bluuebunny/crossref_metadata_2025 huggingface dataset:
Numerical simulations of miscible viscous fingering involving viscosity changes of the displacing fluid by A + B → C chemical reactions
Authors: Omori Keiichiro , Nagatsu Yuichiro
Published: September 2020

Nagatsu and De Wit [“Viscous fingering of a miscible reactive A + B → C interface for an infinitely fast chemical reaction: Nonlinear simulations,” Phys. Fluids 23, 043103 (2011)] simulated the nonlinear evolution of reactive miscible viscous fingering (VF) where the viscosity of the more viscous displaced fluid was changed by an instantaneous A + B → C chemical reaction. They analyzed the dynamics from the viewpoint of an underlying viscosity profile reconstructed from the concentrations of chemical species obtained by a one-dimensional diffusion–reaction equation. The present study develops a mathematical model for reactive miscible VF where the viscosity of the less viscous displacing fluid is changed by an instantaneous A + B → C chemical reaction. We obtain the same underlying viscosity profile as Nagatsu and De Wit by employing appropriate parameters. We perform numerical simulations of the nonlinear evolution of VF under these appropriate parameters. The results show that the present numerical solutions are exactly the same as those obtained by Nagatsu and De Wit, i.e., the same VF pattern is obtained. This numerically proves that the effects of a viscosity change by the chemical reaction on VF are independent of whether the viscosity of the displaced or displacing fluid changes. We obtain a mathematical formula to describe the switch from the parameters used by Nagatsu and De Wit to those used in this study to obtain the same shape of the underlying viscosity profile. This finding will lead to easier and more flexible VF chemical control methods in geoscience processes, where it is difficult to manipulate the properties of more viscous fluids, by manipulating the properties of less viscous fluids.
Canids potentially threaten bilbies at Astrebla Downs National Park
Authors: Augusteyn John , Rich Maree , Story Georgeanna , Nolan Barry
Published: September 2020

The ecological role of canids in arid Australia is unresolved. Some argue they play a role regulating populations of herbivores and introduced mesopredators such as feral cats (Felis catus) and foxes (Vulpes vulpes). However, evidence also suggests they pose a threat to native species populations. The aims of this study were to determine the extent of canid predation on the bilby population at Astrebla Downs National Park, Queensland, to improve our understanding of the ecological role that canids serve in the park and to determine whether seasonal changes in the canid diet can be used to predict if and when management should intervene. Canid scats (n=723) were collected over seven years and their content examined. The percentage of bilby remains in the canid scats varied from 13 to 85% (mean=43%) and was 20–100% by volume. In total, 23 vertebrate species were identified in canid scats. The percentage of cat remains was 0–44% (mean=11%), peaking in 2013 during a cat plague and coinciding with canids actively hunting cats. Fox remains were not detected in dog scats. These results indicate that canids had a varied diet and at times threatened the bilby population at Astrebla.
Structural Characteristics of Low-Aromaticity Marine and Lacustrine Oil Shales and their NaOH-HCl Kerogens Determined Using 13C NMR and XPS
Authors: Amer Mohammad W. , Alhesan Jameel S. Aljariri , Gengenbach Thomas , Marshall Marc , Fei Yi , Jackson W. Roy , Chaffee Alan L.
Published: September 2020

Few comparisons have been made between low-aromaticity marine and lacustrine oil shales and their kerogens, because the reliability of structural analyses has been limited by a reliance on only one method of kerogen isolation, HCl-HF. Therefore, a detailed analysis by 13C NMR and X-ray photoelectron spectroscopy (XPS) was made for Attrat marine oil shale (Jordan) and Colorado (Green River) lacustrine oil shale (USA) and their NaOH-HCl kerogens. Some differences between oil shales and their kerogens were noted, but many structural features were considered to be true characteristics of the organic matter. The results emphasise the importance of comparing the analyses of kerogens isolated by different methods to ensure that features of the organic matter are not an artefact of the method of kerogen isolation. For both oil shales, the predominantly aliphatic character of the organic part was confirmed and the long average chain length of the aliphatic hydrocarbons was established. All shales and their kerogens showed a small cluster size for the aromatic rings. The elemental analysis obtained by XPS, compared with the bulk elemental analysis, indicated major differences between the near-surface region sampled by XPS and the bulk. The organic S was determined to be aliphatic and aromatic S with possibly small amounts of sulfoxide. Most of the N was pyrrolic with smaller amounts in pyridinic or quaternary form. Nearly all of the surface organic C in both kerogens was bonded to C and H. Two major forms of organic O were distinguishable. A good correlation between the proportion of aliphatic S and pyrolysis reactivity is suggested.
Plant water relations.
Authors: Girón Amaranta , Alcocer Christian , Espadas Francisco , Talavera Carlos , Estrella Humberto , Chan Arianna , Fuentes Gabriela , Mitra Sisir , Santamaria Jorge M.
Published: September 2020

This chapter provides information on the common response of pawpaws (Carica papaya) to water stress, including chlorophyll fluorescence, electrolyte leakage, water potential, photosynthesis, stomatal conductance and intercellular CO2. Pawpaw can tolerate some water deficit without significant reduction in yield components, indicating that the full amount of the recommended irrigation can be reduced but there is little or no benefit to partial root drying. Experimental evidence suggests that pawpaws exhibit some signs of stress memory, but that rapid short-term acclimatization responses dominate pawpaw's response to soil water deficit. Decreased plant growth under water deficit is due to reductions in the carbon balance in the plant which affects photosynthesis. However, it is still not clear whether the restrictive factor for photosynthesis under water deficit stress is due to stomatal closure or is due to incomplete metabolism.
Insect and nematode pests.
Authors: Khan Matiyar Rahaman , Ghosh Amalendu
Published: September 2020

This chapter describes some insect, arthropod and nematode pests of pawpaws (Carica papaya): Paracoccus marginatus, Ferrisia virgata, Aonidiella orientalis, Toxotrypana curvicauda [Anastrepha curvicauda], Thrips parvispinus, Bemisia tabaci, Myzus persicae, Aphis gossypii, A. craccivora, Tetranychus urticae, Amblypelta nitida, Meloidogyne incognita, M. javanica, Rotylenchulus reniformis, R. parvus and Xiphinema basiri. Information is given on their biology, crop damage and control.
Postharvest handling, storage and quality.
Authors: Muda Pauziah , Chen Nancy Jung , Paull Robert E.
Published: September 2020

This chapter provides information on the various factors to consider during the harvesting and handling of pawpaw fruits, such as fruit maturity and visual and sensorial quality characteristics. The benefits of the use of coatings and wraps, optimum temperatures and various packing and storage methods for prolonging the fruit quality of pawpaws during storage and transport are also pointed out. Information on the ethylene sensitivity of pawpaw fruits, postharvest quality losses and postharvest handling and storage-related disorders, insect pests and diseases are also discussed.
Ultrafast Quasiparticle Dynamics and Electron-Phonon Coupling in (Li0.84Fe0.16)OHFe0.98Se
Authors: Wu Qiong , Zhou Huaxue , Wu Yanling , Hu Lili , Ni Shunli , Tian Yichao , Sun Fei , Zhou Fang , Dong Xiaoli , Zhao Zhongxian , Zhao Jimin
Published: September 2020

Distinctive superconducting behaviors between bulk and monolayer FeSe make it challenging to obtain a unified picture of all FeSe-based superconductors. We investigate the ultrafast quasiparticle (QP) dynamics of an intercalated superconductor (Li1 – x
Fe
x
)OHFe1 – y
Se, which is a bulk crystal but shares a similar electronic structure with single-layer FeSe on SrTiO3. We obtain the electron-phonon coupling (EPC) constant λ

A
1g
(0.22 ± 0.04), which well bridges that of bulk FeSe crystal and single-layer FeSe on SrTiO3. Significantly, we find that such a positive correlation between λ

A
1g
and superconducting T
c holds among all known FeSe-based superconductors, even in line with reported FeAs-based superconductors. Our observation indicates possible universal role of EPC in the superconductivity of all known categories of iron-based superconductors, which is a critical step towards achieving a unified superconducting mechanism for all iron-based superconductors.
Revisiting radiative leptonic B decay *
Authors: Shen Yue-Long , Wei Yan-Bing , Zhao Xue-Chen , Zhou Si-Hong
Published: September 2020

In this paper, we summarize the existing methods of solving the evolution equation of the leading-twist B-meson LCDA. Then, in the Mellin space, we derive a factorization formula with next-to-leading-logarithmic (NLL) resummation for the form factors

in the

decay at leading power in

. Furthermore, we investigate the power suppressed local contributions, factorizable non-local contributions (which are suppressed by

and

), and soft contributions to the form factors. In the numerical analysis, which employs the two-loop-level hard function and the jet function, we find that both the resummation effect and the power corrections can sizably decrease the form factors. Finally, the integrated branching ratios are also calculated for comparison with future experimental data.
SECONIC: Towards multi-compartmental models for ultrasonic brain stimulation by intramembrane cavitation
*
Authors: Tarnaud Thomas , Joseph Wout , Schoeters Ruben , Martens Luc , Tanghe Emmeric
Published: September 2020

Objective. To design a computationally efficient model for ultrasonic neuromodulation (UNMOD) of morphologically realistic multi-compartmental neurons based on intramembrane cavitation. Approach. A Spatially Extended Neuronal Intramembrane Cavitation model that accurately predicts observed fast Charge Oscillations (SECONIC) is designed. A regular spiking cortical Hodgkin-Huxley type nanoscale neuron model of the bilayer sonophore and surrounding proteins is used. The accuracy and computational efficiency of SECONIC is compared with the Neuronal Intramembrane Cavitation Excitation (NICE) and multiScale Optimized model of Neuronal Intramembrane Cavitation (SONIC). Main results. Membrane charge redistribution between different compartments should be taken into account via fourier series analysis in an accurate multi-compartmental UNMOD-model. Approximating charge and voltage traces with the harmonic term and first two overtones results in reasonable goodness-of-fit, except for high ultrasonic pressure (adjusted R-squared ≥0.61). Taking into account the first eight overtones results in a very good fourier series fit (adjusted R-squared ≥0.96) up to 600 kPa. Next, the dependency of effective voltage and rate parameters on charge oscillations is investigated. The two-tone SECONIC-model is one to two orders of magnitude faster than the NICE-model and demonstrates accurate results for ultrasonic pressure up to 100 kPa. Significance. Up to now, the underlying mechanism of UNMOD is not well understood. Here, the extension of the bilayer sonophore model to spatially extended neurons via the design of a multi-compartmental UNMOD-model, will result in more detailed predictions that can be used to validate or falsify this tentative mechanism. Furthermore, a multi-compartmental model for UNMOD is required for neural engineering studies that couple finite difference time domain simulations with neuronal models. Here, we propose the SECONIC-model, extending the SONIC-model by taking into account charge redistribution between compartments.
Material and Geometry Selection of a Multi-layer Microcantilever Thermal Sensor with Piezoresistive Readout
Authors: Mathew Ribu , Krishna Amal , Nag Kunal , Sathvik S , Sharma Aditi
Published: September 2020

In recent years, micro cantilever thermal sensors with integrated piezoresistive readout have been extensively explored. In this paper, we perform the material and geometry selection of a multi-layer cantilever thermal sensor for maximizing its thermal sensitivity. Present work is performed in two phases. In the first phase, material selection of constituent layers of the cantilever thermal sensor is performed considering various material set reported in the literature. Subsequently, impact of sensor geometry on thermal and electrical sensitivities of the sensor is investigated using computations. Results show that for the chosen material set compared to various cantilever shapes reported in the literature, slender rectangular cantilever platform depicts higher thermal sensitivity. Further, it is observed that the sensor depicts an electrical sensitivity in the range of 1*10−2.
Contemporary development state of reservoir Yu1, the Verkh-Tarskoe oilfield (south of Western Siberia)
Authors: Novikov D A , Pavlova S A , Yu Kuznetsov D , Ryzhkova S V , Chernikov A A
Published: September 2020

The paper provides results of the field-geological information analysis in order to evaluate the current development stage of reservoir Yu1 of the Verkh-Tarskoe oilfield. The main recoverableasset is currently indevelopment phase III (declining production). The total well stock consists of 175 wells, of which 134 are producing.The monthly volume of water injection into the reservoir pressure maintenance (RPM) system reaches 100, 000 m3, and fluidproductionis about 170, 000 m3 with averagewater flooding of producing wells is90.4%. The structures with complex geometry thatformedwithin thehydrodynamic field where the deep pressure sinks are associated withproduction wells, and piezomaximawith injection wells.Given the multi-facies pattern of thesandstone depositional environmentsand secondary processes ofrocks metamorphismduringcatagenesis, thetarget reservoirhas a complex structure and its study in greater detail willrequirebuilding a new geological modelof the oilfieldand more precisedefinition engineeringto achieve maximumrecovery.
Calculation of the neutron flux distribution in the accelerator driven subcritical reactor with (Th-233U)O2 and (Th-235U)O2 mix fuel
Authors: Minh Tien Tran , Quoc Dung Tran
Published: September 2020

This paper presents results of calculating the neutron flux distribution in an accelerator driven subcritical reactor (ADSR) with (Th-233U)O2 and (Th-235U)O2mixed fuel. An ADSR consists of 90 fuel rods, and 10 graphite reflector rods. All objects are placed in liquid lead. Thorium is replaced by mixture of (Th-233U)O2 and (Th-235U)O2; MCNP5 program has been used to calculate radial distribution of the neutron flux, axial distribution and energy distribution from (p, n) reaction.The calculation results show that the axial distribution of the thermal and fast neutron flux reduce from the center of core but reduction rate is different.The thermal neutron flux decreases gradually from 0 to 2.5cm; decreases rapidly from 25cm to 5cm. In comparison, the thermal neutron flux is smaller than fast neutron flux from 0 to 4cm along the radius but the thermal neutron flux is larger than fast neutron flux at distances greater than 5cm along the radius of the reactor.
Influence of dispersity of reinforcing polymer to the polymer-fiber composite materials’ rigidity
Authors: Kornilova N L , Koksharov S A , Shammut U A , Radchenko O V , Nikiforova E N
Published: September 2020

This research aims at validation of the technological approaches to the provision of penetrating the polymer binder into the structure of the filament carrier in order to construct a developed interfacial layer in the form of molecular brushes. Brush “bristles”, enshrined by the outer end in the layer of the copolymer binder, can give elastic properties to the composite material obtained by duplicating the shell material with reinforced adhesive interlining materials.

As a large part of the interlining materials range comprises a mixture of polyester fiber with cotton or viscose, the problem of accessibility of textile liner web for reinforcing polymer is originally considered in relation to the cellulosic component, which has a developed system of pore spaces.

This work defines the technical possibility of regulating the elastic-deformation properties of the fused panels of garment by changing the degree of reinforcing polymer (RP) dispersion fineness, providing different terms for penetration into the structure of fiber material. To change the capacity of the RP to penetrate into the fiber structure a method of ultra-dispergation was used by the mechanical activation of hydrosols in a colloid mill. There is an experimental prove of the decisive role of the reinforcing polymer penetration into the pore spaces of the cellulose component of the interlining material for the formation the branched comb structure of interfacial layer, which provides a comprehensive improvement in the ability of materials to form the bulk shape of the garment and its preservation while distorting.
Asymmetric CPW Fed Miniaturized dual polarized monopole Antenna for WLAN/WiMAX Applications
Authors: Naresh Kumar D.
Published: September 2020

An Asymmetric coplanar waveguide (CPW) Fed Miniaturized dual polarized (linear Polarized and Circularly Polarized) monopole Antenna Implemented. The Inverted-L Strip monopole antenna and the asymmetric ground plane for WLAN/Wi MAX applications are presented. Monopole antenna mainly icludes asymmetric ground plane which are fed with Coplanar Wave inverted L-shape strip and a slit embedded on the ground plane providing an orthogonal phase difference were designed to generate CP radiation. Inverted-L shape strip resonance and matching condition are examined by high-frequency structure simulator (HFSS) and the prototype is designed and measured. The measure simulated results shows that the monopole antenna impedance band-width with at −10 dB of 92.5 %( 3.36-6.66GHz) and a 3-dB axial-ratio bandwidth of 53.9 %( 5.4 -6.39 GHz) could be completed which could absolutely cover the WLAN (5.725 GHz - 5.85 GHz) band. Meanwhile, a linear polarization is also bought which could absolutely cover the WiMAX (3.3 GHz -3.7 GHz) bands. Orthogonal phase difference and average peak gain for lower band 1.9 dB and upper band 2.48 dB have been achieved, respectively.
Construction of the difference problem and error estimation of the approximate solution of the nonlocal problem for the nonlinear equation.
Authors: Aliyev AY , Aliyev AA , Kazimov JK
Published: September 2020

In this paper, we consider a nonlocal problem. It is used in the rectangular area. For this problem, a difference problem is constructed, based on a rectangular grid. The error of theapproximatesolutionsfor a nonlocal problemis estimated. Many applied problems, in particular heat conductivity [1], [2], fluid mechanics [3], the theory of elasticity and shells [4], etc. are reduced to solving nonlocal boundary value problems for elliptical type equations. When solving nonlocal boundaryvalueproblems, nonlocal boundaryconditions complicate the justification of finite difference schemes due to the complexity of matrices obtained from systemsof equation.This complexity is especially evident for numerical methods, fornon-linear equations[5]. Here we consider a nonlocal boundary value problem for a quasi-linear equation. To solve the problem numerically we use the finite difference method. The error estimate of the approximate solution of the nonlocal problem is found.
Step-Up Resonant Converter For Induction Motor Drive Applications
Authors: Chandran Lekha , Manogna B , Sridhar P
Published: September 2020

A new approach for resonant step-up converter which is connected to hybrid micro grid is discussed in this paper. A micro grid has a local source of supply and loads to function as an electrical network either independently or when connected to a grid.A micro grid can integrate effectively distributed generation sources and renewable generation systems like PV, wind and fuel cell generation systems to the existing distribution system. A hybrid micro grid can be connected to DC and AC grids with the help of power electronic interfaces and manage effective power flow throughout the sub grid. The proposed DC–DC converter can be coupled to a AC-DC micro grid with solar energy and when the system operates in isolated mode battery connected to the DC bus maintain the energy requirement. The key principle of power flow control of these devices helps in increase of system stability. The system is simulated in Matlab/Simulink.
Spatial patterning of nanofibrous collagen scaffolds modulates fibroblast morphology
Authors: Suter Naiana , Stebel Sophie , Rianna Carmela , Radmacher Manfred , Brüggemann Dorothea
Published: September 2020

Current knowledge about cell-biomaterial interactions is often based on two-dimensional (2D) cell culture systems like protein-coated glass slides. However, such smooth surfaces cannot mimic the nanofibrous environment of the native extracellular matrix (ECM). It is therefore a major challenge to transfer the results from 2D surfaces to 3D protein scaffolds with biomimetic nanofiber architecture. To understand the influence of different protein topographies on the cell response we introduce a new process to fabricate binary collagen scaffolds of variable thickness with spatially controlled regions of nanofibrous and smooth topography. We used pH-induced self-assembly to prepare collagen nanofibers with diameters between 130 and 150 nm on glass surfaces, which were partly covered with a polymer mask. After cross-linking with glutaraldehyde, smooth collagen films were prepared on the remaining glass regions. Atomic force microscopy revealed a much lower surface roughness of smooth collagen compared to nanofibers. Subsequently, we studied the viability, morphology and migration of 3T3 fibroblasts on both collagen topographies. We found small, elongated fibroblasts with few, long filopodia on collagen nanofibers whereas large, flat fibroblasts with many short filopodia were observed on smooth collagen. Actin stress fibers on collagen nanofibers were substantially reduced in comparison to smooth collagen. Live cell tracking revealed that fibroblasts on thin nanofibrous collagen migrated faster than on smooth collagen. In summary, binary collagen scaffolds enabled us for the first time to study cell responses to topographical cues on a single protein scaffold. In future, it will be intriguing to transfer our patterning process to other proteins to study fundamental principles of topography-dependent cell recognition processes.
The 2021 quantum materials roadmap
Authors: Giustino Feliciano , Lee Jin Hong , Trier Felix , Bibes Manuel , Winter Stephen M , Valentí Roser , Son Young-Woo , Taillefer Louis , Heil Christoph , Figueroa Adriana I , Plaçais Bernard , Wu QuanSheng , Yazyev Oleg V , Bakkers Erik P A M , Nygård Jesper , Forn-Díaz Pol , De Franceschi Silvano , McIver J W , Torres L E F Foa , Low Tony , Kumar Anshuman , Galceran Regina , Valenzuela Sergio O , Costache Marius V , Manchon Aurélien , Kim Eun-Ah , Schleder Gabriel R , Fazzio Adalberto , Roche Stephan
Published: September 2020

In recent years, the notion of ‘Quantum Materials’ has emerged as a powerful unifying concept across diverse fields of science and engineering, from condensed-matter and coldatom physics to materials science and quantum computing. Beyond traditional quantum materials such as unconventional superconductors, heavy fermions, and multiferroics, the field has significantly expanded to encompass topological quantum matter, two-dimensional materials and their van der Waals heterostructures, Moiré materials, Floquet time crystals, as well as materials and devices for quantum computation with Majorana fermions. In this Roadmap collection we aim to capture a snapshot of the most recent developments in the field, and to identify outstanding challenges and emerging opportunities. The format of the Roadmap, whereby experts in each discipline share their viewpoint and articulate their vision for quantum materials, reflects the dynamic and multifaceted nature of this research area, and is meant to encourage exchanges and discussions across traditional disciplinary boundaries. It is our hope that this collective vision will contribute to sparking new fascinating questions and activities at the intersection of materials science, condensed matter physics, device engineering, and quantum information, and to shaping a clearer landscape of quantum materials science as a new frontier of interdisciplinary scientific inquiry. We stress that this article is not meant to be a fully comprehensive review but rather an up-to-date snapshot of different areas of research on quantum materials with a minimal number of references focusing on the latest developments.
Effects of magnetite and titania nanoparticles on properties of transformer insulating oil
Authors: Pillai S Savitha , Aarathy A R , Gopinath Dinesh , Aryanandiny B , Sankar Binu
Published: September 2020

Transformer oil-based nanofluids have become popular research topic due to their enhanced dielectric and thermal properties. Considering the sustainability aspects of extending the life of transformer oil, it is imperative to conduct research on the effect of transformer oil with nanofillers. In the present work, the influence of conducting magnetite (Fe3O4), semiconducting titania (TiO2) nanoparticles and combination of Fe3O4 and TiO2 nanoparticles (multi-nanoparticle) on AC breakdown voltage are investigated for various concentrations. Nanofluid prepared using multi-nanoparticle shows enhanced AC breakdown voltage (BDV) of transformer oil compared with unfilled oil. Enhancement in BDV of 22% is observed with combination of 0.0025 wt% Fe3O4 and 0.0075 wt% TiO2. In addition, the effect of titania nanoparticles dispersed into service-aged transformer oil with a weight percentage of 0.01% is investigated. Comparative study of breakdown strength and viscosity of nanofluid with unfilled oil is performed. Service-aged oil sample shows increased BDV of 15% with TiO2 nanoparticles. The degradation in service-aged transformer oil is analyzed using UV–vis and Fourier Transform Infrared (FTIR) spectroscopy. The characteristics of oil samples are analyzed using fluorescence spectroscopy.
Knockoff boosted tree for model-free variable selection
Authors: Jiang Tao , Li Yuanyuan , Motsinger-Reif Alison A
Published: September 2020

Motivation

The recently proposed knockoff filter is a general framework for controlling the false discovery rate (FDR) when performing variable selection. This powerful new approach generates a ‘knockoff’ of each variable tested for exact FDR control. Imitation variables that mimic the correlation structure found within the original variables serve as negative controls for statistical inference. Current applications of knockoff methods use linear regression models and conduct variable selection only for variables existing in model functions. Here, we extend the use of knockoffs for machine learning with boosted trees, which are successful and widely used in problems where no prior knowledge of model function is required. However, currently available importance scores in tree models are insufficient for variable selection with FDR control.

Results

We propose a novel strategy for conducting variable selection without prior model topology knowledge using the knockoff method with boosted tree models. We extend the current knockoff method to model-free variable selection through the use of tree-based models. Additionally, we propose and evaluate two new sampling methods for generating knockoffs, namely the sparse covariance and principal component knockoff methods. We test and compare these methods with the original knockoff method regarding their ability to control type I errors and power. In simulation tests, we compare the properties and performance of importance test statistics of tree models. The results include different combinations of knockoffs and importance test statistics. We consider scenarios that include main-effect, interaction, exponential and second-order models while assuming the true model structures are unknown. We apply our algorithm for tumor purity estimation and tumor classification using Cancer Genome Atlas (TCGA) gene expression data. Our results show improved discrimination between difficult-to-discriminate cancer types.

Availability and implementation

The proposed algorithm is included in the KOBT package, which is available at https://cran.r-project.org/web/packages/KOBT/index.html.

Supplementary information

Supplementary data are available at Bioinformatics online.
FBA reveals guanylate kinase as a potential target for antiviral therapies against SARS-CoV-2
Authors: Renz Alina , Widerspick Lina , Dräger Andreas
Published: September 2020

Motivation

The novel coronavirus (SARS-CoV-2) currently spreads worldwide, causing the disease COVID-19. The number of infections increases daily, without any approved antiviral therapy. The recently released viral nucleotide sequence enables the identification of therapeutic targets, e.g. by analyzing integrated human-virus metabolic models. Investigations of changed metabolic processes after virus infections and the effect of knock-outs on the host and the virus can reveal new potential targets.

Results

We generated an integrated host–virus genome-scale metabolic model of human alveolar macrophages and SARS-CoV-2. Analyses of stoichiometric and metabolic changes between uninfected and infected host cells using flux balance analysis (FBA) highlighted the different requirements of host and virus. Consequently, alterations in the metabolism can have different effects on host and virus, leading to potential antiviral targets. One of these potential targets is guanylate kinase (GK1). In FBA analyses, the knock-out of the GK1 decreased the growth of the virus to zero, while not affecting the host. As GK1 inhibitors are described in the literature, its potential therapeutic effect for SARS-CoV-2 infections needs to be verified in in-vitro experiments.

Availability and implementation

The computational model is accessible at https://identifiers.org/biomodels.db/MODEL2003020001.
Fold recognition by scoring protein maps using the congruence coefficient
Authors: Di Lena Pietro , Baldi Pierre
Published: September 2020

Motivation

Protein fold recognition is a key step for template-based modeling approaches to protein structure prediction. Although closely related folds can be easily identified by sequence homology search in sequence databases, fold recognition is notoriously more difficult when it involves the identification of distantly related homologs. Recent progress in residue–residue contact and distance prediction opens up the possibility of improving fold recognition by using structural information contained in predicted distance and contact maps.

Results

Here we propose to use the congruence coefficient as a metric of similarity between maps. We prove that this metric has several interesting mathematical properties which allow one to compute in polynomial time its exact mean and variance over all possible (exponentially many) alignments between two symmetric matrices, and assess the statistical significance of similarity between aligned maps. We perform fold recognition tests by recovering predicted target contact/distance maps from the two most recent Critical Assessment of Structure Prediction editions and over 27 000 non-homologous structural templates from the ECOD database. On this large benchmark, we compare fold recognition performances of different alignment tools with their own similarity scores against those obtained using the congruence coefficient. We show that the congruence coefficient overall improves fold recognition over other methods, proving its effectiveness as a general similarity metric for protein map comparison.

Availability and implementation

The congruence coefficient software CCpro is available as part of the SCRATCH suite at: http://scratch.proteomics.ics.uci.edu/.

Supplementary information

Supplementary data are available at Bioinformatics online.
A potential role of fatty acid binding protein 4 in the pathophysiology of autism spectrum disorder
Authors: Maekawa Motoko , Ohnishi Tetsuo , Toyoshima Manabu , Shimamoto-Mitsuyama Chie , Hamazaki Kei , Balan Shabeesh , Wada Yuina , Esaki Kayoko , Takagai Shu , Tsuchiya Kenji J , Nakamura Kazuhiko , Iwata Yasuhide , Nara Takahiro , Iwayama Yoshimi , Toyota Tomoko , Nozaki Yayoi , Ohba Hisako , Watanabe Akiko , Hisano Yasuko , Matsuoka Shigeru , Tsujii Masatsugu , Mori Norio , Matsuzaki Hideo , Yoshikawa Takeo
Published: September 2020

Autism spectrum disorder is a neurodevelopmental disorder characterized by difficulties in social communication and interaction, as well as repetitive and characteristic patterns of behaviour. Although the pathogenesis of autism spectrum disorder is unknown, being overweight or obesity during infancy and low weight at birth are known as risks, suggesting a metabolic aspect. In this study, we investigated adipose tissue development as a pathophysiological factor of autism spectrum disorder by examining the serum levels of adipokines and other metabolic markers in autism spectrum disorder children (n = 123) and typically developing children (n = 92) at 4–12 years of age. Among multiple measures exhibiting age-dependent trajectories, the leptin levels displayed different trajectory patterns between autism spectrum disorder and typically developing children, supporting an adipose tissue-dependent mechanism of autism spectrum disorder. Of particular interest, the levels of fatty acid binding protein 4 (FABP4) were significantly lower in autism spectrum disorder children than in typically developing subjects, at preschool age (4–6 years old: n = 21 for autism spectrum disorder and n = 26 for typically developing). The receiver operating characteristic curve analysis discriminated autism spectrum disorder children from typically developing children with a sensitivity of 94.4% and a specificity of 75.0%. We re-sequenced the exons of the FABP4 gene in a Japanese cohort comprising 659 autism spectrum disorder and 1000 control samples, and identified two rare functional variants in the autism spectrum disorder group. The Trp98Stop, one of the two variants, was transmitted to the proband from his mother with a history of depression. The disruption of the Fabp4 gene in mice evoked autism spectrum disorder-like behavioural phenotypes and increased spine density on apical dendrites of pyramidal neurons, which has been observed in the postmortem brains of autism spectrum disorder subjects. The Fabp4 knockout mice had an altered fatty acid composition in the cortex. Collectively, these results suggest that an ‘adipo-brain axis’ may underlie the pathophysiology of autism spectrum disorder, with FABP4 as a potential molecule for use as a biomarker.
Walking the financialized city: confronting capitalist urbanization through mobile popular education
Authors: Silver Jonathan , Fields Desiree , Goulding Rich , Rose Isaac , Donnachie Siobhan
Published: September 2020

How do communities understand the highly abstract process of housing financialization? In this paper we argue that walking tours offer the capacity to develop new forms of mobile, public education to learn about the capitalist urbanization process, especially as the financialization of housing accelerates. Based on walking the city of Manchester we show that this type of learning may improve public literacy concerning the opaque and extended ways in which housing in central areas has increasingly been shaped by new types of real estate finance. Although many people in Manchester have understood the outline of these dramatic transformations, and could connect the new skyscrapers to their struggles for everyday survival, there remained a gap in detailed literacy of the actors, finances and dynamics that had changed the city so quickly. We contextualize the rapidly changing global landscape of housing since the global financial crisis of 2008 before showing how these transformations have reshaped housing in Manchester. We then describe the motivations for developing the tour, and the details of the walk itself. We conclude by suggesting that the walking tour offers new types of possibility in necessary learning and subsequent action to address capitalist urbanization.
CircR2Cancer: a manually curated database of associations between circRNAs and cancers
Authors: Lan Wei , Zhu Mingrui , Chen Qingfeng , Chen Baoshan , Liu Jin , Li Min , Chen Yi-Ping Phoebe
Published: September 2020

Accumulating evidences have shown that the deregulation of circRNA has close association with many human cancers. However, these experimental verified circRNA–cancer associations are not collected in any database. Here, we develop a manually curated database (circR2Cancer) that provides experimentally supported associations between circRNAs and cancers. The current version of the circR2Cancer contains 1439 associations between 1135 circRNAs and 82 cancers by extracting data from existing literatures and databases. In addition, circR2Cancer contains the information of cancer exacted from Disease Ontology and basic biological information of circRNAs from circBase. At the same time, circR2Cancer provides a simple and friendly interface for users to conveniently browse, search and download the data. It will be a useful and valuable resource for researchers to understanding the regulation mechanism of circRNA in cancers.

Database URL

http://www.biobdlab.cn:8000
CRISPR sequences are sometimes erroneously translated and can contaminate public databases with spurious proteins containing spaced repeats
Authors: Rubio Alejandro , Mier Pablo , Andrade-Navarro Miguel A , Garzón Andrés , Jiménez Juan , Pérez-Pulido Antonio J
Published: September 2020

The genomics era is resulting in the generation of a plethora of biological sequences that are usually stored in public databases. There are many computational tools that facilitate the annotation of these sequences, but sometimes they produce mistakes that enter the databases and can be propagated when erroneous data are used for secondary analyses, such as gene prediction or homology searching. While developing a computational gene finder based on protein-coding sequences, we discovered that the reference UniProtKB protein database is contaminated with some spurious sequences translated from DNA containing clustered regularly interspaced short palindromic repeats. We therefore encourage developers of prokaryotic computational gene finders and protein database curators to consider this source of error.
Midterm result of custom-made iliac branch device for common iliac aneurysm with and without abdominal aortic aneurysm
Authors: Huang Chun-Yang , Chen Po-Lin , Lu Hsin-Ying , Hsu Hung-Lung , Kuo Tzu-Ting , Chen I.-Ming , Hsu Chiao-Po , Shih Chun-Che
Published: September 2020

OBJECTIVES

Although commercial iliac branch devices offer a new and valid endovascular approach to treating iliac aneurysm and effectively preserve antegrade flow of the internal iliac artery, their use may not be suited for all types of challenging anatomy, especially isolated common iliac artery aneurysm. Our custom-made iliac bifurcation device has a unique design and excludes both combined and isolated iliac branch aneurysm. This study validated the efficacy and safety of the custom device by comparing clinical outcomes between groups receiving commercial and custom devices.

METHODS

Data of consecutive patients receiving iliac bifurcation device implantation for iliac aneurysm with or without concomitant endovascular repair for abdominal aortic aneurysm from January 2010 to May 2019 were reviewed.

RESULTS

Iliac bifurcation device implantation with or without concomitant abdominal aortic aneurysm stent grafting was completed in 46 patients (commercial, n = 35; custom, n = 11). No significant differences were observed regarding postoperative complications, occlusion or endoleak. Comparisons of primary (80.8% vs 85.7%, P = 0.88) and secondary (86.5% vs 85.7%, P = 0.85) patency and freedom from reintervention (88.2% vs 100%, P = 0.33), all-cause mortality (78.6% vs 100%, P = 0.25) and aneurysm-related mortality (100% vs 100%, P = 1.00) also indicated no differences at a 5-year surveillance point. Furthermore, the iliac aneurysms of the groups displayed similar shrinkage 1 year after procedures.

CONCLUSIONS

For iliac aneurysm, the novel custom-made iliac bifurcation device is an adaptable design not inferior to commercial devices with regard to postoperative complications, bridge occlusion, endoleak and short-term aneurysm remodelling. It provides an alternative for treatment, particularly when certain anatomic challenges are present.

Clinical trial registration

2018-07-050BC, 2017-01-023ACF.
Average Bound Toward the Generalized Ramanujan Conjecture and Its Applications on Sato–Tate Laws for GL(n)
Authors: Lau Yuk-Kam , Ho Ng Ming , Wang Yingnan
Published: September 2020

We give the 1st non-trivial estimate for the number of $GL(n)$ ($n\ge 3$) Hecke–Maass forms whose Satake parameters at any given prime $p$ fail the Generalized Ramanujan Conjecture and study some applications on the (vertical) Sato–Tate laws.
Building the evidence-base to reduce electronic health record–related clinician burden
Authors: Dymek Christine , Kim Bryan , Melton Genevieve B , Payne Thomas H , Singh Hardeep , Hsiao Chun-Ju
Published: September 2020

Clinicians face competing pressures of being clinically productive while using imperfect electronic health record (EHR) systems and maximizing face-to-face time with patients. EHR use is increasingly associated with clinician burnout and underscores the need for interventions to improve clinicians’ experiences. With an aim of addressing this need, we share evidence-based informatics approaches, pragmatic next steps, and future research directions to improve 3 of the highest contributors to EHR burden: (1) documentation, (2) chart review, and (3) inbox tasks. These approaches leverage speech recognition technologies, natural language processing, artificial intelligence, and redesign of EHR workflow and user interfaces. We also offer a perspective on how EHR vendors, healthcare system leaders, and policymakers all play an integral role while sharing responsibility in helping make evidence-based sociotechnical solutions available and easy to use.
Burn Injuries in Hospitalized Australian Children—An Epidemiological Profile
Authors: Ryder Courtney , Mackean Tamara , Hunter Kate , Rogers Kris , Holland Andrew J A , Ivers Rebecca
Published: September 2020

Globally, First Nations children sustain burns at a higher rate than other children. Little is understood about how health inequities contribute, especially from an Indigenous viewpoint. We analyzed data from the Burns Registry of Australian and New Zealand (BRANZ) for acute burns in children (<16 years) admitted to hospital between October 2009 and July 2018. Descriptive statistics examined equity variables in patient and injury characteristics. Poisson regression was used to describe factors associated with bacterial infection. Indigenous research methods were used throughout. Aboriginal and Torres Strait Islander children represented 10.4% of the study population. Health inequities were present for Aboriginal and Torres Strait Islander children with longer hospital length of stay (9.5 vs 4.6 days), rural residency (61.3% vs 13.9%), lower socioeconomic status (72.2% vs 34.9%), and more flame burns (19.5% vs 10.6%) compared to other Australian children. Streptococcus sp. infection risk was four times greater in Aboriginal and Torres Strait Islander children compared to other Australian children. Flame burns and high percentage total body surface area burns were a risk for Staphylococcus sp. and Streptococcus sp. infection in all children. The epidemiological profile for burn injuries managed in Australian burns centers differs between Aboriginal and Torres Strait Islander children and other children, indicating persistent health inequities. These differences should be considered in the development of injury prevention strategies and the clinical management of burn injuries for Aboriginal and Torres Strait Islander children and their families.
Scalp mass: an atypical presentation of multiple myeloma
Authors: Tift Benjamin D , Prickett Joshua T , Sampson Lorenzo K
Published: September 2020

A 64-year-old male with no history of trauma presented to the general surgery clinic with a 6-month history of an asymptomatic left parietal scalp mass. The differential included benign etiologies such as lipoma or sebaceous cyst. At surgery, a hemorrhagic soft tissue mass with underlying defect in the parietal calvarium was noted. The initial attempt at resection was abandoned and neurosurgical consultation was requested. Magnetic resonance imaging demonstrated an enhancing scalp mass with a lytic lesion of the parietal calvarium with no intradural extension. Craniectomy with mass resection and mesh cranioplasty were performed. Pathology confirmed plasma cell neoplasm; serum protein electrophoresis and lytic skull lesions confirmed multiple myeloma. This rare presentation of multiple myeloma serves as a call for providers to maintain a broad differential when evaluating a seemingly benign mass, consider rare etiologies when appropriate and maintain vigilance for abnormal findings during any procedure.
Associations Among Behavioral Risk, Sociodemographic Identifiers, and Sexually Transmitted Infections in Male and Female Army Enlisted Personnel
Authors: Hood Kristina B , Pollack Lance M , Jackson Dawnyéa D , Boyer Cherrie B
Published: September 2020

Introduction

Rates of sexually transmitted infections (STIs) are higher among U.S. military personnel than their civilian counterparts. Yet there is a paucity of military-specific research that has utilized theoretical frameworks to describe the relative influence of the multiple and interrelated risk factors associated with STIs in this population of young, healthy men and women. The aim of this study was to examine the relative influence of Information, Motivation, and Behavioral Skills Model (IMB) factors known to be associated with condom use and STI diagnosis, as well as examine gender differences among a cohort of young, active duty enlistees who are in the very early stages of their military careers.

Materials and Methods

Data were collected in 2011 to 2013 through self-administered questionnaires and laboratory-confirmed tests of STIs. Logistic regression analyses were used to assess IMB constructs, behavioral risk variables, and sociodemographic factors associated with STI diagnosis and condom use separately among female and male military personnel.

Results

STIs among males were significantly associated with nonwhite race, lower STI behavioral intentions and STI behavioral skills, and engaging in sex after drinking alcohol. Further, males who reported more positive attitudes toward using condoms, higher confidence in preventing drinking, higher alcohol prevention norms among peers, a lower frequency of drinking alcohol before engaging in sexual intercourse, more sexual partners, and higher STI behavioral intentions were significantly more likely to report using condoms consistently during sexual encounters. Among female participants, a history of STIs was significantly associated with higher numbers of reported sexual partners and greater alcohol prevention efficacy while lifetime consistent condom use was significantly associated only with stronger intentions to avoid behaviors that might result in STI acquisition.

Conclusion

Our findings support the need for development of STI prevention strategies that include education and skills-building approaches to reduce alcohol misuse among enlisted military personnel, and especially male personnel. Such programs should include factors that uniquely influence the experiences of males and females in the military context.