bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Genome Sequence of the Eastern Woodchuck (Marmota monax) – A Preclinical Animal Model for Chronic Hepatitis B
Authors: Alioto Tyler S , Cruz Fernando , Gómez-Garrido Jèssica , Triyatni Miriam , Gut Marta , Frias Leonor , Esteve-Codina Anna , Menne Stephan , Kiialainen Anna , Kumpesa Nadine , Birzele Fabian , Schmucki Roland , Gut Ivo G , Spleiss Olivia 
Published: October 2019

Abstract
The Eastern woodchuck (Marmota monax) has been extensively used in research of chronic hepatitis B and liver cancer because its infection with the woodchuck hepatitis virus closely resembles a human hepatitis B virus infection. Development of novel immunotherapeutic approaches requires genetic information on immune pathway genes in this animal model. The woodchuck genome was assembled with a combination of high-coverage whole-genome shotgun sequencing of Illumina paired-end, mate-pair libraries and fosmid pool sequencing. The result is a 2.63 Gigabase (Gb) assembly with a contig N50 of 74.5 kilobases (kb), scaffold N50 of 892 kb, and genome completeness of 99.2%. RNA sequencing (RNA-seq) from seven different tissues aided in the annotation of 30,873 protein-coding genes, which in turn encode 41,826 unique protein products. More than 90% of the genes have been functionally annotated, with 82% of them containing open reading frames. This genome sequence and its annotation will enable further research in chronic hepatitis B and hepatocellular carcinoma and contribute to the understanding of immunological responses in the woodchuck.
Machine Learning Enables High-Throughput Phenotyping for Analyses of the Genetic Architecture of Bulliform Cell Patterning in Maize
Authors: Qiao Pengfei , Lin Meng , Vasquez Miguel , Matschi Susanne , Chamness James , Baseggio Matheus , Smith Laurie G , Sabuncu Mert R , Gore Michael A , Scanlon Michael J 
Published: October 2019

AbstractBulliform cells comprise specialized cell types that develop on the adaxial (upper) surface of grass leaves, and are patterned to form linear rows along the proximodistal axis of the adult leaf blade. Bulliform cell patterning affects leaf angle and is presumed to function during leaf rolling, thereby reducing water loss during temperature extremes and drought. In this study, epidermal leaf impressions were collected from a genetically and anatomically diverse population of maize inbred lines. Subsequently, convolutional neural networks were employed to measure microscopic, bulliform cell-patterning phenotypes in high-throughput. A genome-wide association study, combined with RNAseq analyses of the bulliform cell ontogenic zone, identified candidate regulatory genes affecting bulliform cell column number and cell width. This study is the first to combine machine learning approaches, transcriptomics, and genomics to study bulliform cell patterning, and the first to utilize natural variation to investigate the genetic architecture of this microscopic trait. In addition, this study provides insight toward the improvement of macroscopic traits such as drought resistance and plant architecture in an agronomically important crop plant.
Tel1 Activation by the MRX Complex Is Sufficient for Telomere Length Regulation but Not for the DNA Damage Response in Saccharomyces cerevisiae
Authors: Keener Rebecca , Connelly Carla J , Greider Carol W 
Published: October 2019

Abstract
Previous models suggested that regulation of telomere length in Saccharomyces cerevisiae by Tel1(ATM) and Mec1(ATR) would parallel the established pathways regulating the DNA damage response. Here, we provide evidence that telomere length regulation differs from the DNA damage response in both the Tel1 and Mec1 pathways. We found that Rad53 mediates a Mec1 telomere length regulation pathway but is dispensable for Tel1 telomere length regulation, whereas in the DNA damage response, Rad53 is regulated by both Mec1 and Tel1. Using epistasis analysis with a Tel1 hypermorphic allele, Tel1-hy909, we found that the MRX complex is not required downstream of Tel1 for telomere elongation but is required downstream of Tel1 for the DNA damage response. Our data suggest that nucleolytic telomere end processing is not a required step for telomerase to elongate telomeres.
Numerical Solutions for Micropolar Transport Phenomena over a Nonlinear Stretching Sheet
Authors: Bhargava R. , Sharma S. , Takhar H. S. S. , Bég O. A. A. , Bhargava P. 
Published: October 2019

We present a numerical study for the steady, coupled, hydrodynamic, heat and mass transfer of an incompressible micropolar fluid flowing over a nonlinear stretching sheet. The governing differential equations are partially decoupled using a similarly transformation and then solved by two numerical techniques – the finite element method and the finite difference method. The dimensionless translational velocity, microrotation (angular velocity), temperature and mass distribution function are computed for the different thermophysical parameters controlling the flow regime, viz the nonlinear (stretching) parameter, b, Grashof number, G and Schmidt number, Sc. All results are shown graphically. Additionally skin friction and Nusselt number, which provide an estimate of the surface shear stress and the rate of cooling of the surface, respectively, are also computed. Excellent agreement is obtained between both numerical methods. The dimensionless translational velocity (f′) for both micropolar and Newtonian fluids is shown to decrease with an increase in nonlinear parameter b. Dimensionless microrotation (angular velocity), g, generally increases with a rise in nonlinear parameter b (in particular in the vicinity of the wall) and decreases with a rise in convective parameter, G. The effects of other parameters on the flow variables are also discussed. The flow regime has significant applications in polymer processing technology and metallurgy.
Dynamical Complexity in Some Ecological Models: Effects of Toxin Production by Phytoplankton
Authors: Upadhyay R. K. K. , Naji R. K. K. , Kumari N. 
Published: October 2019

We investigate dynamical complexities in two types of chaotic tri-trophic aquatic food-chain model systems representing a real situation in the marine environment. Phytoplankton produce chemical substances known as toxins to reduce grazing pressure by zooplankton [1]. The role of toxin producing phytoplankton (TPP) on the chaotic behavior in these food chain systems is investigated. Holling type I, II, and III functional response forms are considered to study the interference between phytoplankton and zooplankton populations in the presence of toxic chemical. Our study shows that chaotic dynamics is robust to changes in the rates of toxin release as well as the toxin release functions. The present study also reveals that the rate of toxin production by toxin producing phytoplankton plays an important role in controlling oscillations in the plankton system. The different mortality functions of zooplankton due to toxin producing phytoplankton have significant influence in controlling oscillations, coexistence, survival or extinction of the zooplankton population. Further studies are needed to ascertain if this defence mechanism suppresses chaotic dynamics in model aquatic systems.
A Study of Steady Buoyancy-Driven Dissipative Micropolar Free Convection Heat and Mass Transfer in a Darcian Porous Regime with Chemical Reaction
Authors: Bég O. Anwar Anwar , Bhargava R. , Rawat S. , Takhar H. S. S. , Bég Tasweer A. A. 
Published: October 2019

In the present paper we examine the steady double-diffusive free convective heat and mass transfer of a chemically-reacting micropolar fluid flowing through a Darcian porous regime adjacent to a vertical stretching plane. Viscous dissipation effects are included in the energy equation. Assuming incompressible, micro-isotropic fluid behaviour the transport equations are formulated in a two-dimensional coordinate system (x, y) using boundary-layer theory. The influence of the bulk porous medium retardation is modeled as a drag force term in the translational momentum equation. Transformations render the conservation equations into dimensionless form in terms of a single independent variable, η, transverse to the stretching surface. A simplified first order homogenous reaction model is also used to simulate chemical reaction in the flow. Using the finite element method solutions are generated for the angular velocity field, translational velocity field, temperature and species transfer fields. The effects of buoyancy, porous drag and chemical reaction rate are studied. Chemical reaction is shown to decelerate the flow and also micro-rotation values, in particular near the wall. Mass transfer is also decreased with increasing chemical reaction rate. Increasing Darcy number is shown to accelerate the flow. Applications of the study include cooling of electronic circuits, packed-bed chemical reactors and also the near field flows in radioactive waste geo-repositories.
Dependence on Initial Conditions of Attainable Sets of Control Systems with p-Integrable Controls
Authors: Akyar E. 
Published: October 2019

Quasi-linear systems governed by p-integrable controls, for 1 < p < ∞ with constraint ‖u(·)‖p ≤ µ0 are considered. Dependence on initial conditions of attainable sets are studied.
Joule Heating Effect on the Coupling of Conduction with Magnetohydrodynamic Free Convection Flow from a Vertical Flat Plate
Authors: Alim M. A. A. , Alam Md. M. M. , Al-Mamun Abdullah 
Published: October 2019

The present work describes the effect of magnetohydrodynamic (MHD) natural convection flow along a vertical flat plate with Joule heating and heat conduction. The governing boundary layer equations are first transformed into a non-dimensional form and resulting nonlinear system of partial differential equations are then solved numerically by using the implicit finite difference method with Keller box scheme. The results of the skin friction co-efficient, the surface temperature distribution, the velocity and the temperature profiles over the whole boundary layer are shown graphically for different values of the Prandtl number Pr (Pr = 1.74, 1.00, 0.72, 0.50, 0.10), the magnetic parameter M (M = 1.40, 0.90, 0.50, 0.10) and the Joule heating parameter J (J = 0.90, 0.70, 0.40, 0.20). Numerical values of the skin friction coefficients and surface temperature distributions for different values of Joule heating parameter have been presented in tabular form.
Fuzzy Probabilistic Analysis of Steel Structure Focused on Reliability Design Concept of Eurocodes
Authors: Kala Z. 
Published: October 2019

The modern unification of the European standards EUROCODE requires securing a constant quality of metallurgical production in the EU countries. In this paper, experimentally found statistical characteristics of yield stress, ultimate tensile strength and ductility of Czech and Austrian steel are presented. In the probabilistic reliability analysis, the experimentally found yield stress histograms of structural steel S235 of both Czech and Austrian manufacturing processes are considered as basic parameters. The reliability of steel members designed according to EUROCODE 3 is investigated. The objective of the studies is the verification of partial safety factors of load-carrying capacity, and of load action given in the standard EN1990. Differences in failure probabilities of steel members of Czech and Austrian production are studied in connection with the influence of model fuzzy uncertainties in the determination of load action and load-carrying capacity values.
The Effectiveness of Synergistic Enzymatic Reaction with Limited Mediator
Authors: Kulys J. , Dapkūnas Ž. 
Published: October 2019

Kinetics of biocatalytical synergistic reactions has been analyzed with special emphasis on stability and reactivity of mediators. The application to the model of kinetic constants taken from the experiments showed that the quasi steady state (QSS) for reduced and oxidized enzyme was achieved in 0.001 s. However, the QSS for the mediator was not established during measurable time. For this reason the kinetics of biocatalytical synergistic reactions was modeled by solving the ordinary differential equations using software package KinFitSim©.
The calculations showed the increase of an apparent life-time of the mediator in the synergistic reaction. The apparent life-time was most affected by reactivity of mediator. The change of the mediator reactivity from 1 M−1s−1 to 105 M−1s−1 increased the apparent life-time from 19 s to 1538 s. This mediator reactivity can be achieved even for strongly endothermic reaction when difference of redox potential of substrate and mediator is 0.35 V. The increase of mediator life-time increased product yield.
Numerical Investigation of Combined Buoyancy and Surface Tension Driven Convection in an Axi-Symmetric Cylindrical Annulus
Authors: Sankar M. , Venkatachalappa M. 
Published: October 2019

A numerical study is conducted to understand the effect of surface tension on buoyancy driven convection in a vertical cylindrical annular cavity filled with a low Prandtl number fluid. The inner and outer cylinders are maintained at different uniform temperatures and the horizontal top and bottom walls are thermally insulated. The upper free surface is assumed to remain flat and non-deformable. A finite difference scheme consisting of the Alternating Direction Implicit method and the Successive Line Over Relaxation method is used to solve the vorticity stream function formulation of the problem. Detailed numerical results of heat transfer rate, temperature and velocity fields have been presented for a wide range of physical parameters of the problem. The flow pattern and temperature distribution in the annular cavity are presented by means of contour plots of streamlines and isotherms. The rate of heat transfer is estimated by evaluating the average Nusselt number. Further, the present numerical results are compared with the existing results and are found to be in good agreement.
Asymptotic Stability, Orbital Stability of Hopf-Bifurcating Periodic Solution of a Simple Three-Neuron Artificial Neural Network with Distributed Delay
Authors: Gupta P. D. D. , Majee N. C. C. , Roy A. B. B. 
Published: October 2019

A distributed delay model of a class of three-neuron network has been investigated. Sufficient conditions for existence of unique equilibrium, multiple equilibria and their local stability are derived. A closed interval for a parameter of the system is identified in which Hopf-bifurcating periodic solution occurs for each point of such interval. The orbital stability of such bifurcating periodic solution at the extreme points of the interval is ascertained. Lastly global bifurcation aspect of such periodic solutions is studied. The results are illustrated by numerical simulations.
Unsteady Laminar Free Convection from a Vertical Cone with Uniform Surface Heat Flux
Authors: Pullepu Bapuji , Ekambavanan K. , Chamkha A. J. J. 
Published: October 2019

Numerical solutions of, unsteady laminar free convection from an incompressible viscous fluid past a vertical cone with uniform surface heat flux is presented in this paper. The dimensionless governing equations of the flow that are unsteady, coupled and non-linear partial differential equations are solved by an efficient, accurate and unconditionally stable finite difference scheme of Crank-Nicolson type. The velocity and temperature fields have been studied for various parameters Prandtl number and semi vertical angle. The local as well as average skin-friction and Nusselt number are also presented and analyzed graphically. The present results are compared with available results in literature and are found to be in good agreement.
Chaotic Dynamics in a Three Species Aquatic Population Model with Holling Type II Functional Response
Authors: Upadhyay R. K. K. 
Published: October 2019

A three-trophic model for marine community is proposed and investigated by means of numerical bifurcation analysis. The proposed model based on a modified version of the Leslie-Gower scheme, incorporates mutual interference in all the three populations and generalizes several other known models in the ecological literature. We investigate the dynamical behavior of the model system by considering the Holling type II functional response of toxin liberation process. Bifurcation diagram and two-dimensional parameter scan suggest that chaotic dynamics is robust to variations in toxin production by phytoplankton. Our study suggests that toxic substances released by TPP population may act as bio-control by changing the state of chaos to order. The mutual interference also induces chaos and acts as both stabilizing and destabilizing factors.
Existence Theorems for Some Classes of Boundary Value Problems Involving the P(X)-Laplacian
Authors: Andrei Ionica 
Published: October 2019

We prove an alternative for a nonlinear eigenvalue problem involving the p(x)-Laplacian and study a subcritical boundary value problem for the same operator. The theoretical approach is the Mountain Pass Lemma and one of its variants, which is very useful in the study of eigenvalue problems.
Transient Mixed Convection Flow of A Second-Grade Visco-Elastic Fluid over a Vertical Surface
Authors: Damseh R. A. A. , Shatnawi A. S. S. , Chamkha A. J. J. , Duwairi H. M. M. 
Published: October 2019

The viscoelastic boundary layer flow and mixed convection heat transfer near a vertical isothermal surface have been examined in this paper. The governing equations are formulated and solved numerically using an explicit finite difference technique. The velocity and temperature profiles, boundary layer thicknesses, Nusselt numbers and the local skin friction coefficients are shown graphically for different values of the viscoelsatic parameter. In general, it is found that the velocity decreases inside the boundary layer as the viscoelsatic parameter is increased and consequently, the local Nusselt number decreases. This is due to higher tensile stresses between viscoelsatic fluid layers which has a retardation effects on the motion of these layers and consequently, on the heat transfer rates for the mixed convection heat transfer problem under investigation. A Comparison with available published results on special cases of the problem shows excellent agreement.
Chaos Synchronization Using Active Control and Backstepping Control: A Comparative Analysis
Authors: Vincent U. E. E. 
Published: October 2019

This paper examines the synchronization performance of two widely used chaos synchronization techniques: active control and backstepping control. It is shown that the two methods have excellent performance, with the active control marginally outperforming the backstepping control in terms of transient analysis. However, the complexity of active controllers suggests that the backstepping control would be more attainable in engineering applications.
Density Dependent Predator Death Prevalence Chaos in a Tri-trophic Food Chain Model
Authors: Bandyopadhyay M. , Chatterjee S. , Chakraborty S. , Chattopadhyay J. 
Published: October 2019

Ecological systems have all the properties to produce chaotic dynamics. To predict the chaotic behavior in an ecological system and its possible control mechanism is interesting. Aziz-Alaoui [1] considered a tri-trophic food-chain model with modified Leslie-Gower type growth rate for top-predator population and established the chaotic dynamics exhibited by the model system for a certain choice of parameter values. We have modified the said model by incorporating density dependent death rate for predator population. Our mathematical findings reveal the fact that there are two coexisting equilibrium points one of which is a source and the other one is a sink. The positive equilibrium point which is sink is actually globally asymptotically stable under certain parametric conditions. Numerical experiment analysis shows that the model system are capable to produce chaotic dynamics when the rate of intra specific completion is very low and chaotic dynamics disappears for a certain value of the rate of intra specific completion for predator species. Our results suggest that the consideration of density dependent death rate for predator species have the ability to control the chaotic dynamics.
The Method of Prime Costs Determination of the Model Row Goods
Authors: Barashkov A. S. S. , Petrosian D. S. S. 
Published: October 2019

The concept of the model row goods is introduced. These are the interchangeable goods differing by quality and price. Cognacs of various vintage years produced on one cognac factory are a typical example of such goods. For the indicated kind of the goods the method of the cost price determination of the goods of competitors is worked out and realized. The initial information for determination is the data on the prices of the goods and sales volumes.
Analysis of a Vaccination Model for Carrier Dependent Infectious Diseases with Environmental Effects
Authors: Naresh Ram , Pandey Surabhi , Misra A. K. K. 
Published: October 2019

We have proposed and analyzed a nonlinear mathematical model for the spread of carrier dependent infectious diseases in a population with variable size structure including the role of vaccination. It is assumed that the susceptibles become infected by direct contact with infectives and/or by the carrier population present in the environment. The density of carrier population is assumed to be governed by a generalized logistic model and is dependent on environmental and human factors which are conducive to the growth of carrier population. The model is analyzed using stability theory of differential equations and numerical simulation. We have found a threshold condition, in terms of vaccine induced reproduction number R(φ) which is, if less than one, the disease dies out in the absence of carriers provided the vaccine efficacy is high enough, and otherwise the infection is maintained in the population. The model also exhibits backward bifurcation at R(φ) = 1. It is also shown that the spread of an infectious disease increases as the carrier population density increases. In addition, the constant immigration of susceptibles makes the disease more endemic.
Numerical Approximation of Some Infinite Gaussian Series and Integrals
Authors: Stoncelis M. , Vaičiulis M. 
Published: October 2019

The paper deals with numerical computation of the asymptotic variance of the so-called increment ratio (IR) statistic and its modifications. The IR statistic is useful for estimation and hypothesis testing on fractional parameter H ∈ (0, 1) of random process (time series), see Surgailis et al. [1], Bardet and Surgailis [2]. The asymptotic variance of the IR statistic is given by an infinite integral (or infinite series) of 4-dimensional Gaussian integrals which depend on parameter H. Our method can be useful for numerical computation of other similar slowly convergent Gaussian integrals/series. Graphs and tables of approximate values of the variances σp2(H) and σˆp2(H), p = 1, 2 are included.
Hopf Bifurcation Analysis in a Delayed Kaldor-Kalecki Model of Business Cycle
Authors: Kaddar A. , Talibi Alaoui H. 
Published: October 2019

In this paper, we analyze the model of business cycle with time delay set forth by A. Krawiec and M. Szydłowski [1]. Our goal in this model is to introduce the time delay into capital stock and gross product in capital accumulation equation. The dynamics are studied in terms of local stability and of the description of the Hopf bifurcation, that is proven to exist as the delay (taken as a parameter of bifurcation) cross some critical value. Additionally we conclude with an application.