barrientos Jaime , Cárdenas Manuel , Guzmán-González Mónica
Published: May 2020

System justification theory posits that perceiving society as fair and legitimate provides palliative benefits to people who endorse such beliefs. Despite mixed evidence among socially disadvantaged groups, recent evidence shows that members of disadvantaged groups minimize perceptions of discrimination in order to reap palliative benefits. We tested this hypothesis in a sample of gay men and lesbians in Chile ( N = 467). Specifically, we examined the effects of system justification on psychological distress, and the mediating role of perceived sexual stigma. As expected, system justification was negatively associated with psychological distress via minimizing perceptions of sexual stigma towards the in-group. Our study replicates previous results, and unveils a soporific mechanism of system-justifying beliefs: that of providing palliative benefits to sexual minorities’ well-being by minimizing perceptions of their in-group as target of sexual stigma. Considerations for the well-being and status of sexual minorities and their unwitting compliance with heteronormativity are further discussed.
Intention to return of Spanish emigrant population and associated psychosocial factors (Intención de retorno de la población emigrante española y factores psicosociales asociados)
Authors: Elgorriaga Edurne , Ibabe Izaskun , Arnoso Ainara
Published: May 2020

This study examines whether social-labour conditions improved for Spanish people after emigrating and if these conditions are similar in Germany and England, as well as psychological adjustment and mental health. It also explores whether there are the factors predicting the intention to return to Spain. The sample consists of 529 Spanish people who emigrated to England (291) or Germany (238) for work reasons. The results indicate that after emigration, their social-labour situation improved, although people who migrated to Germany face greater difficulties. Psychological adjustment and mental health was acceptable and similar in both countries. The intention to return before emigrating and the youngest age of emigrants predict the intention of post-immigration return. In addition, in Germany the return is associated with a negative assessment of the job situation and low identification with Germany, while in England it is associated with a low orientation towards English culture and a high orientation towards Spanish culture.
Improving wafer-scale Josephson junction resistance variation in superconducting quantum coherent circuits
Authors: Kreikebaum J M , O’Brien K P , Morvan A , Siddiqi I
Published: May 2020

Quantum bits, or qubits, are an example of coherent circuits envisioned for next-generation computers and detectors. A robust superconducting qubit with a coherent lifetime of O(100 µs) is the transmon: a Josephson junction functioning as a non-linear inductor shunted with a capacitor to form an anharmonic oscillator. In a complex device with many such transmons, precise control over each qubit frequency is often required, and thus variations of the junction area and tunnel barrier thickness must be sufficiently minimized to achieve optimal performance while avoiding spectral overlap between neighboring circuits. Simply transplanting our recipe optimized for single, stand-alone devices to wafer-scale (producing 64, 1x1 cm dies from a 150 mm wafer) initially resulted in global drifts in room-temperature tunneling resistance of ± 30%. Inferring a critical current

I

c

variation from this resistance distribution, we present an optimized process developed from a systematic 38 wafer study that results in < 3.5% relative standard deviation (RSD) in critical current (

≡

σ

I

c

/

I

c

) for 3000 Josephson junctions (both single-junctions and asymmetric SQUIDs) across an area of 49 cm2. Looking within a 1x1 cm moving window across the substrate gives an estimate of the variation characteristic of a given qubit chip. Our best process, utilizing ultrasonically assisted development, uniform ashing, and dynamic oxidation has shown

σ

I

c

/

I

c

= 1.8% within 1x1 cm, on average, with a few 1x1 cm areas having

σ

I

c

/

I

c

< 1.0% (equivalent to

σ

f

/

f

< 0.5%). Such stability would drastically improve the yield of multi-junction chips with strict critical current requirements.
A composition transferable and time-scale consistent coarse-grained model for cis-polyisoprene and vinyl-polybutadiene oligomeric blends
Authors: Ohkuma Takahiro , Kremer Kurt
Published: May 2020

We study a coarse-grained model for a binary blend system composed of cis-polyisoprene and vinyl-polybutadiene. Since the slow relaxation dynamics of polymers may require very long simulation times, coarse-grained descriptions are regularly used in order to reduce computational cost while keeping the essential physics. Relaxation dynamics of a coarse-grained model is sometimes accelerated by the smooth coarse-grained potentials. However, the magnitude of the acceleration may be different in different components in a multi-component system. In order to simulate a time-scale consistent dynamics, the acceleration effects should be the same across the different components. Here, we investigate a time-scale consistent coarse-grained model for a binary polymer blend. For the coarse-grained equation of motion, we adopt the Langevin equation and adjust the friction coefficients by focusing on the relaxation times of the first normal mode of the polymers. A united-atom model is used as a reference system of the coarse-graining. Since it is found that the solubility parameter of the atomistic model is much larger than the experimental result, our simulation model is not applicable for the quantitative predictions, but we utilize it as a example system to study a time scale mismatch of a coarse-grained model. We find that the coarse-grained potentials and the friction coefficients derived for one blend composition captures different compositions of the blend. Furthermore, it is found that the magnitude of the acceleration effects of the blend rarely depends on the composition ratio. This implies that our coarse-grained model can be used for inhomogeneous systems.
What Adaptations and Adaptation Studies Tell Us (and Sometimes Don't Tell Us) about Politics, Culture, and Social Change
Authors: Grossman Julie
Published: May 2020

This essay explores the implications of a Supreme Court dissent written by US Chief Justice John Roberts in the style of film noir. The article analyses Roberts’s adaptation, discussing more broadly the use of classic literary types such as the hardboiled detective and the western cowboy in social and political discourse. The article argues for the significance of adaptation studies in our polarized contemporary society because its valuing of change counters formulaic appropriations of the past and fixed ideas and models of experience. The essay suggests not only that political leaders mired in the past cannot adapt to changing society and social roles, but also that adaptation studies hones readers’ discernment, especially called for when public figures use fictional patterns to address real-world circumstances.
Construct Validity of the Stroop Color-Word Test: Influence of Speed of Visual Search, Verbal Fluency, Working Memory, Cognitive Flexibility, and Conflict Monitoring
Authors: Periáñez José A , Lubrini Genny , García-Gutiérrez Ana , Ríos-Lago Marcos
Published: May 2020

Objective

85 years after the description of the Stroop interference effect, there is still a lack of consensus regarding the cognitive constructs underlying scores from standardized versions of the test. The present work aimed to clarify the cognitive mechanisms underlying direct (word-reading, color-naming, and color-word) and derived scores (interference, difference, ratio, and relative scores) from Golden’s standardized version of the test.

Method

After a comprehensive review of the literature, five cognitive processes were selected for analysis: speed of visual search, phonemic verbal fluency, working memory, cognitive flexibility, and conflict monitoring. These constructs were operationalized by scoring five cognitive tasks (WAIS-IV Digit Symbol, phonemic verbal fluency [letter A], WAIS-IV Digit Span, TMT B-A, and reaction times to the incongruent condition of a computerized Stroop task, respectively). About 83 healthy individuals (mean age = 25.2 years) participated in the study. Correlation and regression analyses were used to clarify the contribution of the five cognitive processes on the prediction of Stroop scores.

Results

Data analyses revealed that Stroop word-reading reflected speed of visual search. Stroop color-naming reflected working memory and speed of visual search. Stroop color-word reflected working memory, conflict monitoring, and speed of visual search. Whereas the interference score was predicted by both conflict monitoring and working memory, the ratio score (color-word divided by color-naming) was predicted by conflict monitoring alone.

Conclusion

The present results will help neuropsychologists to interpret altered patient scores in terms of a failure of the cognitive mechanisms detailed here, benefitting from the solid background of preceding experimental work.
Temporally variable predation risk and fear retention in Trinidadian guppies
Authors: Crane Adam L , Feyten Laurence E A , Ramnarine Indar W , Brown Grant E
Published: May 2020

Predation fear is a unifying theme across vertebrate taxa. Here, we explored how the frequency and duration of predation risk affects postrisk fear behavior in Trinidadian guppies. We first exposed individuals to visual cues of potential predators for 3 days, either frequently (6×/day) or infrequently (1×/day). Each exposure lasted for either a relatively brief (5 min) or long (30 min) duration, whereas a control group consisted of no risk exposures. One day later, we quantified guppy behavior. All background risk treatments induced a fear response toward a novel odor (i.e., neophobia), and individuals previously exposed to frequent bouts of brief risk showed elevated baseline fear. Although neophobic responses were initially similar across risk treatments (1 day later), retention of this response differed. After 8 days, only individuals previously exposed to brief bouts of risk (both frequent and infrequent) maintained neophobic responses, whereas their initially higher level of baseline fear remained elevated but was no longer significantly different from the control. These results increase our understanding of temporal factors that affect the intensity and retention of fear that persists after risk exposure, which may have applications across vertebrates in relation to problems with fearful phenotypes.
MLCDForest: multi-label classification with deep forest in disease prediction for long non-coding RNAs
Authors: Wang Wei , Dai QiuYing , Li Fang , Xiong Yi , Wei Dong-Qing
Published: May 2020

The long non-coding RNAs (lncRNAs) are subject of intensive recent studies due to its association with various human diseases. It is desirable to build the artificial intelligence-based models for prediction of diseases or tissues based on the lncRNAs data, which will be useful in disease diagnosis and therapy. The accuracy and robustness of existing models based on the machine learning techniques are subject to further improvement. In this study, we propose a deep learning model, called Multi-Label Classifications with Deep Forest, termed MLCDForest, to address multi-label classification on tissue prediction for a given lncRNA, which can be regarded as an implementation of the deep forest model in multi-label classification. The MLCDForest is a sequential multi-label-grained scanning method, which distinguishes from the standard deep forest model. It is proposed to train in sequential of multi-labels with label correlation considered. A systematic comparison using the lncRNA-disease association datasets demonstrates that our method consistently shows superior performance over the state-of-the-art methods in disease prediction. Considering label correlation in the sequential multi-label-grained scanning, our model provides a powerful tool to make multi-label classification and tissue prediction based on given lncRNAs.
MetaBCC-LR: metagenomics binning by coverage and composition for long reads
Authors: Wickramarachchi Anuradha , Mallawaarachchi Vijini , Rajan Vaibhav , Lin Yu
Published: May 2020

Motivation

Metagenomics studies have provided key insights into the composition and structure of microbial communities found in different environments. Among the techniques used to analyse metagenomic data, binning is considered a crucial step to characterize the different species of micro-organisms present. The use of short-read data in most binning tools poses several limitations, such as insufficient species-specific signal, and the emergence of long-read sequencing technologies offers us opportunities to surmount them. However, most current metagenomic binning tools have been developed for short reads. The few tools that can process long reads either do not scale with increasing input size or require a database with reference genomes that are often unknown. In this article, we present MetaBCC-LR, a scalable reference-free binning method which clusters long reads directly based on their k-mer coverage histograms and oligonucleotide composition.

Results

We evaluate MetaBCC-LR on multiple simulated and real metagenomic long-read datasets with varying coverages and error rates. Our experiments demonstrate that MetaBCC-LR substantially outperforms state-of-the-art reference-free binning tools, achieving ∼13% improvement in F1-score and ∼30% improvement in ARI compared to the best previous tools. Moreover, we show that using MetaBCC-LR before long-read assembly helps to enhance the assembly quality while significantly reducing the assembly cost in terms of time and memory usage. The efficiency and accuracy of MetaBCC-LR pave the way for more effective long-read-based metagenomics analyses to support a wide range of applications.

Availability and implementation

The source code is freely available at: https://github.com/anuradhawick/MetaBCC-LR.

Supplementary information

Supplementary data are available at Bioinformatics online.
MHCAttnNet: predicting MHC-peptide bindings for MHC alleles classes I and II using an attention-based deep neural model
Authors: Venkatesh Gopalakrishnan , Grover Aayush , Srinivasaraghavan G , Rao Shrisha
Published: May 2020

Motivation

Accurate prediction of binding between a major histocompatibility complex (MHC) allele and a peptide plays a major role in the synthesis of personalized cancer vaccines. The immune system struggles to distinguish between a cancerous and a healthy cell. In a patient suffering from cancer who has a particular MHC allele, only those peptides that bind with the MHC allele with high affinity, help the immune system recognize the cancerous cells.

Results

MHCAttnNet is a deep neural model that uses an attention mechanism to capture the relevant subsequences of the amino acid sequences of peptides and MHC alleles. It then uses this to accurately predict the MHC-peptide binding. MHCAttnNet achieves an AUC-PRC score of 94.18% with 161 class I MHC alleles, which outperforms the state-of-the-art models for this task. MHCAttnNet also achieves a better F1-score in comparison to the state-of-the-art models while covering a larger number of class II MHC alleles. The attention mechanism used by MHCAttnNet provides a heatmap over the amino acids thus indicating the important subsequences present in the amino acid sequence. This approach also allows us to focus on a much smaller number of relevant trigrams corresponding to the amino acid sequence of an MHC allele, from 9251 possible trigrams to about 258. This significantly reduces the number of amino acid subsequences that need to be clinically tested.

Availability and implementation

The data and source code are available at https://github.com/gopuvenkat/MHCAttnNet.
EasyVS: a user-friendly web-based tool for molecule library selection and structure-based virtual screening
Authors: Pires Douglas E V , Veloso Wandré N P , Myung YooChan , Rodrigues Carlos H M , Silk Michael , Rezende Pâmela M , Silva Francislon , Xavier Joicymara S , Velloso João P L , da Silveira Carlos H , Ascher David B
Published: May 2020

EasyVS is a web-based platform built to simplify molecule library selection and virtual screening. With an intuitive interface, the tool allows users to go from selecting a protein target with a known structure and tailoring a purchasable molecule library to performing and visualizing docking in a few clicks. Our system also allows users to filter screening libraries based on molecule properties, cluster molecules by similarity and personalize docking parameters.

Availability and implementation

EasyVS is freely available as an easy-to-use web interface at http://biosig.unimelb.edu.au/easyvs.

Contact

douglas.pires@unimelb.edu.au or david.ascher@unimelb.edu.au

Supplementary information

Supplementary data are available at Bioinformatics online.
ipcoal: an interactive Python package for simulating and analyzing genealogies and sequences on a species tree or network
Authors: McKenzie Patrick F , Eaton Deren A R
Published: May 2020

ipcoal is a free and open source Python package for simulating and analyzing genealogies and sequences. It automates the task of describing complex demographic models (e.g. with divergence times, effective population sizes, migration events) to the msprime coalescent simulator by parsing a user-supplied species tree or network. Genealogies, sequences and metadata are returned in tabular format allowing for easy downstream analyses. ipcoal includes phylogenetic inference tools to automate gene tree inference from simulated sequence data, and visualization tools for analyzing results and verifying model accuracy. The ipcoal package is a powerful tool for posterior predictive data analysis, for methods validation and for teaching coalescent methods in an interactive and visual environment.

Availability and implementation

Source code is available from the GitHub repository (https://github.com/pmckenz1/ipcoal/) and is distributed for packaged installation with conda. Complete documentation and interactive notebooks prepared for teaching purposes, including an empirical example, are available at https://ipcoal.readthedocs.io/.

Contact

p.mckenzie@columbia.edu