bluuebunny/crossref_metadata_2025 huggingface dataset:
Role of Atwood number on flow morphology of a planar shock-accelerated square bubble: A numerical study
Authors: Singh Satyvir
Published: December 2020

The Atwood number plays a critical role in describing the physics of fluids behind the hydrodynamic instabilities in gas dynamics. In order to investigate the impacts of the Atwood number (At), the evolution of a shock-accelerated square bubble containing either SF6, Kr, Ar, Ne, or He and surrounded by N2 is investigated numerically. For this purpose, the unsteady compressible Navier–Stokes–Fourier equations are solved using an explicit modal discontinuous Galerkin method. For validation, the numerical results are compared with available experimental results and are found to be in good agreement. The results demonstrate that the Atwood number has a significant influence on flow morphology with wave patterns, vortex creation, vorticity generation, and bubble deformation. For At > 0, the speed of the shock wave traveling along with the bubble inner surface is often less than that of the incident shock wave and greater than that of the transmitted shock wave. Moreover, vortex pairs from the upstream and downstream corners are generated, and the former vortex pair ultimately dominates the flow morphology. For At ≈ 0, the incident and transmitted shock waves move at the same speeds, whereas for At < 0, the transmitted shock wave travels faster than the incident shock wave. Moreover, only one vortex pair at the upstream corners is generated, which dominates the flow morphology. Furthermore, a detailed study of Atwood number impacts is investigated through the vorticity generation at interfaces. A quantitative analysis based on the shock trajectories, the interface features, and the integral diagnostics is also studied in detail to investigate the impacts of the Atwood number on the flow structure. Finally, a comparative study of the flow physics between the shock-accelerated square and cylindrical bubbles is conducted to examine their natural differences.
Effects of mask-wearing on the inhalability and deposition of airborne SARS-CoV-2 aerosols in human upper airway
Authors: Xi Jinxiang , Si Xiuhua April , Nagarajan Ramaswamy
Published: December 2020

Even though face masks are well accepted as tools useful in reducing COVID-19 transmissions, their effectiveness in reducing viral loads in the respiratory tract is unclear. Wearing a mask will significantly alter the airflow and particle dynamics near the face, which can change the inhalability of ambient particles. The objective of this study is to investigate the effects of wearing a surgical mask on inspiratory airflow and dosimetry of airborne, virus-laden aerosols on the face and in the respiratory tract. A computational model was developed that comprised a pleated surgical mask, a face model, and an image-based upper airway geometry. The viral load in the nose was particularly examined with and without a mask. Results show that when breathing without a mask, air enters the mouth and nose through specific paths. When wearing a mask, however, air enters the mouth and nose through the entire surface of the mask at lower speeds, which favors the inhalation of ambient aerosols into the nose. With a 65% filtration efficiency (FE) typical for a three-layer surgical mask, wearing a mask reduces dosimetry for all micrometer particles except those of size 1 µm–3 µm, for which equivalent dosimetry with and without a mask in the upper airway was predicted. Wearing a mask reduces particle penetration into the lungs, regardless of the FE of the mask. The results also show that mask-wearing protects the upper airway (particularly the nose and larynx) best from particles larger than 10 µm while protecting the lungs best from particles smaller than 10 µm.
Effects of space sizes on the dispersion of cough-generated droplets from a walking person
Authors: Li Zhaobin , Wang Hongping , Zhang Xinlei , Wu Ting , Yang Xiaolei
Published: December 2020

The dispersion of viral droplets plays a key role in the transmission of COVID-19. In this work, we analyze the dispersion of cough-generated droplets in the wake of a walking person for different space sizes. The air flow is simulated by solving the Reynolds-averaged Navier–Stokes equations, and the droplets are modeled as passive Lagrangian particles. Simulation results show that the cloud of droplets locates around and below the waist height of the manikin after 2 s from coughing, which indicates that kids walking behind an infectious patient are exposed to higher transmission risk than adults. More importantly, two distinct droplet dispersion modes occupying significantly different contamination regions are discovered. A slight change of space size is found being able to trigger the transition of dispersion modes even though the flow patterns are still similar. This shows the importance of accurately simulating the air flow in predicting the dispersion of viral droplets and implies the necessity to set different safe-distancing guidelines for different environments.
Growth of InN ultrathin films on AlN for the application to field-effect transistors
Authors: Jeong Dayeon , Kobayashi Atsushi , Ueno Kohei , Fujioka Hiroshi
Published: December 2020

Herein, we report the growth method of ultrathin indium nitride (InN) films on aluminum nitride (AlN) templates by sputtering and its application to field-effect transistors (FETs). Although island-like InN surfaces were formed at the initial film growth stage, the height of the islands on the surface could be controlled by changing the growth temperature. The height of the InN islands grown at 500 °C was lower than those grown at 440 °C and 480 °C. To demonstrate an application of the InN/AlN heterostructure to FETs, we fabricated FETs using a 2-nm-thick InN film grown on an AlN template. The FET with the InN channel grown at 500 °C exhibited a drain current density of 0.19 mA/mm and an on/off ratio of approximately 102 although the drain current of the FET with the InN grown at 450 °C was not adequately controlled by the gate bias. These results indicate that the growth condition of InN films is responsible for the characteristics of InN/AlN FETs.
The microscopic origins of stretched exponential relaxation in two model glass-forming liquids as probed by simulations in the isoconfigurational ensemble
Authors: Diaz Vela Daniel , Simmons David S.
Published: December 2020

The origin of stretched exponential relaxation in supercooled glass-forming liquids is one of the central questions regarding the anomalous dynamics of these fluids. The dominant explanation for this phenomenon has long been the proposition that spatial averaging over a heterogeneous distribution of locally exponential relaxation processes leads to stretching. Here, we perform simulations of model polymeric and small-molecule glass-formers in the isoconfigurational ensemble to show that stretching instead emerges from a combination of spatial averaging and locally nonexponential relaxation. The results indicate that localities in the fluid exhibiting faster-than-average relaxation tend to exhibit locally stretched relaxation, whereas slower-than-average relaxing domains exhibit more compressed relaxation. We show that local stretching is predicted by loose local caging, as measured by the Debye–Waller factor, and vice versa. This phenomenology in the local relaxation of in-equilibrium glasses parallels the dynamics of out of equilibrium under-dense and over-dense glasses, which likewise exhibit an asymmetry in their degree of stretching vs compression. On the basis of these results, we hypothesize that local stretching and compression in equilibrium glass-forming liquids results from evolution of particle mobilities over a single local relaxation time, with slower particles tending toward acceleration and vice versa. In addition to providing new insight into the origins of stretched relaxation, these results have implications for the interpretation of stretching exponents as measured via metrologies such as dielectric spectroscopy: measured stretching exponents cannot universally be interpreted as a direct measure of the breadth of an underlying distribution of relaxation times.
Seipin regulates the formation of nuclear lipid droplets from a distance
Authors: Du Ximing , Yang Hongyuan
Published: December 2020

Nuclear lipid droplets (nLDs) are poorly characterized outside of the liver. In this issue, Sołtysik et al. (2020. J. Cell Biol.https://doi.org/10.1083/jcb.202005026) show that seipin is absent from the nucleus but seipin deficiency promotes nLD formation by increasing nuclear phosphatidic acid.
Gloomy Prospects and Roller Coasters: Finding Coherence in Genome-Wide Association Studies
Authors: Craver Carl F. , Dozmorov Mikhail , Reimers Mark , Kendler Kenneth S.
Published: December 2020

We address Turkheimer’s argument that genome-wide association studies of behaviors and psychiatric traits will fail to produce coherent explanations. We distinguish two major sources of potential incoherence (heterogeneity and complexity), showing how they independently threaten coherence and considering how they are being and might better be addressed with protein and other databases and network tools.
Generalized Learning and Conditional Expectation
Authors: Huttegger Simon M. , Nielsen Michael
Published: December 2020

Reflection and martingale principles are central to models of rational learning. They can be justified in a variety of ways. In what follows we study martingale and reflection principles in the context of measure theory. We give special attention to two approaches for justifying these principles that have not been studied in that context before: diachronic coherence and the value of information. Together with an extant argument based on expected accuracy, these arguments lend support to the thesis that reflection and martingale principles govern rational learning.
Boolean model for melanogenesis
Authors: Dnyane Pooja , Gadgil Chetan
Published: December 2020

Melanogenesis is a highly regulated process through which the pigment melanin is produced in skin cells. Irregularities in the molecular events that govern the process of skin pigmentation can cause disorders like vitiligo. In order to understand the biology of disease progression, it is important to have an in depth understanding of intracellular events. Mathematical models provide an integrated view of intracellular signalling. There are very few models to date that incorporate intracellular processes relevant to melanogenesis and only one to our knowledge that simulates the dynamics of response to varying levels of input. Here, we report the formulation of the largest Boolean model (265 nodes) for melanogenesis to date. The model was built on the basis of a detailed interaction network graph published by Raghunath et al. Through additional manual curation of the reported interactions, we converted the graph into a set of Boolean rules, following the procedure of the first Boolean model (62 nodes) for melanogenesis published by Lee et al. Simulations show that the predicted response to varying UV levels for most of the nodes is similar to the predictions of the existing model. The greater complexity allows investigation of the sensitivity of melanin to additional nodes. We carried out perturbation analysis of the network through node deletion and constitutive activation to identify sensitivity of outcomes, and compared the nodes identified as sensitive to previous reports.
5 nm-scale surface evenness movement measurement method based on the electron spin in diamond
Authors: Liu Yusong , Wang Shixin , Qin Yue , Guo Hao , Li Zhonghao , Li Yanjun , Tang Jun , Ma Zongmin , Liu Jun
Published: December 2020

The motion of a magnetic levitation structure can lead to low accuracy for magnetically suspended control moment gyros (MSCMG), artificial heart pumps or high precision stable platforms. Measuring this motion is important in orbital navigation and precision measurement technologies, but current methods are unable to measure it with high accuracy under a strong magnetic field around the magnetic levitation structure. Here, we present a method in which nitrogen–vacancy (NV) centers in diamond have been used as a sensor to detect the movement of the magnetic levitation structure. The NV quantum sensors probe the electric field around the suspension magnet induced by the magnet fluctuations. Based on the high sensitivity of 0.3 nT (√Hz)−1, the resolution of motion was about 5 nm. Also, the dynamic movement of the magnetic levitation system has been recorded in real-time with a potential resolution of ∼pm as the magnetic field sensitivity of NV center was improved to ∼pT. Our method offers a novel route to measure and feedback control the magnetic levitation system for MSCMGs in satellite attitude or for magnetic pumps in artificial heart applications.
Bidirectional highly-efficient quantum routing in a T-bulge-shaped waveguide*
Authors: Zhang Jia-Hao , He Da-Yong , Luo Gang-Yin , Wang Bi-Dou , Huang Jin-Song
Published: December 2020

Quantum routing in a T-bulge-shaped waveguide system coupled with a driven cyclic three-level atom and a two-level atom is investigated theoretically. By employing the discrete-coordinate scattering method, exact expressions of the transport coefficients along three ports of the waveguide channels are derived. Our results show that bidirectional high transfer-rate single-photon routing between two channels can be effectively implemented, with the help of the effective potential generated by two atoms and the external driving. Moreover, multiple band zero-transmission emerges in the scattering spectra, arising from the quantum interferences among photons scattered by the boundary and the bulged resonators. The proposed system may suggest an efficient duplex router with filtering functions.
Design and optimization of nano-antenna for thermal ablation of liver cancer cells
Authors: Rabienejhad Mohammad Javad , Mazaheri Azardokht , Davoudi-Darareh Mahdi
Published: December 2020

One method of cancer therapy is to utilize nano-antenna for thermal ablation. In this method, the electromagnetic waves emitted from the nano-antenna are absorbed by the tissue and lead to heating of cancer cells. If temperature of cancer cells reaches a threshold, they will begin to die. For this purpose, an L-shaped frame nano-antenna (LSFNA) is designed to introduce into the biological tissue. Thus, the radiation characteristics of the LSFNA such as near and far-field intensities, directivity, and sensitivity to its gap width are studied to the optimization of the nano-antenna. The bio-heat and Maxwell equations are solved using the finite element method. To prevent damage to healthy tissues in this method, the antenna radiation must be completely controlled and performed carefully. Thus, penetration depth, special absorption rate, temperature distribution, and the fraction of tissue necrosis are analyzed in the biological tissue. That is why the design and optimization of the nano-antennas as a radiation source is important. Also, a pulsed source is used to excite the LSFNA. Furthermore, focusing and efficiency of the nano-antenna radiation on the cancer cell is tuned using an adjustable liquid crystal lens. The focus of this lens is changing under an electric field applied to its surrounding cathode.
Equilibrium dynamics of the sub-ohmic spin-boson model at finite temperature*
Authors: Yang Ke , Tong Ning-Hua
Published: December 2020

We use the full-density matrix numerical renormalization group method to calculate the equilibrium dynamical correlation function C(ω) of the spin operator σz
at finite temperature for the sub-ohmic spin-boson model. A peak is observed at the frequency ω
T ∼ T in the curve of C(ω). The curve merges with the zero-temperature C(ω) in ω ≫ ω
T and deviates significantly from the zero-temperature curve in ω ≪ ω
T.
Temperature-induced phase transition of two-dimensional semiconductor GaTe*
Authors: Wang Xiaoyu , Wang Xue , Zou Hongshuai , Fu Yuhao , He Xin , Zhang Lijun
Published: December 2020

GaTe is a two-dimensional III–VI semiconductor with suitable direct bandgap of ∼ 1.65 eV and high photoresponsivity, which makes it a promising candidate for optoelectronic applications. GaTe exists in two crystalline phases: monoclinic (m-GaTe, with space group C2/m) and hexagonal (h-GaTe, with space group P63/mmc). The phase transition between the two phases was reported under temperature-varying conditions, such as annealing, laser irradiation, etc. The explicit phase transition temperature and energy barrier during the temperature-induced phase transition have not been explored. In this work, we present a comprehensive study of the phase transition process by using first-principles energetic and phonon calculations within the quasi-harmonic approximation framework. We predicted that the phase transition from h-GaTe to m-GaTe occurs at the temperature decreasing to 261 K. This is in qualitative agreement with the experimental observations. It is a two-step transition process with energy barriers 199 meV and 288 meV, respectively. The relatively high energy barriers demonstrate the irreversible nature of the phase transition. The electronic and phonon properties of the two phases were further investigated by comparison with available experimental and theoretical results. Our results provide insightful understanding on the process of temperature-induced phase transition of GaTe.
Digital and analog memory devices based on 2D layered MPS3 (M = Mn, Co, Ni) materials*
Authors: Zhao Guihua , Wang Li , Ke Xi , Yu Zhiyi
Published: December 2020

We demonstrate digital and analog devices with an Ag/MPS3/Au structure based on layered MPS3 (M = Mn, Co, Ni) 2D materials. All devices show the bipolar behavior of resistive switching. In addition, Ag/MnPS3/Au and Ag/NiPS3/Au devices show synaptic characteristics of potentiation and depression. The digital and analog characteristics of resistance states enable Ag/MPS3/Au devices to work as both binary memory and artificial synapse devices. The Ag/MPS3/Au memory devices are promising for applications of flexible eye-like and brain-like systems on a chip when they are integrated with photodetectors and FETs composed of full MPS3 materials.
Multi-layer structures including zigzag sculptured thin films for corrosion protection of AISI 304 stainless steel*
Authors: Abdi Fateme
Published: December 2020

To increase corrosion resistance of the sample, its electrical impedance must be increased. Due to the fact that electrical impedance depends on elements such as electrical resistance, capacitance, and inductance, by increasing the electrical resistance, reducing the capacitance and inductance, electrical impedance and corrosion resistance can be increased. Based on the fact that these elements depend on the type of material and the geometry of the material, multilayer structures with different geometries are proposed. For this purpose, conventional multilayer thin films, multilayer thin film including zigzag structure (zigzag 1) and multilayer thin film including double zigzag structure (zigzag 2) of manganese nitride are considered to protect AISI 304 stainless steel against corrosion in salt solution. These multilayer coatings including zigzag structures are prepared by alternately using the conventional deposition of thin film and glancing angle deposition method. After deposition, the samples are placed in a furnace under nitrogen flux for nitriding. The cross sections of the structures are observed by field emission scanning electron microscopy (FESEM). Atomic force microscope (AFM) is used to make surface analyses of the samples. The results show that the multilayer thin films including zigzag structures have smaller grains than conventional multilayer thin films, and the zigzag 2 structure has the smaller grain than the other two samples, which is attributed to the effect of shadowing and porosity on the oblique angle deposition method. Crystallography structures of the samples are studied by using x-ray diffraction (XRD) pattern and the results show that nitride phase formation in zigzag 2 structure is better than that in zigzag 1 structure and conventional multilayer thin film. To investigate the corrosion resistances of the structures, electrochemical impedance spectroscopy (EIS) and potentiodynamic polarization tests are performed. The results reveal that the multilayer thin films with zigzag structures have better corrosion protection than the conventional multilayer thin films, and the zigzag structure 2 has the smallest corrosion current and the highest corrosion resistance. The electrical impedances of the samples are investigated by simulating equivalent circuits. The high corrosion resistance of zigzag 2 structure as compared with conventional multilayer structure and zigzag 1 structure, is attributed to the high electrical impedance of the structure due to its small capacitance and high electrical resistance. Finally, the surfaces of corroded samples are observed by scanning electron microscope (SEM).
Power exhaust by core radiation at COMPASS tokamak
Authors: Komm M. , Mancini D. , Morbey M. , Cavalier J. , Adamek J. , Bernert M. , Bilkova P. , Bohm P. , Brida D. , Février O. , Henderson S. , Hron M. , Jerab M. , Imrisek M. , Kripner L. , Naydenkova D. , Panek R. , Sos M. , Vondracek P. , EUROfusion MST1 team the
Published: December 2020

Substantial power dissipation in the edge plasma is required for the safe operation of ITER and next-step fusion reactors, otherwise unmitigated heat fluxes at the divertor plasma-facing components (PFCs) would easily exceed their material limits. Traditionally, such heat flux mitigation is linked to the regime of detachment, which is characterised by a significant pressure gradient between upstream and downstream scrape-off layer (SOL). However, the physics phenomena responsible for power dissipation and pressure loss are distinctly different, especially when the power dissipation is achieved by impurity seeding. In principle, it is possible to achieve substantial mitigation of the heat fluxes while maintaining conservation of the pressure along the open field lines in the SOL. This regime can be accessed by injection of medium- or high-Z impurities, which mostly radiate inside the last closed flux surface. The critical question related to such an approach is the effect on confinement and perspective fusion power generation in future thermonuclear reactors. In this work, we report on experiments at COMPASS tokamak, where neon and argon impurities were injected in ohmic or NBI-heated low confinement plasmas. With appropriate seeding waveform, stable scenarios were achieved, avoiding the radiative collapse of plasmas. Significant reduction of heat fluxes at the outer target was observed, with heat flux pattern similar to the one previously achieved by nitrogen seeding. The reduction of downstream pressure was, however, accompanied by an equal reduction of upstream pressure, indicating that the power dissipation occurred inside the separatrix. Indeed, the impurity cooling is causing a significant drop of edge temperature; however, the effect in the plasma centre is much less pronounced.
Herbivore absence can shift dry heath tundra from carbon source to sink during peak growing season
Authors: Min Elizabeth , Wilcots Megan E , Naeem Shahid , Gough Laura , McLaren Jennie R , Rowe Rebecca J , Rastetter Edward B , Boelman Natalie T , Griffin Kevin L
Published: December 2020

In arctic tundra, large and small mammalian herbivores have substantial impacts on the vegetation community and consequently can affect the magnitude of carbon cycling. However, herbivores are often absent from modern carbon cycle models, partly because relatively few field studies focus on herbivore impacts on carbon cycling. Our objectives were to quantify the impact of 21 years of large herbivore and large and small herbivore exclusion on carbon cycling during peak growing season in a dry heath tundra community. When herbivores were excluded, we observed a significantly greater leaf area index as well as greater vascular plant abundance. While we did not observe significant differences in deciduous dwarf shrub abundance across treatments, evergreen dwarf shrub abundance was greater where large and small herbivores were excluded. Both foliose and fruticose lichen abundance were higher in the large herbivore, but not the small and large herbivore exclosures. Net ecosystem exchange (NEE) likewise indicated the highest carbon uptake in the exclosure treatments and lowest uptake in the control (CT), suggesting that herbivory decreased the capacity of dry heath tundra to take up carbon. Moreover, our calculated NEE for average light and temperature conditions for July 2017, when our measurements were taken, indicated that the tundra was a carbon source in CT, but was a carbon sink in both exclosure treatments, indicating removal of grazing pressure can change the carbon balance of dry heath tundra. Collectively, these findings suggest that herbivore absence can lead to changes in plant community structure of dry heath tundra that in turn can increase its capacity to take up carbon.
Evaluating accuracy of four MODIS-derived burned area products for tropical peatland and non-peatland fires
Authors: Vetrita Yenni , Cochrane Mark A , Suwarsono  , Priyatna Muhammad , Sukowati Kusumaning A D , Khomarudin Muhammad R
Published: December 2020

Satellite-based burned area products are accurate for many regions. However, only limited assessments exist for Indonesia despite extensive burning and globally important carbon emissions. We evaluated the accuracy of four MODIS-derived (moderate resolution imaging spectroradiometer) burned area products (MCD45A1 collection 5.1, MCD64A1 (collection 5.1 and 6), FireCCI51), and their sensitivity to burned-area size and temporal window length used for detection. The products were compared to reference burned areas from SPOT 5 imagery using error matrices and linear regressions. The MCD45A1 product detected <1% of burned areas. The other products detected 38%–48% of burned area with accuracies increasing modestly (45%–57%) when smaller burns (<100 ha) were excluded, with MCD64A1 C6 performing best. Except for the MCD45 product, linear regressions showed generally good agreement in peatlands (R
2 ranging from 0.6 to 0.8) but detections were less accurate in non-peatlands (R
2 ranging from 0.2 to 0.5). Despite having higher spatial resolution, the FireCCI51 product (250 m) showed lower accuracy (OE = 0.55–0.88, CE = 0.33–0.50) than the 500 m MCD64A1 C6 product (OE = 0.43–0.79, CE = 0.36–0.51) but it was comparable to the C5.1 product (OE = 0.52–0.91, CE = 0.37–0.67). Dense clouds and smoke limited the accuracies of all burned area products, even when the temporal window for detection was lengthened. This study shows that emissions calculations based on burned area in peatlands remain highly uncertain. Given the globally significant amount of emissions from burning peatlands, specific attention is required to improve burned area mapping in these regions in order for global emissions models to accurately reflect when, where, and how much emissions are occurring.
Analysing the effect of climate policies on poverty through employment channels
Authors: Malerba Daniele , Wiebe Kirsten S
Published: December 2020

The recently proposed Green Deals and ‘building back better’ plans have affirmed the importance to make green transitions inclusive. This is particularly related to the labour market, which may witness significant changes. Empirically, this issue has until now received limited attention. The links between poverty and climate change are explored mainly through the lenses of climate change adaptation, or via the effects of rising energy prices on the purchasing power of poor households. We aim to address this gap by using results from a simulation of the global energy transition required to meet the 2-degree target, and compare this to a 6-degree baseline scenario. The simulation with a multi-regional input–output model finds that, overall, this transition results in a small net job increase of 0.3% globally, with cross-country heterogeneity. We complement this macro-level analysis with cross-country household data to draw implications of the effects on poverty through labour market outcomes. The few job losses will be concentrated in specific industries, while new jobs will be created in industries that currently witness relatively high in-work poverty rates, such as construction. We show that high in-work poverty in the industries of interest, and especially in middle-income countries, is often associated with low skills and an insufficient reach of social protection mechanisms. We conclude that green transitions must ensure that the jobs created are indeed decent including fair wages, adequate working conditions, sufficient social protection measures, and accessible to the vulnerable and poorest households.
An algebraic approach to discrete time integrability
Authors: Doikou Anastasia , Findlay Iain
Published: December 2020

We propose the systematic construction of classical and quantum two-dimensional space-time lattices primarily based on algebraic considerations, i.e. on the existence of associated r-matrices and underlying spatial and temporal classical and quantum algebras. This is a novel construction that leads to the derivation of fully discrete integrable systems governed by sets of consistent integrable non-linear space-time difference equations. To illustrate the proposed methodology, we derive two versions of the fully discrete non-linear Schrödinger type system. The first one is based on the existence of a rational r-matrix, whereas the second one is the fully discrete Ablowitz–Ladik model and is associated to a trigonometric r-matrix. The Darboux-dressing method is also applied for the first discretization scheme, mostly as a consistency check, and solitonic as well as general solutions, in terms of solutions of the fully discrete heat equation, are also derived. The quantization of the fully discrete systems is then quite natural in this context and the two-dimensional quantum lattice is thus also examined.
Contact tracing in configuration models
Authors: Kryven Ivan , Stegehuis Clara
Published: December 2020

Quarantining and contact tracing are popular ad hoc practices for mitigating epidemic outbreaks. However, few mathematical theories are currently available to asses the role of a network in the effectiveness of these practices. In this paper, we study how the final size of an epidemic is influenced by the procedure that combines contact tracing and quarantining on a network null model: the configuration model. Namely, we suppose that infected vertices may self-quarantine and trace their infector with a given success probability. A traced infector is, in turn, less likely to infect others. We show that the effectiveness of such tracing process strongly depends on the network structure. In contrast to previous findings, the tracing procedure is not necessarily more effective on networks with heterogeneous degrees. We also show that network clustering influences the effectiveness of the tracing process in a non-trivial way: depending on the infectiousness parameter, contact tracing on clustered networks may either be more, or less efficient than on networks without clustering.
Introducing Materials for Quantum Technology
Authors: Smith Jason M
Published: December 2020

Developed in close consultation with the research community, Materials for Quantum Technology is a unique multidisciplinary, open access journal that recognises the significant long-term contribution materials science will have in overcoming wide-ranging challenges associated with realising future real-world quantum technologies. This editorial introduces the goals of the journal and describes how it will add to the publishing landscape.
ASCB Keith Porter Lecture
Authors: Hyman Anthony A.
Published: December 2020

Although we attempt to plan the way we live, perhaps the best description of life is from the words of Yogi Berra: “It’s tough to make predictions, especially about the future.” A little over a year ago, I thought my future was predictable; after a fulfilling career, I would enjoy a last decade of research before a comfortable retirement. Then I lost my beloved wife and life partner, Suzanne Eaton to a senseless act of violence, and all assumptions were called into question.
Discovery of Specialist Beech-Feeding Underwing Moths From Taiwan (Lepidoptera: Erebidae: Catocalinae) and Its Implication to Biodiversity Conservation of Taiwan Beech Forests
Authors: Hsu Yu-Feng , Wang Li-Hao , Huang Chia-Lung , Braby Michael F , Lin Wen-Jie , Lin Rung-Juen , Hsu Yu-Ming
Published: December 2020

Deciduous Beech (Fagus spp.) forests have a highly disjunct distribution in the Northern Hemisphere, with greatest diversity in eastern Asia. Although Fagus supports a rich phytophagous insect fauna, the diversity, composition, and host specialization of insects associated with these trees in Asia are less well known compared with Europe and North America. For instance, two species of Catocala moths, both considered endemic to Japan, were previously known as the only beech-feeding specialists of this genus. However, two Catocala species were recently discovered from Taiwan during a survey of phytophagous insects on Taiwan Beech Fagus hayatae, a threatened plant. Identification of these two species of moths was determined by mtDNA (COI barcodes), adult morphology, including wing pattern and genitalia, and biology. Based on these multiple sources of evidence, we conclude that one species represents an undescribed species and the other a new subspecies of a species previously known only from mainland China. The taxonomic treatments in the present work include Catocala seiohbo sanctocula Hsu & Huang, subsp. nov., C. nimbosa Hsu & Wang, sp. nov. and C. nubila ohshimai, stat. nov. In Taiwan, Catocala spp. occur mainly in large, undisturbed patches of Taiwan Beech forest and are codependent on F. hayatae. Thus, they are not only considered to be at risk of co-extinction, but may serve as potential indicator species to monitor the extent and health of this threatened ecological community.
Why we need to evaluate long-term antidepressant use in older patients with depression
Authors: Batelaan Neeltje , Scholten Willemijn , Rhebergen Didi , Van Balkom Anton
Published: December 2020

In this commentary, we address current clinical practice of long-term antidepressant use in older adults with depression, and recommend improvements. Compared with younger adults, older adults more frequently use antidepressants in the long term, although they may not always benefit from them, and in spite of an increased risk for adverse events. Unfortunately, evaluations of long-term antidepressant use are sparse, especially in older age groups. To prevent and reduce inappropriate long-term use and adverse events, antidepressant use in older age groups should be regularly evaluated.
Individual Factors of Botulinum Type A in Treatment of Gummy Smile: A Prospective Study
Authors: Gong Xi , Huang Hongyuan , Gu Chenyang , Li Facheng , Zou Lidong , An Yang , Han Xuefeng , Tang Zhihui
Published: December 2020

Background

Botulinum type A (BTX-A) injection is a promising treatment for gummy smile (GS), although its effects are varied and inconsistent.

Objectives

The aim of this study was to explore the effect of individual factors on BTX-A treatment for GS, and to establish treatment expectations.

Methods

In this prospective clinical study, a standardized technique comprising bilateral single-point injections of 2 U BTX-A (total, 4 U) was administered to all GS patients. Data were collected at baseline and after 4, 12, and 32 weeks of follow-up. Twenty-nine potential individual factors were analyzed by correlation and regression analysis to exclude confounding bias.

Results

Ninety-four patients completed the BTX-A treatment. After adjusting for potential confounding factors, the correlation and regression analysis confirmed the following formula: anterior gingival exposure (GE) at 4 weeks = 1.44 + (0.94 × baseline anterior GE) − (1.88 × sex) (where male = 1 and female = 2). The confidence interval (CI) of the prediction showed that for all female participants with baseline anterior GE <5.3 mm, the 95% CI of anterior GE was 0.3 to 3.0 mm after 4 weeks of treatment, and 3.0 to 8.9 mm with baseline anterior GE ≥6 mm. For male patients with baseline anterior GEs of 3 and ≥4.6 mm, the 95% CIs were 1.5 to 3.3 mm and 3.2 to 8.9 mm, respectively.

Conclusions

The effect of average-dose BTX-A treatment for GS depended on GS severity and patient’s sex, rather than GS etiology and other factors. Female participants with baseline anterior GE <5.3 mm were more likely to show complete improvement after 4 weeks of treatment. However, female participants with baseline anterior GE ≥6.0 mm or male participants were less likely to show complete improvement at 4 weeks.

Level of Evidence: 4
Riboexp: an interpretable reinforcement learning framework for ribosome density modeling
Authors: Hu Hailin , Liu Xianggen , Xiao An , Li YangYang , Zhang Chengdong , Jiang Tao , Zhao Dan , Song Sen , Zeng Jianyang
Published: December 2020

Translation elongation is a crucial phase during protein biosynthesis. In this study, we develop a novel deep reinforcement learning-based framework, named Riboexp, to model the determinants of the uneven distribution of ribosomes on mRNA transcripts during translation elongation. In particular, our model employs a policy network to perform a context-dependent feature selection in the setting of ribosome density prediction. Our extensive tests demonstrated that Riboexp can significantly outperform the state-of-the-art methods in predicting ribosome density by up to 5.9% in terms of per-gene Pearson correlation coefficient on the datasets from three species. In addition, Riboexp can indicate more informative sequence features for the prediction task than other commonly used attribution methods in deep learning. In-depth analyses also revealed the meaningful biological insights generated by the Riboexp framework. Moreover, the application of Riboexp in codon optimization resulted in an increase of protein production by around 31% over the previous state-of-the-art method that models ribosome density. These results have established Riboexp as a powerful and useful computational tool in the studies of translation dynamics and protein synthesis. Availability: The data and code of this study are available on GitHub: https://github.com/Liuxg16/Riboexp. Contact:zengjy321@tsinghua.edu.cn; songsen@tsinghua.edu.cn
IGD: high-performance search for large-scale genomic interval datasets
Authors: Feng Jianglin , Sheffield Nathan C
Published: December 2020

Databases of large-scale genome projects now contain thousands of genomic interval datasets. These data are a critical resource for understanding the function of DNA. However, our ability to examine and integrate interval data of this scale is limited. Here, we introduce the integrated genome database (IGD), a method and tool for searching genome interval datasets more than three orders of magnitude faster than existing approaches, while using only one hundredth of the memory. IGD uses a novel linear binning method that allows us to scale analysis to billions of genomic regions.

Availabilityand implementation

https://github.com/databio/IGD.

Supplementary information

Supplementary data are available at Bioinformatics online.
The software for interactive evaluation of mass spectra stability and reproducibility
Authors: Zhvansky E S , Sorokin A A , Bormotov D S , Bocharov K V , Zavorotnyuk D S , Ivanov D G , Nikolaev E N , Popov I A
Published: December 2020

Mass spectrometry (MS) methods are widely used for the analysis of biological and medical samples. Recently developed methods, such as DESI, REIMS and NESI allow fast analyses without sample preparation at the cost of higher variability of spectra. In biology and medicine, MS profiles are often used with machine learning (classification, regression, etc.) algorithms and statistical analysis, which are sensitive to outliers and intraclass variability. Here, we present spectra similarity matrix (SSM) Display software, a tool for fast visual outlier detection and variance estimation in mass spectrometric profiles. The tool speeds up the process of manual spectra inspection, improves accuracy and explainability of outlier detection, and decreases the requirements to the operator experience. It was shown that the batch effect could be revealed through SSM analysis and that the SSM calculation can also be used for tuning novel ion sources concerning the quality of obtained mass spectra.

Availability and implementation

Source code, example datasets, binaries and other information are available at https://github.com/EvgenyZhvansky/R_matrix.

Supplementary information

Supplementary data are available at Bioinformatics online.
Improving circRNA–disease association prediction by sequence and ontology representations with convolutional and recurrent neural networks
Authors: Lu Chengqian , Zeng Min , Wu Fang-Xiang , Li Min , Wang Jianxin
Published: December 2020

Motivation

Emerging studies indicate that circular RNAs (circRNAs) are widely involved in the progression of human diseases. Due to its special structure which is stable, circRNAs are promising diagnostic and prognostic biomarkers for diseases. However, the experimental verification of circRNA–disease associations is expensive and limited to small-scale. Effective computational methods for predicting potential circRNA–disease associations are regarded as a matter of urgency. Although several models have been proposed, over-reliance on known associations and the absence of characteristics of biological functions make precise predictions are still challenging.

Results

In this study, we propose a method for predicting CircRNA–disease associations based on sequence and ontology representations, named CDASOR, with convolutional and recurrent neural networks. For sequences of circRNAs, we encode them with continuous k-mers, get low-dimensional vectors of k-mers, extract their local feature vectors with 1D CNN and learn their long-term dependencies with bi-directional long short-term memory. For diseases, we serialize disease ontology into sentences containing the hierarchy of ontology, obtain low-dimensional vectors for disease ontology terms and get terms’ dependencies. Furthermore, we get association patterns of circRNAs and diseases from known circRNA–disease associations with neural networks. After the above steps, we get circRNAs’ and diseases’ high-level representations, which are informative to improve the prediction. The experimental results show that CDASOR provides an accurate prediction. Importing the characteristics of biological functions, CDASOR achieves impressive predictions in the de novo test. In addition, 6 of the top-10 predicted results are verified by the published literature in the case studies.

Availability and implementation

The code and data of CDASOR are freely available at https://github.com/BioinformaticsCSU/CDASOR.
The Use of Digital Platforms for Community-Based Monitoring
Authors: Johnson Noor , Druckenmiller Matthew L , Danielsen Finn , Pulsifer Peter L
Published: December 2020

Environmental observing programs that are based on Indigenous and local knowledge increasingly use digital technologies. Digital platforms may improve data management in community-based monitoring (CBM) programs, but little is known about how their use translates into tangible results. Drawing on published literature and a survey of 18 platforms, we examine why and how digital platforms are used in CBM programs and illuminate potential challenges and opportunities. Digital platforms make it easy to collect, archive, and share CBM data, facilitate data use, and support understanding larger-scale environmental patterns through interlinking with other platforms. Digital platforms, however, also introduce new challenges, with implications for the sustainability of CBM programs and communities’ abilities to maintain control of their own data. We expect that increased data access and strengthened technical capacity will create further demand within many communities for ethically developed platforms that aid in both local and larger-scale decision-making.
Great Expectations: Deconstructing the Process Pathways Underlying Beaver-Related Restoration
Authors: Nash Caroline S , Grant Gordon E , Charnley Susan , Dunham jason B , Gosnell Hannah , Hausner Mark B , Pilliod David S , Taylor Jimmy D
Published: December 2020

Beaver-related restoration is a process-based strategy that seeks to address wide-ranging ecological objectives by reestablishing dam building in degraded stream systems. Although the beaver-related restoration has broad appeal, especially in water-limited systems, its effectiveness is not yet well documented. In this article, we present a process-expectation framework that links beaver-related restoration tactics to commonly expected outcomes by identifying the set of process pathways that must occur to achieve those expected outcomes. We explore the contingency implicit within this framework using social and biophysical data from project and research sites. This analysis reveals that outcomes are often predicated on complex process pathways over which humans have limited control. Consequently, expectations often shift through the course of projects, suggesting that a more useful paradigm for evaluating process-based restoration would be to identify relevant processes and to rigorously document how projects do or do not proceed along expected process pathways using both quantitative and qualitative data.
How does Lived Experience of Incarceration Impact Upon the Helping Process in Social Work Practice?: A Scoping Review
Authors: Duvnjak Angella , Stewart Victoria , Young Peter , Turvey Leah
Published: December 2020

Whilst the value of lived experience in the helping process is recognised in a range of settings including mental health, disability and substance addiction, the understanding of therole of lived experience of incarceration in the helping process is less developed. This is relevant to the question of gatekeeping into the social work profession. A heightened focus on risk has resulted in limited opportunity for those with a history of incarceration from studying and practising social work. Little is known about how a lived experience of incarceration influences the helping relationship, and in turn we know very little about the implications for service users of having reduced access to social workers who have experienced imprisonment. To better understand the current state of knowledge regarding the role of lived experience of incarceration in the helping process, a scoping review of the literature was undertaken. A thematic analysis of sixty-one articles published before 2019 was undertaken and consensus was achieved on four themes: stigma and discrimination; trust and authenticity; role modelling and hope; and, power and agency. The findings include recommendations for more nuanced policy regarding the restriction of those with a lived experience of incarceration entering the social work profession.