bluuebunny/crossref_metadata_2025 huggingface dataset:
Mathematical modeling of the dynamics of layered and block media with nonlinear contact conditions on supercomputers
Authors: Nikitin I. S. , Burago N. G. , Golubev V. I. , Nikitin A. D.
Published: December 2019

Continual models of solid media with a discrete set of slip planes (layered, block media) and with nonlinear slip conditions at the contact boundaries of structural elements are constructed. The constitutive equations of the resulting system of equations contain a small viscosity parameter in the denominator of nonlinear free terms. For a stable numerical solution of a system of differential equations, an explicit-implicit method is proposed with an explicit approximation of the equations of motion and an implicit approximation of the constitutive relations containing a small parameter. From implicit nonlinear difference approximations analytically, using the perturbation method, various effective formulas for the correction of stress components after an elastic time step are obtained. To calculate the elastic step, we used a grid-characteristic method on hexahedral grids, which allowed us to significantly increase the speed of calculations and simulate a non-stationary three-dimensional problem of generating a response from an oriented layered or block cracked cluster located in a homogeneous medium.
Mathematical model of decomposition of hydrates in a reservoir
Authors: Popov V.V
Published: December 2019

A mathematical model of the process of decomposition of hydrates in a reservoir by reducing pressure is implemented numerically. The dependence of results obtained on main parameters of the problem such as initial hydrate saturation, initial water saturation, depression on the formation, permeability coefficient, porosity has been studied. We compare results of the numerical implementation of the original model with results obtained after linearization of the heat equation, equations of gas flow continuity both separately and simultaneously. It is shown that with relatively low permeability, initial water saturation and depression one can use the model with linearized equations. The relative difference of the calculated hydrate saturation is a few percent. For the distribution of temperature and pressure, this difference is even smaller. The developed algorithm can easily be expanded for a multidimensional problem.
Mathematical technology for solving the Kardar-Parisi-Zhang equation with a source
Authors: Rassadin A E , Stepanov A V
Published: December 2019

The description of an algorithm for numerical solution of the two-dimensional Kardar-Parisi-Zhang equation with fractal initial condition and spatially inhomogeneous stochastic source of particles has been presented. Using the Cole-Hopf substitution, the KardarParisi-Zhang equation is reduced to an auxiliary linear parabolic equation with a variable coefficient. This reduction provides both compatibility of the algorithm with the concept of mathematical technology and possibility of its practical realization on supercomputer using the MPI parallel programming technology and the ROOT framework. The required profile of the evolving surface is restored by the inverse substitution by solving the auxiliary equation, Opportunity of estimation of its autocorrelation function and its spectral power density, as well as the time dynamics of Shannon surface information, have been discussed.
Multiscale Finite Element Method for scattering problem in heterogeneous domain
Authors: Gavrilieva Uygulaana , Vasilyeva Maria , Harris Isaac , Chung Eric T. , Efendiev Yalchin
Published: December 2019

In this paper, we consider the wave scattering problem in heterogeneous domain. The mathematical model is described by the Helmholtz equation for time-harmonic wave propagation with absorbing boundary condition. We construct a coarse grid approximation for the efficient numerical solution on coarse grids using the Multiscale Finite Element Method (MsFEM), where we construct a multiscale space using solution of some local problems in each local domain. Numerical results are presented to illustrate the performance of the method.
Neural networks for multicontinuum models
Authors: Grigorev A. , Stepanov S. , Nikiforov Dj.
Published: December 2019

Neural networks are developed for multicontinuum models. Multicontinuum models [1] assume that processes divided into several continuums and they are connected by some exchange member. In problems connected with PDE not only solution, but also coefficients can depends on time. First we construct LSTM neural network for exchange coefficient that depend on time. We compare the results obtained on the basis of the reference coefficient and on the basis of the neural network. Next we apply same neural network on the solutions. The proposed approach involves the use of a neural network for the approximate generation of a solutions and the further adaptation of the solution of a neural network for generate coarse grid solution based on DG finite elements.
GMsFEM on unstructured grids for single-phase flow in fractured porous media
Authors: Nikiforov Djulustan , Vasilyeva Maria , Efendiev Yalchin , Vasil’ev Vasily
Published: December 2019

In this work, we consider an unstructured Generalized Multiscale Finite Element Method (GMsFEM) for solution of the filtration problem in a fractured media. The basic idea is that coarse grid blocks are formed as sets of fine grid triangular cells and, thus, can be of an almost arbitrary polygonal shape. In this approach, when constructing the fine grid, the faces of coarse blocks are not considered. Discrete fractured model is used to describe a flows in a fractured media.
Embedded fracture model in numerical simulation of the fluid flow and geo-mechanics using Generalized Multiscale Finite Element Method
Authors: Tyrylgin Aleksei , Vasilyeva Maria , Chung Eric T.
Published: December 2019

In this work, we consider a pororelasticity problem in fractured porous media. Mathematical model contains a coupled system of equations for pressure and displacements, for which we use an embedded fracture model. The fine grid approximation is constructed based on the finite volume approximation for the pressure in fractured media and finite element method for the displacements. Multiscale approximation is developed using a structured coarse grid and is based on the Generalized Multiscale Finite Element Method for pressures and displacements. The performance of the method is tested using a two-dimensional model problem with different number of the multiscale basis functions.
Numerical calculation of spectral problems in SP3 approximation by FEM
Authors: Vasilev A. O. , Avvakumov A. V. , Strizhov V. F. , Vabishchevich P. N.
Published: December 2019

The SP3 approximation of the neutron transport equation allows improving the accuracy for both static and transient simulations for reactor core analysis compared with the neutron diffusion theory. Besides, the SP3 calculation costs are much less than higher order transport methods (SN or PN). Another advantage of the SP3 approximation is a similar structure of equations that is used in the diffusion method. Therefore, there is no difficulty to implement the SP3 solution option to the multi-group neutron diffusion codes. In this work, the application of the SP3 methodology based on solution of the - and -spectral problems has been tested for reactor benchmarks. The FEM is chosen to achieve the geometrical generality. The results calculated with the diffusion and SP3 methods are compared with the reference calculation results.
Development of algorithms for the formation of steady-state modes based on the topology of electric power systems
Authors: Akhmetbaev D S , Dzhandigulov A R
Published: December 2019

Implementation of the new algorithm for the formation of the steady state mode based on the distribution coefficients of the driving currents in complex electrical networks. is proposed.

The advantage of the proposed approach, in contrast to previously known ones, is that it is not necessary to calculate all 2-trees, as is done in previously known topological methods, which reduces the number of operations by n
2 times.

The results of calculations by the proposed method on various test examples 99% coincided with the results of calculations obtained using the industrial software RastrWin3.
A computational algorithm for constructing a two-dimensional heat wave generated by a non-stationary boundary condition
Authors: Kazakov A L , Spevak L F , Lempert A A , Nefedova O A
Published: December 2019

The paper discusses solutions of the nonlinear heat equation, which have the form of a heat wave propagating on a zero background with a finite velocity. Such solutions are not typical for parabolic equations, and their existence is associated with the degeneration of the problem at the wave (zero) front. We propose a numerical algorithm for constructing a two-dimensional heat wave, symmetrical with respect to the origin, with a non-zero boundary condition defined on the moving boundary. The main difficulty of the new task is that at each time point a heat wave front (a domain boundary) is unknown. The solution is carried out in two stages. At first, we change the roles of unknown function and radial polar coordinate. For a new unknown function at each time point, we obtain a boundary value problem for the Poisson equation in a known region. The step-by-step solving of this problem by the method of boundary elements at a given time interval allows us to determine the law of the zero front moving. At second, we approximate the found zero front by an analytical function and construct a generalized self-similar solution. The developed algorithm is implemented and tested on a task set.
Management of thermal process for polyethylene gas pipes welding with built-in heater
Authors: Starostin N P , Vasileva M A , Ammosova O A
Published: December 2019

Based on the thermal process control, rapid welding technology for polyethylene pipes with built-in heater in the open air at temperatures below standard is proposed. Technological parameters of welding are determined by calculation from the condition of temperature field dynamics in heat-affected zone according to regularities, that are peculiar to welding at permissible temperatures. The results of determining the welding parameters during electrofusion welding and welding of the saddle branch to the polyethylene pipe of the gas pipeline, as well as the results of tests of the joints obtained by the proposed welding technology are presented.
IDENTIFICATION OF HEAT EXCHANGE BOUNDARY CONDITIONS AT VARIOUS NATURAL AND TECHNOGENIC FACTORS
Authors: Vinokurova T.A , Permyakov P.P
Published: December 2019

The development of permafrost areas requires reliable and long-term projected estimates in a changing climate and man-made impacts. Dangerous natural and man-made factors, such as snowfall, infiltration of precipitation, ice, thermokarst, etc., interact with the ground and determine the stability of the territories of the cryolithozone. In this regard, the work is devoted to the development of new algorithms and software for identifying the boundary conditions on the surface of frozen soil, taking into account the actual process of freezing and thawing of the pore solution of the soil.
A physical-biogeochemical mechanism for negative feedback between marsh crabs and carbon storage
Authors: Guimond Julia A , Seyfferth Angelia L , Moffett Kevan B , Michael Holly A
Published: December 2019

Tidal marshes are valuable global carbon sinks, yet large uncertainties in coastal marsh carbon budgets and mediating mechanisms limit our ability to estimate fluxes and predict feedbacks with global change. To improve mechanistic understanding, we assess how net carbon storage is influenced by interactions between crab activity, water movement, and biogeochemistry. We show that crab burrows enhance carbon loss from tidal marsh sediments by physical and chemical feedback processes. Burrows increase near-creek sediment permeability in the summer by an order of magnitude compared to the winter crab dormancy period, promoting carbon-rich fluid exchange between the marsh and creek. Burrows also enhance vertical exchange by increasing the depth of the strongly carbon-oxidizing zone and reducing the capacity for carbon sequestration. Results reveal the mechanism through which crab burrows mediate the movement of carbon through tidal wetlands and highlight the importance of considering burrowing activity when making budget projections across temporal and spatial scales.
Effect of inhaled acetone concentrations on exhaled breath acetone concentrations at rest and during exercise
Authors: Ager Clemens , Mochalski Pawel , King Julian , Mayhew Chris A , Unterkofler Karl
Published: December 2019

Real-time measurements of the differences in inhaled and exhaled, unlabeled and fully deuterated acetone concentration levels, at rest and during exercise, have been conducted using proton transfer reaction mass spectrometry. A novel approach to continuously differentiate between the inhaled and exhaled breath acetone concentration signals is used. This leads to unprecedented fine grained data of inhaled and exhaled concentrations. The experimental results obtained are compared with those predicted using a simple three compartment model that theoretically describes the influence of inhaled concentrations on exhaled breath concentrations for volatile organic compounds with high blood:air partition coefficients, and hence is appropriate for acetone. An agreement between the predicted and observed concentrations is obtained. Our results highlight that the influence of the upper airways cannot be neglected for volatiles with high blood:air partition coefficients, i.e. highly water soluble volatiles.
4. The plane and other spaces
Authors: Earl Richard
Published: December 2019

Most functions have several numerical inputs and produce more than one numerical output. But even generally continuity requires that we can constrain the difference in outputs by suitably constraining the difference in inputs. ‘The plane and other spaces’ asks more general questions such as ‘is the distance a car has travelled a continuous function of its speed?’ This is a subtle question as neither the input nor output are numbers, but rather functions of time, with input the speed function s(t) and output the distance function d(t). In answering the question, it considers continuity between metric spaces, equivalent metrics, open sets, convergence, and compactness and connectedness, the last two being topological invariants that can be used to differentiate between spaces.
5. Flavours of topology
Authors: Earl Richard
Published: December 2019

From the mid-19th century, topological understanding progressed on various fronts. ‘Flavours of topology’ considers other areas such as differential topology, algebraic topology, and combinatorial topology. Geometric topology concerned surfaces and grew out of the work of Euler, Möbius, Riemann, and others. General topology was more analytical and foundational in nature; Hausdorff was its most significant progenitor and its growth mirrored other fundamental work being done in set theory. The chapter introduces the hairy ball theorem, and the work of great French mathematician and physicist Henri Poincaré, which has been rigorously advanced over the last century, making algebraic topology a major theme of modern mathematics.
The Latent-Variable Structure of the Addenbrooke’s Cognitive Examination-Revised
Authors: Connolly Madeleine L , Bowden Stephen C , Simpson Leonie C , Horne Malcolm , McGregor Sarah
Published: December 2019

Objectives

To establish a theoretically justified factor structure for the Addenbrooke’s Cognitive Examination-Revised (ACE-R).

Methods

Our sample comprised 288 patients with Parkinson’s disease (179 men and 109 women). The mean age of participants was 66.66 (SD = 8.93). Confirmatory factor analysis (CFA) was used to evaluate the test developers’ five-factor model of the ACE-R, and alternative models as guided by the Cattell–Horn–Carroll (CHC) theory. Exploratory structural equation modeling (ESEM) was also employed to examine alternative factor structures to ensure that a good candidate model was not overlooked.

Results

A three-factor CHC-guided CFA and a similar three-factor ESEM model both showed acceptable overall fit, and interpretable factor structures. The three-factor CFA model showed two factors of pure CHC constructs: acquired knowledge (Gc), and visuospatial ability (Gv), and one combined factor, namely, long-term memory retrieval, fluency, and working memory (Glr-Gsm). The three-factor ESEM model showed three factors essentially in line with the CFA results.

Conclusion

The three-factor CHC-guided CFA model was selected as the best model to guide clinical interpretation of cognitive variables underlying ACE-R scores.
Establishment and Early Development of Even-Age Shortleaf Pine–Hardwood Mixtures Using Artificially Regenerated Shortleaf Pine and Various Site Preparation and Release Treatments
Authors: Clabo David C , Clatterbuck Wayne K
Published: December 2019

Shortleaf pine (Pinus echinata)–hardwood mixtures were once a common forest type on upland sites throughout the southeastern United States. These forest types have declined throughout much of shortleaf pine’s native range. Information on restoring shortleaf pine–hardwood types when a shortleaf pine seed source is not present is lacking. The objectives of this study were to investigate the effects of four site-preparation and release treatments (control, burn, herbicide, and herbicide and burn) on the development of even-aged mixtures of planted shortleaf pine and natural hardwoods located on the Highland Rim physiographic province of Tennessee, USA. Three years after study establishment, statistical differences among treatments occurred for shortleaf pine survival and basal diameter. Survival was greatest in the herbicide-only treatment. Height and basal diameter growth were greatest in the herbicide and burn treatment. Stem densities were greater in treatments that did not include a herbicide release than those where herbicide was used alone or combined with prescribed burning. The herbicide and burn treatment had the greatest potential after 3 years for developing into a balanced, mixed shortleaf pine–hardwood stand, whereas most treatments had an influx of exotic, invasive species such as Chinese privet (Ligustrum sinense) and callery pear (Pyrus calleryana).
High Transcriptional Error Rates Vary as a Function of Gene Expression Level
Authors: Meer Kendra M , Nelson Paul G , Xiong Kun , Masel Joanna
Published: December 2019

Errors in gene transcription can be costly, and organisms have evolved to prevent their occurrence or mitigate their costs. The simplest interpretation of the drift barrier hypothesis suggests that species with larger population sizes would have lower transcriptional error rates. However, Escherichia coli seems to have a higher transcriptional error rate than species with lower effective population sizes, for example Saccharomyces cerevisiae. This could be explained if selection in E. coli were strong enough to maintain adaptations that mitigate the consequences of transcriptional errors through robustness, on a gene by gene basis, obviating the need for low transcriptional error rates and associated costs of global proofreading. Here, we note that if selection is powerful enough to evolve local robustness, selection should also be powerful enough to locally reduce error rates. We therefore predict that transcriptional error rates will be lower in highly abundant proteins on which selection is strongest. However, we only expect this result when error rates are high enough to significantly impact fitness. As expected, we find such a relationship between expression and transcriptional error rate for non-C→U errors in E. coli (especially G→A), but not in S. cerevisiae. We do not find this pattern for C→U changes in E. coli, presumably because most deamination events occurred during sample preparation, but do for C→U changes in S. cerevisiae, supporting the interpretation that C→U error rates estimated with an improved protocol, and which occur at rates comparable with E. coli non-C→U errors, are biological.
Genome Sequences of 72 Bacterial Strains Isolated from Ectocarpus subulatus: A Resource for Algal Microbiology
Authors: Karimi Elham , Geslain Enora , KleinJan Hetty , Tanguy Gwenn , Legeay Erwan , Corre Erwan , Dittami Simon M
Published: December 2019

Brown algae are important primary producers and ecosystem engineers in the ocean, and Ectocarpus has been established as a laboratory model for this lineage. Like most multicellular organisms, Ectocarpus is associated with a community of microorganisms, a partnership frequently referred to as holobiont due to the tight interconnections between the components. Although genomic resources for the algal host are well established, its associated microbiome is poorly characterized from a genomic point of view, limiting the possibilities of using these types of data to study host–microbe interactions. To address this gap in knowledge, we present the annotated draft genome sequences of seventy-two cultivable Ectocarpus-associated bacteria. A screening of gene clusters related to the production of secondary metabolites revealed terpene, bacteriocin, NRPS, PKS-t3, siderophore, PKS-t1, and homoserine lactone clusters to be abundant among the sequenced genomes. These compounds may be used by the bacteria to communicate with the host and other microbes. Moreover, detoxification and provision of vitamin B pathways have been observed in most sequenced genomes, highlighting potential contributions of the bacterial metabolism toward host fitness and survival. The genomes sequenced in this study form a valuable resource for comparative genomic analyses and evolutionary surveys of alga-associated bacteria. They help establish Ectocarpus as a model for brown algal holobionts and will enable the research community to produce testable hypotheses about the molecular interactions within this complex system.
Geodetic evidence for shallow creep along the Quito fault, Ecuador
Authors: Mariniere J , Nocquet J-M , Beauval C , Champenois J , Audin L , Alvarado A , Baize S , Socquet A
Published: December 2019

Quito, the capital city of Ecuador hosting ∼2 million inhabitants, lies on the hanging wall of a ∼60-km-long reverse fault offsetting the Inter-Andean Valley in the northern Andes. Such an active fault poses a significant risk, enhanced by the high density of population and overall poor building construction quality. Here, we constrain the present-day strain accumulation associated with the Quito fault with new Global Positioning System (GPS) data and Persistent Scatterer Interferometric Synthetic Aperture Radar (PS-InSAR) analysis. Far field GPS data indicate 3–5 mm yr–1 of horizontal shortening accommodated across the fault system. In the central segment of the fault, both GPS and PS-InSAR results highlight a sharp velocity gradient, which attests for creep taking place along the shallowest portion of the fault. Smoother velocity gradients observed along the other segments indicate that the amount of shallow creep decreases north and south of the central segment. 2-D elastic models using GPS horizontal velocity indicate very shallow (<1 km) locking depth for the central segment, increasing to a few kilometres south and north of it. Including InSAR results in the inversion requires locking to vary both along dip and along strike. 3-D spatially variable locking models show that shallow creep occurs along the central 20-km-long segment. North and south of the central segment, the interseismic coupling is less resolved, and data still allows significant slip deficit to accumulate. Using the interseismic moment deficit buildup resulting from our inversions and the seismicity rate, we estimate recurrence time for magnitude 6.5 + earthquake to be between 200 and 1200 yr. Finally, PS-InSAR time-series identify a 2 cm transient deformation that occurred on a secondary thrust, east of the main Quito fault between 1995 and 1997.
Ultra-low palaeointensities from East European Craton, Ukraine support a globally anomalous palaeomagnetic field in the Ediacaran
Authors: Shcherbakova V V , Bakhmutov V G , Thallner D , Shcherbakov V P , Zhidkov G V , Biggin A J
Published: December 2019

The time-averaged geomagnetic field is generally purported to be uniformitarian across Earth history—close to a geocentric axial dipole, with average strength within one order of magnitude of that at present. Nevertheless, recent studies have reported that the field was approximately ten times weaker than present in the mid-Palaeozoic (∼410–360 Ma) and late Ediacaran (∼565 Ma). Here we present the first whole-rock palaeointensity determinations of Ediacaran age outside of Laurentia. These were obtained by the Thellier-Coe, Wilson and microwave methods for basaltic rocks of 560–580 Ma age of the Ediacaran traps, southwestern margin of the East European Craton, Ukraine. All four studied sites showed extremely low instantaneous field values of (3–7) μT with corresponding VDMs of (0.4–1) × 1022 Am2. Summarizing all available data, the Ediacaran field appears to be anomalously characterized by ultra-low dipole moment and ultra-high reversal frequency. According to some geodynamo models, this state could indicate a weak dipole field regime prior to the nucleation of the solid inner core. However, given that ultra-low field intensities have also been detected in the Devonian, and that virtually no palaeointensity data exist for the intervening ∼150 Ma, the date of inner core nucleation remains extremely uncertain. Our new evidence of persistent ultra-weak magnetospheric shielding in the Ediacaran may be considered consistent with the recently hypothesized link between enhanced UV-B radiation in this interval and the subsequent Cambrian evolutionary radiation.
The state of diet-related NCD policies in Afghanistan, Bangladesh, Nepal, Pakistan, Tunisia and Vietnam: a comparative assessment that introduces a ‘policy cube’ approach
Authors: Buse Kent , Aftab Wafa , Akhter Sadika , Phuong Linh Bui , Chemli Haroun , Dahal Minakshi , Feroz Anam , Hofiani Sayad , Pradhan Nousheen Akber , Anwar Iqbal , Skhiri Hajer Aounallah , El Ati Jalila , Giang Kim Bao , Puri Mahesh , Noormal Bashir , Rabbani Fauziah , Hawkes Sarah
Published: December 2019

We assessed the technical content of sugar, salt and trans-fats policies in six countries in relation to the World Health Organization ‘Best Buys’ guidelines for the prevention and control of non-communicable diseases (NCDs). National research teams identified policies and strategies related to promoting healthy diets and restricting unhealthy consumption, including national legislation, development plans and strategies and health sector-related policies and plans. We identified relevant text in relation to the issuing agency, overarching aims, goals, targets and timeframes, specific policy measures and actions, accountability systems, budgets, responsiveness to inequitable vulnerabilities across population groups (including gender) and human rights. We captured findings in a ‘policy cube’ incorporating three dimensions: policy comprehensiveness, political salience and effectiveness of means of implementation, and equity/rights. We compared diet-related NCD policies to human immunodeficiency virus policies in relation to rights, gender and health equity. All six countries have made high-level commitments to address NCDs, but dietary NCDs policies vary and tend to be underdeveloped in terms of the specificity of targets and means of achieving them. There is patchwork reference to internationally recognized, evidence-informed technical interventions and a tendency to focus on interventions that will encounter least resistance, e.g. behaviour change communication in contrast to addressing food reformulation, taxation, subsidies and promotion/marketing. Policies are frequently at the lower end of the authoritativeness spectrum and have few identified budgetary commitments or clear accountability mechanisms. Of concern is the limited recognition of equity and rights-based approaches. Healthy diet policies in these countries do not match the severity of the NCDs burden nor are they designed in such a way that government action will focus on the most critical dietary drivers and population groups at risk. We propose a series of recommendations to expand policy cubes in each of the countries by re-orienting diet-related policies so as to ensure healthy diets for all.
Serum Newborn Screening Blood Metabolites Are not Associated With Childhood-onset Inflammatory Bowel Disease: A Population-based Matched Case-control Study
Authors: Kuenzig M Ellen , Hawken Steven , Wilson Kumanan , Talarico Robert , Chakraborty Pranesh , Sood Manish M , Benchimol Eric I
Published: December 2019

Background

Originally used for screening of inborn errors of metabolism, routine metabolite profiles of newborns have also been associated with prematurity and some childhood diseases. We sought to determine whether metabolites measured during routine newborn screening could identify infants who develop inflammatory bowel disease (IBD) in childhood.

Methods

We conducted a population-based matched case-control study using health administrative data from Ontario, Canada. Children born 2006 to 2015 with IBD were identified using a validated algorithm and matched to 5 controls based on birth date, sex, rural/urban household, and mean neighborhood income quintile at birth. Cases and controls were linked deterministically to metabolic profiles from Newborn Screening Ontario. We fit a lasso penalized logistic regression model and used 10-fold cross-validation to obtain internally valid performance measures. Models included metabolites, amino acids, and endocrine markers. Models also included ratios of metabolites, gestational age, birth weight, mode of delivery, age at serum collection, maternal age at delivery, maternal history of IBD, and parity.

Results

Three hundred eight cases of IBD, diagnosed at 5.5 ± 2.8 years, were matched to 1540 controls. No individual metabolites were associated with IBD. The c-statistic was 0.50 for the training data. After 10-fold cross-validation the C statistic was 0.50, indicating no significant association between metabolites and IBD diagnosis.

Conclusions

Newborn screening serum metabolites could not identify children who will develop IBD in this population-based cohort. Future studies with an expanded panel of metabolites may provide improved prediction of IBD.
Things and Terms: Relations Between Materiality, Language, and Politics in Post-revolutionary Iran
Authors: Sefat Kusha
Published: December 2019

Departing from the canons of the cultural and material turns, this paper emphasizes the shortcomings that each body of work has shown in addressing political transformations. So doing, it argues that shifting relations between materiality and language occasion different kinds of politics. Specifically, the paper offers a new interpretation of one of the most critical epochs in the political history of modern Iran, by illustrating that the confluence of the material and linguistic worlds in the Islamic Republic during the 1980s, brought about a distinct political field in which relations between words and their material referents became fixed at the level of multitudes. This blocked public processes of performativity and resignification of signs in ways that might have threatened the centrality of the revolutionary leader, Imam Khomeini. What developed was a social milieu in which Khomeini never faced the possibility of defeat in politics.
Metabolic studies reveal that ruminal microbes of adult steers do not degrade rumen-protected or unprotected L-citrulline
Authors: Gilbreath Kyler R , Nawaratna Gayan I , Wickersham Tryon A , Satterfield M Carey , Bazer Fuller W , Wu Guoyao
Published: December 2019

In vitro and in vivo experiments were conducted to determine the metabolism of rumen-protected or unprotected l-citrulline (Cit) plus l-glutamine (Gln) by ruminal microbes. In the in vitro experiment, whole ruminal fluid (3 mL, containing microorganisms) from steers was incubated at 37 ºC with 5 mM Cit plus 6 mM Gln (in a rumen-protected or unprotected form) for 0, 0.5, 2, or 4 h after which times 50 µL samples were collected for AA and ammonia analyses. In the in vivo experiment, at 0.5 h before and 0, 0.5, 1, 2, 4, and 6 h after cannulated adult steers consumed 0.56 kg dried-distillers’ grain mixed with 70 g Cit plus 70 g Gln (in a rumen-protected or unprotected form), samples of ruminal fluid and jugular venous blood were obtained for AA analyses. Results from both in vitro and in vivo experiments demonstrated extensive hydrolysis of rumen-unprotected Gln into glutamate, but little degradation of the rumen-protected Gln or rumen-protected and unprotected Cit by ruminal microbes. Concentrations of Cit and arginine in the plasma of steers consuming rumen-protected or unprotected AA increased at 1 and 2 h after the meal, respectively, when compared with values at 0 h. Collectively, these novel findings indicate that ruminal microbes of adult steers do not degrade extracellular Cit in a rumen-protected or unprotected form. Our results refute the view that all dietary AAs are extensively catabolized by ruminal microorganisms and also have important implications for dietary supplementation with Cit to ruminants to enhance the concentration of arginine in their plasma and their productivity.
Contrast-Enhanced Mammography: A Scientific Review
Authors: Lewin John M , Patel Bhavika K , Tanna Aneri
Published: December 2019

In this paper we provide an overview of contrast-enhanced mammography (CEM) and a review of the published literature in order to provide a picture of the current state of the evidence on the performance of CEM. Clinical research was fairly sparse following the demonstration of the technique in research subjects about 18 years ago, but the number of publications rapidly increased following commercialization 9 years ago, and even more so in the last 5 years. Initial studies compared CEM with mammography, and clearly showed that CEM could detect cancers not visible on mammography. More recent studies have primarily focused on comparing the performance of CEM with contrast-enhanced magnetic resonance imaging (MRI) in selected cohorts. These studies have almost uniformly shown CEM and MRI to have similar sensitivities, with sensitivity and accuracy showing more variability from study to study. With increasing clinical use, a large number of retrospective reviews of CEM have appeared, showing utility of CEM in the diagnostic clinical setting. Most recently, a small number of papers have been published looking at CEM for high-risk and dense breast screening, two potentially large applications of the technique, showing it to outperform mammography in both populations. CEM has clearly been shown to have clinical utility, but more prospective studies, including screening studies, are needed to further evaluate its performance, especially in comparison with MRI.
Implementation of a Diagnostic-Concentration Bioassay for Detection of Susceptibility to Pyrethroids in Soybean Aphid (Hemiptera: Aphididae)
Authors: Menger James , Beauzay Patrick , Chirumamilla Anitha , Dierks Cole , Gavloski John , Glogoza Phillip , Hamilton Krista , Hodgson Erin W , Knodel Janet J , MacRae Ian V , Pezzini Daniela T , Potter Bruce D , Varenhorst Adam J , Koch Robert L
Published: December 2019

Soybean aphid, Aphis glycines Matsumura, remains the most economically damaging arthropod pest of soybean in the midwestern United States and southern Canada. Foliar applications of a limited number of insecticide modes of action have been the primary management tactic, and pyrethroid resistance was documented recently with full concentration–response leaf-dip and glass-vial bioassays. Full concentration–response bioassays can be cumbersome, and a more efficient assessment tool was needed. In this study, we implemented a diagnostic-concentration glass-vial bioassay using bifenthrin and λ-cyhalothrin. Bioassays were conducted with field-collected soybean aphid populations to assess the geographic extent and severity of resistance to pyrethroids. In 2017, 10 of 18 and 11 of 21 field populations tested with bifenthrin and λ-cyhalothrin, respectively, had mean proportion mortalities less than the susceptible laboratory population. In 2018, 17 of 23 and 13 of 23 field populations tested with bifenthrin and λ-cyhalothrin, respectively, had mean proportion mortalities less than the susceptible laboratory population. Populations collected after reported field failures of a pyrethroid insecticide generally had mean proportion mortalities less than the susceptible laboratory population. In both years, there was a strong correlation between chemistries, which suggests cross-resistance between these insecticides. The diagnostic-concentration glass-vial bioassays reported here will provide the foundation for an insecticide resistance monitoring program with the ability to determine practical levels and geographic extent of insecticide resistance.
Flea Beetle (Coleoptera: Chrysomelidae) Populations, Effects of Feeding Injury, and Efficacy of Insecticide Treatments on Eggplant and Cabbage in Southwest Virginia
Authors: Mason James , Michael Alford Adam , Patrick Kuhar Thomas
Published: December 2019

Flea beetles, are common pests of cabbage Brassica oleracea L. (Brassicales: Brassicaceae) and eggplant Solanum melongena L. (Solanales: Solanaceae), but little is known about the flea beetle populations in Virginia, their impact on yield, or the most effective control methods. This research investigates flea beetle populations and the impact of their feeding injury on cabbage and eggplant in Southwest Virginia and determines the most efficacious control methods. In Whitethorne, VA, cabbage and eggplant crops were vacuum sampled weekly throughout two summers (2015, 2016). Crucifer flea beetle, Phyllotreta cruciferae (Goeze) (Coleoptera: Chrysomelidae), and striped flea beetle, Phyllotreta striolata Fabr. (Coleoptera: Chrysomelidae) were found on cabbage; whereas, eggplant flea beetle, Epitrix fucula (Crotch) (Coleoptera: Chrysomelidae), and the tobacco flea beetle, Epitrix hirtipennis (Melsheimer) (Coleoptera: Chrysomelidae) were found on eggplant. To evaluate the impact of flea beetle feeding on these plants flea beetle densities and defoliation were assessed weekly and individual plant, as well as whole plot yields, assessed at harvest. For cabbage, significant yield reductions were observed between 1 and 20% and >60% defoliation. Similarly, significant yield reductions were observed between 41 and 60% and >60% defoliation for eggplant. The efficacy of various insecticides was also evaluated. Soil application of the systemic neonicotinoid dinotefuran, imidacloprid, and the foliar-applied bifenthrin resulted in the fewest beetles, the least amount of leaf defoliation, and the highest yield in cabbage and eggplant. This research helps vegetable growers to better understand the severity of these pests and how to effectively combat them.
Performance of Field-Collected Spodoptera frugiperda (Lepidoptera: Noctuidae) Strains Exposed to Different Transgenic and Refuge Maize Hybrids in Argentina
Authors: Murúa María G , Vera Martín A , Michel Andrew , Casmuz Augusto S , Fatoretto Julio , Gastaminza Gerardo
Published: December 2019

Spodoptera frugiperda (J. E. Smith) is one of the major pests of maize in Argentina. The main tool for its control is the use of genetically modified maize hybrids expressing Bacillus thuringiensis (Bt) insecticidal proteins. Maize growers in Argentina initially controlled this pest with Bt maize that expressed a single Bt protein (Cry1Ab or Cry1F). Currently it is necessary to plant maize cultivars that produce two Bt proteins to achieve the satisfactory control. Recently, Cry1F field-evolved resistant populations of this species were confirmed in Argentina. The objective of this study was to evaluate the performance of S. frugiperda field-collected strains on different Bt and non-Bt maize hybrids. Strains were collected from non-Bt maize (T1), Agrisure TDMax (T2), Agrisure Viptera (T3), Agrisure Viptera 3110 (T4), Genuity VT Triple Pro (T5), and Power Core (T6). Three experiments were performed to 1) determine the survivorship and reproduction of field-collected larvae (F0) from Bt maize hybrids, 2) evaluate Cry1F resistance using an F1 screen, and 3) assess the performance of F1 strains on different maize hybrids. In the F0, the survivorship from larva to adult ranged from 0 to 63%. We obtained adults from only the T1, T2, T5, and T6 strains with no significant differences in the reproductive parameters. Continuously rearing F1 larvae on their collected hosts affected larval duration, which was significantly shorter for a known-laboratory Bt-susceptible strain than the field-collected strains. Our results support the existence of Cry1F-resistance alleles in S. frugiperda field populations in Argentina.
Genetic Diversity of Pediculus humanus capitis (Phthiraptera: Pediculidae) in Peninsular Malaysia and Molecular Detection of Its Potential Associated Pathogens
Authors: Mokhtar Aida Syafinaz , Ling Lau Yee , Wilson John-James , Abdul-Aziz Noraishah Mydin
Published: December 2019

Pediculosis capitis caused by Pediculus humanus capitis (De Geer) is endemic all over the world, and children are mostly affected, particularly those living in overcrowded institutions. Several studies have shown that P. h. capitis carried human pathogenic bacteria, suggesting the potential role of head lice in the transmission of pathogens to humans. In this study, we determined the genetic diversity of head lice collected from welfare homes sheltering underprivileged children by using DNA barcoding and demonstrated the presence of Acinetobacter spp., Serratia marcescens, and Staphylococcus aureus in head lice, which have never been investigated before in Malaysia. Cox1 DNA barcoding identified the head lice, P. h. capitis collected from welfare homes across two geographical areas of Peninsular Malaysia as belonging to clades A, B, and D. Acinetobacter bacteria: Acinetobacter guillouiae, Acinetobacter junii, Acinetobacter baumannii, and Acinetobacter nosocomialis were detected in head lice belonging to clades A and also D. In addition, DNA from S. marcescens and S. aureus were also detected in both clades A and D. To our knowledge, this is the first report on the genetic diversity of head lice in Malaysia through DNA barcoding, as well as the first to provide molecular evidence on the type of bacteria occurring in head lice in Malaysia. It is anticipated that the DNA barcoding technique used in this study will be able to provide rapid and accurate identification of arthropods, in particular, medically important ectoparasites.
Swift UVOT grism observations of nearby Type Ia supernovae – II. Probing the progenitor metallicity of SNe Ia with ultraviolet spectra
Authors: Pan Y-C , Foley R J , Jones D O , Filippenko A V , Kuin N P M
Published: December 2019

Ultraviolet (UV) observations of Type Ia supernovae (SNe Ia) are crucial for constraining the properties of their progenitor systems. Theoretical studies predicted that the UV spectra, which probe the outermost layers of an SN, should be sensitive to the metal content of the progenitor. Using the largest SN Ia UV (λ < 2900 Å) spectroscopic sample obtained from Neil Gehrels Swift Observatory, we investigate the dependence of UV spectra on metallicity. For the first time, our results reveal a correlation (∼2σ) between SN Ia UV flux and host-galaxy metallicities, with SNe in more metal-rich galaxies (which are likely to have higher progenitor metallicities) having lower UV flux level. We find that this metallicity effect is only significant at short wavelengths (λ ≲ 2700 Å), which agrees well with the theoretical predictions. We produce UV spectral templates for SNe Ia at peak brightness. With our sample, we could disentangle the effect of light-curve shape and metallicity on the UV spectra. We also examine the correlation between the UV spectra and SN luminosities as parametrized by Hubble residuals. However, we do not see a significant trend with Hubble residuals. This is probably due to the large uncertainties in SN distances, as the majority of our sample members are extremely nearby (redshift z ≲ 0.01). Future work with SNe discovered in the Hubble flow will be necessary to constrain a potential metallicity bias on SN Ia cosmology.
Reverse genetics-based biochemical studies of the ribosomal exit tunnel constriction region in eukaryotic ribosome stalling: spatial allocation of the regulatory nascent peptide at the constriction
Authors: Takamatsu Seidai , Ohashi Yubun , Onoue Noriyuki , Tajima Yoko , Imamichi Tomoya , Yonezawa Shinya , Morimoto Kyoko , Onouchi Hitoshi , Yamashita Yui , Naito Satoshi
Published: December 2019

A number of regulatory nascent peptides have been shown to regulate gene expression by causing programmed ribosome stalling during translation. Nascent peptide emerges from the ribosome through the exit tunnel, and one-third of the way along which β-loop structures of ribosomal proteins uL4 and uL22 protrude into the tunnel to form the constriction region. Structural studies have shown interactions between nascent peptides and the exit tunnel components including the constriction region. In eukaryotes, however, there is a lack of genetic studies for the involvement of the constriction region in ribosome stalling. Here, we established transgenic Arabidopsis lines that carry mutations in the β-loop structure of uL4. Translation analyses using a cell-free translation system derived from the transgenic Arabidopsis carrying the mutant ribosome showed that the uL4 mutations reduced the ribosome stalling of four eukaryotic stalling systems, including those for which stalled structures have been solved. Our data, which showed differential effects of the uL4 mutations depending on the stalling systems, explained the spatial allocations of the nascent peptides at the constriction that were deduced by structural studies. Conversely, our data may predict allocation of the nascent peptide at the constriction of stalling systems for which structural studies are not done.
Accurate inference of the full base-pairing structure of RNA by deep mutational scanning and covariation-induced deviation of activity
Authors: Zhang Zhe , Xiong Peng , Zhang Tongchuan , Wang Junfeng , Zhan Jian , Zhou Yaoqi
Published: December 2019

Despite the large number of noncoding RNAs in human genome and their roles in many diseases include cancer, we know very little about them due to lack of structural clues. The centerpiece of the structural clues is the full RNA base-pairing structure of secondary and tertiary contacts that can be precisely obtained only from costly and time-consuming 3D structure determination. Here, we performed deep mutational scanning of self-cleaving CPEB3 ribozyme by error-prone PCR and showed that a library of <5 × 104 single-to-triple mutants is sufficient to infer 25 of 26 base pairs including non-nested, nonhelical, and noncanonical base pairs with both sensitivity and precision at 96%. Such accurate inference was further confirmed by a twister ribozyme at 100% precision with only noncanonical base pairs as false negatives. The performance was resulted from analyzing covariation-induced deviation of activity by utilizing both functional and nonfunctional variants for unsupervised classification, followed by Monte Carlo (MC) simulated annealing with mutation-derived scores. Highly accurate inference can also be obtained by combining MC with evolution/direct coupling analysis, R-scape or epistasis analysis. The results highlight the usefulness of deep mutational scanning for high-accuracy structural inference of self-cleaving ribozymes with implications for other structured RNAs that permit high-throughput functional selections.