bluuebunny/crossref_metadata_2025 huggingface dataset:
Pectobacterium parmentieri (black leg disease of potato).
Authors: Lojkowska Ewa
Published: March 2021

Pectobacterium parmentieri is a bacterial pathogen of potato present in Europe since the 1960s. The bacterium was earlier classified as Pectobacterium carotovorum. After reclassification of P. carotovorum subsp. carotovorum SCC3193 to P. wasabiae and later on to P. parmentieri, several studies devoted to identification of pectinolytic bacteria in international collections and identification of the strains isolated from infected potato plants have indicated that this bacteria commonly occurs in several regions of Europe, Canada, USA, New Zealand and South Africa. P. parmentieri can cause symptoms of blackleg and soft rot on potato tubers. These diseases are usually a consequence of latent infection of seed potatoes. In the majority of countries pre-basic and basic seed tuber potatoes intended for the production of seed tuber crops should be free of Pectobacterium spp. and Dickeya spp. P. parmentieri is not present on any international or national alert lists.
Solenopsis invicta (red imported fire ant).
Authors: Gunawardana Disna
Published: March 2021

S. invicta is an ant native to South America. It is an aggressive generalist forager that occurs in high densities and can thus dominate most potential food sources. It breeds and spreads rapidly and, if disturbed, can relocate quickly, ensuring the survival of the colony. S. invicta is highly invasive because of its high reproductive capacity, large colony size, ability to exploit human disturbances, wide food range and ability to sting. Its stinging ability allows it to subdue prey and even repel larger vertebrate competitors from resources (ISSG, 2014). S. invicta has become widespread in the southern USA and Caribbean after its introduction in the 1930s (Morrison et al., 2004). It has also been introduced to parts of Australia and New Zealand. S. invicta is one of the most notorious invasive ants and has been nominated for the 100 World's Worst Invaders list compiled by the Invasive Species Specialist Group (ISSG, 2014).
Uromycladium spp. that cause gall rusts (Acacia gall rusts).
Authors: Wood Alan R.
Published: March 2021

Gall forming rust fungi of the genus Uromycladium are native to Australasia. They are invasive in New Zealand, the Philippines, East Timor, Malaysia and Indonesia. Uromycladium murphyi (as Uromycladium notabile in the literature) causes damage to Acacia decurrens grown for tannin and as an ornamental in New Zealand. Other hosts of U. murphyi are A. baileyana, A. dealbata and A. mearnsii. Uromycladium paradoxae infects Acacia paradoxa in New Zealand. Uromycladium species have been found in New Zealand on A. ulicifolia and A. verticillata, but the taxa on these two hosts is uncertain and await phylogenetic studies. Uromycladium falcatariae causes serious disease in Falcataria moluccana in Southeast Asia. This tree is grown as a shade tree in coffee plantations, for timber and pulp, and for other uses. Uromycladium morrisii and U. woodii were deliberately introduced into South Africa for the biological control of Acacia saligna and Paraserianthes lophantha, respectively.
Didymella fabae (leaf and pod spot).
Authors:   USA, USDA-ARS
Published: March 2021

Ascochyta blight is the most severe disease of cool-season pulses (Davidson and Kimber, 2007). D. fabae (anamorph: Ascochyta fabae) attacks
Vicia faba
and can survive and reproduce in and spread from crop debris or be transported in infected seed. Introduction on infected seed occurred in Australia and Canada in the 1970s, and was probably the means for the pathogen's original spread to countries outside southwestern Asia. Ascospores are disseminated by wind from the debris as primary inoculum and secondary cycles are initiated by conidia spread by rain splash from plant lesions. The fungus is host-specific in causing disease, but may be able to survive in non-host plants and reproduce on their debris. It is not treated as a phytosanitary risk or listed as an invasive pathogen by major organizations. Seed certification is the primary means of preventing its spread to new areas and the importation of new genotypes of the fungus to areas already infested.
Candidatus Phytoplasma asteris (yellow disease phytoplasmas).
Authors: Marcone Carmine
Published: March 2021

Aster yellows (AY) group phytoplasmas affect plants by causing a general reduction in quantity and quality of yield. The most severely affected hosts are carrot, lettuce, onion, spinach and several ornamental crops, including aster, gladiolus, hydrangea, chrysanthemum and purple coneflower. Disease incidence may vary from year to year depending on the population trend of the vectors in the field. Infection rates varying from 20 to 30% were observed in lettuce and ranunculus fields in southern Italy (Marcone et al., 1995; Parrella et al., 2008). In Oklahoma, USA, according to Errampalli et al. (1991), AY group phytoplasma infections occurred in 80% of lettuce plants and 28% of carrots. In Ohio, disease incidence of 100% has been recorded in lettuce fields (Zhang et al., 2004). A major outbreak of AY disease occurred in 2000 in Texas that affected several vegetable crops. Among them, carrot was most severely damaged with infection rates that ranged from to 50 to near 100% (Lee et al., 2003). A severe AY disease of chrysanthemum which induced losses of 70 to 80% of the crop has been reported from China (Min et al., 2008) whereas losses of 90% were recorded in AY-affected aubergines in Bangladesh (Kelly et al., 2009). Infection rates of 60 and 99% were recorded in Hungary for AY-affected sugarbeet plants and India for AY-affected Jatropha curcas plants, respectively (Mumford et al., 2000; Kumar et al., 2010b). However, there are also several reports on sporadic occurrence and generally low incidence of AY group phytoplasmas in vegetable and ornamental crops (Smith et al., 1988; Vibio et al., 1995; Bertaccini et al., 1998). Cassava witches' broom, a disease affecting cassava in South East Asia (Vietnam, Thailand, Cambodia, Laos, China and the Philippines) is caused by 16SrI phytoplasma. The disease has resulted in significant reductions in cassava root starch content and up to 80% yield loss in parts of Vietnam (Anon., 2014).
Cassia fistula (Indian laburnum).
Authors: Datiles Marianne Jennifer , Acevedo-Rodríguez Pedro
Published: March 2021

C. fistula is widely planted in the tropics as an ornamental and avenue tree. The timber is hard, strong and durable, and although not available on a commercial scale, is used for a wide variety of purposes on a local scale. The roots, bark, seeds, leaves and pulp from ripe pods are used medicinally. In India, the bark is also widely used in tannin industry. The flowers are golden-yellow, and are used in religious ceremonies in India and Bangladesh. The flowers and buds may be eaten (Krishnamurthy, 1993).
Arundo donax (giant reed).
Authors: Rojas-Sandoval Julissa , Acevedo-Rodríguez Pedro
Published: March 2021

A. donax has played an important role in the culture of the western world through its influence on the development of music, which can be traced back 5000 years. A. donax cane was the source of the original Pan pipe or syrix and to this day the A. donax culms remain an unrivalled source of reeds for woodwind instruments. A. donax has been purposefully introduced by man and cultivated into many of the subtropical and warm temperate areas of the world for a number of uses. It is planted as an ornamental and cultivated for a variety of uses including erosion control along ditches and drainage canals. It is available via the nursery trade and spreads as a garden escapee and through the disposal of garden waste.
Eucalyptus camaldulensis (red gum).
Authors: Rojas-Sandoval Julissa , Acevedo-Rodríguez Pedro
Published: March 2021

E. camaldulensis is a medium to large tree. It has the widest geographical range of any eucalypt and is extensively planted outside Australia. Its tolerance of extreme drought and high temperature, combined with rapid growth when water is available, deep penetration of roots, tolerance of periodic waterlogging and soil salinity, some tolerance of frost, good coppicing ability, and usefulness of the wood, are the keys to its success. E. camaldulensis wood is used mainly for poles, posts, firewood, charcoal, and paper pulp. Logs may be sawn for construction timber, furniture, and packing cases, although the quality is sometimes poor. It is widely planted for shade, shelter, and amenity purposes, and as a source of nectar in honey production. Some tropical provenances produce medicinal-grade Eucalyptus oil.
Adenanthera pavonina (red-bead tree).
Authors: Rojas-Sandoval Julissa , Acevedo-Rodríguez Pedro
Published: March 2021

A. pavonina is a valuable multipurpose species (Adkins, 1994; Clark and Thaman, 1993). It is a source of food, fodder, green manure, fuel, timber, dye, decoration, medicine and other products. In the South Pacific Islands it is intercropped with spices, coffee, coconuts, or planted along borders as a windbreak in plantations or on agroforestry farms (Adkins, 1994; Clark and Thaman, 1993). Throughout the tropics and sub-tropics it is extensively cultivated as an ornamental tree along roadsides and in communal areas.
Mangifera indica (mango).
Authors: Rojas-Sandoval Julissa , Acevedo-Rodríguez Pedro
Published: March 2021

M. indica is not important as a forest tree as it is seldom found in abundance in forests, but wherever the tree is available it is exploited. It is a multipurpose tree species providing shelterbelts, firewood, timber, fruits, cattle fodder, green manure and medicine. It is primarily used for its edible fruits and extensive plantations have been established throughout the tropics and sub-tropics, under numerous cultivars providing good income for mango growers. Various parts of the mango tree are used in traditional medicines. It also has great significance in Hindu religious ceremonies (Kostermans and Bompard, 1993).
Morus nigra (black mulberry).
Authors: Datiles Marianne Jennifer , Acevedo-Rodríguez Pedro
Published: March 2021

M. nigra is a small to medium-size tree up to 10 m tall. It originates from Iran and is slow growing, deciduous and dioecious. For centuries, it has been cultivated in many countries in the world for leaf and fruit production. The leaves are used for silk worm rearing and as fodder for livestock. The fruits are edible. It has high tolerance to drought, frost, cold and air pollutants. The only unsuitable region is the lowland tropics. It is widely planted as an ornamental tree and many types, varieties, and cultivars exist. It is an ideal wood for sports goods, tool handles, light construction and as a fuel. It can be propagated by seed, nursery seedlings, stem and branch cuttings and tissue culture.
Paulownia tomentosa (paulownia).
Authors: Pasiecznik Nick
Published: March 2021

P. tomentosa is one of the most important tree species in China. It is a fast-growing tree with high-quality wood, and produces approximately 0.4 cubic metres of timber after 10 years' growth. Currently there are about 1.1 billion Paulownia trees planted throughout China and about 3.0 million cubic metres of Paulownia timber worth US$55 million is exported overseas each year; P. tomentosa represents a substantial proportion of this. The wood is used in furniture, decorative products and musical instruments. P. tomentosa is also suitable for use in agroforestry systems in semi-humid temperate areas. A disadvantage is that this species grows well only on fertile land. More research is needed in order to improve its wood properties and stress tolerance, and increase its use in plantations.
Thespesia populnea (portia tree).
Authors: Pasiecznik Nick
Published: March 2021

A small to medium-sized evergreen tree, with a rather dense crown and spreading branches (Troup et al., 1975) which reaches about 18 m in height. It has showy, bell-shaped yellow flowers, long-petioled, heart-shaped leaves, and a tough, fibrous bark. It is indigenous to tropical Asia, but has been widely planted throughout tropical regions, including Africa, and coastal woodlands in the Caribbean and elsewhere in the Neotropics. The seed floats in sea water, and can remain viable in sea water for more than a year, making natural distribution by sea currents possible (Nakanishi, 1989). It prefers well-drained sandy, gravelly and rocky soils derived from coral limestone and volcanic parent materials, and it is salt-tolerant (Desale et al., 1989). It is often found close to, but not growing in, mangrove forests which are occasionally inundated, or on saline sands behind mangrove forests (Siddiqi et al., 1995; Sosef et al., 1998; Morton, 1976). In India growth is reported to be rapid, and it flowers and fruits throughout the year (Sosef et al., 1998). In the Caribbean, flowering occurs primarily from April to January (Parrotta, 1994). T. populnea can be easily raised from seed and from cuttings, usually branch or shoot cuttings up to 2 m in length and 10 cm in diameter, although smaller cuttings are generally preferred (Parrotta, 1994). In India it is often planted to consolidate bunds and ridges in aqua-silvicultural systems for prawn production, or along the coast as protection against erosion (Latiff and Faridah Hanum, 1997; Harikrishnan, 1993). It produces a fine-grained, durable wood (density 400 to 770 kg/cubic metre at 15% moisture content), with a red-brown to dark brown heartwood and a sharply differentiated white sapwood. The wood is valued for furniture, flooring, musical instruments, mouldings, utensils and vehicle bodies. The wood is durable under water, and is therefore used for boat-building. The bark is also utilized for caulking and rope. The wood and a yellow gum from the fruits and flowers yield a dye, and core-wood has medicinal uses. It is a sacred tree in many parts of the Pacific, often planted near temples, and is also grown as an ornamental and roadside tree. Planting T. populnea is outlawed, or strongly discouraged, in some cotton-growing areas, as it is an alternative host of several damaging cotton pests, including the cotton weevil (Anthonomus grandis grandis), the red cotton bug (Dysdercus cingulatus), the Indian dusky cotton bug (Oxycarenus laetus), and Pyroderces simplex (Parrotta, 1994).
Bambusa vulgaris (common bamboo).
Authors: Rojas-Sandoval Julissa , Acevedo-Rodríguez Pedro
Published: March 2021

Bambusa vulgaris is the most commonly encountered bamboo in cultivation in SE Asia but is rarely found in natural forest (although possibly natural, or escaped, naturalized populations exist). It is grown pantropically, and is the only Asian species that is common in the New World. Ease of propagation is the main reason for its success, culms and branches rooting very readily indeed. Infrequency of flowering, failure to produce seed and divert resources away from culm production, and recovery of clumps after flowering are other assets, and may be a result of repeated selection and cloning (Stapleton, 1990). Although not very straight, not easy to split, and inflexible, the culms are thick-walled and initially strong although relatively susceptible to powder-post beetle attack. They find many uses, although structural use is not recommended without preservation to protect against beetles. The ease of propagation, long life expectancy, and high yield make this species better suited to production of pulp and biomass for energy. Susceptibility to bamboo blight is of concern, especially on sites with impeded drainage. Repeated vegetative propagation has resulted in reduced genetic variability. Ornamental clones with all yellow, or yellow striped culms, or shortened, swollen culm internodes ('Wamin') are widely cultivated.
Electron heating mode transitions in radio-frequency driven micro atmospheric pressure plasma jets in He/O2: a fluid dynamics approach
Authors: Liu Yue , Korolov Ihor , Hemke Torben , Bischoff Lena , Hübner Gerrit , Schulze Julian , Mussenbrock Thomas
Published: March 2021

A two-dimensional fluid model is used to investigate the electron heating dynamics and the production of neutral species in a capacitively coupled radio-frequency micro atmospheric pressure helium plasma jet—specifically the COST jet—with a small oxygen admixture. Electron heating mode transitions are found to be induced by varying the driving voltage amplitude and the O2 concentration numerically and experimentally. The helium metastable density, and the charged species densities are highly relevant to the electron heating dynamics. By analyzing the creation and destruction mechanisms of the negative ions, we find that the generation of negative ions strongly depends on the O2 concentration. The increase of the electronegativity with the increasing O2 concentration leads to an enhancement of the bulk drift electric field. The distributions of the different neutral species densities along the direction of the gas flow inside the jet, as well as in the effluent differ a lot due to the relevant chemical reaction rates and the effect of the gas flow. The simulated results show that a fluid model can be an effective tool for qualitative investigations of micro atmospheric pressure plasma jets.
Dynamic remagnetisation of CoFe2O4 nanoparticles: thermal fluctuational thawing of anisotropy
Authors: Balaev D A , Poperechny I S , Krasikov A A , Semenov S V , Popkov S I , Knyazev Y V , Kirillov V L , Yakushkin S S , Martyanov O N , Raikher Yu L
Published: March 2021

We report a study of the magnetodynamics of cobalt ferrite (CoFe2O4) nanoparticles with an average diameter of ∼6 nm. Hysteresis loops were measured under quasi-static conditions and in pulse fields with amplitudes H0 of up to 130 kOe and for durations τ

P
of 8 and 16 ms. The growth of coercivity H

c
observed with an increase in the magnetic field variation rate dH/dt (determined by the values of H
0 and τ

P
) and the reduction of H

c
with temperature is ascribed to the superparamagnetic effect. The proposed theoretical model explains the observed dependences fairly well. Notably, the effective magnetic anisotropy constant obtained exceeds the value for bulk crystals and might be indicative of the contribution of surface magnetic anisotropy.
Plasmon localization by adatoms in gold atomic wires on Si(775)
Authors: Mamiyev Z , Tegenkamp C , Pfnür H
Published: March 2021

Self-organized gold chains on vicinal Si(111) surfaces represent prototype examples of quasi-one-dimensional objects that are stabilized by hybridization with Si surface states. Their plasmons contain important information about the unoccupied bandstructure close to the Fermi level. Using Si(775)–Au as an example, we report here the modifications of the plasmon dispersion by the simple atomic adatom species H and O. Using a combination of low energy electron diffraction and high-resolution electron energy loss spectroscopy, we study the interconnection between plasmonic excitation and the corresponding local surface structure. Both adsorbates do not destroy metallicity, but, similar to Si(553)–Au, atomic hydrogen enhances dimerization of the Au chains, which at small concentrations counteracts the disorder introduced by random adsorption. This effect, most likely caused by electron donation of H to the surface states, is missing in case of adsorbed oxygen, so that only the effect of disorder is observed. For both adsorbates increasing disorder as a function of adsorbate concentration finally results in plasmon localization and opening of a band gap.
Photoluminescence upconversion of 2D materials and applications
Authors: Wang Qixing , Wee Andrew T S
Published: March 2021

Photoluminescence (PL) upconversion is a phenomenon involving light–matter interactions, where the energy of emitted photons is higher than that of the incident photons. PL upconversion is an intriguing process in two-dimensional materials and specifically designed 2D heterostructures, which have potential upconversion applications in optoelectronic devices, bioimaging, and semiconductor cooling. In this review, we focus on the recent advances in photoluminescence upconversion in two-dimensional materials and their heterostructures. We discuss the upconversion mechanisms, applications, and future outlook of upconversion in two-dimensional materials.
Davydov Splitting, Resonance Effect and Phonon Dynamics in Chemical Vapor Deposition Grown Layered MoS2
Authors: Kumar Deepu , Singh Birender , Kumar Rahul , Kumar Mahesh , Kumar Pradeep
Published: March 2021

We present comprehensive temperature dependent Raman measurements for chemical vapor deposition grown horizontally aligned layered MoS2 in a temperature range of 4–330 K under a resonance condition. Our analysis of temperature dependent phonon frequency shift and linewidth suggests a finite role of three and four phonon anharmonic effect. We observe Davydov splitting of the out-of-plane (A
1g
) and in-plane (

E

2
g

1

) modes for both three layer (3L) and few layer (FL) systems. The number of Davydov splitting components are found more in FL compared to 3L MoS2, which suggests that it increases with an increasing number of layers. Further, Davydov splitting is analyzed as a function of temperature. Temperature evaluation of the Raman spectra shows that the Davydov splitting, especially for A
1g
mode, is very strong and well resolved at low temperature. We observe that A
1g
mode shows the splitting at low temperature, while

E

2
g

1

mode is split even at room temperature, which suggests a prominent role of A
1g
mode in the interlayer interaction at low temperature. Further, an almost 60-fold increase in the intensity of the phonon modes at low temperature clearly shows the temperature dependent tuning of the resonance effect.
High conductivity InAlN/GaN multi-channel two-dimensional electron gases
Authors: Sohi P , Carlin J-F , Rossell M D , Erni R , Grandjean N , Matioli E
Published: March 2021

In this study, we propose a novel, high-conductivity multi-channel heterostructure based on lattice-matched InAlN/GaN channels with modulation-doping-induced two-dimensional electron gases (2DEGs). To facilitate device processing, the channel period thickness was minimized while maintaining a high electron mobility in each channel. We demonstrate a 10-channel heterostructure with a period thickness of 14 nm and a total sheet resistance of 82 Ω □−1. By increasing the doping concentration in each channel, much higher carrier densities per channel were achieved, resulting in an ultra-low sheet resistance of 36 Ω □−1. Furthermore, optimizing the heterostructure design enabled high electron mobilities, up to 1530 cm2 V−1 s−1, independent of the number of channels, by secluding the 2DEG from the barrier interfaces in each channel to avoid both strong interface roughness and ionized impurity scattering. This was achieved by modulation-doping of the GaN channel and the insertion of a GaN interlayer between the InAlN barrier and the AlN spacer. This approach offers a new platform for designing high conductivity heterostructures, where the general trade-off between electron mobility and carrier density can be significantly alleviated.
Application of statistical moment method to investigate mechanical properties of yttria-stabilized zirconia
Authors: Thu Lam Le , Van Hung Vu , Thanh Hai Dang , Thi Thanh Huong Le
Published: March 2021

The mechanical properties of yttria-stabilized zirconia (YSZ) crystal under extreme conditions are theoretically investigated using the analytic free energy formulas derived from the statistical moment method. We calculate the elastic moduli and constants under temperature up to 2100 K and pressure up to 20 GPa using Buckingham potential. The dopant concentration, temperature, and pressure dependences of the elastic moduli and constants of YSZ crystal are studied taking into account the anharmonic effects of the lattice vibrations. Our results are in reasonable agreement with previous experiments and simulations. This approach can then be developed extensively to investigate the thermodynamic and mechanical properties of the other ceramic materials used in solid oxide fuel cells.
Asymmetry of the CMB map: local and global anomalies
Authors: Creswell James , Naselsky Pavel
Published: March 2021

We investigate the sources of parity asymmetry in the CMB
temperature maps using a pixel domain approach. We demonstrate that
this anomaly is mainly associated with the presence of two pairs of
high asymmetry regions. The first pair of peaks with Galactic
coordinates (l, b) = (212°, -21°) and (32°,
21°) is associated with the Northern Galactic Spur and the
direction of the dipole modulation of the power spectrum of the CMB
anisotropy. The other pair ((l, b)=(332°, -8°) and
(152°, 8°)) is located within the Galactic plane (the
Galactic Cold Spot and its antipodal partner). Similar asymmetric
peaks, but with smaller amplitudes, belong to the WMAP/Planck Cold
Spot and its partner in the Northern Galactic Spur. These local
anomalies increase the odd-multipole power to a level consistent
with Gaussian simulations. In contrast, the deficit of symmetric
peaks is accompanied by a deficit in the even-multipole power and is
the source of the parity asymmetry of the CMB temperature maps at
the level of about 3 sigma. We also evaluate the influence of the
quadrupole, which is another source of the even-multipole
deficit. If the low quadrupole is an intrinsic feature of the
theoretical model, it will reduce the significance of the parity
asymmetry to around the 2 sigma level. We also investigate the
relationship between the asymmetry of the power spectrum and the
level of the parity asymmetry in the framework of a model with
dipole modulation of a statistically uniform Gaussian signal. We
show that these two anomalies are innately linked to each other.
Influence of laser parameters on superhydrophobicity- A review
Authors: Raja R Samuel Sanjay , Selvakumar P , Babu P Dinesh , Rubasingh B Jacob , Suresh K
Published: March 2021

Superhydrophobicity is also known as lotus effect which makes the water to roll off and bounce when liquid droplets resting on the surface. In nature it is used by plants for self-cleaning purpose and by animals for anti-adhesion skin. The superhydrophobic surface has been mimicked and used in the field of aerospace, textiles, power line, solar cell and so on. In this review we provide the basic theories of wetting, wetting transition models of superhydrophobicity, parameters of laser beam and post processing (heat treatment only) after laser irradiation related to contact angle. Laser parameters play a vital role in producing surface topography. The surface topography may be consists of ripples, dual surface roughness on the laser textured surface. Based on the magnitude of laser parameters the different surface morphology can be obtained. The surface morphology will vary for the different laser system such femto, pico or nano second laser system. The present review aims to report the understanding of laser parameters in order to texture the expected surface structure by controlling the laser parameters.
Actuated bending of a long cantilevered glassy nematic bilayer strip: failure of the beam model
Authors: Lin Y L , He L H
Published: March 2021

Cantilevered long glassy nematic bilayer strips bend in response to light, and thus are attractive for actuation applications. The objective of this work is to examine whether the deformation can be predicted by the one-dimensional beam model as in usual practice. To do so, we consider a bilayer with orthogonal director orientations in the upper and lower layers and analyze its bending in the framework of the classical plate theory. We find that the deflection is much larger than that given by the beam model, because the spontaneous bending in the width direction increases the curvature along the long axis. Therefore, the one-dimensional beam model fails to describe the bending behavior of the cantilevered bilayer strips.
Diagnostic Accuracy Estimates for COVID-19 Real-Time Polymerase Chain Reaction and Lateral Flow Immunoassay Tests With Bayesian Latent-Class Models
Authors: Kostoulas Polychronis , Eusebi Paolo , Hartnack Sonja
Published: March 2021

Our objective was to estimate the diagnostic accuracy of real-time polymerase chain reaction (RT-PCR) and lateral flow immunoassay (LFIA) tests for coronavirus disease 2019 (COVID-19), depending on the time after symptom onset. Based on the cross-classified results of RT-PCR and LFIA, we used Bayesian latent-class models, which do not require a gold standard for the evaluation of diagnostics. Data were extracted from studies that evaluated LFIA (immunoglobulin G (IgG) and/or immunoglobulin M (IgM)) assays using RT-PCR as the reference method. The sensitivity of RT-PCR was 0.68 (95% probability interval (PrI): 0.63, 0.73). IgG/M sensitivity was 0.32 (95% PrI :0.23; 0.41) for the first week and increased steadily. It was 0.75 (95% PrI: 0.67; 0.83) and 0.93 (95% PrI: 0.88; 0.97) for the second and third weeks after symptom onset, respectively. Both tests had a high to absolute specificity, with higher point median estimates for RT-PCR specificity and narrower probability intervals. The specificity of RT-PCR was 0.99 (95% PrI: 0.98; 1.00). and the specificity of IgG/IgM was 0.97 (95% PrI: 0.92, 1.00), 0.98 (95% PrI: 0.95, 1.00) and 0.98 (95% PrI: 0.94, 1.00) for the first, second, and third weeks after symptom onset. The diagnostic accuracy of LFIA varies with time after symptom onset. Bayesian latent-class models provide a valid and efficient alternative for evaluating the rapidly evolving diagnostics for COVID-19, under various clinical settings and different risk profiles.
A comparative analysis of RNA-binding proteins binding models learned from RNAcompete, RNA Bind-n-Seq and eCLIP data
Authors: Tripto Eitamar , Orenstein Yaron
Published: March 2021

Understanding post-transcriptional gene regulation is a key challenge in today’s biology. The new technologies of RNAcompete and RNA Bind-n-Seq enable the measurement of the binding intensities of one RNA-binding protein (RBP) to numerous synthetic RNA sequences in a single experiment. Recently, Van Nostrand et al. reported the results of RNA Bind-n-Seq experiments measuring binding of 78 human RBPs. Because 31 of these RBPs were also covered by RNAcompete technology, a large-scale comparison between implementations of these two in vitro technologies is now possible. Here, we assessed the similarities and differences between binding models, represented as a list of $k$-mer scores, inferred from RNAcompete and RNA Bind-n-Seq, and also measured how well these models predict in vivo binding. Our results show that RNA Bind-n-Seq- and RNAcompete-derived models agree (Pearson correlation $> 0.5$) for most RBPs (23 out of 31). RNA Bind-n-Seq-derived $k$-mer scores predict RNAcompete binding measurements quite well (average Pearson correlation 0.26), and both technologies produce $k$-mer scores that achieve comparable results in predicting in vivo binding (average AUC 0.7). When inspecting RNA structural preferences inferred from the data of RNA Bind-n-Seq and RNAcompete, we observed high concordance in binding preferences. Through our study, we developed a new $k$-mer score for RNA Bind-n-Seq and extended it to include RNA structural preferences.
Phantom limb pain: thinking outside the (mirror) box
Authors: Makin Tamar R
Published: March 2021

Despite our best efforts over the past century, our mechanistic understanding of phantom limb pain and our ability to treat it have remained limited. Tamar Makin invites readers to think more critically about some of the most popular approaches to understanding and treating this condition.
Estimation of Secondary Household Attack Rates for Emergent Spike L452R Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants Detected by Genomic Surveillance at a Community-Based Testing Site in San Francisco
Authors: Peng James , Liu Jamin , Mann Sabrina A , Mitchell Anthea M , Laurie Matthew T , Sunshine Sara , Pilarowski Genay , Ayscue Patrick , Kistler Amy , Vanaerschot Manu , Li Lucy M , McGeever Aaron , Chow Eric D , Marquez Carina , Nakamura Robert , Rubio Luis , Chamie Gabriel , Jones Diane , Jacobo Jon , Rojas Susana , Rojas Susy , Tulier-Laiwa Valerie , Black Douglas , Martinez Jackie , Naso Jamie , Schwab Joshua , Petersen Maya , Havlir Diane , DeRisi Joseph ,   IDseq Team
Published: March 2021

Background

Sequencing of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral genome from patient samples is an important epidemiological tool for monitoring and responding to the pandemic, including the emergence of new mutations in specific communities.

Methods

SARS-CoV-2 genomic sequences were generated from positive samples collected, along with epidemiological metadata, at a walk-up, rapid testing site in the Mission District of San Francisco, California during 22 November to 1 December, 2020, and 10–29 January 2021. Secondary household attack rates and mean sample viral load were estimated and compared across observed variants.

Results

A total of 12 124 tests were performed yielding 1099 positives. From these, 928 high-quality genomes were generated. Certain viral lineages bearing spike mutations, defined in part by L452R, S13I, and W152C, comprised 54.4% of the total sequences from January, compared to 15.7% in November. Household contacts exposed to the “California” or “West Coast” variants (B.1.427 and B.1.429) were at higher risk of infection compared to household contacts exposed to lineages lacking these variants (0.36 vs 0.29, risk ratio [RR] = 1.28; 95% confidence interval [CI]: 1.00–1.64). The reproductive number was estimated to be modestly higher than other lineages spreading in California during the second half of 2020. Viral loads were similar among persons infected with West Coast versus non-West Coast strains, as was the proportion of individuals with symptoms (60.9% vs 64.3%).

Conclusions

The increase in prevalence, relative household attack rates, and reproductive number are consistent with a modest transmissibility increase of the West Coast variants.

Summary: We observed a growing prevalence and modestly elevated attack rate for “West Coast” severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants in a community testing setting in San Francisco during January 2021, suggesting its modestly higher transmissibility.
Isolation and characterization of bacteriophages from the human skin microbiome that infectStaphylococcus epidermidis
Authors: Valente Luca G , Pitton Melissa , Fürholz Monika , Oberhaensli Simone , Bruggmann Rémy , Leib Stephen L , Jakob Stephan M , Resch Grégory , Que Yok-Ai , Cameron David R
Published: March 2021

Phage therapy might be a useful approach for the treatment of nosocomial infections; however, only few lytic phages suitable for this application are available for the opportunistic pathogen, Staphylococcus epidermidis. In the current study, we developed an efficient method to isolate bacteriophages present within the human skin microbiome, by using niche-specific S. epidermidis as the host for phage propagation. Staphylococcus epidermidis was identified on the forehead of 92% of human subjects tested. These isolates were then used to propagate phages present in the same skin sample. Plaques were observable on bacterial lawns in 46% of the cases where S. epidermidis was isolated. A total of eight phage genomes were genetically characterized, including the previously described phage 456. A total of six phage sequences were unique, and spanned each of the major staphylococcal phage families; Siphoviridae (n = 3), Podoviridae (n = 1) and Myoviridae (n = 2). One of the myoviruses (vB_SepM_BE06) was identified on the skin of three different humans. Comparative analysis identified novel genes including a putative N-acetylmuramoyl-L-alanine amidase gene. The host-range of each unique phage was characterized using a panel of diverse staphylococcal strains (n = 78). None of the newly isolated phages infected more than 52% of the S. epidermidis strains tested (n = 44), and non-S. epidermidis strains where rarely infected, highlighting the narrow host-range of the phages. One of the phages (vB_SepM_BE04) was capable of killing staphylococcal cells within biofilms formed on polyurethane catheters. Uncovering a richer diversity of available phages will likely improve our understanding of S. epidermidis-phage interactions, which will be important for future therapy.
Insulin Restriction, Emotion Dysregulation, and Depressive Symptoms in Late Adolescents with Diabetes
Authors: Beam Aislinn B , Wiebe Deborah J , Berg Cynthia A
Published: March 2021

Objective

Insulin restriction occurs when an individual takes less insulin than recommended and is a serious concern for those with diabetes. General insulin restriction (IR) and insulin restriction for weight control (IRWC) have not been clearly distinguished in the literature, creating inconsistencies and limited understanding of factors that underlie this behavior. We examined whether these are distinct, and how emotion dysregulation and depressive symptoms relate to both forms of insulin restriction during late adolescence.

Methods

As part of a larger study, late adolescents (ages 17–18) with type 1 diabetes (N = 236) completed measures of depressive symptoms (Center for Epidemiologic Studies—Depression Scale [CES-D]), facets of Difficulties In Emotion Regulation Scale (DERS), diabetes self-management behaviors, insulin restriction, and hemoglobin A1c (HbA1c).

Results

IR and IRWC were not significantly associated with each other. IR was associated with self-management behaviors but not HbA1c, whereas the opposite was true for IRWC. All DERS subscales (M = 10.60–16.73) and CES-D (M = 16.56) were correlated with greater IRWC; CES-D and all but one DERS subscale were correlated with IR. Covariation with CES-D explained associations between DERS and IRWC. CES-D moderated associations with IR, indicating most subscales of the DERS were associated with IR only when CES-D was higher.

Conclusion

Emotion dysregulation and depressive symptoms are important correlates of the dangerous behavior of insulin restriction, but function differently when insulin is restricted specifically for weight control versus nonspecified reasons. Future research to understand these underlying processes will be necessary to develop emotion-based theory and evidence-based interventions for this dangerous behavior.
Examining transfer of rights surplus—Brazilian case
Authors: David Olavo Bentes , Castro de Carvalho Bruno Eustáquio F , Braga Maria Amélia , Isfer Renata Beckert , Esteves Heloísa Borges , Regra Andre
Published: March 2021

At the end of 2019, Brazil realized an enormous offshore premium assets under the ‘Transfer of Rights’ (TOR) regime. It was a key milestone that later set in motion the largest oil bidding round in history, according to the Brazilian authorities. TOR is a regime that deviates from the general rule of holding bids prior to the granting of oil & natural gas E&P rights. No legal dispositive was able to predict the possibility which impose Brazilian government design an innovative portfolio of regulations in order to achieve high productivity and profitability. A new regulatory framework was created to support the decision makers. Transference of Rights Surplus came to lead with surplus volume bidding rounds. Future biddings will take place at another level of institutional maturity to deal with the situation, and takes advantage of the learning and tools already developed. It is expected that the changes being discussed will bring attractiveness to the offer of the areas in the current scenario.
ℋ-Colouring Dichotomy in Proof Complexity
Authors: Gaysin Azza
Published: March 2021

The $\mathcal {H}$-colouring problem for undirected simple graphs is a computational problem from a huge class of the constraint satisfaction problems (CSPs): an $\mathcal {H}$-colouring of a graph $\mathcal {G}$ is just a homomorphism from $\mathcal {G}$ to $\mathcal {H}$ and the problem is to decide for fixed $\mathcal {H}$, given $\mathcal {G}$, if a homomorphism exists or not. The dichotomy theorem for the $\mathcal {H}$-colouring problem was proved by Hell and Nešetřil (1990, J. Comb. Theory Ser. B, 48, 92–110) (an analogous theorem for all CSPs was recently proved by Zhuk (2020, J. ACM, 67, 1–78) and Bulatov (2017, FOCS, 58, 319–330)), and it says that for each $\mathcal {H}$, the problem is either $p$-time decidable or $NP$-complete. Since negations of unsatisfiable instances of CSP can be expressed as propositional tautologies, it seems to be natural to investigate the proof complexity of CSP. We show that the decision algorithm in the $p$-time case of the $\mathcal {H}$-colouring problem can be formalized in a relatively weak theory and that the tautologies expressing the negative instances for such $\mathcal {H}$ have polynomial proofs in propositional proof system $R^*(log)$, a mild extension of resolution. In fact, when the formulas are expressed as unsatisfiable sets of clauses, they have $p$-size resolution proofs. To establish this, we use a well-known connection between theories of bounded arithmetic and propositional proof systems. This upper bound follows also from a different construction in [1]. We complement this result by a lower bound result that holds for many weak proof systems for a special example of $NP$-complete case of the $\mathcal {H}$-colouring problem, using known results about the proof complexity of the pigeonhole principle. The main goal of our work is to start the development of some of the theories beyond the CSP dichotomy theorem in bounded arithmetic. We aim eventually—in a subsequent work—to formalize in such a theory the soundness of Zhuk’s algorithm, extending the upper bound proved here from undirected simple graphs to the general case of directed graphs in some logical calculi.
Artificial neural network classification of asteroids in the M1:2 mean-motion resonance with Mars
Authors: Carruba V , Aljbaae S , Domingos R C , Barletta W
Published: March 2021

Artificial neural networks (ANNs) have been successfully used in the last years to identify patterns in astronomical images. The use of ANN in the field of asteroid dynamics has been, however, so far somewhat limited. In this work, we used for the first time ANN for the purpose of automatically identifying the behaviour of asteroid orbits affected by the M1:2 mean-motion resonance with Mars. Our model was able to perform well above 85 per cent levels for identifying images of asteroid resonant arguments in term of standard metrics like accuracy, precision, and recall, allowing to identify the orbital type of all numbered asteroids in the region. Using supervised machine learning methods, optimized through the use of genetic algorithms, we also predicted the orbital status of all multi-opposition asteroids in the area. We confirm that the M1:2 resonance mainly affects the orbits of the Massalia, Nysa, and Vesta asteroid families.
MRI-active inner regions of protoplanetary discs. I. A detailed model of disc structure
Authors: Jankovic Marija R , Owen James E , Mohanty Subhanjoy , Tan Jonathan C
Published: March 2021

Short-period super-Earth-sized planets are common. Explaining how they form near their present orbits requires understanding the structure of the inner regions of protoplanetary discs. Previous studies have argued that the hot inner protoplanetary disc is unstable to the magnetorotational instability (MRI) due to thermal ionization of potassium, and that a local gas pressure maximum forms at the outer edge of this MRI-active zone. Here we present a steady-state model for inner discs accreting viscously, primarily due to the MRI. The structure and MRI-viscosity of the inner disc are fully coupled in our model; moreover, we account for many processes omitted in previous such models, including disc heating by both accretion and stellar irradiation, vertical energy transport, realistic dust opacities, dust effects on disc ionization, and non-thermal sources of ionization. For a disc around a solar-mass star with a standard gas accretion rate ($\dot{M}\, \sim \, 10^{-8}$ M⊙ yr−1) and small dust grains, we find that the inner disc is optically thick, and the accretion heat is primarily released near the mid-plane. As a result, both the disc mid-plane temperature and the location of the pressure maximum are only marginally affected by stellar irradiation, and the inner disc is also convectively unstable. As previously suggested, the inner disc is primarily ionized through thermionic and potassium ion emission from dust grains, which, at high temperatures, counteract adsorption of free charges on to grains. Our results show that the location of the pressure maximum is determined by the threshold temperature above which thermionic and ion emission become efficient.
HD 143006: circumbinary planet or misaligned disc?
Authors: Ballabio G , Nealon R , Alexander R D , Cuello N , Pinte C , Price D J
Published: March 2021

Misalignments within protoplanetary discs are now commonly observed, and features such as shadows in scattered light images indicate departure from a co-planar geometry. VLT/SPHERE (Very Large Telescope/Spectro-Polarimetric High-​contrast Exoplanet REsearch) observations of the disc around HD 143006 show a large-scale asymmetry and two narrow dark lanes that are indicative of shadowing. ALMA (Atacama Large Millimeter/submillimeter Array) observations also reveal the presence of rings and gaps in the disc, along with a bright arc at large radii. We present new hydrodynamic simulations of HD 143006, and show that a configuration with both a strongly inclined binary and an outer planetary companion is the most plausible to explain the observed morphological features. We compute synthetic observations from our simulations, and successfully reproduce both the narrow shadows and the brightness asymmetry seen in infrared scattered light. Additionally, we reproduce the large dust observed in the mm continuum, due to a 10 Jupiter-mass planet detected in the CO kinematics. Our simulations also show the formation of a circumplanetary disc, which is misaligned with respect to the outer disc. The narrow shadows cast by the inner disc and the planet-induced ‘kink’ in the disc kinematics are both expected to move on a time-scale of ∼5–10 yr, presenting a potentially observable test of our model. If confirmed, HD 143006 would be the first known example of a circumbinary planet on a strongly misaligned orbit.