bluuebunny/crossref_metadata_2025_split huggingface dataset:
On the Application of OpenFOAM® in Gravity Water Wave Generation and Wave-Structure Interaction
Authors: Chen Hao 
Published: February 2019

This article presents an investigation on the best practice for modeling of water wave generation and wave-structure interaction using a widely spread two-phase flow solver with a specific interface compression technique in OpenFOAM® (OpenFOAM Foundation Ltd., London, United Kingdom). A series of numerical experiments were conducted to examine the effects of the employed schemes, mesh resolution, time step resolution, and compression coefficient. Both surface elevation and velocity profile were considered as the criteria for assessment of the quality of the generated waves. The numerical experiments showed that by using a blending scheme between the Crank-Nicolson and Euler scheme, relatively high quality waves were produced, where the spurious current at the interface region was effectively reduced. Meanwhile, it was also recommended to apply a compression coefficient Cα = 1, the Courant number limit Co = .1, and a mesh resolution of 18 cells per wave height. This set of parameters was used to validate the numerical model for two sets of cases for wave forces on half-immersed horizontal cylinders. The results in general agreed well with the experimental data, although the inline forces were slightly but consistently overestimated.

1. Introduction
In the past few decades, because of the increase in the computing ability and resources, computational fluid dynamic (CFD) approach has been gaining popularity in the naval hydrodynamic communities. Considering that a large portion of naval hydrodynamic problems are concerned with the free-surface flows, e.g., ocean waves and its interaction with structures, a free-surface model is needed to couple with the Navier-Stokes solver. Eventually, as a result of direct application of the first principles, the solver can model both inertia and viscous dominant flows. Even local wave breaking and violent flows can be properly resolved.
Different methods have been proposed to track the interface of free-surface flows. This includes height function method and line segment method, which are the simplest techniques to represent and configure a free surface. However, they have deficiencies when two surfaces intersect or when a surface folds over on itself, which are overcome by the marker and cell method proposed in Harlow and Welch (1965). In their method, massless particles are used to track the free surface in a Lagrangian manner. Alternatively, the level-set (LS) method or volume of fluid (VOF) method can be used to implicitly capture the surface in an Eulerian way. The LS method was introduced in Osher (1988) where the interface is defined as the one on which a level-set function is equal to zero. This LS function is continuous across the interface. Therefore, it is not significantly influenced by the numerical diffusion. However, the originally proposed LS method suffers from mass conservation problems, which has been resolved in, e.g., Olsson and Kreiss (2005) and Olsson et al. (2007).
Barrier Loci and Evolution
Authors: Elmer Kathryn R 
Published: February 2019

Abstract

The evolution and maintenance of new species is a major question in evolutionary biology. During speciation, the genomes of individuals in the splitting populations do not diverge at an equal rate: some parts diverge more quickly while other parts remain more similar. The organisation of genetic diversity and differentiation in the genome is important to how speciation happens and reflective of speciation processes. Barrier loci are parts of the genome that contribute to a restriction of gene flow at that genomic region and are most diverged between young species. The size and distribution of barrier loci is influenced by evolutionary processes such as demography, selection, and gene flow, and by properties of the genome such as mutation rate, gene density, and recombination. Speciation research is in an exciting new era of identifying barrier loci and their distribution in the genome and testing what they reveal about the processes of evolution.

Key Concepts

As populations become more different with divergence and speciation, the rate and pattern at which genetic differences accumulate are not the same across the genome.

Barrier loci are those loci that resist homogenisation with the other genome when gene flow occurs between diverging species, and consequently, they are the most different parts of the genome between divergent populations.

Genomic divergence is affected by many properties of the genome and of the species being studied, and therefore the process of divergence and the effects on barrier loci are complex and variable.

Barrier loci form due to a reduction in gene flow at particular genomic regions. Therefore, they are a function of both population factors (demography, time since divergence, and strength and target of selection) and properties of the genome (recombination rate, mutation rate, gene density, and the organisation of relevant loci).

Barrier loci are inferred with genome‐wide molecular methods and analytical tools.

Barrier loci give important insights into the genetic basis of species differences and the process and rates of speciation.
Eukaryotic and Bacterial Antimicrobial Peptides
Authors: Thomas Benjamin J 
Published: February 2019

Abstract

Antimicrobial peptides (AMPs) form part of the innate immune response found among all classes of life. The term AMPs also encompasses bacteriocins (bacterial AMPs), antimicrobial compounds that bacteria use to gain a competitive advantage against closely related species. AMPs target a wide spectrum of target organisms ranging from bacteria, fungi and viruses to cancer cells and parasites and many are potent antibiotics, which demonstrate potential as novel therapeutic agents. AMPs are characterised by their secondary structural form and have specific biochemical properties conferred by the amino acids that form them that define their bioactivity. Many AMPs destabilise biological membranes by forming transmembrane channels, and some also have the ability to enhance immunity by functioning as immunomodulators.

Key Concepts

AMPs can be ribosomally or nonribosomally synthesised, and they have a wide range of bioactive functions including antibacterial, antiviral and antifungal activity.

Bacterial AMPs (bacteriocins) are produced by bacteria to leverage a competitive advantage in microbiomes and each has a narrow target spectrum of closely related species.

Eukaryotic AMPs have a broader target profile and are part of the innate immune response found among all classes of multi‐celled life.

The bioactive functions of AMPs are conferred by a series of characteristics which may include structure, sequence, amphipathy, hydrophobicity and solubility.

Many AMPs are membrane‐acting and affect bacterial membranes to induce cell lysis.

The role of AMPs as potent, broad‐spectrum antibiotics means they have potential as novel therapeutic agents.
3D Printing of a Thermo‐ and Solvatochromic Composite Material Based on a Cu(II)–Thymine Coordination Polymer with Moisture Sensing Capabilities
Authors: Maldonado Noelia , Vegas Verónica G. , Halevi Oded , Martínez Jose Ignacio , Lee Pooi See , Magdassi Shlomo , Wharmby Michael T. , Platero‐Prats Ana E. , Moreno Consuelo , Zamora Félix , Amo‐Ochoa Pilar 
Published: February 2019

AbstractThis work presents the fabrication of 3D‐printed composite objects based on copper(II) 1D coordination polymer (CP1) decorated with thymine along its chains with potential utility as an environmental humidity sensor and as a water sensor in organic solvents. This new composite object has a remarkable sensitivity, ranging from 0.3% to 4% of water in organic solvents. The sensing capacity is related to the structural transformation due to the loss of water molecules that CP1 undergoes with temperature or by solvent molecules' competition, which induces significant change in color simultaneously. The CP1 and 3D printed materials are stable in air over 1 year and also at biological pHs (5–7), therefore suggesting potential applications as robust colorimetric sensors. These results open the door to generate a family of new 3D printed materials based on the integration of multifunctional coordination polymers with organic polymers.
From Single‐Dimensional to Multidimensional Manipulation of Optical Waves with Metasurfaces
Authors: Chen Shuqi , Li Zhancheng , Liu Wenwei , Cheng Hua , Tian Jianguo 
Published: February 2019

AbstractMetasurfaces, 2D artificial arrays of subwavelength elements, have attracted great interest from the optical scientific community in recent years because they provide versatile possibilities for the manipulation of optical waves and promise an effective way for miniaturization and integration of optical devices. In the past decade, the main efforts were focused on the realization of single‐dimensional (amplitude, frequency, polarization, or phase) manipulation of optical waves. Compared to the metasurfaces with single‐dimensional manipulation, metasurfaces with multidimensional manipulation of optical waves show significant advantages in many practical application areas, such as optical holograms, sub‐diffraction imaging, and the design of integrated multifunctional optical devices. Nowadays, with the rapid development of nanofabrication techniques, the research of metasurfaces has been inevitably developed from single‐dimensional manipulation toward multidimensional manipulation of optical waves, which greatly boosts the application of metasurfaces and further paves the way for arbitrary design of optical devices. Herein, the recent advances in metasurfaces are briefly reviewed and classified from the viewpoint of different dimensional manipulations of optical waves. Single‐dimensional manipulation and 2D manipulation of optical waves with metasurfaces are discussed systematically. In conclusion, an outlook and perspectives on the challenges and future prospects in these rapidly growing research areas are provided.
Grow with the Flow: When Morphogenesis Meets Microfluidics
Authors: Samal Pinak , van Blitterswijk Clemens , Truckenmüller Roman , Giselbrecht Stefan 
Published: February 2019

AbstractDevelopmental biology has advanced the understanding of the intricate and dynamic processes involved in the formation of an organism from a single cell. However, many gaps remain in the knowledge of embryonic development, especially regarding tissue morphogenesis. A possible approach to mimic such phenomena uses pluripotent stem cells in in vitro morphogenetic models. Herein, these systems are summarized with emphasis on the ability to better manipulate and control cellular interfaces with either liquid or solid materials using microengineered tools, which is critical for attaining deeper insights into pattern formation and stem cell differentiation during organogenesis. The role of conventional and customized cell‐culture systems in supporting important advances in the field of morphogenesis is discussed, and the fascinating role that material sciences and microengineering currently play and are expected to play in the future is highlighted. In conclusion, it is proffered that continued microfluidics innovations when applied to morphogenesis promise to provide important insights to advance many multidisciplinary fields, including regenerative medicine.
From DNA Nanotechnology to Material Systems Engineering
Authors: Hu Yong , Niemeyer Christof M. 
Published: February 2019

AbstractIn the past 35 years, DNA nanotechnology has grown to a highly innovative and vibrant field of research at the interface of chemistry, materials science, biotechnology, and nanotechnology. Herein, a short summary of the state of research in various subdisciplines of DNA nanotechnology, ranging from pure “structural DNA nanotechnology” over protein–DNA assemblies, nanoparticle‐based DNA materials, and DNA polymers to DNA surface technology is given. The survey shows that these subdisciplines are growing ever closer together and suggests that this integration is essential in order to initiate the next phase of development. With the increasing implementation of machine‐based approaches in microfluidics, robotics, and data‐driven science, DNA‐material systems will emerge that could be suitable for applications in sensor technology, photonics, as interfaces between technical systems and living organisms, or for biomimetic fabrication processes.
An NIR‐Fluorophore‐Based Inhibitor of SOD1 Induces Apoptosis by Targeting Transcription Cofactor PC4
Authors: Luo Peng , Tan Xu , Luo Shenglin , Wang Ziwen , Long Lei , Wang Yawei , Liao Fengying , Chen Long , Zhang Chi , He Jintao , Huang Yinghui , Liu Zujuan , Gan Yibo , Chen Zelin , Wang Yang , Liu Yunsheng , Wang Yu , Shi Chunmeng 
Published: February 2019

AbstractColorectal cancer (CRC) is one of the leading causes of cancer‐related death worldwide. Development of novel therapies has focused on new oncogenes and few tumor‐targeted theranostic agents. Recent studies show that the increased oxidative stress that results from abnormal metabolism makes cancer cells more dependent on antioxidant systems, indicating a proper therapeutic target. As a major antioxidant enzyme, superoxide dismutase 1 (SOD1) is overexpressed in cancer cells and closely related to carcinogenesis and therapeutic effects. However, there is still a lack of tumor‐targeted agents to effectively inhibit the expression of SOD1. Here, a novel near‐infrared heptamethine cyanine dye, IR‐37, is designed, synthesized, and screened that preferentially accumulates in tumor cells with an intrinsic structure‐inherent targeting property, significantly inhibits the expression of SOD1 and induces excessive reactive oxygen species (ROS)‐mediated apoptosis. IR‐37 also has excellent optical properties, implying its potential application in tumor‐targeted imaging. Moreover, a novel CRC‐related oncogene, positive cofactor 4 (PC4), is identified that is involved in the killing effects of IR‐37 through the SOD1‐ROS‐c‐Jun N‐terminal kinase (JNK) pathway. Together, these findings suggest that IR‐37 may be a promising theranostic agent for personalized tumor‐targeted therapy and imaging, and that PC4 is a novel oncogene for the diagnosis and therapy of CRC.
Infrared Light Management Using a Nanocrystalline Silicon Oxide Interlayer in Monolithic Perovskite/Silicon Heterojunction Tandem Solar Cells with Efficiency above 25%
Authors: Mazzarella Luana , Lin Yen‐Hung , Kirner Simon , Morales‐Vilches Anna B. , Korte Lars , Albrecht Steve , Crossland Ed , Stannowski Bernd , Case Chris , Snaith Henry J. , Schlatmann Rutger 
Published: February 2019

AbstractPerovskite/silicon tandem solar cells are attractive for their potential for boosting cell efficiency beyond the crystalline silicon (Si) single‐junction limit. However, the relatively large optical refractive index of Si, in comparison to that of transparent conducting oxides and perovskite absorber layers, results in significant reflection losses at the internal junction between the cells in monolithic (two‐terminal) devices. Therefore, light management is crucial to improve photocurrent absorption in the Si bottom cell. Here it is shown that the infrared reflection losses in tandem cells processed on a flat silicon substrate can be significantly reduced by using an optical interlayer consisting of nanocrystalline silicon oxide. It is demonstrated that 110 nm thick interlayers with a refractive index of 2.6 (at 800 nm) result in 1.4 mA cm−² current gain in the silicon bottom cell. Under AM1.5G irradiation, the champion 1 cm2 perovskite/silicon monolithic tandem cell exhibits a top cell + bottom cell total current density of 38.7 mA cm−2 and a certified stabilized power conversion efficiency of 25.2%.
Non‐native insects dominate daytime pollination in a high‐elevation Hawaiian dryland ecosystem
Authors: Aslan Clare E. , Shiels Aaron B. , Haines William , Liang Christina T. 
Published: February 2019

Premise of the StudyOver one‐third of the native flowering plant species in the Hawaiian Islands are listed as federally threatened or endangered. Lack of sufficient pollination could contribute to reductions in populations, reproduction, and genetic diversity among these species but has been little studied.MethodsWe used systematic observations and manual flower treatments to quantify flower visitation and outcrossing dependency of eight native (including four endangered) plant species in a dryland ecosystem in Hawaii: Argemone glauca, Bidens menziesii, Dubautia linearis, Haplostachys haplostachya, Sida fallax, Silene lanceolata, Stenogyne angustifolia, and Tetramolopium arenarium.Key ResultsDuring 576.36 h of flower observations, only insects visited the flowers. Out of all recorded flower visits, 85% were performed by non‐native species, particularly the honeybee (Apis mellifera) and flies in the family Syrphidae. Some plant species received little visitation (e.g., S. angustifolia received one visit in 120 h of observation), whereas others were visited by a wide diversity of insects. The endangered plant species were visited by fewer visitor taxa than were the common native plant species. For six of the focal plant species, bagging of flowers to exclude pollinators resulted in significant reductions in seed set.ConclusionsThe flower visitor community in this system, although heavily dominated by non‐native insects, appears to be facilitating pollination for multiple plant species. Non‐native insects may thus be sustaining biotic interactions otherwise threatened with disruption in this island ecosystem. This may be particularly important for the studied endangered plant species, which exhibit fewer partners than the more common plant species.
Microscale trait‐environment associations in two closely‐related South African shrubs
Authors: Mitchell Nora , Holsinger Kent E. 
Published: February 2019

Premise of the StudyPlant traits are often associated with the environments in which they occur, but these associations often differ across spatial and phylogenetic scales. Here we study the relationship between microenvironment, microgeographical location, and traits within populations using co‐occurring populations of two closely related evergreen shrubs in the genus Protea.MethodsWe measured a suite of functional traits on 147 plants along a single steep mountainside where both species occur, and we used data‐loggers and soil analyses to characterize the environment at 10 microsites spanning the elevational gradient. We used Bayesian path analyses to detect trait‐environment relationships in the field for each species. We used complementary data from greenhouse grown seedlings derived from wild collected seed to determine whether associations detected in the field are the result of genetic differentiation.Key ResultsMicroenvironmental variables differed substantially across our study site. We found strong evidence for six trait‐environment associations, although these differed between species. We were unable to detect similar associations in greenhouse‐grown seedlings.ConclusionsSeveral leaf traits were associated with temperature and soil variation in the field, but the inability to detect these in the greenhouse suggests that differences in the field are not the result of genetic differentiation.
Supply and value chain analysis of mixed biomass feedstock supply system for lignocellulosic sugar production
Authors: Baral Nawa Raj , Davis Ryan , Bradley Thomas H. 
Published: February 2019

AbstractThe sustainable supply of high‐quality, low‐cost biomass feedstock to cellulosic biorefineries is still a challenge. Utilizing corn stover as the single feedstock to a biorefinery also poses a source of risk to seasonal feedstock availability, affordability, and sustainability. Implementing a year‐round feedstock switching strategy or utilizing an optimal mixture of corn stover, miscanthus, and switchgrass is demonstrated to diminish these concerns while reducing the cost of sugar production by as much as 3.8% and 13.6%, respectively, when compared to a baseline sugar price of 441.9 $ metric ton−1 (t) attributed to a fixed corn stover feedstock basis. This study determines that a mixing ratio of corn stover, miscanthus, and switchgrass of 36%, 50%, and 14%, respectively, minimizes the selling price of sugar. If miscanthus is sufficiently available in the future, its fraction could be further increased to 70% by reducing the fraction of corn stover. We find that the mixed feedstock considered in this study reduces the nutrient replacement and feedstock transportation costs and improves the quality of feedstock (determined by total carbohydrates and ash) relative to corn stover alone. Results suggest that a high‐quality feedstock with a high carbohydrate content is an important metric for consideration, beyond strictly the feedstock cost, to reduce the selling price of sugar and its uncertainties. In the future this may be supported by the increased availability of higher carbohydrate feedstocks such as miscanthus. © 2019 Society of Chemical Industry and John Wiley & Sons, Ltd.
Differences in the genomic profiles of cell‐free DNA between plasma, sputum, urine, and tumor tissue in advanced NSCLC
Authors: Wu Zhen , Yang Zhen , Li Chun Sun , Zhao Wei , Liang Zhi Xin , Dai Yu , Zhu Qiang , Miao Kai Ling , Cui Dong Hua , Chen Liang An 
Published: February 2019

AbstractLiquid biopsy has provided an efficient way for detection of gene alterations in advanced non‐small‐cell lung cancer (NSCLC). However, the correlation between systematic determination of somatic genomic alterations in liquid biopsy and tumor biopsy still remained unclear, and the concordance rate between cell‐free DNA (cfDNA) and matched tumor tissue DNA needs to be increased. A prospective study was performed to detect differences in genetic profiles of cfDNA in sputum, plasma, urine, and tumor tissue from 50 advanced NSCLC patients in parallel by the same next‐generation sequencing (NGS) platform. Driver genes alterations were identified in cfDNA sample and matched tumor sample, with an overall concordance rate of 86% in plasma cfDNA, 74% in sputum cfDNA, 70% in urine cfDNA, and 90% in cfDNA of combination of plasma, sputum, and urine. And the concordant rate of cfDNA in sputum in patients with smoking history was higher than that in patients without history of smoking (89% vs. 66%, P = 0.033) and equal to that in plasma cfDNA of the smoking patients (89% vs. 89%). In conclusion, sputum cfDNA can be considered as an alternative medium to liquid biopsy, while the complementarity of genomic profiles in cfDNA among plasma, sputum, and urine was beneficial to detect more diver genes alterations and improve the utility of liquid biopsy in advanced NSCLC (Liquid Biopsy for Detection of Driver Mutation in NSCLC; NCT02778854).
Agro Food Wastes and Innovative Pretreatments to Meet Biofuel Demand in Europe
Authors: Procentese Alessandra , Raganati Francesca , Olivieri Giuseppe , Russo Maria Elena , De La Feld Marco , Marzocchella Antonio 
Published: February 2019

AbstractThe use of agricultural residues (AR) and agro‐food waste (AFW) as potential feedstocks for the production of second‐generation ethanol and butanol is reviewed. The maximum biofuel production rate from AR and AFW was estimated on the basis of the feedstock availability rate, the average composition, and the biofuel yields reported in the literature. According to the estimations, the contribution of ethanol and butanol to current European biofuel accounts could be 32 and 23 % if traditional pretreatments are applied, and 40 and 19 % if they are produced by innovative pretreatments, respectively. Finally, the analysis was applied to a local scenario (Campania, Italy), with a view to potential decentralized exploitation of AR and AFW.