bluuebunny/crossref_metadata_2025 huggingface dataset:
Long Term Results of Single-Fraction Carbon-Ion Radiotherapy for Non-small Cell Lung Cancer
Authors: Ono Takashi , Yamamoto Naoyoshi , Nomoto Akihiro , Nakajima Mio , Isozaki Yuka , Kasuya Goro , Ishikawa Hitoshi , Nemoto Kenji , Tsuji Hiroshi
Published: December 2020

Background: The purpose of the present study was to evaluate the efficacy and safety of single-fraction carbon-ion radiotherapy (CIRT) in patients with non-small cell lung cancer. Methods: Patients with histologically confirmed non-small cell lung cancer, stage T1-2N0M0, and treated with single-fraction CIRT (50Gy (relative biological effectiveness)) between June 2011 and April 2016 were identified in our database and retrospectively analyzed. Toxicity was evaluated using the Common Terminology Criteria for Adverse Events version 4.0. Results: The study included 57 patients, 22 (38.6%) of whom had inoperable cancer. The median age was 75 years (range: 42–94 years), and the median follow-up time was 61 months (range: 6–97 months). The 3- and 5-year overall survival rates were 91.2% and 81.7%, respectively. All survivors were followed up for more than three years. The 3- and 5-year local control rates were 96.4% and 91.8%, respectively. No case of ≥ grade 2 pneumonitis was recorded. Conclusions: This study suggests that single-fraction CIRT for T1-2N0M0 non-small cell lung cancer patients is feasible and can be considered as one of the treatment choices, especially in medically inoperable patients.
Targeting Hedgehog Pathway and DNA Methyltransferases in Uterine Leiomyosarcoma Cells
Authors: Garcia Natalia , Al-Hendy Ayman , Baracat Edmund C. , Carvalho Katia Candido , Yang Qiwei
Published: December 2020

Uterine leiomyosarcoma (LMS) is an aggressive tumor that presents a poor prognosis, high rates of recurrence, and metastasis. Because of its rarity, there is no information available concerning LMS molecular mechanisms of origin and development. Here, we assessed the expression profile of Hedgehog (HH) signaling pathway markers and the effects of their pharmacological inhibition on uterine smooth muscle (UTSM), leiomyoma, and LMS cells. Additionally, we also evaluated the effects of DNMTs inhibition on LMS cell behavior. Cell proliferation, migration and apoptosis rates were evaluated by MTT, Scratch, and Annexin V assays, respectively. RNA expression and protein levels were assessed by qRT-PCR and Western blot. We found that SMO and GLIs (1, 2, and 3) expression was upregulated in LMS cells, with increased nuclear levels of GLI proteins. Treatment with LDE225 (SMOi) and Gant61 (GLIi) resulted in a significant reduction in Glis protein levels in LMS (p < 0.05). Additionally, the expression of DNMT (1, 3a, and 3b), as well as GLI1 nuclear expression, was significantly decreased after treatment with HH inhibitor in LMS cells. Our results showed that blocking of SMO, GLI, and DNMTs is able to inhibit LMS proliferation, migration, and invasion. Importantly, the combination of those treatments exhibited a potentiated effect on LMS malignant features due to HH pathway deactivation.
Partly-Pseudo-Linear Cryptanalysis of Reduced-Round Speck
Authors: Alzakari Sarah A. , Vora Poorvi L.
Published: December 2020

We apply McKay’s pseudo-linear approximation of addition modular 2n to lightweight ARX block ciphers with large words, specifically the Speck family. We demonstrate that a pseudo-linear approximation can be combined with a linear approximation using the meet-in-the-middle attack technique to recover several key bits. Thus we illustrate improvements to Speck linear distinguishers based solely on Cho–Pieprzyk approximations by combining them with pseudo-linear approximations, and propose key recovery attacks.
High-Pressure Spectroscopy Study of Zn(IO3)2 Using Far-Infrared Synchrotron Radiation
Authors: Liang Akun , Turnbull Robin , Bandiello Enrico , Yousef Ibraheem , Popescu Catalin , Hebboul Zoulikha , Errandonea Daniel
Published: December 2020

We report the first high-pressure spectroscopy study on Zn(IO3)2 using synchrotron far-infrared radiation. Spectroscopy was conducted up to pressures of 17 GPa at room temperature. Twenty-five phonons were identified below 600 cm−1 for the initial monoclinic low-pressure polymorph of Zn(IO3)2. The pressure response of the modes with wavenumbers above 150 cm−1 has been characterized, with modes exhibiting non-linear responses and frequency discontinuities that have been proposed to be related to the existence of phase transitions. Analysis of the high-pressure spectra acquired on compression indicates that Zn(IO3)2 undergoes subtle phase transitions around 3 and 8 GPa, followed by a more drastic transition around 13 GPa.
Time Dependent Lyotropic Chromonic Textures in Microfluidic Confinements
Authors: Sharma Anshul , Ong Irvine Lian Hao , Sengupta Anupam
Published: December 2020

Nematic and columnar phases of lyotropic chromonic liquid crystals (LCLCs) have been long studied for their fundamental and applied prospects in material science and medical diagnostics. LCLC phases represent different self-assembled states of disc-shaped molecules, held together by noncovalent interactions that lead to highly sensitive concentration and temperature dependent properties. Yet, microscale insights into confined LCLCs, specifically in the context of confinement geometry and surface properties, are lacking. Here, we report the emergence of time dependent textures in static disodium cromoglycate (DSCG) solutions, confined in PDMS-based microfluidic devices. We use a combination of soft lithography, surface characterization, and polarized optical imaging to generate and analyze the confinement-induced LCLC textures and demonstrate that over time, herringbone and spherulite textures emerge due to spontaneous nematic (N) to columnar M-phase transition, propagating from the LCLC-PDMS interface into the LCLC bulk. By varying the confinement geometry, anchoring conditions, and the initial DSCG concentration, we can systematically tune the temporal dynamics of the N- to M-phase transition and textural behavior of the confined LCLC. Overall, the time taken to change from nematic to the characteristic M-phase textures decreased as the confinement aspect ratio (width/depth) increased. For a given aspect ratio, the transition to the M-phase was generally faster in degenerate planar confinements, relative to the transition in homeotropic confinements. Since the static molecular states register the initial conditions for LC flows, the time dependent textures reported here suggest that the surface and confinement effects—even under static conditions—could be central in understanding the flow behavior of LCLCs and the associated transport properties of this versatile material.
Laser Floating Zone Growth: Overview, Singular Materials, Broad Applications, and Future Perspectives
Authors: Rey-García Francisco , Ibáñez Rafael , Angurel Luis Alberto , Costa Florinda M. , de la Fuente Germán F.
Published: December 2020

The Laser Floating Zone (LFZ) technique, also known as Laser-Heated Pedestal Growth (LHPG), has been developed throughout the last several decades as a simple, fast, and crucible-free method for growing high-crystalline-quality materials, particularly when compared to the more conventional Verneuil, Bridgman–Stockbarger, and Czochralski methods. Multiple worldwide efforts have, over the years, enabled the growth of highly oriented polycrystalline and single-crystal high-melting materials. This work attempted to critically review the most representative advancements in LFZ apparatus and experimental parameters that enable the growth of high-quality polycrystalline materials and single crystals, along with the most commonly produced materials and their relevant physical properties. Emphasis will be given to materials for photonics and optics, as well as for electrical applications, particularly superconducting and thermoelectric materials, and to the growth of metastable phases. Concomitantly, an analysis was carried out on how LFZ may contribute to further understanding equilibrium vs. non-equilibrium phase selectivity, as well as its potential to achieve or contribute to future developments in the growth of crystals for emerging applications.
Emission of Dislocations from Grain Boundaries and Its Role in Nanomaterials
Authors: Li James C. M. , Feng C. R. , Rath Bhakta B.
Published: December 2020

The Frank-Read model, as a way of generating dislocations in metals and alloys, is widely accepted. In the early 1960s, Li proposed an alternate mechanism. Namely, grain boundary sources for dislocations, with the aim of providing a different model for the Hall-Petch relation without the need of dislocation pile-ups at grain boundaries, or Frank-Read sources inside the grain. This article provides a review of his model, and supporting evidence for grain boundaries or interfacial sources of dislocations, including direct observations using transmission electron microscopy. The Li model has acquired new interest with the recent development of nanomaterial and multilayers. It is now known that nanocrystalline metals/alloys show a behavior different from conventional polycrystalline materials. The role of grain boundary sources in nanomaterials is reviewed briefly.
Bacterial Composition and Diversity in Deep-Sea Sediments from the Southern Colombian Caribbean Sea
Authors: Franco Nelson Rivera , Giraldo Miguel Ángel , López-Alvarez Diana , Gallo-Franco Jenny Johana , Dueñas Luisa F. , Puentes Vladimir , Castillo Andrés
Published: December 2020

Deep-sea sediments are considered an extreme environment due to high atmospheric pressure and low temperatures, harboring novel microorganisms. To explore marine bacterial diversity in the southern Colombian Caribbean Sea, this study used 16S ribosomal RNA (rRNA) gene sequencing to estimate bacterial composition and diversity of six samples collected at different depths (1681 to 2409 m) in two localities (CCS_A and CCS_B). We found 1842 operational taxonomic units (OTUs) assigned to bacteria. The most abundant phylum was Proteobacteria (54.74%), followed by Bacteroidetes (24.36%) and Firmicutes (9.48%). Actinobacteria and Chloroflexi were also identified, but their dominance varied between samples. At the class-level, Alphaproteobacteria was most abundant (28.4%), followed by Gammaproteobacteria (24.44%) and Flavobacteria (16.97%). The results demonstrated that some bacteria were common to all sample sites, whereas other bacteria were unique to specific samples. The dominant species was Erythrobacter citreus, followed by Gramella sp. Overall, we found that, in deeper marine sediments (e.g., locality CCS_B), the bacterial alpha diversity decreased while the dominance of several genera increased; moreover, for locality CCS_A, our results suggest that the bacterial diversity could be associated with total organic carbon content. We conclude that physicochemical properties (e.g., organic matter content) create a unique environment and play an important role in shaping bacterial communities and their diversity.
Enhancing Chaos Complexity of a Plasma Model through Power Input with Desirable Random Features
Authors: Natiq Hayder , Kamel Ariffin Muhammad Rezal , Asbullah Muhammad Asyraf , Mahad Zahari , Najah Mohammed
Published: December 2020

The present work introduces an analysis framework to comprehend the dynamics of a 3D plasma model, which has been proposed to describe the pellet injection in tokamaks. The analysis of the system reveals the existence of a complex transition from transient chaos to steady periodic behavior. Additionally, without adding any kind of forcing term or controllers, we demonstrate that the system can be changed to become a multi-stable model by injecting more power input. In this regard, we observe that increasing the power input can fluctuate the numerical solution of the system from coexisting symmetric chaotic attractors to the coexistence of infinitely many quasi-periodic attractors. Besides that, complexity analyses based on Sample entropy are conducted, and they show that boosting power input spreads the trajectory to occupy a larger range in the phase space, thus enhancing the time series to be more complex and random. Therefore, our analysis could be important to further understand the dynamics of such models, and it can demonstrate the possibility of applying this system for generating pseudorandom sequences.
Measure Theoretic Entropy of Discrete Geodesic Flow on Nagao Lattice Quotient
Authors: Kwon Sanghoon
Published: December 2020

The discrete geodesic flow on Nagao lattice quotient of the space of bi-infinite geodesics in regular trees can be viewed as the right diagonal action on the double quotient of PGL2Fq((t−1)) by PGL2Fq[t] and PGL2(Fq[[t−1]]). We investigate the measure-theoretic entropy of the discrete geodesic flow with respect to invariant probability measures.
Expectation-Maximization Algorithm for the Calibration of Complex Simulator Using a Gaussian Process Emulator
Authors: Seo Yun Am , Park Jeong-Soo
Published: December 2020

The approximated non-linear least squares (ALS) tunes or calibrates the computer model by minimizing the squared error between the computer output and real observations by using an emulator such as a Gaussian process (GP) model. A potential defect of the ALS method is that the emulator is constructed once and it is no longer re-built. An iterative method is proposed in this study to address this difficulty. In the proposed method, the tuning parameters of the simulation model are calculated by the conditional expectation (E-step), whereas the GP parameters are updated by the maximum likelihood estimation (M-step). These EM-steps are alternately repeated until convergence by using both computer and experimental data. For comparative purposes, another iterative method (the max-min algorithm) and a likelihood-based method are considered. Five toy models are tested for a comparative analysis of these methods. According to the toy model study, both the variance and bias of the estimates obtained from the proposed EM algorithm are smaller than those from the existing calibration methods. Finally, the application to a nuclear fusion simulator is demonstrated.
Optimal Randomness for Stochastic Configuration Network (SCN) with Heavy-Tailed Distributions
Authors: Niu Haoyu , Wei Jiamin , Chen YangQuan
Published: December 2020

Stochastic Configuration Network (SCN) has a powerful capability for regression and classification analysis. Traditionally, it is quite challenging to correctly determine an appropriate architecture for a neural network so that the trained model can achieve excellent performance for both learning and generalization. Compared with the known randomized learning algorithms for single hidden layer feed-forward neural networks, such as Randomized Radial Basis Function (RBF) Networks and Random Vector Functional-link (RVFL), the SCN randomly assigns the input weights and biases of the hidden nodes in a supervisory mechanism. Since the parameters in the hidden layers are randomly generated in uniform distribution, hypothetically, there is optimal randomness. Heavy-tailed distribution has shown optimal randomness in an unknown environment for finding some targets. Therefore, in this research, the authors used heavy-tailed distributions to randomly initialize weights and biases to see if the new SCN models can achieve better performance than the original SCN. Heavy-tailed distributions, such as Lévy distribution, Cauchy distribution, and Weibull distribution, have been used. Since some mixed distributions show heavy-tailed properties, the mixed Gaussian and Laplace distributions were also studied in this research work. Experimental results showed improved performance for SCN with heavy-tailed distributions. For the regression model, SCN-Lévy, SCN-Mixture, SCN-Cauchy, and SCN-Weibull used less hidden nodes to achieve similar performance with SCN. For the classification model, SCN-Mixture, SCN-Lévy, and SCN-Cauchy have higher test accuracy of 91.5%, 91.7% and 92.4%, respectively. Both are higher than the test accuracy of the original SCN.
Second-Order Phase Transition in Counter-Rotating Taylor–Couette Flow Experiment
Authors: Avila Kerstin , Hof Björn
Published: December 2020

In many basic shear flows, such as pipe, Couette, and channel flow, turbulence does not arise from an instability of the laminar state, and both dynamical states co-exist. With decreasing flow speed (i.e., decreasing Reynolds number) the fraction of fluid in laminar motion increases while turbulence recedes and eventually the entire flow relaminarizes. The first step towards understanding the nature of this transition is to determine if the phase change is of either first or second order. In the former case, the turbulent fraction would drop discontinuously to zero as the Reynolds number decreases while in the latter the process would be continuous. For Couette flow, the flow between two parallel plates, earlier studies suggest a discontinuous scenario. In the present study we realize a Couette flow between two concentric cylinders which allows studies to be carried out in large aspect ratios and for extensive observation times. The presented measurements show that the transition in this circular Couette geometry is continuous suggesting that former studies were limited by finite size effects. A further characterization of this transition, in particular its relation to the directed percolation universality class, requires even larger system sizes than presently available.
A New Extension of Thinning-Based Integer-Valued Autoregressive Models for Count Data
Authors: Liu Zhengwei , Zhu Fukang
Published: December 2020

The thinning operators play an important role in the analysis of integer-valued autoregressive models, and the most widely used is the binomial thinning. Inspired by the theory about extended Pascal triangles, a new thinning operator named extended binomial is introduced, which is a general case of the binomial thinning. Compared to the binomial thinning operator, the extended binomial thinning operator has two parameters and is more flexible in modeling. Based on the proposed operator, a new integer-valued autoregressive model is introduced, which can accurately and flexibly capture the dispersed features of counting time series. Two-step conditional least squares (CLS) estimation is investigated for the innovation-free case and the conditional maximum likelihood estimation is also discussed. We have also obtained the asymptotic property of the two-step CLS estimator. Finally, three overdispersed or underdispersed real data sets are considered to illustrate a superior performance of the proposed model.
Do Agrochemical-Free Paddy Fields Serve as Refuge Habitats for Odonata?
Authors: Huynh Thien , Oyabu Aisha , Nomura Shinya , Takashima Tadao , Usio Nisikawa
Published: December 2020

Agrochemical-free rice farming has attracted interest for restoring paddy field biodiversity and producing safe food. Odonata are commonly used as a biodiversity indicator in these low-input farms. However, the effect of agrochemical-free rice farming on odonate diversity has rarely been assessed over the entire emergence period of these insects. We investigated whether different farming practices, such as conventional or natural (agrochemical-and fertilizer-free) cultivation, and associated water management strategies affect the emergence rates of Odonata in paddy field landscapes in central Japan. Weekly exuviae sampling in 2017 and 2019 suggested that odonate assemblages differed between conventional and natural paddy fields, with a higher number of taxa emerging from natural paddy fields. Contrary to expectations, conventional paddy fields had equivalent or higher emergence rates of all Odonata and two numerically dominant Sympetrum species. Peak emergence periods for numerically dominant taxa differed between the farming types, with the emergence of three Sympetrum species peaking in late June in conventional paddy fields and that of S. frequens peaking in early to mid-July in natural paddy fields. Our findings suggest that both conventional and natural paddy fields are important habitats for Odonata in Japan.
Research on the Possible Application of Polyolefin Waste-Derived Pyrolysis Oils for ANFO Manufacturing
Authors: Biessikirski Andrzej , Czerwonka Dominik , Biegańska Jolanta , Kuterasiński Łukasz , Ziąbka Magdalena , Dworzak Michał , Twardosz Michał
Published: December 2020

This work aims to evaluate the possible application of pyrolysis fuel oils obtained through the pyrolysis of waste plastics. by comparing both the blasting properties and morphology results of Ammonium Nitrate Fuel Oil (ANFO), which is applied in the mining industry, and ANFO based on pyrolysis fuel oils (FOs), as well as low-temperature properties of all tested FO samples. The low-temperature research includes the measurements of density, kinematic viscosity, flash point, pour point, and cloud point. Moreover, a stability analysis was carried out based on the Turbiscan Stability Index (TSI) coefficient. Based on the obtained results it was concluded that despite pyrolysis FOs showing some differences in comparison with index FO, none of their properties indicated that pyrolysis FOs should be excluded from possible application in ANFO. Additionally, IR, XRD, and SEM analyses were conducted for all ANFO samples. The instrumental analysis did not show any dribbling effect. The blasting tests such as velocity of detonation (VOD), the heat of explosion, and post-blast fumes revealed that VOD values were lower in comparison to the reference ANFO sample. However, the observed differences were either negligible (heat of explosion) or small enough (VOD) to conclude that polyolefin waste-derived pyrolysis fuel oils can be applied as ANFO’s fuel component.
Hybrid Tuning of a Boost Converter PI Voltage Compensator by Means of the Genetic Algorithm and the D-Decomposition
Authors: Nalepa Radosław , Najdek Karol , Strong Błażej
Published: December 2020

In this paper the D-decomposition technique is investigated as a source of non-linear boundaries used with the Genetic Algorithm (GA) search of a PI voltage compensator gains of the boost converter operating in Continuous Conduction Mode (CCM). The well known and appreciated boost converter has been chosen as a test object due to its right-half plane zero in the control-to-output (c2o) voltage transfer function. The D-decomposition, as a technique relying on the frequency sweeping, clearly indicates not only the global stability but, in its extended version, regions satisfying the required gain (GM) and phase (PM) margins. Such results are in form of easy to interpret functions KI=f(KP). The functions are easy to convert to the GA constraints. The GA search, with three different performance indexes as the fitness functions, is applied to a control structure with time delays basing on identified c2o voltage transfer functions. The identification took place in an experiment and in simulation. Outcomes of the identification are compared to mathematically derived formula taking into account certain parasitics. A complete set of practically useful mathematical formulas together with their validation in simulation and experiment is included.
Thermal Systems—An Overview
Authors: Tam Ivan CK , Agnew Brian
Published: December 2020

We live in interesting times in which life as we know it is being threatened by human-made changes to the atmosphere we live [...]
Vanadium Redox Flow Batteries: A Review Oriented to Fluid-Dynamic Optimization
Authors: Aramendia Iñigo , Fernandez-Gamiz Unai , Martinez-San-Vicente Adrian , Zulueta Ekaitz , Lopez-Guede Jose Manuel
Published: December 2020

Large-scale energy storage systems (ESS) are nowadays growing in popularity due to the increase in the energy production by renewable energy sources, which in general have a random intermittent nature. Currently, several redox flow batteries have been presented as an alternative of the classical ESS; the scalability, design flexibility and long life cycle of the vanadium redox flow battery (VRFB) have made it to stand out. In a VRFB cell, which consists of two electrodes and an ion exchange membrane, the electrolyte flows through the electrodes where the electrochemical reactions take place. Computational Fluid Dynamics (CFD) simulations are a very powerful tool to develop feasible numerical models to enhance the performance and lifetime of VRFBs. This review aims to present and discuss the numerical models developed in this field and, particularly, to analyze different types of flow fields and patterns that can be found in the literature. The numerical studies presented in this review are a helpful tool to evaluate several key parameters important to optimize the energy systems based on redox flow technologies.
Experimental Determination of the Heat Transfer Coefficient of Real Cooled Geometry Using Linear Regression Method
Authors: Ali Asif , Cocchi Lorenzo , Picchi Alessio , Facchini Bruno
Published: December 2020

The scope of this work was to develop a technique based on the regression method and apply it on a real cooled geometry for measuring its internal heat transfer distribution. The proposed methodology is based upon an already available literature approach. For implementation of the methodology, the geometry is initially heated to a known steady temperature, followed by thermal transient, induced by injection of ambient air to its internal cooling system. During the thermal transient, external surface temperature of the geometry is recorded with the help of infrared camera. Then, a numerical procedure based upon a series of transient finite element analyses of the geometry is applied by using the obtained experimental data. The total test duration is divided into time steps, during which the heat flux on the internal surface is iteratively updated to target the measured external surface temperature. The final procured heat flux and internal surface temperature data of each time step is used to find the convective heat transfer coefficient via linear regression. This methodology is successfully implemented on three geometries: a circular duct, a blade with U-bend internal channel, and a cooled high pressure vane of real engine, with the help of a test rig developed at the University of Florence, Italy. The results are compared with the ones retrieved with similar approach available in the open literature, and the pros and cons of both methodologies are discussed in detail for each geometry.
Numerical Study on Sectional Loads and Structural Optimization of an Elastic Semi-Submersible Floating Platform
Authors: Liu Yuliang , Ishihara Takeshi
Published: December 2020

This study investigates the sectional loads on an elastic semi-submersible platform for a 2 MW FOWT (floating offshore wind turbine) used in the Fukushima demonstration project. A water tank test is firstly carried out with an elastic model to study the dynamic responses and sectional loads of the platform in regular and irregular waves. Numerical simulations are then performed using multiple hydrodynamic bodies connected by elastic beams. The dynamic responses of the elastic model are compared to those of a rigid model to clarify the influence of the structural stiffness on the platform motion and mooring tension. The predicted sectional loads on the deck, brace and pontoon by the proposed nonlinear hydrodynamic models show good agreement with the experimental data obtained from the water tank test and a simplified formula is proposed to evaluate the distribution of the moments on the platform. Finally, the structural optimization of the elastic semi-submersible platform is conducted. The sectional moments and fatigue loadings on the pontoons are significantly reduced using the strut between the pontoons since the horizontal wave loads on the side column are dominant and the vertical wave loads acting on the platform are relatively small due to the deep draft.
Hybrid Pine (Pinus attenuata × Pinus radiata) Somatic Embryogenesis: What Do You Prefer, Mother or Nurse?
Authors: Montalbán Itziar A. , Castander-Olarieta Ander , Hargreaves Cathy L. , Gough Keiko , Reeves Cathie B. , van Ballekom Shaf , Goicoa Tomás , Ugarte María Dolores , Moncaleán Paloma
Published: December 2020

Development of hybrid pines of Pinus radiata D. Don for commercial forestry presents an opportunity to diversify the current resource of plant material. Climate change and different land uses pose challenges, making alternative species necessary to guarantee wood and non-wood products in the future. Pinus radiata var. cedrosensis × Pinus attenuata hybrid possesses different attributes, such as tolerance to drought conditions, better growth and resistance to snow damage at higher altitudes, and more importantly, different wood quality characteristics. Embryogenic cell lines were successfully initiated reciprocal hybrids using as initial explants megagametophytes, excised zygotic embryos and excised zygotic embryos plus nurse culture. However, the questions raised were: does the initiation environment affect the conversion to somatic plantlets months later? Does the mother tree or the cross have an effect on the conversion to somatic plantlets? In the present work we analysed the maturation rate, number of somatic embryos, germination rate, and the ex-vitro growth in cell lines derived from different initiation treatments, mother tree species, and crosses. Differences were not observed for in vitro parameters such as maturation and germination. However, significant differences were observed due to the mother tree species in relation with the ex-vitro growth rates observed, being higher those in which P. radiata acted as a mother. Moreover, embryogenic cell lines from these hybrids were stored at −80 °C and regenerated after one and five years.
Numerical Investigation of Two-Phase Flows in Corrugated Channel with Single and Multiples Drops
Authors: Anjos Gustavo R.
Published: December 2020

This work aims at investigating numerically the effects of channel corrugation in two-phase flows with single and multiples drops subject to buoyancy-driven motion. A state-of-the-art model is employed to accurately compute the dynamics of the drop’s interface deformation using a modern moving frame/moving mesh technique within the arbitrary Lagrangian–Eulerian framework, which allows one to simulate very large domains. The results reveal a complex and interesting dynamics when more than one drop is present in the system, leading eventually in coalescence due to the amplitude of the corrugated sinusoidal channel and distance between drops.
Analysis and Modelling of the Commutation Error
Authors: Klein Markus , Germano Massimo
Published: December 2020

A multiscale dynamic analysis of the commutation error, based on the filtering approach is performed. The similarity multiscale hypothesis proposed by Bardina (1983) and extended by Geurts and Holm (2006) to the commutation error is examined in detail and an extension of the Germano identity to the analysis and the modelling of the commutation error is proposed. For a detailed analysis under controlled condition the method is first applied to synthetic turbulence and subsequently to the a-priori analysis of a turbulent channel flow at Reτ=590. The results illustrate the flexibility of the dynamic modelling approach. Combined with a scale similarity assumption for the commutation error very satisfactory results have been obtained for first order derivatives and reasonable results for second order derivatives. In all cases the modelling of the commutation error resulted in smaller errors than the error obtained by neglecting the commutation error.
New Horizons in Hydrogels for Methotrexate Delivery
Authors: Dehshahri Ali , Kumar Anuj , Madamsetty Vijay Sagar , Uzieliene Ilona , Tavakol Shima , Azedi Fereshteh , Fekri Hojjat Samareh , Zarrabi Ali , Mohammadinejad Reza , Thakur Vijay Kumar
Published: December 2020

Since its first clinical application, methotrexate (MTX) has been widely used for the treatment of human diseases. Despite great advantages, some properties such as poor absorption, short plasma half-life and unpredictable bioavailability have led researchers to seek novel delivery systems to improve its characteristics for parenteral and oral administration. Recently, great attention has been directed to hydrogels for the preparation of MTX formulations. This review describes the potential of hydrogels for the formulation of MTX to treat cancer, rheumatoid arthritis, psoriasis and central nervous system diseases. We will delineate the state-of-the-art and promising potential of hydrogels for systemic MTX delivery as well as transdermal delivery of the drug-using hydrogel-based formulations.
A Constitutive Model for Alginate-Based Double Network Hydrogels Cross-Linked by Mono-, Di-, and Trivalent Cations
Authors: Külcü İsmail Doğan
Published: December 2020

In this contribution, a micro-mechanically based constitutive model is proposed to describe the nonlinear inelastic rubber-like features of alginate-based double network hydrogel cross-linked via various counterions. To this end, the lengthening of the polysaccharide polymer chain after a fully stretched state is characterized. A polymer chain is firstly considered behaving entropically up to the fully stretched state. Then, enthalpic behavior is accounted for concerning the following lengthening. To calculate enthalpic behavior, the macroscopic material properties, such as elastic modulus, are integrated into the proposed model. Thus, a new energy concept for a polymer chain is proposed. The model is constituted by the proposed energy concept, the network decomposition model, the Arruda–Boyce eight chain model and the network alteration theory. The model is compared against the cyclic tensile test data of alginate-based double network hydrogels cross-linked via mono-, di-, and trivalent cations. Good agreement between the model and experiments is obtained.
Re-Evaluating the Internal Phylogenetic Relationships of Collembola by Means of Mitogenome Data
Authors: Cucini Claudio , Fanciulli Pietro P. , Frati Francesco , Convey Peter , Nardi Francesco , Carapelli Antonio
Published: December 2020

Collembola are an ancient and early diverging lineage of basal hexapods that occur in virtually all terrestrial habitats on Earth. Phylogenetic relationships between the different orders of Collembola are fiercely debated. Despite a range of studies and the application of both morphological and genetic approaches (singly or in combination) to assess the evolutionary relationships of major lineages in the group, no consensus has been reached. Several mitogenome sequences have been published for key taxa of the class (and their number is increasing rapidly). Here, we describe two new Antarctic Collembola mitogenomes and compare all complete or semi-complete springtail mitogenome sequences available on GenBank in terms of both gene order and DNA sequence analyses in a genome evolution and molecular phylogenetic framework. With minor exceptions, we confirm the monophyly of Poduromorpha and Symphypleona sensu stricto (the latter placed at the most basal position in the springtail phylogenetic tree), whereas monophyly of Neelipleona and Entomobryomorpha is only supported when a handful of critical taxa in these two lineages are excluded. Finally, we review gene order models observed in the class, as well as the overall mitochondrial nucleotide composition.
MiR-146a Regulates Migration and Invasion by Targeting NRP2 in Circulating-Tumor Cell Mimicking Suspension Cells
Authors: Do Yeojin , Cho Jin Gu , Park Ji Young , Oh Sumin , Park Doyeon , Yoo Kyung Hyun , Lee Myeong-Sok , Kwon Byung Su , Kim Jongmin , Yang Young
Published: December 2020

Cancer metastasis is the primary cause of cancer-related death and metastatic cancer has circulating-tumor cells (CTCs), which circulate in the bloodstream before invading other organs. Thus, understanding the precise role of CTCs may provide new insights into the metastasis process and reduce cancer mortality. However, the molecular characteristics of CTCs are not well understood due to a lack of number of CTCs. Therefore, suspension cells were generated from MDA-MB-468 cells to mimic CTCs, and we investigate the microRNA (miRNA)-dependent molecular networks and their role in suspension cells. Here, we present an integrated analysis of mRNA and miRNA sequencing data for suspension cell lines, through comparison with adherent cells. Among the differentially regulated miRNA–mRNAs axes, we focus on the miR-146a-Neuropilin2 (NRP2) axis, which is known to influence tumor aggressiveness. We show that miR-146a directly regulates NRP2 expression and inhibits Semaphorin3C (SEMA3C) signaling. Functional studies reveal that miR-146a represses SEMA3C-induced invasion and proliferation by targeting NRP2. Finally, high-NRP2 is shown to be associated with poor outcomes in breast cancer patients. This study identifies the key role of the miR-146a–NRP2 signaling axis that is critical for the regulation of migration and invasion in CTC-mimicking cells.
DIANA-mAP: Analyzing miRNA from Raw NGS Data to Quantification
Authors: Alexiou Athanasios , Zisis Dimitrios , Kavakiotis Ioannis , Miliotis Marios , Koussounadis Antonis , Karagkouni Dimitra , Hatzigeorgiou Artemis G.
Published: December 2020

microRNAs (miRNAs) are small non-coding RNAs (~22 nts) that are considered central post-transcriptional regulators of gene expression and key components in many pathological conditions. Next-Generation Sequencing (NGS) technologies have led to inexpensive, massive data production, revolutionizing every research aspect in the fields of biology and medicine. Particularly, small RNA-Seq (sRNA-Seq) enables small non-coding RNA quantification on a high-throughput scale, providing a closer look into the expression profiles of these crucial regulators within the cell. Here, we present DIANA-microRNA-Analysis-Pipeline (DIANA-mAP), a fully automated computational pipeline that allows the user to perform miRNA NGS data analysis from raw sRNA-Seq libraries to quantification and Differential Expression Analysis in an easy, scalable, efficient, and intuitive way. Emphasis has been given to data pre-processing, an early, critical step in the analysis for the robustness of the final results and conclusions. Through modularity, parallelizability and customization, DIANA-mAP produces high quality expression results, reports and graphs for downstream data mining and statistical analysis. In an extended evaluation, the tool outperforms similar tools providing pre-processing without any adapter knowledge. Closing, DIANA-mAP is a freely available tool. It is available dockerized with no dependency installations or standalone, accompanied by an installation manual through Github.
From the Outside to the Inside: New Insights on the Main Factors That Guide Seed Dormancy and Germination
Authors: Longo Chiara , Holness Soyanni , De Angelis Veronica , Lepri Andrea , Occhigrossi Sara , Ruta Veronica , Vittorioso Paola
Published: December 2020

The transition from a dormant to a germinating seed represents a crucial developmental switch in the life cycle of a plant. Subsequent transition from a germinating seed to an autotrophic organism also requires a robust and multi-layered control. Seed germination and seedling growth are multistep processes, involving both internal and external signals, which lead to a fine-tuning control network. In recent years, numerous studies have contributed to elucidate the molecular mechanisms underlying these processes: from light signaling and light-hormone crosstalk to the effects of abiotic stresses, from epigenetic regulation to translational control. However, there are still many open questions and molecular elements to be identified. This review will focus on the different aspects of the molecular control of seed dormancy and germination, pointing out new molecular elements and how these integrate in the signaling pathways already known.
Progressive External Ophthalmoplegia in Polish Patients—From Clinical Evaluation to Genetic Confirmation
Authors: Kierdaszuk Biruta , Kaliszewska Magdalena , Rusecka Joanna , Kosińska Joanna , Bartnik Ewa , Tońska Katarzyna , Kamińska Anna M. , Kostera-Pruszczyk Anna
Published: December 2020

Mitochondrial encephalomyopathies comprise a group of heterogeneous disorders resulting from impaired oxidative phosphorylation (OxPhos). Among a variety of symptoms progressive external ophthalmoplegia (PEO) seems to be the most common. The aim of this study is to present clinical and genetic characteristics of Polish patients with PEO. Clinical, electrophysiological, neuroradiological, and morphological data of 84 patients were analyzed. Genetic studies of mitochondrial DNA (mtDNA) were performed in all patients. Among nuclear DNA (nDNA) genes POLG was sequenced in 41 patients, TWNK (C10orf2) in 13 patients, and RNASEH1 in 2 patients. Total of 27 patients were included in the chronic progressive external ophthalmoplegia (CPEO) group, 24 in the CPEO+ group. Twenty-six patients had mitochondrial encephalomyopathy (ME), six patients Kearns–Sayre syndrome (KSS), and one patient sensory ataxic neuropathy, dysarthria, ophthalmoparesis (SANDO) syndrome. Genetic analysis of nDNA genes revealed the presence of pathogenic or possibly pathogenic variants in the POLG gene in nine patients, the TWNK gene in five patients and the RNASEH1 gene in two patients. Detailed patients’ history and careful assessment of family history are essential in the diagnostic work-up. Genetic studies of both mtDNA and nDNA are necessary for the final diagnosis of progressive external ophthalmoplegia and for genetic counseling.
Comparative Transcriptome Profiling of Ovary Tissue between Black Muscovy Duck and White Muscovy Duck with High- and Low-Egg Production
Authors: Bao Xiuyu , Song Yiping , Li Tao , Zhang Shanshan , Huang Lihua , Zhang Shuya , Cao Junting , Liu Xiaolin , Zhang Jianqin
Published: December 2020

The egg-laying rate is an important indicator for evaluating fertility of poultry. In order to better understand the laying mechanism of Muscovy ducks, gene expression profiles and pathways of ovarian tissues in high- and low-laying black (BH and BL) and white Muscovy ducks (WH and WL) during the peak production period were performed by using RNA-seq. The total number of reads produced for each ovarian sample ranged from 44,344,070 to 47,963,328. A total of 113, 619 and 87 differentially expressed genes (DEGs) were identified in BH-vs-WH, BL-vs-BH and BL-vs-WL, respectively. Among them, 54, 356 and 49 genes were up regulated and 59, 263 and 38 genes were down regulated. In addition, there were only 10 up-regulated genes in WL-vs-WH. In the comparison of DEGs in black and white Muscovy ducks, two co-expressed DEG genes were detected between BH-vs-WH and BL-vs-WL and seven DEGs were co-expressed between BL-vs-BH and WL-vs-WH. The RNA-Seq data were confirmed to be reliable by qPCR. Numerous DEGs known to be involved in ovarian development were identified, including TGFβ2, NGFR, CEBPD, CPEB2, POSTN, SMOC1, FGF18, EFNA5 and SDC4. Gene Ontology (GO) annotations indicated that DEGs related to ovarian development were mainly enriched in biological processes of “circadian sleep/wake cycle process,” “negative regulation of transforming growth factor-β secretion,” “positive regulation of calcium ion transport” in BH-vs-WH and “cell surface receptor signaling pathway,” “Notch signaling pathway” and “calcium ion transport” in BL-vs-BH. Besides, “steroid biosynthetic process,” “granulosa cell development” and “egg coat formation” were mainly enriched in BL-vs-WL and “reproduction,” “MAPK cascade” and “mitotic cell cycle” were mainly enriched in WL-vs-WH. KEGG pathway analysis showed that the PI3K-Akt signaling pathway and ovarian steroidogenesis were the most enriched in Muscovy duck ovary transcriptome data. This work highlights potential genes and pathways that may affect ovarian development in Muscovy duck.
The Relationship between Adverse Childhood Experiences and Sleep Problems among Adolescent Students: Mediation by Depression or Anxiety
Authors: Park E-Jin , Kim Shin-Young , Kim Yeeun , Sung Dajung , Kim Bora , Hyun Yerin , Jung Kyu-In , Lee Seung-Yup , Kim Hayeon , Park Subin , Kim Bung-Nyun , Park Min-Hyeon
Published: December 2020

Adverse childhood experiences (ACEs) are known to be closely related to depression, anxiety and sleep problems. However, it remains unclear whether adolescents with ACEs have sleep problems regardless of depression or anxiety or under a mediating effect from depression or anxiety. Therefore, our aim was to examine whether depression or anxiety mediates the relationship between ACEs and sleep problems in adolescents by using a community sample. The Early Trauma Inventory Self Report–Short Form (ETISR-SF) and List of Threatening Experiences Questionnaire (LTE-Q) were used to assess traumatic ACEs. Ultimately, data from 737 students (M = 448, F = 289, 15.1 ± 1.4 years old) were included in the statistical analysis. A total of 576 (78.1%) participants reported that they had experienced one or more ACEs. Adolescents with ACEs had higher levels of depression, anxiety and sleep problems than did adolescents without ACEs, and boys tended to experience more trauma than girls. Depression and anxiety partially mediated the relationship between ACEs and sleep problems. The results of this study suggest the need for depression and anxiety interventions for adolescents with ACEs to reduce the long-term consequences, including sleep problems and physical health problems.
Influence of Public Oral Health Services and Socioeconomic Indicators on the Frequency of Hospitalization and Deaths due to Oral Cancer in Brazil, between 2002–2017
Authors: Freire Aldelany R. , Freire Deborah E. W. G. , Araújo Elza C. F. de , de Lucena Edson H. G. , Cavalcanti Yuri W.
Published: December 2020

Background: Oral cancer is a frequent neoplasm worldwide, and socioeconomic factors and access to health services may be associated with its risk. Aim: To analyze effect of socioeconomic variables and the influence of public oral health services availability on the frequency of new hospitalized cases and mortality of oral cancer in Brazil. Materials and Methods: This observational study analyzed all Brazilian cities with at least one hospitalized case of oral cancer in the National Cancer Institute database (2002–2017). For each city were collected: population size, Municipal Human Development Index (MHDI), Gini Coefficient, oral health coverage in primary care, number of Dental Specialized Centers (DSC) and absolute frequency of deaths after one year of the first treatment. The risk ratio was determined by COX regression, and the effect of the predictor variables on the incidence of cases was verified by the Hazard Ratio measure. Poisson regression was used to determine factors associated with higher mortality frequency. Results: Cities above 50,000 inhabitants, with high or very high MHDI, more unequal (Gini > 0.4), with less oral health coverage in primary care (<50%) and without DSC had a greater accumulated risk of having 1 or more cases (p < 0.001). Higher frequency of deaths was also associated with higher population size, higher MHDI, higher Gini and lower oral health coverage in primary care (p < 0.001). Conclusions: The number hospitalization and deaths due to oral cancer in Brazil was influenced by the cities’ population size, the population’s socioeconomic status and the availability of public dental services.