bluuebunny/crossref_metadata_2025 huggingface dataset:
The crystal structure of a 250-kDa heterotetrameric particle explains inhibition of sheddase meprin β by endogenous fetuin-B
Authors: Eckhard Ulrich , Körschgen Hagen , von Wiegen Nele , Stöcker Walter , Gomis-Rüth F. Xavier
Published: March 2021

Significance

Membrane-bound metallopeptidases cut substrates as “sheddases” on the cell surface. Due to the irreversibility of peptide bond cleavage, they are regulated by specific, colocalizing protein inhibitors. We solved the crystal structure of the complex between the ectomoiety of the human integral membrane sheddase, meprin β (Mβ), and its only reported endogenous protein inhibitor, fetuin-B (FB), which reveals a large particle of ∼250-kDa and ∼160-Å maximal dimension. Our results unveiled a sophisticated “raised elephant trunk” mechanism as the structural basis for the very strong inhibition of Mβ by FB. Moreover, we derived a functional model for Mβ on the cell membrane, which foresees a transition between a membrane-proximal and a membrane-distal position for catalytic and inhibitory functions, respectively.
Deep genetic affinity between coastal Pacific and Amazonian natives evidenced by Australasian ancestry
Authors: Castro e Silva Marcos Araújo , Ferraz Tiago , Bortolini Maria Cátira , Comas David , Hünemeier Tábita
Published: March 2021

Different models have been proposed to elucidate the origins of the founding populations of America, along with the number of migratory waves and routes used by these first explorers. Settlements, both along the Pacific coast and on land, have been evidenced in genetic and archeological studies. However, the number of migratory waves and the origin of immigrants are still controversial topics. Here, we show the Australasian genetic signal is present in the Pacific coast region, indicating a more widespread signal distribution within South America and implicating an ancient contact between Pacific and Amazonian dwellers. We demonstrate that the Australasian population contribution was introduced in South America through the Pacific coastal route before the formation of the Amazonian branch, likely in the ancient coastal Pacific/Amazonian population. In addition, we detected a significant amount of interpopulation and intrapopulation variation in this genetic signal in South America. This study elucidates the genetic relationships of different ancestral components in the initial settlement of South America and proposes that the migratory route used by migrants who carried the Australasian ancestry led to the absence of this signal in the populations of Central and North America.
The diversity of stomatal development regulation in
Callitriche
is related to the intrageneric diversity in lifestyles
Authors: Doll Yuki , Koga Hiroyuki , Tsukaya Hirokazu
Published: March 2021

Significance

Plant stomata are produced through divisions and differentiation of stem cells, termed meristemoids. During stomatal development, we see diverse patterns of meristemoid behavior among land plant lineages. However, both the ecological significance and the diversification processes of this diversity remain mostly unknown. Here we report that the ecologically diverse genus
Callitriche
shows unprecedented intrageneric diversity in meristemoid behavior. While meristemoids in terrestrial species of
Callitriche
undergo a series of asymmetric divisions before differentiation, those in amphibious species skip the divisions and directly differentiate into stomata. The simple shift in the expression times of two key transcription factors underlies these different patterns. This study provides important insights into the evolution and ecological significance of stomatal patterning.
Turn-on mode diarylethenes for bioconjugation and fluorescence microscopy of cellular structures
Authors: Uno Kakishi , Aktalay Ayse , Bossi Mariano L. , Irie Masahiro , Belov Vladimir N. , Hell Stefan W.
Published: March 2021

Significance

In superresolution fluorescence microscopy, employing synthetic dyes that can be reversibly photoswitched between a nonfluorescent (“dark”) and a fluorescent (“bright”) state has been an attractive alternative to using photoswitchable fluorescent proteins. However, employing such synthetic dyes has been elusive because they have defied reliable attachment to proteins and required UV light for photoswitching. Here we prepared “turn-on mode” fluorescent diarylethenes (fDAEs) that are switchable with visible rather than UV light and blink between a bright fluorescent and a dark state in aqueous buffers. Moreover, our thienyl-substituted fDAEs effectively labeled two thiol groups on nanobodies bearing a single maleimide tag. With these small-sized probes, we acquired superresolution images of vimentin filaments in cells by applying just yellow (561 nm) light.
Lepidium draba (hoary cress).
Authors: Weyl Philip
Published: March 2021

Lepidium draba is found in a wide range of habitats ranging from roadsides (highly disturbed sites) to rangelands, meadows and pastures, cultivated fields, home gardens, national parks and wasteland. It exists at high and low latitudes, above and below sea level. It is found under irrigation and in soils of high moisture content and also exists in arid regions. It invades all soil types, although it prefers alkaline conditions and can germinate in saline soils. All of these characteristics and adaptations provide exceptional advantages for this noxious weed and reflect its high potential to invade different agricultural systems. The absence of L. draba plants from plantations or sites where it has not been reported may not be due to the species' ability to invade, survive, grow or develop in these sites but rather to the absence of initial infestation. The weed can invade both agricultural and natural ecosystems (Larson et al., 2000). In summary, L. draba is a serious threat to agriculture and the environment. It is of a high ecological tolerance and is potentially harmful to human and animal health. Its ability to invade and reproduce by different means and to host plant pathogenic agents make this weed invasive with significant problems to man and natural resources.
Senna occidentalis (coffee senna).
Authors: Vélez-Gavilán Jeanine
Published: March 2021

S. occidentalis is an annual to short lived perennial herb to small shrub with a pantropical distribution (PROTA, 2016). It is reported as invasive throughout Oceania, and various countries in Asia and Africa, where is reported as introduced (BioNET-EAFRINET, 2016; PIER, 2016). Within its native range S. occidentalis is listed as invasive for Cuba by Oviedo Prieto et al. (2012). This species is recognised as an invasive herb or a problematic weed that affects crops and plantations all over its range (PIER, 2016). For example, in the Northern Territory, Australia, it is a class B declared weed, i.e. spread to be controlled in all of the Territory (Flanagan, 1998). This weed is a problem in seven states of the USA and is increasing in eight others (Teem et al., 1980). Its ability to colonize a wide range of climatic and edaphic conditions is epitomized by its occurrence in East Africa where it is found at altitudes of 0-1740 metres above sea level (Brenan, 1967). Though probably less important than the related weeds, S. obtusifolia and S. tora, S. occidentalis has the potential to become a weed of more widespread significance. In the USA it is on the regulated invasive list for Florida (Invasive Plant Atlas of the United States, 2016).
Liberibacter asiaticus (Asian greening).
Authors: Arengo Esther
Published: March 2021

The Asian form of Huanglongbing is considered very invasive due to the cryptic nature of the disease and its ability to be transported either in infected plant material or infective psyllids, in which the disease can persist for up to 3 months (da Graca and Korsten, 2004). Yield losses due to this disease have been estimated to be between 30% and 100%, depending on the proportion of the canopy affected and the age of the trees during inoculation (Gottwald, 2010; Ammar et al., 2011). History has shown that the appearance of the vector in a country will almost guarantee the appearance of the disease in the future, e.g. in Brazil and Florida, USA. The species and its vector are on several alert lists including the EPPO A1 Regulated Quarantine Plant Pests.
Chromolaena odorata (Siam weed).
Authors: Pasiecznik Nick
Published: March 2021

C. odorata is a very widely distributed tropical shrub that is still expanding its range, and is considered one of the world's worst weeds. It continues to spread due to its effective short- and long-distance dispersal. It can form pure stands where established, often in disturbed areas, grasslands, fallow areas and forestry plantations, and is highly competitive. It is viewed as a major environmental weed, but is appreciated by some agriculturalists as it shortens fallow time in shifting cultivation.
Halyomorpha halys (brown marmorated stink bug).
Authors: Leskey Tracey C. , Hamilton George C. , Biddinger David J. , Buffington Matthew L. , Dieckhoff Christine , Dively Galen P. , Fraser Hannah , Gariepy Tara , Hedstrom Christopher , Herbert D. Ames , Hoelmer Kim A. , Hooks Cerruti R. R. , Inkley Douglas , Krawczyk Greg , Kuhar Thomas P. , Lee Doo-Hyung , Nielsen Anne L. , Pfeiffer Douglas G. , Rodriguez-Saona Cesar , Shearer Peter W. , Talamas Elijah , Tomasino Elizabeth , Tooker John , Venugopal P. Dilip , Whalen Joanne , Walton Vaughn , Wiman Nik
Published: March 2021

Following the accidental introduction and initial discovery of H. halys in Allentown, Pennsylvania, USA, this species has been detected in 41 states and the District of Columbia in the USA. Isolated populations also exist in Switzerland, France, Italy and Canada. Recent detections also have been reported in Germany and Liechtenstein. BMSB has become a major nuisance pest in the mid-Atlantic region and Pacific Northwest, USA, due to its overwintering behaviour of entering human-made structures in large numbers. BMSB also feeds on numerous tree fruits, vegetables, field crops, ornamental plants, and native vegetation in its native and invaded ranges. In the mid-Atlantic region, serious crop losses have been reported for apples, peaches, sweetcorn, peppers, tomatoes and row crops such as field maize and soyabeans since 2010. Crop damage has also been detected in other states recently including Oregon, Ohio, New York, North Carolina and Tennessee.
Lantana camara (lantana).
Authors: Thomas Sarah E. , Rojas-Sandoval Julissa , Acevedo-Rodríguez Pedro
Published: March 2021

L. camara is a highly variable ornamental shrub, native of the neotropics. It has been introduced to most of the tropics and subtropics as a hedge plant and has since been reported as extremely weedy and invasive in many countries. It is generally deleterious to biodiversity and has been reported as an agricultural weed resulting in large economic losses in a number of countries. In addition to this, it increases the risk of fire, is poisonous to livestock and is a host for numerous pests and diseases. L. camara is difficult to control. In Australia, India and South Africa aggressive measures to eradicate L. camara over the last two centuries have been largely unsuccessful, and the invasion trajectory has continued upwards despite control measures. This species has been the target of biological control programmes for over a century, with successful control only being reported in a few instances.
Meloidogyne incognita (root-knot nematode).
Authors: Eisenback Jonathan D.
Published: March 2021

Introduction: The root knot nematode species, M. incognita, is the most widespread and probably the most serious plant parasitic nematode pest of tropical and subtropical regions throughout the world (Sasser, 1979). It occurs as a pest on a very wide range of crops. Most estimates of yield loss come from the use of nematicides and it should be noted that these can possibly cause other beneficial growth effects.
Mononychellus tanajoa (cassava green mite).
Authors: Pollangyo Beatrice , Odour George
Published: March 2021

The cassava green mite, M. tanajoa, is of Neotropical origin but was accidentally introduced to Africa in 1971 (Nyiira, 1972). By 1985, the pest had spread throughout the cassava belt of Africa (Yaninek and Heren, 1988). M. tanajoa affects the important annual crop cassava (Manihot esculenta) and can cause a reduction of about 50% in leaf weight, and up to 80% tuber yield loss (Shukla, 1976; Gutierrez et al., 1988; Pallangyo et al., 2004). M. tanajoa is mainly dispersed by human activity, whereby infested plant materials and contaminated media are transported over long distances. Natural dispersion by wind and water may also spread the cassava green mite. In areas where both the pest and host plant are exotic, there is no evidence that indigenous natural enemies are significant factors in limiting the mite population growth rates. M. tanajoa can feed and reproduce on other plant species (Moraes et al., 1995) and is reported as a quarantine pest (Delalibera et al., 1992; EPPO, 2009).
Candidatus Phytoplasma trifolii (clover proliferation phytoplasma).
Authors: Zhao Yan , Wei Wei
Published: March 2021

The reference strain of 'Ca. Phytoplasma trifolii' is the causative agent of clover proliferation (CP) disease of alsike clover (Trifolium hybridum). The CP disease was first reported in Canada in the early 1960s when the aetiological agent was mistakenly presumed to be a yellows-type virus (Chiykowski, 1965). Subsequent investigations revealed that the disease was associated with infection by a mycoplasma-like organism (Chen and Hiruki, 1975; Hiruki and Chen, 1984), now termed phytoplasma, strain CPR (Hiruki and Wang, 2004). Later, phytoplasmas of the same lineage (subgroup 16SrVI-A) were found in the USA, Mexico, and many countries in Europe and Asia, causing diseases in diverse leguminous and vegetable crops, responsible for significant yield losses and quality reductions. Phytoplasmas of the same lineage also caused disease in elm trees in the USA. Phytoplasmas of closely-related lineages (various subgroups of group 16SrVI) also have wide distributions around the world.
Vincetoxicum rossicum (European swallowwort).
Authors: Gassmann André
Published: March 2021

V. rossicum is a herbaceous perennial climbing vine native to Ukraine and southwestern European Russia. It was introduced into North America for ornamental purposes and has spread extensively throughout the lower Great Lakes Basin, particularly Lake Ontario, including New York State, USA and Ontario, Canada. Self-fertility and large numbers of wind-borne seeds ensure rapid dispersal of V. rossicum to new sites. Small patches of V. rossicum can coalesce to form very large, monospecific stands which can outcompete native vegetation resulting in a change in habitats and a decrease in biodiversity. V. rossicum is allelopathic and can alter the microbial composition in the rhizosphere preventing the growth of sensitive plant species. In the USA, competition from V. rossicum is putting pressure on the rare and endangered species Asplenium scolopendrium var. americanum. In addition to this, V. rossicum has been shown to decrease insect biodiversity and may have negative impact on the reproduction of the Monarch butterfly, Danaus plexippus.
Banana bunchy top virus (bunchy top of banana).
Authors: Kumar Lava
Published: March 2021

BBTV is the most serious virus disease of bananas and plantains. It occurs in Africa, Asia, Australia and South Pacific islands. The virus is transmitted in a persistent, circulative, non-propagative manner by the banana aphid, Pentalonia nigronervosa, which has worldwide distribution. The virus is also spread through infected planting material. All banana cultivars are thought to be susceptible, with no known sources of resistance. The typical symptoms of bunchy top of banana are very distinctive and readily distinguished from those caused by other viruses of banana. Infected plants exhibit a rosetted or 'bunchy top' appearance. Once infected, plants do not recover. The disease is a major constraint to production in many areas where it occurs. Devastating epidemics occurred early in the twentieth century in Fiji and Australia. In the 1920s, the disease had a dramatic economic effect on the banana industry in parts of Australia (Dale, 1987). More recently, BBTV has been decimating the banana industry in Pakistan (Jones, 1994) and in sub-Saharan Africa, BBTV was the main contributor to a reduction in banana bunch production by up to 70-90% in disease affected areas (Kumar et al., 2015). BBTV is listed by ISSG as one of the world's 100 worst invasive alien species.
Pore-forming transmembrane domains control ion selectivity and selectivity filter conformation in the KirBac1.1 potassium channel
Authors: Matamoros Marcos , Nichols Colin G.
Published: March 2021

Potassium (K+) channels are membrane proteins with the remarkable ability to very selectively conduct K+ ions across the membrane. High-resolution structures have revealed that dehydrated K+ ions permeate through the narrowest region of the pore, formed by the backbone carbonyls of the signature selectivity filter (SF) sequence TxGYG. However, the existence of nonselective channels with similar SF sequences, as well as effects of mutations in other regions on selectivity, suggest that the SF is not the sole determinant of selectivity. We changed the selectivity of the KirBac1.1 channel by introducing mutations at residue I131 in transmembrane helix 2 (TM2). These mutations increase Na+ flux in the absence of K+ and introduce significant proton conductance. Consistent with K+ channel crystal structures, single-molecule FRET experiments show that the SF is conformationally constrained and stable in high-K+ conditions but undergoes transitions to dilated low-FRET states in high-Na+/low-K+ conditions. Relative to wild-type channels, I131M mutants exhibit marked shifts in the K+ and Na+ dependence of SF dynamics to higher K+ and lower Na+ concentrations. These results illuminate the role of I131, and potentially other structural elements outside the SF, in controlling ion selectivity, by suggesting that the physical interaction of these elements with the SF contributes to the relative stability of the constrained K+-induced SF configuration versus nonselective dilated conformations.
Degenerate Hořava gravity
Authors: Barausse Enrico , Crisostomi Marco , Liberati Stefano , ter Haar Lotte
Published: March 2021

Hořava gravity breaks Lorentz symmetry by introducing a dynamical timelike scalar field (the khronon), which can be used as a preferred time coordinate (thus selecting a preferred space–time foliation). Adopting the khronon as the time coordinate, the theory is invariant only under time reparametrizations and spatial diffeomorphisms. In the infrared limit, this theory is sometimes referred to as khronometric theory. Here, we explicitly construct a generalization of khronometric theory, which avoids the propagation of Ostrogradski modes as a result of a suitable degeneracy condition (although stability of the latter under radiative corrections remains an open question). While this new theory does not have a general-relativistic limit and does not yield a Friedmann–Robertson–Walker-like cosmology on large scales, it still passes, for suitable choices of its coupling constants, local tests on Earth and in the Solar System, as well as gravitational-wave tests. We also comment on the possible usefulness of this theory as a toy model of quantum gravity, as it could be completed in the ultraviolet into a ‘degenerate Hořava gravity’ theory that could be perturbatively renormalizable without imposing any projectability condition.
Gravitational decoherence of photons
Authors: Lagouvardos Michalis , Anastopoulos Charis
Published: March 2021

Models of gravitational decoherence are not commonly applied to ultra-relativistic systems, including photons. As a result, few quantum optical tests of gravitational decoherence have been developed. In this paper, we generalize the gravitational decoherence model of Anastopoulos and Hu (2013 Class. Quantum Grav.
30 165007) to photons. In this model, decoherence originates from a bath of stochastic gravitational perturbations, possibly of fundamental origin. We derive a master equation for general states of the electromagnetic field; the only free parameter is a noise temperature Θ of the gravitational fluctuations. We find that interference experiments with long baselines, accessible in near-future experiments, can, in principle, lead to strong constraints in Θ.
Constructing black holes in Einstein–Maxwell-scalar theory
Authors: Yu Shuang , Qiu Jianhui , Gao Changjun
Published: March 2021

Exact black hole solutions in the Einstein–Maxwell-scalar theory are constructed. They are the extensions of dilaton black holes in de Sitter or anti de Sitter universe. As a result, except for a scalar potential, a coupling function between the scalar field and the Maxwell invariant is present. Then the corresponding Smarr formula and the first law of thermodynamics are investigated.
Development of microfluidic cartridge for culture-free detection of Staphylococcus aureus in blood
Authors: Zhou Weidong , Wu Ruige , Duraiswamy Suhanya , Wang Wei , Zhu Liang , Wang Zhiping
Published: March 2021

Rapid detection of small amounts of Staphylococcus aureus (S. aureus) in whole blood and the corresponding diagnosis of S. aureus is a complicated and time-consuming process. Gold standard is to culture and grow bacteria before detection, which typically takes several days and requires skilled personnel. Here, we developed a microfluidic cartridge for the culture-free isolation of S. aureus in blood and diagnosed them using a multiplex polymerase chain reaction (PCR) method. Isolation of S. aureus was achieved from large volumes of blood (typically of the order of 5 ml) using Apolipoprotein H coated magnetic beads followed by ultrasonication, a similar kind of agitation utilized in an ultrasonic bath, to lyse the enriched bacteria. The designed cartridge consisted of a rotary valve to control the sample flow and, also to direct the samples to the designated chambers for the pre-processing and bacteria isolation. By comparing PCR results from batch process and cartridge based method, we proved that the current cartridge design was capable of S. aureus detection in whole blood sample.
Enhancement of passive mixing via arc microchannel with sharp corner structure
Authors: Huang Long-Run , Fan Liang-Liang , Liu Qi , Zhao Zhi , Zhe Jiang , Zhao Liang
Published: March 2021

A novel microfluidic device for efficient passive mixing is reported. A series of sharp corner structures designed on side wall of an arc microchannel was utilized to induce three-dimensional vortices, which strongly stretched and folded the interface and significantly increased the interfacial contact area between different fluids. Additionally, the sharp corner structure induced high radial velocity and reduced the diffusion length because of the restricted effect of the geometrical structure. Eventually, the fluid mixing was significantly enhanced, and a mixing efficiency from ∼87% to 92% was achieved at moderate Reynolds number (Re) from 3.0 to 24.2 (10 to 80 μl min−1). The influence of the sharp corner position on the mixing was also investigated by the experiment and the numerical simulation. With single-layer structure and high mixing efficiency, the present device has great potential in the mixing process in variety of lab-chip applications, such as clinic diagnosis and analytic chemistry.
On the oscillating properties of a two-electron quantum dot in the presence of a magnetic field
Authors: Maniero A M , de Carvalho C R , Prudente F V , Jalbert Ginette
Published: March 2021

We give a basic explanation for the oscillating properties of some physical quantities of a two-electron quantum dot in the presence of a static magnetic field. This behaviour was discussed in a previous work of ours (Maniero et al 2020 J. Phys. B: At. Mol. Opt. Phys.
53 185001) and was identified as a manifestation of the de Haas–van Alphen effect, originally observed in the framework of diamagnetism of metals in the 30s. We show that this behaviour is a consequence of different eigenstates of the system assuming, in a certain interval of the magnetic field, the condition of the lowest energy singlet and triplet states.
High quality factor, protein-based microlasers from self-assembled microcracks
Authors: Nguyen Tam Trong , Mai Hanh Hong , Pham Thin Van , Nguyen Thau Xuan , Ta Van Duong
Published: March 2021

In the last decade, microlasers with biological origin have shown their great potential in biosensing and bioimaging. Several micro-structures have been developed for high quality (Q) factor biolasers including Fabry–Pérot, distributed feedback and whispering gallery mode cavities. However, the fabrication of these lasers is generally complicated and their operation is strongly affected by cavity defects. In this work, we demonstrate random protein-based microlasers fabricated by a simple one-step self-assembled method. The lasing can be achieved from microcracks with random structures. The lasing threshold is around 14 mJ cm−2 and the quality factor of lasing modes can be up to

3
×

10
3

which are comparable with other conventional biolasers. Our work opens a new possibility for the fabrication of high Q factor microlasers from biocompatible materials, with great potential for biosensing and biomedical applications.
Error propagation dynamics of velocimetry-based pressure field calculations (2): on the error profile
Authors: Faiella Matthew , Grant Jeon Macmillan Corwin , Whitehead Jared P , Pan Zhao
Published: March 2021

A recent study investigated the propagation of error in a velocimetry-based pressure (V-pressure) field reconstruction problem by directly analyzing the properties of the pressure Poisson equation (Pan et al 2016 Meas. Sci. Technol.
27 084012). In the present work, we extend these results by quantifying the effect of the error profile in the data field (shape/structure of the error in space) on the resultant error in the reconstructed pressure field. We first calculate the mode of the error in the data that maximizes error in the pressure field, which is the most dangerous error (called the worst error in the present work). This calculation of the worst error is equivalent to finding the principle mode of, for example, an Euler–Bernoulli beam problem in one-dimension and the Kirchhoff–Love plate in two-dimensions, thus connecting the V-pressure problem from experimental fluid mechanics to buckling elastic bodies from elastic mechanics. Taking advantage of this analogy, we then analyze how the error profile (e.g. spatial frequency of the error and the location of the most concentrated error) in the data field coupled with fundamental features of the flow domain (i.e. size, shape, and dimension of the domain, and the configuration of boundary conditions) significantly affects the error propagation from data to the reconstructed pressure. Our analytical results lend to practical applications in two ways. First, minimization of error propagation can be achieved by avoiding low frequency error profiles in data similar to the worst case scenarios and error concentrated at sensitive locations. Second, small amounts of the error in the data, if the error profile is similar to the worst error case, can cause significant error in the reconstructed pressure field; such a synthetic error can be used to benchmark V-pressure algorithms.
Male pelvic CT multi-organ segmentation using synthetic MRI-aided dual pyramid networks
Authors: Lei Yang , Wang Tonghe , Tian Sibo , Fu Yabo , Patel Pretesh , Jani Ashesh B , Curran Walter J , Liu Tian , Yang Xiaofeng
Published: March 2021

The delineation of the prostate and organs-at-risk (OARs) is fundamental to prostate radiation treatment planning, but is currently labor-intensive and observer-dependent. We aimed to develop an automated computed tomography (CT)-based multi-organ (bladder, prostate, rectum, left and right femoral heads (RFHs)) segmentation method for prostate radiation therapy treatment planning. The proposed method uses synthetic MRIs (sMRIs) to offer superior soft-tissue information for male pelvic CT images. Cycle-consistent adversarial networks (CycleGAN) were used to generate CT-based sMRIs. Dual pyramid networks (DPNs) extracted features from both CTs and sMRIs. A deep attention strategy was integrated into the DPNs to select the most relevant features from both CTs and sMRIs to identify organ boundaries. The CT-based sMRI generated from our previously trained CycleGAN and its corresponding CT images were inputted to the proposed DPNs to provide complementary information for pelvic multi-organ segmentation. The proposed method was trained and evaluated using datasets from 140 patients with prostate cancer, and were then compared against state-of-art methods. The Dice similarity coefficients and mean surface distances between our results and ground truth were 0.95 ± 0.05, 1.16 ± 0.70 mm; 0.88 ± 0.08, 1.64 ± 1.26 mm; 0.90 ± 0.04, 1.27 ± 0.48 mm; 0.95 ± 0.04, 1.08 ± 1.29 mm; and 0.95 ± 0.04, 1.11 ± 1.49 mm for bladder, prostate, rectum, left and RFHs, respectively. Mean center of mass distances was within 3 mm for all organs. Our results performed significantly better than those of competing methods in most evaluation metrics. We demonstrated the feasibility of sMRI-aided DPNs for multi-organ segmentation on pelvic CT images, and its superiority over other networks. The proposed method could be used in routine prostate cancer radiotherapy treatment planning to rapidly segment the prostate and standard OARs.
Spatial characteristics of luminous hydrocarbon pellet clouds in the large helical device
Authors: Sharov I A , Sergeev V Yu , Miroshnikov I V , Tamura N , Sudo S
Published: March 2021

This study analyzes the dependences of the size of the luminous region of hydrocarbon pellet cloud on the ablation rate, as well as on the ambient plasma electron density and temperature. The data were obtained in a series of experiments where spherical solid polystyrene pellets with a diameter of ≈900 μm at a speed of ≈450 m s−1 were injected into hydrogen plasma of the large helical device. The ambient plasma with an electron temperature of 0.5–1.5 keV and a density of (1–7) × 1019 m−3 was maintained by injection of neutral atom beams with total the heating power of 3–14 MW. A scaling law was derived for determining the transverse size of the cloud’s luminous region from the known values of the pellet’s current radius as well as the values of the density and temperature of the ambient plasma at the place of image acquisition. The interdependencies between various dimensions of the luminous region obtained in the line spectrum are established. The presence of such dependences makes it possible to describe the dimensions of the luminous region comprehensively by means of the scaling law for its transverse size.
Modeling active control of resistive wall mode with power saturation and sensor noise on HL-2M
Authors: Wang S , Liu Y Q , Xia G L , Song X M , Hao G Z , Li L , Li B , Zhang N , Dong G Q , Bai X , Zheng G Y
Published: March 2021

The resistive wall mode (RWM) control on the HL-2M tokamak is simulated with the MARS-F code (Liu et al 2000 Phys. Plasmas
7 3681), aiming at quantifying control current and voltage requirements when more realistic issues are taken into account, i.e. the control power saturation and the sensor signal noise. The fluid model predicts a narrow stability region for the n = 1 RWM without magnetic feedback, in the 2D parameter space of the plasma pressure versus the toroidal flow speed. Magnetic feedback can fully stabilize the RWM on HL-2M. Without considering the voltage limitation and the sensor signal noise, it is found that plasma flow helps active control of the mode, by reducing the required critical feedback gain for both flux-to-current and flux-to-voltage control schemes. In the absence of the sensor signal noise, the lowest control voltage saturation level, below which the RWM control is lost, is found to roughly satisfy a linear relation to the plasma flow frequency, indicating that subsonic plasma flow is effective in relaxing the control power requirement for the RWM feedback stabilization. The presence of the sensor signal noise substantially modifies the feedback results. A statistical study finds that the sensor signal noise, with the standard deviation of 0.1 G on HL-2M, roughly doubles the required control voltage for successful mode control. The synergistic stabilization effect due to plasma flow is somewhat weakened by the presence of the sensor signal noise. At a given rotation, the tolerable voltage limit generally increases with increasing feedback gain due to the sensor signal noise.
2D particle-in-cell simulations of geometrically asymmetric low-pressure capacitive RF plasmas driven by tailored voltage waveforms
Authors: Wang Li , Hartmann Peter , Donkó Zoltán , Song Yuan-Hong , Schulze Julian
Published: March 2021

The effects of the simultaneous presence of two different types of plasma asymmetry, viz, geometric and electrical, on low-pressure capacitively coupled argon discharges are studied by 2D3V graphics-processing-unit-based particle-in-cell/Monte Carlo simulations. The geometric asymmetry originates from the different powered vs grounded electrode surface areas, while the electrical asymmetry is established by applying peaks/valleys and sawtooth-up/-down driving voltage waveforms. While in geometrically symmetric discharges, the {peaks ↔ valleys} and the {sawtooth-down ↔ sawtooth-up} switching of the waveforms is equivalent to exchanging the powered and grounded electrodes, this transformation is violated when the geometric symmetry is broken. Under such conditions, the plasma characteristics and the DC self-bias generation behave differently, compared to the geometrically symmetric case. This leads to different sheath dynamics and, therefore, strongly influences the electron power absorption dynamics. For identical peak-to-peak voltages, the plasma density obtained for such tailored voltage waveforms is found to be higher compared to the classical single-frequency waveform case. Reduced plasma densities are found in the valleys- and sawtooth-down waveform cases, compared to the peaks- and sawtooth-up waveforms. By including realistic energy and material-dependent secondary electron emission (SEE) coefficients in the simulations, the electron-induced SEE is found to be reduced in the valleys- and sawtooth-down waveform cases, which explains the behaviour of the plasma density. Using such tailored waveforms in geometrically asymmetric discharges is also found to lead to the formation of different charged particle energy distributions at the boundary surfaces, compared to those in geometrically symmetric plasma sources.
Structure of DC magnetron sputtering discharge at various gas pressures: a two-dimensional particle-in-cell Monte Carlo collision study
Authors: Ryabinkin A N , Serov A O , Pal A F , Mankelevich Yu A , Rakhimov A T , Rakhimova T V
Published: March 2021

We report the results of a particle-in-cell Monte-Carlo collision simulation of an axially symmetric DC magnetron discharge with a 5 cm diameter flat cathode in argon at pressures from 1 to 10 mTorr at a constant discharge current of about 0.5 A. Calculations show that the cathode region, where almost the entire discharge voltage drops, consists of a cathode sheath 0.1–0.2 mm wide and a presheath about 2 cm wide, where most of the ionizations occur, separated by a region 0.25–0.35 mm wide, where the plasma potential remains almost unchanged and the plasma density reaches its maximum value. Most of the discharge voltage drops in the presheath at low gas pressure, and in cathode sheath at high pressure. The ratio of sheath to presheath voltages increases linearly with pressure. The distribution of the ionization rate has two maxima: near the cathode sheath and in the presheath. The fraction of ionizations near the cathode sheath increases with pressure. The electron energy distribution function (EEDF) is generally a two-temperature function. At low pressures at a distance of less than 1 cm from the cathode, the EEDF becomes one-temperature. A high-energy tail is observed on the EEDF near the cathode; the fraction of electrons in the tail (in the order of tenths of a percent at 10 mTorr) and their energy, determined by the sheath voltage, increase with pressure. The electron temperature decreases with pressure due to a decrease of the electric field in the presheath, which leads to a decrease of energetically accessible regions of collisionless electron motion and to a corresponding decrease in the energy that electrons can obtain in these regions. The dependence of the discharge voltage on the gas pressure has a minimum at about 3 mTorr, which occurs due to the competition of two processes on pressure increase: a decrease in the electron temperature and a decrease in the fraction of electrons returning back to the cathode. Plasma density waves are observed in the presheath region at pressures of 1–3 mTorr.
Genuine monogamy relations in no-signaling theories—a geometric approach
Authors: Ryu Junghee , Lee Daemin , Lee Jinhyoung , Kurzyński Paweł , Kaszlikowski Dagomir
Published: March 2021

Quantum correlations are subject to certain distribution rules represented by so-called monogamy relations. Derivation of monogamy relations for multipartite systems is a non-trivial problem, as the multipartite correlations reveal their behaviors in a way different from bipartite systems. We here show that simple geometric properties of probabilistic spaces, in conjunction with no-signaling principle, lead to genuine monogamy relations for a large class of Bell type inequalities for many qubits. The term of ‘genuine’ implies that only one out of N Bell inequalities exhibits a quantum violation. We also generalize our method to qudits. Using the similar geometric approach with a quasi-distance employed, we derive Svetlichny–Zohren–Gill type Bell inequalities for d-dimensional tripartite systems, and show their monogamous nature.
Redshift-space distortions in Lagrangian perturbation theory
Authors: Chen Shi-Fan , Vlah Zvonimir , Castorina Emanuele , White Martin
Published: March 2021

We present the one-loop 2-point function of biased tracers
in redshift space computed with Lagrangian perturbation theory,
including a full resummation of both long-wavelength (infrared)
displacements and associated velocities. The resulting model
accurately predicts the power spectrum and correlation function of
halos and mock galaxies from two different sets of N-body
simulations at the percent level for quasi-linear scales, including
the damping of the baryon acoustic oscillation signal due to the
bulk motions of galaxies. We compare this full resummation with
other, approximate, techniques including the moment expansion and
Gaussian streaming model. We discuss infrared resummation in detail
and compare our Lagrangian formulation with the Eulerian theory
augmented by an infrared resummation based on splitting the input
power spectrum into “wiggle” and “no-wiggle” components. We
show that our model is able to recover unbiased cosmological
parameters in mock data encompassing a volume much larger than what
will be available to future galaxy surveys. We demonstrate how to
efficiently compute the resulting expressions numerically, making
available a fast Python code capable of rapidly computing these
statistics in both configuration and Fourier space.
Optimization of the computation of total and local radiated power at ASDEX Upgrade
Authors: David P. , Bernert M. , Pütterich T. , Fuchs C. , Glöggler S. , Eich T. , the ASDEX Upgrade Team
Published: March 2021

Radiation losses are measured as a line integrated quantity from the plasma, on ASDEX Upgrade using foil bolometers. Based on these measurements, the computation of the radiated power from either the whole volume or any sub region requires post processing including key assumptions. A new algorithm to improve this computation was recently developed and benchmarked. The algorithm is based on a routinely used tomography method and allows for local radiative events to be properly taken into account. It is compared to two other methods used at ASDEX Upgrade: the generic one based on flux tube symmetry and a more specific method using a 1D fit to compute the radiation excluding the divertor. In benchmarks with phantom radiation distributions, the new method shows a significantly better accuracy of −2.9 ± 5.2% in comparison to the previous algorithm accuracy of −27.8 ± 21.4% (average ± standard deviation on all test cases of the benchmark). The new code also allows the systematic computation of the radiated power from four sub regions, such as the divertor, the main chamber and inside the separatrix.
Modification of favorable average curvature effect by changing parallel sound wave behavior in tokamak plasmas
Authors: Bai Xue , Liu Yueqiang , Hao Guangzhou
Published: March 2021

The favorable average curvature effect, also known as the GGJ effect (Glasser et al 1975 Phys. Fluids
18 875), is intrinsically associated with parallel sound wave propagation in a tokamak plasma. This work investigates how the GGJ effect is modified by changing the parallel sound wave behavior. Two physics models beyond the standard single fluid theory, i.e. an anisotropic thermal transport model and a parallel sound wave damping model, are employed to change parallel sound waves in a toroidal plasma, and the consequence on the GGJ effect is demonstrated for two important classes of problems, i.e. the resistive plasma response to the applied resonant magnetic perturbation and the stability of the tearing mode. Toroidal modeling reveals that the GGJ effect is significantly altered by both of the aforementioned physics effects. Compared to the thermal transport physics, which completely removes the GGJ effect, the sound wave damping effect only offers partial mitigation. The differences between these two models are further illustrated in terms of the radial structure of the shielding current and the eigenfunction of the tearing instability. In particular, a fundamental reason for complete suppression of the GGJ effect by the thermal transport is identified as an extra toroidal coupling of the poloidal harmonics.
Comparison of Colorectal Cancer Classification between K-Nearest Neighbors (K-NN) and Neural Network
Authors: Zhafarina F , Rustam Z , Amalia Y , Wirasati I
Published: March 2021

Machine learning is one of the technologies used in medicine. Machine learning can help detect various kinds of problems in the medical field and enables a process to be faster and more efficient. Cancer is one of the most dangerous diseases in the world. Machine learning is widely used in bioinformatics and particularly in cancer diagnosis. One of the most popular methods is K-nearest neighbors (K-NN) and Neural Network. There are supervised learning methods. Using K-NN, the quality of the results depends largely on the distance and the value of the parameter “k” which represents the number of the nearest neighbors. This research is explains the classification of colorectal cancer by using K-NN with different k values and Neural Network Classification. Our work will be performed on the Colorectal Cancer dataset obtained by the Al-Islam Hospital, Bandung, Indonesia and it consists of benign cases 163 and malignant cases 47 samples. Thus, the final result indicates better performance for K-nearest neighbors’ accuracy is 0.786 in K-parameter equal to 7, 9, 11 has the same accuracy with 60% data training and Neural Network reached 0.904 with 90% of data training.
Mathematical model of schistosomiasis with health education and molluscicide intervention
Authors: Nur W , Trisilowati  , Suryanto A , Kusumawinahyu W M
Published: March 2021

In this article, a mathematical model is developed to study the impact of health education and molluscicide intervention on the spread of schistosomiasis. The model constructed consists of seven ordinary differential equations that describe susceptible human, latent human, infectious human, susceptible snail, infected snail, miracidia and cercarie. After analyzing non-negativity and boundedness of solutions of the model, we determine the disease free equilibrium point and the endemic equilibrium point as well as their existence conditions. The basic reproduction number is determined using the next generation matrix approach. The local stability condition of the disease-free equilibrium point is proved by using linearization and Descartes’ sign rule.. The Center Manifold Theory is used to prove the local stability condition of the endemic equilibrium point and to identify the existence of bifurcation. We constructed Lyapunov function to show that the disease-free equilibrium point is globally asymptotically stable under sufficient condition. We present numerical simulations to support our theoretical study. Numerical simulations show that health education and molluscicide intervention are able to reduce schistosomiasis cases in human and snail populations. Molluscicide intervention is a very effective method to control the spread of schistosomiasis.
An epidemic model with age structured of rubella virus: threshold and stability
Authors: Abadi  , Artiono Rudianto , Prawoto Budi Priyo
Published: March 2021

This study aimed to explore the dynamic behaviour of rubella virus model which considers age-structured. It was not only to figure out the stability analysis of the model but also the judgement of the result through numerical simulation. Firstly, we constructed model for the disease spread based on the characteristic of rubella virus. The basic model of the disease spread (SEIR) had been used as a fundamental model. In the beginning, human population have been divided into two age groups; children and adults. Furthermore, based on the characteristic of rubella, we separated each group into four sub populations, i.e., Susceptible, Exposed, Infected, and Recovered. The transmission routes of the disease were formulated mathematically based on the real problem. In the second step, two disease equilibrium points had been obtained. There were a disease-free equilibrium and an endemic equilibrium. Moreover, by using Next Generation Matrix method, the basic reproduction number also had been determined. Finally, stability analysis had been done to explore the persistence of the disease. This results also had been supported by the numerical simulation.
About the Creation of Sensor of New Firefighting, Devices Based on Nanostructures for Determination of Carbon Monoxide and Carbon Dioxide Components
Authors: Boroznin S V , Zaporotskova I V , Boroznina N P
Published: March 2021

The article is devoted to the study of methods of detecting CO2 molecules using boroncarbon nanotubes of type BC5. The article also compares the mechanisms of attachment of the molecule CO2 to the surface of the modified carboxyl group of the nanotube. The main method used in the work is the density functional theory (DFT) method within the B3LYP functional. As a result of the work, the most likely method of catching carbon dioxide molecules using boroncarbon nanotubes was established and the physicochemical characteristics of these phenomena were determined
Numerical Simulation of Stratified Values of the Vertical Gravity Gradient Generated by a Pair of Closely Spaced Isolated Inhomogeneities with Excessive Density
Authors: Chashchin O N , Podoinikov D A
Published: March 2021

In the article is presented a mathematical model and a computational algorithm for solving the inverse problem of gravity gradiometry – a problem of localization (separability) of a pair of gravitational inhomogeneities – isolated ore bodies (oil and gas domes) with excessive positive (negative) density based on the gravitational anomalies generated by them. Anomalies are empirical data for solving the inverse problem, which is relevant for geological exploration, monitoring and geophysical support of developed fields, as well as for practical problems of engineering geology.