bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular dynamics simulation for interfacial properties of carbon nanotube reinforced aluminum composites
Authors: Patel Pramod Rakt , Sharma Sumit , Tiwari S K 
Published: November 2020

Abstract
A molecular dynamics (MD) simulation method has been used to predict the interfacial behavior of single-wall carbon nanotube (CNT) reinforced aluminum (Al) composites. At the interface of the CNT and the Al, only van der Waals interaction was considered. The effect of CNT volume fraction and chirality on CNT pull-out has been studied for the first time with a proper distinction between them. The length of all the CNTs was kept constant throughout the study. The approach used in this work was validated with an earlier study. The present study revealed that the average pull-out load was found proportional to both the CNT volume fraction as well as the diameter. The smaller diameter CNTs improved the interfacial shear strength (ISS) at lower volume fraction significantly in comparison to that of the larger diameter CNTs. The highest improvement of 38.7% was observed in the ISS during pull-out of (6, 6) CNT at a CNT volume fraction of 3.17%. The average energy increment was found to be increasing with CNT volume fraction and was higher for larger diameter CNTs.
The unique global solvability and optimal time decay rates for a multi-dimensional compressible generic two-fluid model with capillarity effects
*
Authors: Xu Fuyi , Chi Meiling 
Published: November 2020

Abstract
The present paper deals with the Cauchy problem of a compressible generic two-fluid model with capillarity effects in any dimension N ⩾ 2. We first study the unique global solvability of the model in spaces with critical regularity indices with respect to the scaling of the associated equations. Due to the presence of the capillary terms, we exploit the parabolic properties of the linearized system for all frequencies which enables us to apply contraction mapping principle to show the unique global solvability of strong solutions close to a stable equilibrium state. Furthermore, under a mild additional decay assumption involving only the low frequencies of the data, we establish the optimal time decay rates for the constructed global solutions.
Global existence of the nonisentropic compressible Euler equations with vacuum boundary surrounding a variable entropy state
Authors: Rickard Calum , Hadžić Mahir , Jang Juhi 
Published: November 2020

Abstract
Global existence for the nonisentropic compressible Euler equations with vacuum boundary for all adiabatic constants γ > 1 is shown through perturbations around a rich class of background nonisentropic affine motions. The notable feature of the nonisentropic motion lies in the presence of non-constant entropies, and it brings a new mathematical challenge to the stability analysis of nonisentropic affine motions. In particular, the estimation of the curl terms requires a careful use of algebraic, nonlinear structure of the pressure. With suitable regularity of the underlying affine entropy, we are able to adapt the weighted energy method developed for the isentropic Euler Hadžić and Jang (2018 Inventiones Mathematicae
214 1205–1266) to the nonisentropic problem. For large γ values, inspired by Shkoller and Sideris (2019 Arch. Ration. Mech. Anal.
234 115), we use time-dependent weights that allow some of the top-order norms to potentially grow as the time variable tends to infinity. We also exploit coercivity estimates here via the fundamental theorem of calculus in time variable for norms which are not top-order.
Signal intensity form of the Tofts model for quantitative analysis of prostate dynamic contrast enhanced MRI data
Authors: Fan Xiaobing , Chatterjee Aritrick , Medved Milica , Oto Aytekin , Karczmar Gregory S 
Published: November 2020

Abstract
The aim of this study is to develop a signal intensity (S(t)) form of the standard Tofts pharmacokinetic model that avoids the need to calculate tissue contrast agent concentration (C(t)) as function of time (t). We refer to this as ‘SI-Tofts’ model. Physiological parameters (K
trans and v
e) calculated using the SI-Tofts and standard Tofts models were compared by using simulations and human prostate dynamic contrast enhanced (DCE) MRI data. This approach was also applied to the Patlak model to compare K
trans values calculated from C(t) and S(t). Simulations were performed on DCE-MRI data from the quantitative imaging biomarkers alliance to validate SI-Tofts model. In addition, ultrafast DCE-MRI data were acquired from 18 prostate cancer patients on a Philips Achieva 3T-TX scanner. Regions-of-interest (ROIs) for prostate cancer, normal tissue, gluteal muscle, and iliac artery were manually traced. The C(t) was calculated for each ROI using the standard model with measured pre-contrast tissue T
1 values. Both the simulation and clinical results showed strong correlation (r = 0.87–0.99, p < 0.001) for K
trans and v
e calculated from the SI-Tofts and standard Tofts models. The SI-Tofts model with a correction factor using the T
1 ratio of blood to tissue significantly improved the K
trans estimates. The correlation of K
trans obtained from the Patlak model with C(t) vs S(t) was also strong (r = 0.95–0.99, p < 0.001). These preliminary results suggest that physiological parameters from DCE-MRI can be reliably estimated from the SI-Tofts model without contrast agent concentration calculation.
Experimental determination of magnetic field correction factors for ionization chambers in parallel and perpendicular orientations
Authors: Pojtinger Stefan , Nachbar Marcel , Ghandour Sarah , Pisaturo Olivier , Pachoud Marc , Kapsch Ralf-Peter , Thorwarth Daniela 
Published: November 2020

Abstract
Magnetic field correction factors are needed for absolute dosimetry in magnetic resonance (MR)-linacs. Currently experimental data for magnetic field correction factors, especially for small volume ionization chambers, are largely lacking. The purpose of this work is to establish, independent methods for the experimental determination of magnetic field correction factors

k

B
⃗

,
Q

in an orientation in which the ionization chamber is parallel to the magnetic field. The aim is to confirm previous experiments on the determination of Farmer type ionization chamber correction factors and to gather information about the usability of small-volume ionization chambers for absolute dosimetry in MR-linacs. The first approach to determine

k

B
⃗

,
Q

is based on a cross-calibration of measurements using a conventional linac with an electromagnet and an MR-linac. The absolute influence of the magnetic field in perpendicular orientation is quantified with the help of the conventional linac and the electromagnet. The correction factors for the parallel orientation are then derived by combining these measurements with relative measurements in the MR-linac. The second technique utilizes alanine electron paramagnetic resonance dosimetry. The alanine system as well as several ionization chambers were directly calibrated with the German primary standard for absorbed dose to water. Magnetic field correction factors for the ionization chambers were determined by a cross-calibration with the alanine in an MR-linac. Important quantities like

k

B
⃗

,
Q

for Farmer type ionization chambers in parallel orientation and the change of the dose to water due the magnetic field

c

B
⃗

have been confirmed. In addition, magnetic field correction factors have been determined for small volume ionization chambers in parallel orientation. The electromagnet-based measurements of

k

B
⃗

,
Q

for

7

MV

/

1.5

T

MR-linacs and parallel ionization chamber orientations resulted in 0.9926(22), 0.9935(31) and 0.9841(27) for the PTW 30013, the PTW 31010 and the PTW 31021, respectively. The measurements based on the second technique resulted in values for

k

B
⃗

,
Q

of 0.9901(72), 0.9955(72), and 0.9885(71). Both methods show excellent accuracy and reproducibility and are therefore suitable for the determination of magnetic field correction factors. Small-volume ionization chambers showed a variation in the resulting values for

k

B
⃗

,
Q

and should be cross-calibrated instead of using tabulated values for correction factors.
Bronchoscope motion tracking using centerline-guided Gaussian mixture model in navigated bronchoscopy
Authors: Navaei Lavasani Saeedeh , Farnia Parastoo , Najafzadeh Ebrahim , Saghatchi Samaneh , Samavati Mehdi , Abtahi Hamidreza , Deevband Mohammadreza , Ahmadian Alireza 
Published: November 2020

Abstract
Electromagnetic-based navigation bronchoscopy requires accurate and robust estimation of the bronchoscope position inside the bronchial tree. However, respiratory motion, coughing, patient movement, and airway deformation inflicted by bronchoscope significantly hinder the accuracy of intraoperative bronchoscopic localization. In this study, a real-time and automatic registration procedure was proposed to superimpose the current location of the bronchoscope to corresponding locations on a centerline extracted from bronchial computed tomography (CT) images. A centerline-guided Gaussian mixture model (CG-GMM) was introduced to register a bronchoscope’s position concerning extracted centerlines. A GMM was fitted to bronchoscope positions where the orientation likelihood was chosen to assign the membership probabilities of the mixture model, which led to preserving the global and local structures. The problem was formulated and solved under the expectation maximization framework, where the feature correspondence and spatial transformation are estimated iteratively. Validation was performed on a dynamic phantom with four different respiratory motions and four human real bronchoscopy (RB) datasets. Results of the experiments conducted on the bronchial phantom showed that the average positional tracking error using the proposed approach was equal to 1.98

±

0.98 mm that was reduced in comparison with independent electromagnetic tracking (EMT), iterative closest point (ICP), and coherent point drift (CPD) methods by 64%, 58%, and 53%, respectively. In the patient assessment part of the study, the average positional tracking error was 4.73

±

4.76 mm and compared to ICP, and CPD methods showed 31.4% improvement of successfully tracked frames. Our approach introduces a novel method for real-time respiratory motion compensation that provides reliable guidance during bronchoscopic interventions and, thus could increase the diagnostic yield of transbronchial biopsy.
Spatio-temporal dynamics of a nanosecond pulsed microwave plasma ignited by time reversal
Authors: Valentin Mazières , Pascaud Romain , Pascal Olivier , Clergereaux Richard , Stafford Luc , Dap Simon , Liard Laurent 
Published: November 2020

Abstract
In the present paper, a detailed investigation of the spatio-temporal dynamics of the recently developed time reversal microwave plasma source is presented. This novel source allows to ignite a plasma at a desired location in a reverberant cavity by focusing the electromagnetic energy in time and space. An important feature is the possibility to control the plasma position only by changing the input microwave waveform. The source is operated in a repetitive pulsed mode with very low duty cycle (typically 5 × 10−2%). Nanosecond pulses have rise time lower than 1 ns. The generated plasmas have typical sizes in the millimeter range and are observed using imaging for dozens of nanoseconds. The plasma behavior is investigated for different pressures and repetition frequencies. A strong dependence is observed between each discharge pulse suggesting the existence of an important memory effect. The latter is probably due to argon metastable atoms and/or residual charges remaining in the post-discharge and allowing the next breakdown to occur at a moderate electric field.
A metamaterial for wearable piezoelectric energy harvester
Authors: Gao Shanshi , Gain Asit Kumar , Zhang Liangchi 
Published: November 2020

Abstract
In this study, a metamaterial is developed and manufactured by additive manufacturing technique for a novel wearable piezoelectric energy harvester (PEH). This PEH converts electricity from the kinetic energy associated with walking by attached polyvinylidene fluoride (PVDF) membranes. Finite element method analysis was conducted to simulate the dynamic compression on insoles corresponding to actual walking or running. The simulation results were verified by experiments. It was found that a triple-layer PVDF structure can produce an output voltage of 4.15 V and one insole with a triple-layer PVDF structure array can provide an 8.6 mW output power at running.
The flow of fluid-particle suspension between two rotating stretchable disks with the effect of the external magnetic field
Authors: Radhika M , Sowmya G , Siddabasappa  , Prasannakumara B C , Alam Manawwer , Rahimi-Gorji Mohammad , Rahaman Mostafizur 
Published: November 2020

Abstract
This paper explores the compressible dusty fluid flow between two spinning disks. The upper and lower disks rotate at an angular velocity equal to

Ω

1

and

Ω

2

respectively. Fluid and dust particles are considered to be dispersed axisymmetrically. The equations which represents the described flow are transformed into a set of ordinary differential equations which are nonlinear and coupled by opting suitable similarity variables. These equations are solved using the built-in bvp4c algorithm of MATLAB. The profiles of axial, radial, azimuthal velocity and thermal profiles are discussed through graphs for variations of non-dimensional parameters. It has been observed that the friction factor enhances with the upsurge in values of Hartmann number Ha and the Nusselt number declines for shoot up values of Eckert number. Also, the stretching parameter amplifies the friction factor and the Nusselt number.
Noise and the molecular processes underlying cell fate decision-making
Authors: Guillemin Anissa , Stumpf Michael P H 
Published: November 2020

Abstract
Cell fate decision-making events involve the interplay of many molecular processes, ranging from signal transduction to genetic regulation, as well as a set of molecular and physiological feedback loops. Each aspect offers a rich field of investigation in its own right, but to understand the whole process, even in simple terms, we need to consider them together. Here we attempt to characterise this process by focussing on the roles of noise during cell fate decisions. We use a range of recent results to develop a view of the sequence of events by which a cell progresses from a pluripotent or multipotent to a differentiated state: chromatin organisation, transcription factor stoichiometry, and cellular signalling all change during this progression, and all shape cellular variability, which becomes maximal at the transition state.
Dust acoustic rogue waves of fractional-order model in dusty plasma
Authors: Sun Jun-Chao , Zhang Zong-Guo , Dong Huan-He , Yang Hong-Wei 
Published: November 2020

Abstract
In this paper, the fractional-order model is used to study dust acoustic rogue waves in dusty plasma. Firstly, based on control equations, the multi-scale analysis and reduced perturbation method are used to derive the (3+1)-dimensional modified Kadomtsev–Petviashvili (MKP) equation. Secondly, using the semi-inverse method and the fractional variation principle, the (3+1)-dimensional time-fractional modified Kadomtsev–Petviashvili (TF-MKP) equation is derived. Then, the Riemann–Liouville fractional derivative is used to study the symmetric property and conservation laws of the (3+1)-dimensional TF-MKP equation. Finally, the exact solution of the (3+1)-dimensional TF-MKP equation is obtained by using fractional order transformations and the definition and properties of Bell polynomials. Based on the obtained solution, we analyze and discuss dust acoustic rogue waves in dusty plasma.
Newtonian gravitational constant measurement. All atomic variables become extreme when using a source mass consisting of three or more parts
Authors: Dubetsky B 
Published: November 2020

Abstract
Atomic interferometry methods used to measure the Newtonian gravitational constant. To improve the accuracy, one should measure the phase of an atomic interferometer at extreme values of atomic vertical velocities and coordinates. Owing to symmetry, the horizontal components of atomic velocities and coordinates are also extreme. We propose using a source mass consisting of three or more parts, since only in this case one can find such an arrangement of parts that all atomic variables become extreme. Nonlinear dependences of the phase on the uncertainties of atomic positions and velocities near those extreme values required us to modify the expression for the phase relative standard deviation. Moreover, taking into account nonlinear terms in the phase dependence on the atomic coordinates and velocities leads to a phase shift. In the last experiment to measure the Newtonian gravitational constant by atomic interferometry, this shift was not included. We took the shift into account, got a value of 199 ppm for it, and this leads to a decrease in the value of the Newton constant by 0.02%. In addition, we showed that at equal sizes of the atomic cloud in the vertical and horizontal directions, as well as at equal atomic vertical and transverse temperatures, systematic errors due to the finite size and temperature of the cloud disappear. The calculation also showed that when using the 13-ton source mass proposed recently, the measurement accuracy can reach 17 ppm for a source mass consisting of four quarters. We assumed that the source mass consisting of a set of cylinders is used for measurements. We have obtained a new analytical expression for the gravitational field of a homogeneous cylinder.
Invited Commentary: Epigenetic Clocks and Obesity—Towards the Next Frontier Using Integrative Approaches and Early-Life Models
Authors: Tekola-Ayele Fasil 
Published: November 2020

Abstract
Why people of the same age show differences in age-related functional decline and whether biological aging can be slowed down through lifestyle changes and therapeutics are active research topics. Molecular tools that predict biological age based on DNA methylation markers, known as epigenetic clocks, are facilitating these efforts. In this issue, Kresovich et al. (Am J Epidemiol. 2021;190(6):984–993) investigated a cohort of non-Hispanic White women, demonstrating positive relationships between adiposity measures and the ticking rate of epigenetic clocks in blood. This commentary emphasizes that integrating molecular and genetic epidemiology approaches is crucial to dissecting the complex relationship between obesity and epigenetic aging. The early-life period is explored as a unique opportunity to gain novel insights into links between developmental processes and aging in later life. Last, the landscape of the next frontier in aging research is described in light of the imperative for transdisciplinary approaches to outline a shared vision and public health implementation dilemmas.
Type II achalasia is associated with a comparably favorable outcome following per oral endoscopic myotomy
Authors: Tomizawa Yutaka , Mahmud Nadim , Dasher Kevin , Triggs Joseph R , Saumoy Monica , Falk Gary W , Ginsberg Gregory G 
Published: November 2020

Summary
Per oral endoscopic myotomy (POEM) is a safe and effective treatment for esophageal motility disorder in treatment-naïve patients as well as salvage therapy. Though type II achalasia, compared to other subtypes, is reported to have a more favorable outcome with pneumatic dilation (PD) or Heller myotomy (HM), it is unclear whether achalasia subtype predicts symptom response to POEM. We aimed to evaluate whether type II achalasia is associated with a comparably favorable outcome following POEM. We performed a retrospective review of patients with esophageal motility disorder who were referred for POEM from April 2014 to June 2017. The main outcome was clinical success based on Eckardt score ≤3 and its association with subtype and safety. A total of 63 patients (mean age 51 years [SD 15]; 63% male) underwent a total of 68 POEMs with median of 263 days follow-up. Of these, 45 (71.3%) patients were type II achalasia. In all, 29 (46%) patients were treatment-naïve and 34 (54%) patients had previous endoscopic or surgical therapy including botulinum toxin injection in 16 (25%), PD in 10 (16%), both botulinum toxin injection and PD in 8 (13%) and HM in 3 (5%). Technical success was 100% and clinical success was achieved in 51 (81%) patients. The rate of clinical success was higher in patients with type II achalasia compared to the other subtypes (88.9% vs. 61.1% [P = 0.028]) and type II achalasia patients required fewer redo POEM (2.2% vs. 22.2% [P = 0.021]). Multivariate logistic regression analysis demonstrated the positive prediction of clinical success for type II achalasia following POEM (P = 0.046). As observed with PD and HM, type II achalasia was associated with a favorable clinical outcome following POEM.
D-EE: Distributed software for visualizing intrinsic structure of large-scale single-cell data
Authors: An Shaokun , Huang Jizu , Wan Lin 
Published: November 2020

Abstract

Background
Dimensionality reduction and visualization play vital roles in single-cell RNA sequencing (scRNA-seq) data analysis. While they have been extensively studied, state-of-the-art dimensionality reduction algorithms are often unable to preserve the global structures underlying data. Elastic embedding (EE), a nonlinear dimensionality reduction method, has shown promise in revealing low-dimensional intrinsic local and global data structure. However, the current implementation of the EE algorithm lacks scalability to large-scale scRNA-seq data.

Results
We present a distributed optimization implementation of the EE algorithm, termed distributed elastic embedding (D-EE). D-EE reveals the low-dimensional intrinsic structures of data with accuracy equal to that of elastic embedding, and it is scalable to large-scale scRNA-seq data. It leverages distributed storage and distributed computation, achieving memory efficiency and high-performance computing simultaneously. In addition, an extended version of D-EE, termed distributed optimization implementation of time-series elastic embedding (D-TSEE), enables the user to visualize large-scale time-series scRNA-seq data by incorporating experimentally temporal information. Results with large-scale scRNA-seq data indicate that D-TSEE can uncover oscillatory gene expression patterns by using experimentally temporal information.

Conclusions
D-EE is a distributed dimensionality reduction and visualization tool. Its distributed storage and distributed computation technique allow us to efficiently analyze large-scale single-cell data at the cost of constant time speedup. The source code for D-EE algorithm based on C and MPI tailored to a high-performance computing cluster is available at https://github.com/ShaokunAn/D-EE.