bluuebunny/crossref_metadata_2025 huggingface dataset:
Research on the discharge characteristics of XLPE insulated DC cables
Authors: Liu Ying , Zheng Xinlong
Published: December 2021

This paper focuses on the discharge of cross-linked polyethylene (XLPE) insulated DC cables, which has become a concern of power utilities when carrying out a voltage withstand test or an outage maintenance. Based on the electrical tree initiation test of XLPE block samples under grounded DC voltages, the main cause and key factors for damages of DC insulation resulted by grounding discharge were investigated, and the allowable voltage level to start the accelerated discharge operation was estimated. By the laboratory tests of two XLPE cable samples discharged under different conditions, the basic discharge rules were observed, the equivalent circuit was set up, and the equipment parameters were determined. In addition, a method to estimate the discharge time for cable lines with different lengths was proposed. Finally, the on-site measured data of decay voltage and leakage current were presented for a 200 kV DC XLPE cable line which had been discharged steppedly through a resistance grounding device after the DC voltage withstand test, and the experimental results were found to be in good agreement with the theoretical data.
Electrical conductivity of nanoring-based transparent conductive films: A mean-field approach
Authors: Tarasevich Yuri Yu. , Eserkepov Andrei V. , Vodolazskaya Irina V.
Published: December 2021

We have studied the electrical conductivity of nanoring-based, transparent conductive films, these being promising elements for flexible electronic devices. Both the wire resistance and the junction resistance were taken into account. We have calculated the dependency of the electrical conductivity on the number density of the rings. We have proposed a mean-field approach to estimate the dependency of the electrical conductivity on the main parameters. Comparison of direct computations of the electrical conductivity and the estimates provided by the mean-field approach evidenced the applicability of this approach for those cases where the wire resistance dominates over the junction resistance and where both resistances are of the same order. For these two cases, both the direct computations and the mean-field approach evidenced a linear dependence of the electrical conductivity of the films on the number density of the conductive rings. By contrast, the dependence of the electrical conductivity on the number density of the conductive rings is quadratic when the junction resistance dominates over the wire resistance. In this case, the mean-field approach significantly overestimates the electrical conductivity since the main assumptions underlying this approach are no longer fulfilled.
Residual feed intake and the inclusion of crude glycerin in the diet of feedlot-finished Nellore cattle
Authors: Silva Gabriele Voltareli da , Batalha Camila Delveaux Araujo , Cyrillo Joslaine Noely dos Santos Gonçalves , Canesin Roberta Carrilho , Barducci Robson Sfaciotti , Bonilha Sarah Figueiredo Martins
Published: December 2021

Context The beef market faces an increasing demand for an environmentally friendly production system with high-quality final products. The use of strategies that improve system efficiency without detriment on quality are desired for both producers and consumer. Aims This study aimed to evaluate the effects of residual feed intake (RFI) and dietary inclusion of crude glycerin on carcass and meat quality traits of feedlot-finished Nellore cattle. Methods Nellore bulls selected for growth and classified as high (n = 14) and low (n = 14) RFI, with average liveweight of 328 kg and age of 552 days were used. Bulls received a high-concentrate diet for 96 days before slaughter and were randomly allocated to two experimental diets in a 2 × 2 factorial arrangement: RFI class (low or high) and dietary inclusion (CG) or not (WCG) of crude glycerin (20% on dry-matter basis). Data were analysed with the SAS MIXED procedure considering RFI class and diet as fixed effects and selection line as a random effect. Key results There were no significant differences between RFI classes for dry-matter intake during finishing or production traits. Dry-matter intake tended to be reduced by 16% in CG bulls, without alterations in production. Dietary glycerin inclusion tended to increase the protein content in the Longissimus muscle and significantly reduced the fat content. In low-RFI bulls, shear force was higher in unaged beef, and shear force and myofibrillar fragmentation index tended to be higher in meat aged for 14 days. RFI class did not affect Longissimus muscle fatty acid profile, which was highly influenced by dietary glycerin inclusion. Bulls allocated to the CG treatment had a reduction in saturated fatty acids, an increase in odd-chain fatty acids, and a trend towards increased omega-3 fatty acids, which significantly increased the omega-3:omega-6 ratio. Conclusions The use of Nellore bulls classified as low-RFI and crude glycerin inclusion in finishing diets of Nellore cattle do not compromise production, carcass traits or beef properties. Implications This approach increases the efficiency and sustainability of the production process and improves the nutritional characteristics of beef for human consumption.
A review of the classification and taxonomic and geographic distribution of cleistogamy in Australian grasses
Authors: Thompson E. J.
Published: December 2021

Cleistogamy, self-fertilisation within a closed flower, was found in 135 Australian grass species from 46 genera within 5 subfamilies representing 14% of the species and 30% of the genera. This represents an increase from 4% of species and 12% of genera from previous records. Expressions of cleistogamy were classified into three main categories on the basis of: presence or absence of anther dimorphism, presence of amphigamy with or without spikelet peculiarities, and chasmogamous and cleistogamous spikelets on separate plants. One category of these dimorphisms involves species that have differing terminal and axillary inflorescences (amphigamy) with corresponding spikelets so different that the axillary ones appear to belong to a different genus. Dimorphisms within cleistogamous species were found in inflorescences, spikelets, florets, anthers and caryopses. The highest concentration of Australian cleistogamous grasses occurs in the subtropical climatic zone and more than three-quarters of the species are chloridoid and panicoid with nearly equal proportions. Of Australian cleistogamous grasses, 33% have C3 photosynthetic pathway and 67% have C4, and the largest taxonomic groups are panicoid with 38% and chloridoid with 39%.
RNA-Seq analysis of resistant and susceptible soybean genotypes in response to stress from soybean cyst nematode (
Authors: Jiang Haipeng , Bu Fanshan , Yan Shixin , Li Yi , Wu Tong , Bai RuiYao , Xu Aitong , Zhao Xue , Han Yingpeng
Published: December 2021

The soybean cyst nematode (SCN, Heterodera glycine Ichinohe) is a major disease affecting soybean (Glycine max (L.) Merr.) production and yield. Breeding of new SCN-resistant cultivars and understanding their resistance mechanisms are valuable for improving SCN resistance of soybean. However, we still know little about resistance mechanisms to SCN. The purpose of our analysis was to understand the different resistance mechanisms of resistant and susceptible lines to SCN by dissecting their transcriptional changes during infection by SCN HG type 1.2.3.5.7. In this study, 119 recombinant inbred lines derived from a cross of cv. Dongnong L-204 (SCN resistant) and cv. Heinong 37 (SCN susceptible) were identified for resistance status to SCN HG type 1.2.3.5.7. Roots of the lines identified as extremely resistant or susceptible (L5, L89) were sequenced by transcriptome, and we obtained 66.61 Gb of data. Compared with the untreated control, there were 8394 and 6899 differentially expressed genes in SCN-infected roots of L5 and L89, respectively. Genes of metabolic pathways, biosynthesis of secondary metabolites, plant hormone signal transduction, and plant–pathogen interaction pathway were significantly expressed in both resistant and susceptible genotypes. The expression of genes of phenylpropanoid biosynthesis, flavonoid biosynthesis, thiamine metabolism, cutin, suberin and wax biosynthesis, and endocytosis pathway was significantly higher in the resistant line than the susceptible line. Transcription factor analysis showed that 88 transcription factors from 18 transcription factor families responded to SCN stress. Nine genes were identified by reverse transcriptase qPCR to be associated with SCN resistance. This study helps us to understand better the mechanism of soybean resistance to SCN.
Are canid pest ejectors an effective control tool for wild dogs in an arid rangeland environment?
Authors: Kreplins T. L. , Miller J. , Kennedy M. S.
Published: December 2021

Abstract Context Wild dogs are a significant pest species of livestock production and native wildlife in Australia. A suite of control tools is used to mitigate predation impacts. Baiting with sodium fluoroacetate is the most commonly used control tool in Australia; however, its effectiveness can be reduced by interference by non-target species, and in some contexts by microbial degradation of the toxin. Canid pest ejectors (CPEs) are a mechanical device with an attractant ‘lure head’ designed to eject a lethal toxin into the mouth of canids pulling on the lure head. A range of lure heads can be used to attract canids to pull, and trigger CPEs. Aims We aimed to determine whether uptake of CPEs by wild dogs in an arid rangeland environment could cause a decline in a wild dog population. We also aimed to determine whether there are particular lure heads that increase the rate of CPEs being triggered by wild dogs. Methods We deployed one hundred CPEs over four sessions of control across three properties in the southern rangelands of Western Australia from 2018 to 2020. Each session consisted of 2 months of CPE deployment with two different lure heads, totalling eight lure head types over the entire study. All CPEs were monitored using camera traps. Key results Wild dog density varied over the study period. In all four control sessions, a decrease in wild dog density was recorded (–46%, –5%, –13%, –38%). Wild dog activity events on camera and their interest in CPEs differed between sessions and lures (i.e. higher with scent-based lures). Non-target species did not interfere with CPEs significantly, despite a higher number of activity events by non-target species than wild dogs. Conclusions CPEs caused a reduction of 5–46% of wild dog density when deployed in the southern rangelands of Western Australia. Non-target interference was minimal when using CPEs for wild dog control. Implications Use of scent-based lures on felt lure heads is recommended for successful use of CPEs for wild dog control in arid rangeland environments. Future on-ground wild dog control should include CPEs as a complementary tool for the reduction of wild dog density.
SARS-CoV-2 spreads through cell-to-cell transmission
Authors: Zeng Cong , Evans John P. , King Tiffany , Zheng Yi-Min , Oltz Eugene M. , Whelan Sean P. J. , Saif Linda J. , Peeples Mark E. , Liu Shan-Lu
Published: December 2021

Significance

It is currently unknown if SARS-CoV-2 can spread through cell–cell contacts, and if so, the underlying mechanisms and implications. In this work, we show, by using lentiviral pseudotyped virus, that the spike protein of SARS-CoV-2 mediates the viral cell-to-cell transmission, with an efficiency higher than that of SARS-CoV. We also find that cell–cell fusion contributes to cell-to-cell transmission, yet ACE2 is not absolutely required. While the authentic variants of concern (VOCs) B.1.1.7 (alpha) and B.1.351 (beta) differ in cell-free infectivity from wild type and from each other, these VOCs have similar cell-to-cell transmission capability and exhibit differential sensitivity to neutralization by vaccinee sera. Results from our study will contribute to a better understanding of SARS-CoV-2 spread and pathogenesis.
Minimally-modeled search of higher multipole gravitational-wave radiation in compact binary coalescences
Authors: Vedovato G , Milotti E , Prodi G A , Bini S , Drago M , Gayathri V , Halim O , Lazzaro C , Lopez D , Miani A , O’Brien B , Salemi F , Szczepanczyk M , Tiwari S , Virtuoso A , Klimenko S
Published: December 2021

As the Advanced LIGO and Advanced Virgo interferometers, soon to be joined by the KAGRA interferometer, increase their sensitivity, they detect an ever-larger number of gravitational waves with a significant presence of higher multipoles (HMs) in addition to the dominant (2, 2) multipole. These HMs can be detected with different approaches, such as the minimally-modeled burst search methods, and here we discuss one such approach based on the coherent WaveBurst (cWB) pipeline. During the inspiral phase the HMs produce chirps whose instantaneous frequency is a multiple of the dominant (2, 2) multipole, and here we describe how cWB can be used to detect these spectral features. The search is performed within suitable regions of the time-frequency representation; their shape is determined by optimizing the receiver operating characteristics. This novel method has already been used in the GW190814 discovery paper (Abbott et al 2020 Astrophys. J. Lett.
896 L44) and is very fast and flexible. Here we describe in full detail the procedure used to detect the (3, 3) multipole in GW190814 as well as searches for other HMs during the inspiral phase, and apply it to another event that displays HMs, GW190412, replicating the results obtained with different methods. The procedure described here can be used for the fast analysis of HMs and to support the findings obtained with the model-based Bayesian parameter estimates.
Effect of the electric field profile on the accuracy of E-FISH measurements in ionization waves
Authors: Chng Tat Loon , Pai David Z , Guaitella Olivier , Starikovskaia Svetlana M , Bourdon Anne
Published: December 2021

Electric field induced second harmonic (E-FISH) generation has emerged as a versatile tool for measuring absolute electric field strengths in time-varying, non-equilibrium plasmas and gas discharges. Yet recent work has demonstrated that the E-FISH signal, when produced with tightly focused laser beams, exhibits a strong dependence on both the length and shape of the applied electric field profile (along the axis of laser beam propagation). In this paper, we examine the effect of this dependence more meaningfully, by predicting what an E-FISH experiment would measure in a plasma, using 2D axisymmetric numerical fluid simulations as the true value. A pin-plane nanosecond discharge at atmospheric pressure is adopted as the test configuration, and the electric field evolution during the propagation of the ionization wave (IW) is specifically analysed. We find that the various phases of this evolution (before and up to the front arrival, immediately behind the front and after the connection to the grounded plane) are quite accurately described by three unique electric field profile shapes, each of which produces a different response in the E-FISH signal. As a result, the accuracy of an E-FISH measurement is generally predicted to be comparable in the first and third phases of the IW evolution, and significantly poorer in the second (intermediate) phase. Fortunately, even though the absolute error in the field strength at certain time instants could be large, the overall shape of the field evolution curve is relatively well captured by E-FISH. Guided by the simulation results, we propose a procedure for estimating the error in the initial phase of the IW development, based on the presumption that the starting field profile mirrors that of its corresponding Laplacian conditions before evolving further. We expect that this approach may be readily generalized and applicable to other IW problems or phenomena, thus extending the utility of the E-FISH diagnostic.
Characterization of FBK 3D pixel sensor modules based on RD53A readout chip for the ATLAS ITk
Authors: Samy Md.A.A. , Lapertosa A. , Vannoli L. , Gemme C. , Dalla Betta G.-F.
Published: December 2021

CERN is planning to upgrade its Large Hadron Collider to the High Luminosity phase (HL-LHC), pushing detector technologies to cope with unprecedently demanding performance in terms of particle rate and radiation hardness. The ATLAS experiment decided to equip the innermost layer (L0) of its Inner Tracker (ITk) with small-pitch 3D pixels of two different geometries, i.e., 25 µm × 100 µm for the central barrel and 50 µm × 50 µm for the lateral rings. A new generation of 3D pixels featuring these small-pitch dimensions and reduced active thickness (∼150 µm) has been developed to this purpose within a collaboration of INFN and FBK since 2014. Recently, the R&D activities have been focused on the characterization of modules based on sensors compatible with the RD53A readout chip, which were tested in laboratory and at beam lines. In this paper, we report on the characterization of modules irradiated with protons up to a fluence of 1 × 1016 neq/cm2, including threshold tuning and noise measurements, and results from beam tests performed at DESY. Moreover, we will discuss about the electrical characteristics at wafer level and at module level before and after irradiation.
Helium isotope separation by bi-layer membranes of g-C3N4
Authors: Poteryaeva Valentina A , Bubenchikov Alexey M , Bubenchikov Michael A , Lun-Fu Alexandr V , Jambaa Soninbayar
Published: December 2021

The problem of helium isotope separation via bi-layer membranes of graphitic carbon nitride g-C3N4 has been studied. The probability of passing isotopes through the membrane is derived from solving the Schrödinger integral equation using Hermite polynomials. The potential energy of the membrane is calculated based on modified Lennard-Johnes potential. The separation degree of the 3He/4He reaches the value of 1045 due to the resonant effect.
Dual-function of the ZnO nano-sheets as light absorber scaffold and electron transport material in perovskite solar cells
Authors: Bui Cong-Dan , Cao Van-Phuoc , Nguyen Van-Quy , Bui Thi-Hang , Tran Van-Dang
Published: December 2021

Recent advances in the development of perovskite solar cells using CH3NH3PbI3 as the absorber material have reached over 18.7% in power conversion efficiency. The best performance perovskite-based cells required support of a mesoporous charge collector. In this work we present a new process for preparing perovskite solar cells with the structure of AZO/Au/AZO(AAA)/ZnO-sheets/CH3NH3PbI3/HTM/Au. Herein, ZnO nanosheets layer was prepared by electrochemical deposition method using zinc nitrate hexahydrate as nutrient solution, then annealed at 150 °C in ambient air. The results show that high crystal ZnO sheets assembled simply from AZO top layer could act as electron transporter and scaffold for perovskite layer. The presentation of ZnO scaffold was exploited to improve 19% in power conversion efficiency, offering great promise for further improvement of the low-temperature, low-cost processing solar technology.
Biological synthesis, physico-chemical characterization of undoped and Co doped α-Fe2O3 nanoparticles using Tribulus terrestris leaf extract and its antidiabetic, antimicrobial applications
Authors: Sakthi Athithan A S , Jeyasundari J , Jacob Y B A
Published: December 2021

Hematite (α-Fe2O3) nanoparticles (NPs) were chemically and thermodynamically more stable among iron oxide nanoparticles. Doping of Co2+ metal ion in α-Fe2O3 can modify the structural, optical and magnetic properties of NPs and also enhances the potential of the biomedical applications. In the current study, undoped and Co doped hematite nanoparticles were synthesised by co-precipitation method using Tribulus terrestris L. leaf extract as bio-reductant. The magnetic, optical and structural investigations were studied with the help of Ultraviolet-visible (UV-Vis), Fourier Transform Infrared (FTIR), Scanning Electron Microscopy equipped with Energy Dispersive X-ray (SEM-EDX) Spectroscopy, Vibrating Sample Magnetometer (VSM) and X-ray Diffraction (XRD) Spectroscopy. XRD analysis shows that synthesized nanoparticles were in hematite phase, rhombohedral in structure. XRD spectral pattern clearly evidenced that prepared α-Fe2O3 and Co-Fe2O3 NPs were highly crystalline with no impurity peaks. Using VSM spectra, the M-H curve indicates that saturation magnetisation (Ms) value increases for Co-Fe2O3 NPs than undoped α-Fe2O3 NPs, it can be clearly seen that doping largely affects the magnetic nature of nanoparticles. In the UV-Vis spectra, absorption maxima increases and band gap value decreases for cobalt doped hematite nanoparticles indicating the substitution of Fe2+ ions by Co2+ ions in α-Fe2O3 lattice sites. Antidiabetic and antimicrobial activity of the synthesized undoped and Co doped hematite NPs were tested by alpha-amylase inhibitory and disc diffusion method. The Co-Fe2O3 NPs have greatly inhibited the digestive enzyme and microbial strains as compared to undoped α-Fe2O3 NPs.
The investigation of the effect of nano particles on dry sliding wear and corrosion behavior of Al-Mg/Al2O3 composites
Authors: A Chandrashekar , Mohanavel V , Kaladgi Abdul Razak , R Vinod Kumar , Ravichandran M , Arunkumar G L , Basheer Dadapeer
Published: December 2021

Aluminum matrix composites were extensively used as structural material as it possesses good surface properties such as wear and corrosion resistance. The practical importance of nano particles in composite materials has triggered widespread attention towards the enhancement of its properties. In this study, Al-Mg/Al2O3 (0–8 wt%) metal matrix nano composites fabricated by two step stir casting route was investigated to comprehend its wear and corrosion behaviour. The Pin-on-Disc dry sliding wear test was performed on Al-Mg/Al2O3 (0–8 wt%) by adopting Design of Experiments under the action of different contact loads and sliding distance following the ASTM G99 Standard. The experimental results conveyed that specific wear rate decreases with increase in sliding distance. Statistical analysis was performed by Taguchi’s Technique and Analysis of Variance (ANOVA) to determine the most dominating factor that influences specific wear rate for the optimum weight percentage of reinforcement. Analysis revealed adequacy with the constructed model in predicting the wear behavior of composite and unreinforced Al-Mg alloy. The corrosion behaviour of the base alloy and composites was analysed by static immersion and electrochemical assessments, by immersing prepared specimens in aqueous sodium chloride (3.5%) solution. The dependance of corrosion rate of the composites with the weight percentage of Al2O3, exposure duration and temperature of the corrosive medium was studied in detail. Corrosion test results exhibit that corrosion rate decreases with increase in weight percentage of Al2O3 particles and exposure duration, whereas it follows reverse trend with increase in corrosion medium temperature.
Effect of electrochemical modification of titanium hydride fraction on oxygen content in surface and deep layers
Authors: Yastrebinsky R N , Pavlenko V I , Gorodov A I , Karnauhov A A , Cherkashina N I , Yastrebinskay A V
Published: December 2021

The paper presents a study of the microstructure and oxygen concentration in the surface and deep layers of fractions of unmodified titanium hydride and titanium hydride modified by electrodeposited layers of Ti and Cu at temperatures of 300 °C–900 °C. The composition of the oxide layer and the concentration of titanium and oxygen atoms are estimated. It is shown that an increase in the thickness and compaction of the oxide layer with increasing temperature prevents the penetration of oxygen into the deep layers of the unmodified fraction of titanium hydride. Modification of titanium hydride by electrochemical deposition of metallic titanium at a temperature of 700 °C reduces the oxygen concentration in titanium hydride at a layer depth of 50 μm from 35 wt% to 12.5 wt%. Electrodeposition of coatings based on titanium and copper at 700 °C reduces the oxygen concentration to 9.2 wt%, which may be due to the protective mechanism of the formed copper titanate layer. At 900 °C, in the modification layer based on titanium and copper, due to the eutectoid transformation of the β-phase of titanium, the process of contact melting occurs and a multiphase zone is formed. The oxygen concentration at a layer depth of 50 μm is no more than 12.4 wt%.
Women are more likely to experience author disputes
Authors: Allen Michael
Published: December 2021

Female academics are more likely to have authorship disagreements when publishing their research than their male colleagues, according to a global survey.
The nuclear fight
Authors: Crease Robert P
Published: December 2021

Robert P Crease talks to William D Magwood IV, director-general of the Nuclear Energy Agency, about the battle to keep nuclear power on the agenda.
Going in circles
Authors: England Nick
Published: December 2021

In response to Michael Allen’s Feature article “Twists, turns, thrills and spills” in which he explains the physics behind the sensations that we experience on rollercoasters.
The right to flight
Authors: Holmes Steve
Published: December 2021

In response to Peter Wright’s letter “Spaced out” in which he questions the value of billionaires’ space travel, such as the 20 July flight of Jeff Bezos on the rocket New Shepard, built by his aerospace company Blue Origin.
Scanning the cosmos for signs of technology
Authors: Appell David
Published: December 2021

Ever since planets beyond our solar system were first discovered, astronomers have been hunting life beyond our world. While biological signatures are crucial, the idea of scouring the skies for signs of technosignatures from advanced civilizations is gaining momentum, as David Appell discovers.
Chain mail fabric shown to stiffen under pressure
Authors: Jarman Sam
Published: December 2021

Physicists have designed a chain mail fabric that can be easily folded but becomes much stiffer when compressed.
Bose–Einstein condensates hit record low temperature
Authors: Boerkamp Martijn
Published: December 2021

Researchers have used a new way of controlling the expansion of matter in a free-falling Bose–Einstein condensate to produce the coldest effective temperature ever measured.
Chinese photographer wins astronomy prize
Authors: Banks Michael
Published: December 2021

Chinese photographer Shuchang Dong has won the 2021 Astronomy Photographer of the Year for an image depicting the annular solar eclipse on 21 June 2020.
Geophysics fellow nominations hit by lack of diversity
Authors: Gwynne Peter
Published: December 2021

A section of the American Geophysical Union (AGU) has declined to recommend any of its members for a 2021 fellowship following a lack of diversity among potential nominees.
Join a prize-winning field if you want science success
Authors: Allen Michael
Published: December 2021

The productivity of scientists working in a field that has recently won a high-profile award increases rapidly in the following decade according to an analysis.
Ideals and ideologies
Authors: Young Alison
Published: December 2021

In response to Ling Xin’s news analysis article “Tibet seen as ideal stargazing spot” in which she reports that Chinese astronomer Licai Deng has found that Saishiteng Mountain in the Tibetan Plateau has ideal conditions for future gigantic optical telescopes.
Food for thought
Authors: Murnaghan David
Published: December 2021

In response to the “Physics on holiday” special issue of Physics World, which included articles on the science of sandcastles, rollercoasters and food and drink.
High-spec open-source microscopy for all
Authors: Bowman Richard , Stirling Julian
Published: December 2021

Open-science hardware offers unprecedented technological access to researchers and enthusiasts all over the globe. Richard Bowman and Julian Stirling of the Bath Open Instrumentation Group describe the lessons learnt in developing a low-cost, laboratory-grade microscope.
Advice for post-COVID careers
Authors: Hirst Andrew , Benson Veronica
Published: December 2021

COVID-19 has changed some aspects of the world of work forever, but others have stayed much the same. Andrew Hirst and Veronica Benson look at how physics students can prepare for careers in the post-pandemic world, and what universities and employers can do to help them.
International quantum year proposed for 2025
Authors: Hiscott Laura
Published: December 2021

Physicists around the world are drawing up plans for a year-long celebration of quantum science and technology in 2025.
A quantum promise
Authors: Boerkamp Martijn
Published: December 2021

Freeke Heijman from Quantum Delta NL tells Martijn Boerkamp how the Netherlands is forging ahead in quantum technologies.
Going global
Authors: Philpot Julian
Published: December 2021

A response to Andrew Hirst and Veronica Benson’s article “Advice for post-COVID careers”, in which they argue that universities should consider the needs of local employers when designing their degree courses.
Sensing gravity, the quantum way
Authors: Allen Michael , Hiscott Laura , Harris Margaret , Banks Michael
Published: December 2021

Devices that exploit the extreme sensitivity of quantum states are making their way out of the lab and into everything from construction and healthcare to seismology. Michael Allen learns more about the technology that goes into building a quantum gravity sensor, and its multitude of uses in research and industry.
A tale of two scientists
Authors: Hiscott Laura , Benson Veronica
Published: December 2021

Laura Hiscott reviews Flashes of Creation: George Gamow, Fred Hoyle, and the Great Big Bang Debate by Paul Halpern.
Joining the dots
Authors: Hiscott Laura
Published: December 2021

Laura Hiscott reviews Eight Improbable Possibilities: the Mystery of the Moon and Other Implausible Scientific Truths by John Gribbin.
Strictly convex entropy and entropy stable schemes for reactive Euler equations
Authors: Zhao Weifeng
Published: December 2021

This paper presents entropy analysis and entropy stable (ES) finite difference schemes for the reactive Euler equations with chemical reactions. For such equations we point out that the thermodynamic entropy is no longer strictly convex. To address this issue, we propose a strictly convex entropy function by adding an extra term to the thermodynamic entropy. Thanks to the strict convexity of the proposed entropy, the Roe-type dissipation operator in terms of the entropy variables can be formulated. Furthermore, we construct two sets of second-order entropy preserving (EP) numerical fluxes for the reactive Euler equations. Based on the EP fluxes and the Roe-type dissipation operators, high-order EP/ES fluxes are derived. Numerical experiments validate the designed accuracy and good performance of our schemes for smooth and discontinuous initial value problems. The entropy decrease of ES schemes is verified as well.
Modeling myosin Va liposome transport through actin filament networks reveals a percolation threshold that modulates transport properties
Authors: Walcott S. , Warshaw D. M.
Published: December 2021

Myosin Va-mediated transport of liposomes through actin filament networks transitions, with increasing actin density, from directed transport to random walks interspersed with pauses. The density at which this phase transition occurs varies inversely with liposome diameter. Cells can tune actin density and cargo size to regulate cargo delivery.
Uncovering the phylogeography of Schinus terebinthifolia in South Africa to guide biological control
Authors: Canavan Kim , Magengelele Nwabisa L , Paterson Iain D , Williams Dean A , Martin Grant D
Published: December 2021

Schinus terebinthifolia is a problematic invasive alien plant (IAP) in South Africa that is a high priority target for biological control. Biological control has been implemented in the states of Florida and Hawaii (USA), where S. terebinthifolia is also an IAP. Phylogeographic work determined that there have been multiple introductions of two lineages (haplotype A and B) into the USA. Haplotype A was introduced to western Florida and Hawaii, while haplotype B was introduced to eastern Florida. Haplotypes A and B have subsequently hybridized in Florida, resulting in novel plant genotypes. Biological control agents in the USA are known to vary in efficacies on the two different haplotypes and hybrids. This study used molecular techniques to uncover the source populations of S. terebinthifolia in South Africa using chloroplast DNA and microsatellites. Populations from the introduced ranges in Florida (east, west and hybrids) and Hawaii were included (n = 95). All South Africa populations (n = 51) were found to be haplotype A. Microsatellite analysis determined shared alleles with western Florida and Hawaiian populations. The likely source of South African S. terebinthifolia was determined to be western Florida through the horticultural trade. These results will help guide a biological control programme to source agents that perform well on these populations in the USA. Furthermore, the presence of only one haplotype in South Africa highlights the need to ensure no further introductions of other haplotypes of the plant are made, in order to avoid similar hybridization events like those recorded in Florida.
In vitro transcytosis of Helicobacter pylori histidine-rich protein through gastric epithelial-like cells and the blood–brain barrier
Authors: Iwasaki Takashi , Maruyama Aiki , Inui Yurika , Sakurai Toshihiko , Kawano Tsuyoshi
Published: December 2021

Recent epidemiological studies have supported the correlation between Helicobacter pylori infection and the development of Alzheimer’s disease. HpHpn, a histidine-rich H. pylori protein, forms amyloid-like oligomers; it may be a pathogenic factor for Alzheimer’s disease progression. HpHpn may also be transported from the gastric epithelium to the brain. However, HpHpn is secreted from H. pylori on the outer surface of gastric epithelia; therefore, the hypothesized movement of HpHpn across the gastric epithelium to the blood remains controversial. Here, we found the HpHpn showed acidic pH-dependent cellular uptake and subsequent secretion in human gastric epithelial-like carcinoma cells. Furthermore, HpHpn exhibited in vitro permeability across the blood–brain barrier. Although further in vivo experiments are required, our findings suggest that in vitro transcytosis of HpHpn in gastric epithelial cells and the blood–brain barrier may provide new insights into the correlation between H. pylori infections and Alzheimer’s disease progression.
LYRUS: a machine learning model for predicting the pathogenicity of missense variants
Authors: Lai Jiaying , Yang Jordan , Gamsiz Uzun Ece D , Rubenstein Brenda M , Sarkar Indra Neil
Published: December 2021

Single amino acid variations (SAVs) are a primary contributor to variations in the human genome. Identifying pathogenic SAVs can provide insights to the genetic architecture of complex diseases. Most approaches for predicting the functional effects or pathogenicity of SAVs rely on either sequence or structural information. This study presents 〈Lai Yang Rubenstein Uzun Sarkar〉 (LYRUS), a machine learning method that uses an XGBoost classifier to predict the pathogenicity of SAVs. LYRUS incorporates five sequence-based, six structure-based and four dynamics-based features. Uniquely, LYRUS includes a newly proposed sequence co-evolution feature called the variation number. LYRUS was trained using a dataset that contains 4363 protein structures corresponding to 22 639 SAVs from the ClinVar database, and tested using the VariBench testing dataset. Performance analysis showed that LYRUS achieved comparable performance to current variant effect predictors. LYRUS’s performance was also benchmarked against six Deep Mutational Scanning datasets for PTEN and TP53.

Availability and implementation

LYRUS is freely available and the source code can be found at https://github.com/jiaying2508/LYRUS.

Supplementary information

Supplementary data are available at Bioinformatics Advances online.
RAxML Grove: an empirical phylogenetic tree database
Authors: Höhler Dimitri , Pfeiffer Wayne , Ioannidis Vassilios , Stockinger Heinz , Stamatakis Alexandros
Published: December 2021

The assessment of novel phylogenetic models and inference methods is routinely being conducted via experiments on simulated as well as empirical data. When generating synthetic data it is often unclear how to set simulation parameters for the models and generate trees that appropriately reflect empirical model parameter distributions and tree shapes. As a solution, we present and make available a new database called ‘RAxML Grove’ currently comprising more than 60 000 inferred trees and respective model parameter estimates from fully anonymized empirical datasets that were analyzed using RAxML and RAxML-NG on two web servers. We also describe and make available two simple applications of RAxML Grove to exemplify its usage and highlight its utility for designing realistic simulation studies and analyzing empirical model parameter and tree shape distributions.

Availability and implementation

RAxML Grove is freely available at https://github.com/angtft/RAxMLGrove.

Supplementary information

Supplementary data are available at Bioinformatics online.
Junctional instability in neuroepithelium and network hyperexcitability in a focal cortical dysplasia human model
Authors: Avansini Simoni H , Puppo Francesca , Adams Jason W , Vieira Andre S , Coan Ana C , Rogerio Fabio , Torres Fabio R , Araújo Patricia A O R , Martin Mariana , Montenegro Maria A , Yasuda Clarissa L , Tedeschi Helder , Ghizoni Enrico , França Andréa F E C , Alvim Marina K M , Athié Maria C , Rocha Cristiane S , Almeida Vanessa S , Dias Elayne V , Delay Lauriane , Molina Elsa , Yaksh Tony L , Cendes Fernando , Lopes Cendes Iscia , Muotri Alysson R
Published: December 2021

Focal cortical dysplasia is a highly epileptogenic cortical malformation with few treatment options.

Here, we generated human cortical organoids from patients with focal cortical dysplasia type II. Using this human model, we mimicked some focal cortical dysplasia hallmarks, such as impaired cell proliferation, the presence of dysmorphic neurons and balloon cells, and neuronal network hyperexcitability. Furthermore, we observed alterations in the adherens junctions zonula occludens-1 and partitioning defective 3, reduced polarization of the actin cytoskeleton, and fewer synaptic puncta. Focal cortical dysplasia cortical organoids showed downregulation of the small GTPase RHOA, a finding that was confirmed in brain tissue resected from these patients. Functionally, both spontaneous and optogenetically-evoked electrical activity revealed hyperexcitability and enhanced network connectivity in focal cortical dysplasia organoids.

Taken together, our findings suggest a ventricular zone instability in tissue cohesion of neuroepithelial cells, leading to a maturational arrest of progenitors or newborn neurons, which may predispose to cellular and functional immaturity and compromise the formation of neural networks in focal cortical dysplasia.
Identifying Sepsis From Foodborne Hospitalization: Incidence and Hospitalization Cost by Pathogen
Authors: Ahn Jae Wan , Scallan Walter Elaine , White Alice E , McQueen R Brett , Hoffmann Sandra
Published: December 2021

Background

Sepsis causes a major health burden in the United States. To better understand the role of sepsis as a driver of the burden and cost of foodborne illness in the United States, we estimated the frequency and treatment cost of sepsis among US patients hospitalized with 31 pathogens commonly transmitted through food or with unspecified acute gastrointestinal illness (AGI).

Methods

Using data from the National Inpatient Sample from 2012 to 2015, we identified sepsis hospitalizations using 2 approaches—explicit ICD-9-CM codes for sepsis and a coding scheme developed by Angus that identifies sepsis using specific ICD-9-CM diagnosis codes indicating an infection plus organ failure. We examined differences in the frequency and the per-case cost of sepsis across pathogens and AGI and estimated total hospitalization costs using prior estimates of foodborne hospitalizations.

Results

Using Explicit Sepsis Codes, sepsis hospitalizations accounted for 4.6% of hospitalizations with a pathogen commonly transmitted through food or unspecified AGI listed as a diagnosis; this was 33.2% using Angus Sepsis Codes. The average per-case cost was $35 891 and $20 018, respectively. Applying the proportions of hospitalizations with sepsis from this study to prior estimates of the number foodborne hospitalizations, the total annual cost was $248 million annually using Explicit Sepsis Codes and $889 million using Angus Sepsis Codes.

Conclusions

Sepsis is a serious complication among patients hospitalized with a foodborne pathogen infection or AGI resulting in a large burden of illness. Hospitalizations that are diagnosed using explicit sepsis codes are more severe and costly, but likely underestimate the burden of foodborne sepsis.
Coronavirus Disease 2019 (COVID-19) Breakthrough Infection and Post-Vaccination Neutralizing Antibodies Among Healthcare Workers in a Referral Hospital in Tokyo: A Case-Control Matching Study
Authors: Yamamoto Shohei , Maeda Kenji , Matsuda Kouki , Tanaka Akihito , Horii Kumi , Okudera Kaori , Takeuchi Junko S , Mizoue Tetsuya , Konishi Maki , Ozeki Mitsuru , Sugiyama Haruhito , Aoyanagi Nobuyoshi , Mitsuya Hiroaki , Sugiura Wataru , Ohmagari Norio
Published: December 2021

Background

While increasing coverage of effective vaccines against coronavirus disease 2019 (COVID-19), emergent variants raise concerns about breakthrough infection. Data are limited, however, whether breakthrough infection during the epidemic of the variant is ascribed to insufficient vaccine-induced immunogenicity.

Methods

We describe incident COVID-19 in relation to the vaccination program among workers of a referral hospital in Tokyo. During the predominantly Delta epidemic, we followed 2415 fully vaccinated staff (BNT162b2) for breakthrough infection and selected 3 matched controls. We measured post-vaccination neutralizing antibodies against the wild-type, Alpha (B.1.1.7), and Delta (B.1.617.2) strains using live viruses and anti-spike antibodies using quantitative assays, and compared them using the generalized estimating equation model between the 2 groups.

Results

No COVID-19 cases occurred 1–2 months after the vaccination program during the fourth epidemic wave in Japan, dominated by the Alpha variant, while 22 cases emerged 2–4 months after the vaccination program during the fifth wave, dominated by the Delta variant. In the vaccinated cohort, all 17 cases of breakthrough infection were mild or asymptomatic and participants had returned to work early. There was no measurable difference between cases and controls in post-vaccination neutralizing antibody titers against the wild-type, Alpha, Delta, and anti-spike antibody titers, while neutralizing titers against the variants were considerably lower than those against the wild-type.

Conclusions

Post-vaccination neutralizing antibody titers were not decreased among patients with breakthrough infection relative to their controls under the Delta variant outbreak. The result points to the importance of infection-control measures in the post-vaccination era, irrespective of immunogenicity profile.
How much progress have we made?: a 20-year experience regarding esophageal stents for the palliation of malignant dysphagia
Authors: Kumar Shria , Bahdi Firas , Emelogu Ikenna K , Yu Abraham C , Coronel Martin , Ge Philip S , Coronel Emmanuel , Ajani Jaffer A , Weston Brian , Lynch Patrick , Ross William A , Lee Jeffrey H
Published: December 2021

Esophageal stents are widely used for the palliation of malignant esophageal obstruction. Advances in technology have made esophageal stenting technically feasible and widespread for such obstruction, but complications remain frequent. We present outcomes of a large cohort undergoing esophageal stent placement for malignant esophageal obstruction at a tertiary care cancer center. Patients who underwent placement of esophageal stents for malignancy-related esophageal obstruction between 1 January 2001 and 31 July 2020 were identified. Exclusion criteria included stents placed for benign stricture, fistulae, obstruction of proximal esophagus (proximal to 24 cm from incisors), or post-surgical indications. Patient charts were reviewed for demographics, procedure and stent characteristics, complications, and follow-up. A total of 242 patients underwent stent placement (median age: 64 years, 79.8% male). The majority, 204 (84.3%), had esophageal cancer. During the last two decades, there has been an increasing trend in the number of esophageal stents placed. Though plastic stents were previously used, these are no longer utilized. Complications are frequent and include early complications of pain in 68 (28.1%) and migration in 21 (8.7%) and delayed complications of recurrent symptoms of dysphagia in 46 (19.0%) and migration in 26 (10.7%). Over the study period, there has not been a significant improvement in the rate of complications. During follow-up, 92 (38%) patients required other enteral nutrition modalities after esophageal stent placement. No patient, treatment, or stent characteristics were significantly associated with stent complication or outcome. Esophageal stent placement is an increasingly popular method for palliation of malignant dysphagia. However, complications, particularly pain, migration, and recurrent symptoms of dysphagia are common. Almost 40% of patients may also require other methods of enteral access after esophageal stent placement. Given the high complication rates and suboptimal outcomes, removable stents should be considered as first-line in the case of poor palliative response.
Geriatric patients with esophageal motility disorders benefit more from minimally invasive peroral endoscopic myotomy: a multicenter study in Japan
Authors: Ujiie Naoto , Sato Hiroki , Fujiyoshi Mary Raina Angeli , Tanaka Shinwa , Shiwaku Hironari , Shiota Junya , Ogawa Ryo , Yokomichi Hiroshi , Kamei Takashi , Inoue Haruhiro
Published: December 2021

Geriatric patients with existing studies on the safety and efficacy of peroral endoscopic myotomy (POEM) for achalasia involve small sample sizes and single institutions. However, multi-center, large-scale data analyses are lacking. The study aimed to clarify the characteristics of geriatric patients with esophageal motility disorders (EMDs) and determine the procedure-related outcomes and clinical course following POEM. This cohort study included 2,735 patients with EMDs who were treated at seven Japanese facilities between 2010 and 2019. The patients’ characteristics and post-POEM clinical courses were compared between the geriatric (age ≥ 75 years; n = 321) and non-geriatric (age < 75 years; n = 2,414) groups. Compared with the non-geriatric group, the geriatric group had higher American Society of Anesthesiologists physical status scores; more recurrent cases; lower incidence of chest pain; and higher incidence of type III achalasia, distal esophageal spasm, and Jackhammer esophagus. Furthermore, the incidence of sigmoid esophagus was higher, although esophageal dilation was not severe in this group. POEM was safe and effective for geriatric patients with treatment-naïve and recurrent EMDs. Furthermore, compared with the non-geriatric group, the geriatric group had lower post-POEM Eckardt scores, fewer complaints of refractory chest pain, and a lower incidence rate of post-POEM reflux esophagitis. Geriatric patients are characterized by worse clinical conditions, more spastic disorders, and greater disease progression of EMDs, which are also the indications for minimally invasive POEM. POEM is more beneficial in geriatric patients as it has lowering symptom scores and incidence rates of reflux esophagitis.