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“Floquet engineering of axion and high-Chern number phases in a topological insulator under illumination”. Shafiei M, Fazileh F, Peeters FM, Milošević, MV, SciPost Physics Core 7, 024 (2024). http://doi.org/10.21468/SCIPOSTPHYSCORE.7.2.024
Abstract: Quantum anomalous Hall, high-Chern number, and axion phases in topological insulators are characterized by its Chern invariant C (respectively, C = 1, integer C > 1, and C = 0 with half-quantized Hall conductance of opposite signs on top and bottom surfaces). They are of recent interest because of novel fundamental physics and prospective applications, but identifying and controlling these phases has been challenging in practice. Here we show that these states can be created and switched between in thin films of Bi2Se3 by Floquet engineering, using irradiation by circularly polarized light. We present the calculated phase diagrams of encountered topological phases in Bi2Se3, as a function of wavelength and amplitude of light, as well as sample thickness, after properly taking into account the penetration depth of light and the variation of the gap in the surface states. These findings open pathways towards energy-efficient optoelectronics, advanced sensing, quantum information processing and metrology.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
DOI: 10.21468/SCIPOSTPHYSCORE.7.2.024
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“Tuning the quantum phase transition of an ultrathin magnetic topological insulator”. Shafiei M, Fazileh F, Peeters FM, Milošević, MV, Physical review materials 8, 074201 (2024). http://doi.org/10.1103/PHYSREVMATERIALS.8.074201
Abstract: We explore the effect of thickness, magnetization direction, strain, and gating on the topological quantum phase transition of a thin-film magnetic topological insulator. Reducing the film thickness to the ultrathin regime couples the edge states on the two surfaces, opening a gap known as the hybridization gap, and causing a phase transition from a topological insulator to a normal insulator (NI). An out-of-plane/in-plane magnetization of size proportional to the hybridization gap triggers a phase transition from a normal insulator state to a quantum anomalous Hall (QAH)/semimetal state. A magnetization tilt by angle 0 from the out-of-plane axis influences the topological phase transition in a way that for sufficiently large 0, no phase transition from NI to QAH can be observed regardless of the sample thickness or magnetization, and for 0 close to pi /2 the system transits to a semimetal phase. Furthermore, we demonstrate that compressive/tensile strain can be used to decrease/increase the magnetization threshold for the topological phase transition. Finally, we reveal the effect of a vertical potential acting on the film, be it due to the substrate or applied gating, which breaks inversion symmetry and raises the magnetization threshold for the transition from NI to QAH state.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 3.4
DOI: 10.1103/PHYSREVMATERIALS.8.074201
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“Skin penetration of minerals in psoriatics and guinea-pigs bathing in hypertonic salt solutions”. Shani J, Barak S, Levi D, Ram M, Schachner ER, Schlesinger T, Robberecht H, Van Grieken R, Avrach WW, Pharmacological research communications 17, 501 (1985). http://doi.org/10.1016/0031-6989(85)90123-7
Abstract: Penetration of electrolytes through the human skin was measured in healthy volunteers and in psoriatic patients after bathing in the Dead-Sea or in simulated bath-salt solutions. Significant increases in the levels of serum Br, Rb, Ca and Zn were noticed only in the psoriatic patients after daily bathing in the Dead-Sea for a 4-week regimen. Guinea-pigs bathed in simulated Dead-Sea bath-salt solutions containing radionuclides of Ca, Mg, K and Br. Traces of each radionuclide were detected in the blood and in some internal organs after 60 minutes of bathing. The radionuclides showed a physiological pattern in their organ distribution. Even though the whole investigation was carried out in hypertonic solutions, there is a definite penetration of salts through healthy (human and guinea-pigs) and damaged (psoriatic) epidermis. This finding suggests that improvement of the psoriatic condition after bathing in the Dead-Sea, may be partly attributed (in addition to ultraviolet irradiation) to the minerals' effect on the psoriatic skin.
Keywords: A3 Journal article; Pharmacology. Therapy; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
DOI: 10.1016/0031-6989(85)90123-7
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“Serum bromine levels in psoriasis”. Shani J, Barak S, Ram M, Levi D, Pfeifer Y, Schlesinger T, Avrach WW, Robberecht H, Van Grieken R, Pharmacology 25, 297 (1982). http://doi.org/10.1159/000137756
Abstract: Serum bromine levels in psoriatic Danes increased 2- to 3-fold during a 4-week bathing course in the Dead Sea. This increase correlated well with the improvement in their clinical and psychic condition. Serum bromine levels in psoriatic Danes were somewhat lower than those in healthy subjects residing in Denmark, but the difference was not significant. Israelis working in the open air in the Dead Sea area (air bromine 20-fold higher than in Jerusalem) had higher bromine levels than psoriatic or healthy Israelis residing in Jerusalem or healthy Israelis working in air-conditioned rooms in the Dead Sea area (p < 0.05), but those levels were still within the normal range. As our animal experimentation indicates that the skin is a major target organ for 82Br, applied either by bathing or as an aerosol, we conclude that the higher bromine levels noticed in the psoriatic Danes after their 4-week stay at the Dead Sea may be equally due to their contact with the bromine-containing aerosol and the high bromine level of the Dead Sea waters.
Keywords: A1 Journal article; Pharmacology. Therapy; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
DOI: 10.1159/000137756
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“Increased erythrocyte glutathione peroxidase activity in psoriatics consuming high-selenium drinking water at the dead-sea psoriasis treatment center”. Shani J, Livshitz T, Robberecht H, Van Grieken R, Rubinstein N, Even-Paz Z, Pharmacological research communications 17, 479 (1985). http://doi.org/10.1016/0031-6989(85)90083-9
Abstract: Erythrocyte selenium-dependent glutathione peroxidase activity was measured in psoriatic Danes, before and after their four-week balneological therapy at the Ein-Bokek International Psoriasis Treatment Center, on the Dead-Sea shore in Israel. The drinking water in Ein-Bokek was found to be rich in selenium, a trace element with anticarcinogenic properties and of great importance in human nutrition and health. The most reliable biological parameter for increase in selenium bioavailability is the erythrocytes' glutathione-peroxidase activity. As psoriasis is a proliferative skin disease, the activity of this enzyme was assayed in 35 psoriatic Danes and in 25 long-term local hotel workers, as well as in 34 volunteers drinking low-selenium water. The glutathione peroxidase activity in the psoriatic patients increased significantly during their four-week stay in Ein-Bokek. Erythrocyte glutathione peroxidase activity in the hotel workers was 50% higher than that in the healthy volunteers consuming low-selenium water. A possible role of selenium in psoriasis is suggested.
Keywords: A3 Journal article; Pharmacology. Therapy; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
DOI: 10.1016/0031-6989(85)90083-9
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“Farmers' decision to use drought early warning system in developing countries”. Sharafi L, Zarafshani K, Keshavarz M, Azadi H, Van Passel S, Science Of The Total Environment 758, 142761 (2021). http://doi.org/10.1016/J.SCITOTENV.2020.142761
Abstract: Drought is a persistent, sluggish natural disaster in developing countries that has generated a financial burden and an unstable climate. Farmers should adopt early warning systems (EWS) in their strategies for monitoring drought to reduce its serious consequences. However, farmers in developing countries are reluctant to use EWS as their management strategies. Hence, the aim of this study was to investigate the decision of farmers to use climate knowledge through the model of farming activity in Kermanshah Township, Iran. A surveyor questionnaire was used to gather data from 370 wheat farmers using random sampling methods inmulti-stage clusters. Results revealed that the decision to use climate information is affected by personal factors, attitude towards climate information, objectives of using climate information, and external/physical farming factors. The result of this study has implications for drought management practitioners. To be specific, the results can aid policymakers to design early alert programs to minimize the risk of drought and thus move from conventional to climate smart agriculture. (C) 2020 Elsevier B.V. All rights reserved.
Keywords: A1 Journal article; Engineering Management (ENM)
Impact Factor: 4.9
DOI: 10.1016/J.SCITOTENV.2020.142761
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Shaw P (2021) Dual action of reactive species as signal and stress agents in plasma medicine : combined computational and experimental research. 191 p
Abstract: Reactive oxygen and nitrogen species (RONS) generated by cold atmospheric plasma (CAP) can activate discrete signaling transduction pathways or disrupt redox cellular homeostasis, depending on their concentration. This makes that CAP possesses therapeutic potential towards wound healing, cancer, and other diseases. In order to effectively use CAP in the clinic, a clear understanding of the interaction of RONS with biomolecules (lipids, proteins and nucleic acids) from the atomic to the macro scale, and their biological significance, is needed. In this work, I have therefore studied the dual role of CAP-derived RONS, i.e., (i) in the signaling pathways involved in wound healing, and (ii) in their reaction with biomolecules to cause oxidation-mediated damage. I performed computer simulations to provide fundamental insight about the occurring processes that are difficult or even impossible to obtain experimentally. Furthermore, next to computational studies, I used both 2D and 3D tissue cultures. 3D model allows proliferation in a more physiologically relevant geometry that stimulates the production of extracellular matrix proteins. I investigated the treatment of human gingival fibroblasts with low doses of CAP-generated RONS. This treatment demonstrated that it can inhibit colony formation but does not induce cell death, induce the expression of metalloprotease proteins, induce extracellular matrix degradation, and promote cell migration, which could result in enhanced wound healing. In contrast, at high concentrations, RONS can disrupt the cell membrane integrity and induce cancer cell death through oxidative stress-mediated pathways. I discovered how oxidation of the cell membrane (lipid-peroxidation) can facilitate the access of a drug (Melittin) into cancer cells, and in this way, reduce the required therapeutic dose of Melittin in melanoma and breast cancer cells (demonstrated using in vitro, in ovo and in silico approaches). Furthermore, I studied how excessive lipid-oxidation in chemoresistant pancreatic cancer cells promotes ferroptotic cell death. This was due to the stimulation of the iron-dependent Fenton reaction by targeting a redox specific signaling network. However, upon oxidative stress, cells protect themselves via a sophisticated intracellular antioxidant system that involves the regulation of glutathione/glutathione peroxidase 4 (lipid repair enzyme). Cancer cells exhibited increased levels of intracellular RONS due to their hyper metabolism, leading to high expression of anti-oxidant systems. I therefore focus on the effect of reactive species on the intracellular anti-oxidant system and corresponding DNA damages in both temozolomide-sensitive as well as temozolomide-resistant glioblastoma spheroids, in a 3-dimensional tumor model with a more complex tumor microenvironment than cell monolayers.
Keywords: Doctoral thesis; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Center for Oncological Research (CORE)
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“Preconcentration of precious metals by tellurium sulphide fire-assay followed by instrumental neutron activation analysis”. Shazali I, Van 't dack L, Gijbels R, , 29 (1988)
Keywords: P3 Proceeding; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
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“Structures and magnetic ordering in layered Cr oxide arsenides Sr₂CrO₂Cr₂OAs₂, and Sr₂CrO₃CrAs”. Sheath BC, Xu X, Manuel P, Hadermann J, Batuk M, O'Sullivan J, Bonilla RS, Clarke SJ, Inorganic chemistry 61, 10 (2022). http://doi.org/10.1021/ACS.INORGCHEM.2C01773
Abstract: Two novel chromium oxide arsenide materials have been synthesized, Sr2CrO2Cr2OAs2 (i.e., Sr2Cr3As2O3) and Sr2CrO3CrAs (i.e., Sr2Cr2AsO3), both of which contain chromium ions in two distinct layers. Sr2CrO2Cr2OAs2 was targeted following electron microscopy measurements on a related phase. It crystallizes in the space group P4/mmm and accommodates distorted CrO4As2 octahedra containing Cr2+ and distorted CrO(2)As(4 )octahedra containing Cr3+. In contrast, Sr2CrO3CrAs incorporates Cr3+ in CrO5 square-pyramidal coordination in [Sr2CrO3](+) layers and Cr2+ ions in CrAs(4 )tetrahedra in [CrAs](-) layers and crystallizes in the space group P4/nmm. Powder neutron diffraction data reveal antiferromagnetic ordering in both compounds. In Sr2CrO3CrAs the Cr2+ moments in the [CrAs](-) layers exhibit long-range ordering, while the Cr3+ moments in the [Sr2CrO3](+) layers only exhibit short-range ordering. However, in Sr2CrO2Cr2OAs2, both the Cr(2+ )moments in the CrO4As2 environments and the Cr3+ moments in the CrO2As4 polyhedra are long-range-ordered below 530(10) K. Above this temperature, only the Cr3+ moments are ordered with a Neel temperature slightly in excess of 600 K. A subtle structural change is evident in Sr2CrO2Cr2OAs2 below the magnetic ordering transitions.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 4.6
DOI: 10.1021/ACS.INORGCHEM.2C01773
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“Competition between the Ni and Fe redox in the O3-NaNi1/3Fe1/3Mn1/3O2 cathode material for Na-ion batteries”. Shevchenko VA, Glazkova IS, Novichkov DA, Skvortsova I, V Sobolev A, Abakumov AM, Presniakov IA, Drozhzhin OA, V Antipov E, Chemistry of materials 35, 4015 (2023). http://doi.org/10.1021/ACS.CHEMMATER.3C00338
Abstract: Sodium-ion batteries are attracting great attention due to their low cost and abundance of sodium. The O3-type NaNi1/3Fe1/3Mn1/3O2 layered oxide material is a promising candidate for positive electrodes (cathodes) in Na-ion batteries. However, its stable electrochemical performance is restricted by the upper voltage limit of 4.0 V (vs Na/Na+), which allows for reversibly removing 0.5-0.55 Na+ per formula unit, corresponding to the capacity of 120-130 mAh.g(-1). Further reduction of sodium content inevitably accelerates capacity degradation, and this issue calls for a detailed study of the redox reactions that accompany the electrochemical (de)intercalation of a large amount of sodium. Here, we present operando and ex situ studies using powder X-ray diffraction and X-ray absorption spectroscopy combined with Fe-57 Mossbauer spectroscopy. Our approach reveals the sequence of the redox transitions that occur during the charge and discharge of O3-NaNi1/3Fe1/3Mn1/3O2. Our data show that in addition to nickel and iron cations oxidizing to M+4, a part of iron transforms into the “3 + delta” state owing to the fast electron exchange Fe3+ + Fe4+ <-> Fe4+ + Fe3+. This process freezes upon cooling the material to 35 K, producing Fe4+ cations, some of which occupy tetrahedral positions.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 8.6
DOI: 10.1021/ACS.CHEMMATER.3C00338
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“Composition of aerosols in the surface boundary layer of the atmosphere over the seas of the Western Russian Arctic”. Shevchenko VP, Lisitsin AP, Kuptsov VM, van Malderen H, Martin JM, Van Grieken R, Huang WW, Oceanology 39, 128 (1999)
Keywords: A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
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“Composition of aerosols over the Laptev, the Kara, the Barents, the Greenland and the Norwegian seas”. Shevchenko VP, Lisitzin AP, Kuptzov VM, Ivanov GI, Lukashin VN, Martin JM, Rusakov VY, Safarova SA, Serova VV, Van Grieken R, van Malderen H page 7 (1995).
Keywords: H3 Book chapter; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
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“Composition of aerosols in the marine boundary layer over the seas of the western Russian Arctic”. Shevchenko VP, Lisitzin AP, Kuptzov VM, Van Malderen H, Martin JM, Van Grieken R, Huang WW, Omnia therapeutica. supplemento 39, 142 (1999)
Abstract: During the SPASIBA expedition (Scientific Program on Arctic and Siberian Aquatorium) on board RV “Yakov Smirnitzky” to the Laptev Sea 10 samples of aerosols in the marine boundary layer have been collected by nylon meshes in August-September 1991. The composition of the samples was studied by a combined approach of different analytical techniques (single-particle analysis, instrumental neutron activation analysis, and atomic absorption spectrometry). The mass concentration of coarse (>1 mu m) insoluble fraction of aerosols was from 0.08 to 0.46 mu g/m(3). In all samples remains of land vegetation were found as the main component. The organic carbon content of the aerosols ranged from 23 to 49%. The inorganic part of the samples is represented mainly by alumosilicates and quartz, In all samples anthropogenic fly ash particles were detected, Temporal variations of the element concentrations are caused by various air masses transported to the study area.
Keywords: A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
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“Composition of individual aerosol particles in the marine boundary layer over seas of the Western Russian Arctic”. Shevchenko VP, Van Grieken RE, van Malderen H, Lisitzin AP, Kuptsov VM, Serova VV, Doklady earth sciences 366, 546 (1999)
Keywords: A1 Journal article; Engineering sciences. Technology; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
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Shi H (2014) From functional properties to micro/nano-structures : a TEM study of NiTiNb shape memory alloys. Antwerpen
Keywords: Doctoral thesis; Electron microscopy for materials research (EMAT)
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“Correlation effects of DX centers on electron mobility in delta doped semiconductors investigated by Monte Carlo simulations”. Shi JM, Farias GA, Koenraad PM, van de Stadt AFW, Peeters FM, Wolter JH, Devreese JT, Brazilian journal of physics 27, 327 (1997)
Keywords: A1 Journal article; Condensed Matter Theory (CMT); Theory of quantum systems and complex systems
Impact Factor: 0.732
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“Charged-impurity correlations in Si ?-doped GaAs”. Shi JM, Koenraad PM, van de Stadt AFW, Peeters FM, Devreese JT, Wolter JH, , 2351 (1996)
Keywords: P3 Proceeding; Condensed Matter Theory (CMT); Theory of quantum systems and complex systems
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“Effects of DX centers on electronic structure of a ?-doped quantum barrier”. Shi JM, Koenraad PM, van de Stadt AFW, Peeters FM, Devreese JT, Wolter JH, , 2355 (1996)
Keywords: P3 Proceeding; Condensed Matter Theory (CMT); Theory of quantum systems and complex systems
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“Effects of the DX centers on electronic structure of a δ-doped quantum barrier”. Shi JM, Koenraad PM, van de Stadt AFW, Peeters FM, Devreese JT, Wolter JH, , 2355 (1996)
Keywords: P3 Proceeding; Condensed Matter Theory (CMT); Theory of quantum systems and complex systems
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“Shallow-donor states in strongly-coupled super-lattices”. Shi JM, Peeters FM, Devreese JT, Bulletin of the American Physical Society 39, 488 (1994)
Keywords: A3 Journal article; Condensed Matter Theory (CMT); Theory of quantum systems and complex systems
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“Effects of confinement in strongly-coupled superlattices on impurity bound magneto-polarons”. Shi JM, Peeters FM, Devreese JT, Cheng J-P, Kono J, McCombe BD, Proceedings of the International Conference on the Physics of Semiconductors 22, 2267 (1994)
Keywords: P3 Proceeding; Condensed Matter Theory (CMT); Theory of quantum systems and complex systems
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“Comparison of dwarf bamboos (Indocalamus sp.) leaf parameters to determine relationship between spatial density of plants and total leaf area per plant”. Shi P-J, Xu Q, Sandhu HS, Gielis J, Ding Y-L, Li H-R, Dong X-B, Ecology and evolution 5, 4578 (2015). http://doi.org/10.1002/ECE3.1728
Abstract: The relationship between spatial density and size of plants is an important topic in plant ecology. The self-thinning rule suggests a −3/2 power between average biomass and density or a −1/2 power between stand yield and density. However, the self-thinning rule based on total leaf area per plant and density of plants has been neglected presumably because of the lack of a method that can accurately estimate the total leaf area per plant. We aimed to find the relationship between spatial density of plants and total leaf area per plant. We also attempted to provide a novel model for accurately describing the leaf shape of bamboos. We proposed a simplified Gielis equation with only two parameters to describe the leaf shape of bamboos one model parameter represented the overall ratio of leaf width to leaf length. Using this method, we compared some leaf parameters (leaf shape, number of leaves per plant, ratio of total leaf weight to aboveground weight per plant, and total leaf area per plant) of four bamboo species of genus Indocalamus Nakai (I. pedalis (Keng) P.C. Keng, I. pumilus Q.H. Dai and C.F. Keng, I. barbatus McClure, and I. victorialis P.C. Keng). We also explored the possible correlation between spatial density and total leaf area per plant using log-linear regression. We found that the simplified Gielis equation fit the leaf shape of four bamboo species very well. Although all these four species belonged to the same genus, there were still significant differences in leaf shape. Significant differences also existed in leaf area per plant, ratio of leaf weight to aboveground weight per plant, and leaf length. In addition, we found that the total leaf area per plant decreased with increased spatial density. Therefore, we directly demonstrated the self-thinning rule to improve light interception.
Keywords: A1 Journal article; Engineering sciences. Technology; Sustainable Energy, Air and Water Technology (DuEL)
DOI: 10.1002/ECE3.1728
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“A simple way to calculate the volume and surface area of avian eggs”. Shi P, Chen L, Quinn BK, Yu K, Miao Q, Guo X, Lian M, Gielis J, Niklas KJ, Annals of the New York Academy of Sciences 1524, 118 (2023). http://doi.org/10.1111/NYAS.15000
Abstract: Egg geometry can be described using Preston's equation, which has seldom been used to calculate egg volume (V) and surface area (S) to explore S versus V scaling relationships. Herein, we provide an explicit re-expression of Preston's equation (designated as EPE) to calculate V and S, assuming that an egg is a solid of revolution. The side (longitudinal) profiles of 2221 eggs of six avian species were digitized, and the EPE was used to describe each egg profile. The volumes of 486 eggs from two avian species predicted by the EPE were compared with those obtained using water displacement in graduated cylinders. There was no significant difference in V using the two methods, which verified the utility of the EPE and the hypothesis that eggs are solids of revolution. The data also indicated that V is proportional to the product of egg length (L) and maximum width (W) squared. A 2/3-power scaling relationship between S and V for each species was observed, that is, S is proportional to (LW2)(2/3). These results can be extended to describe the shapes of the eggs of other species to study the evolution of avian (and perhaps reptilian) eggs.
Keywords: A1 Journal article; Engineering sciences. Technology; Sustainable Energy, Air and Water Technology (DuEL)
Impact Factor: 5.2
DOI: 10.1111/NYAS.15000
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“Comparison of a universal (but complex) model for avian egg shape with a simpler model”. Shi P, Gielis J, Niklas KJ, Annals of the New York Academy of Sciences 1514, 34 (2022). http://doi.org/10.1111/NYAS.14799
Abstract: Recently, a universal equation by Narushin, Romanov, and Griffin (hereafter, the NRGE) was proposed to describe the shape of avian eggs. While NRGE can simulate the shape of spherical, ellipsoidal, ovoidal, and pyriform eggs, its predictions were not tested against actual data. Here, we tested the validity of the NRGE by fitting actual data of egg shapes and compared this with the predictions of our simpler model for egg shape (hereafter, the SGE). The eggs of nine bird species were sampled for this purpose. NRGE was found to fit the empirical data of egg shape well, but it did not define the egg length axis (i.e., the rotational symmetric axis), which significantly affected the prediction accuracy. The egg length axis under the NRGE is defined as the maximum distance between two points on the scanned perimeter of the egg's shape. In contrast, the SGE fitted the empirical data better, and had a smaller root-mean-square error than the NRGE for each of the nine eggs. Based on its mathematical simplicity and goodness-of-fit, the SGE appears to be a reliable and useful model for describing egg shape.
Keywords: Editorial; Engineering sciences. Technology; Sustainable Energy, Air and Water Technology (DuEL)
Impact Factor: 5.2
DOI: 10.1111/NYAS.14799
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“Leaf functional traits : ecological and evolutionary implications”. Shi P, Gielis J, Niklas KJ, Niinemets Ü, Schrader J page 185 p. (2023).
Keywords: ME3 Book as editor; Sustainable Energy, Air and Water Technology (DuEL)
DOI: 10.3389/978-2-83252-086-4
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“‘biogeom&rsquo, : an R package for simulating and fitting natural shapes”. Shi P, Gielis J, Quinn BK, Niklas KJ, Ratkowsky DA, Schrader J, Ruan H, Wang L, Niinemets Ü, Niinennets U, Annals of the New York Academy of Sciences 1516, 123 (2022). http://doi.org/10.1111/NYAS.14862
Abstract: Many natural objects exhibit radial or axial symmetry in a single plane. However, a universal tool for simulating and fitting the shapes of such objects is lacking. Herein, we present an R package called 'biogeom' that simulates and fits many shapes found in nature. The package incorporates novel universal parametric equations that generate the profiles of bird eggs, flowers, linear and lanceolate leaves, seeds, starfish, and tree-rings, and three growth-rate equations that generate the profiles of ovate leaves and the ontogenetic growth curves of animals and plants. 'biogeom' includes several empirical datasets comprising the boundary coordinates of bird eggs, fruits, lanceolate and ovate leaves, tree rings, seeds, and sea stars. The package can also be applied to other kinds of natural shapes similar to those in the datasets. In addition, the package includes sigmoid curves derived from the three growth-rate equations, which can be used to model animal and plant growth trajectories and predict the times associated with maximum growth rate. 'biogeom' can quantify the intra- or interspecific similarity of natural outlines, and it provides quantitative information of shape and ontogenetic modification of shape with important ecological and evolutionary implications for the growth and form of the living world.
Keywords: A1 Journal article; Engineering sciences. Technology; Sustainable Energy, Air and Water Technology (DuEL)
Impact Factor: 5.2
DOI: 10.1111/NYAS.14862
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“Leaf area-length allometry and its implications in leaf shape evolution”. Shi P, Liu M, Ratkowsky DA, Gielis J, Su J, Yu X, Wang P, Zhang L, Lin Z, Schrader J, Trees: structure and function 33, 1073 (2019). http://doi.org/10.1007/S00468-019-01843-4
Abstract: According to Thompson’s principle of similarity, the area of an object should be proportional to its length squared. However, leaf area–length data of some plants have been demonstrated not to follow the principle of similarity. We explore the reasons why the leaf area–length allometry deviates from the principle of similarity and examine whether there is a general model describing the relationship among leaf area, width and length. We sampled more than 11,800 leaves from six classes of woody and herbaceous plants and tested the leaf area–length allometry. We compared six mathematical models based on root-mean-square error as the measure of goodness-of-fit. The best supported model described a proportional relationship between leaf area and the product of leaf width and length (i.e., the Montgomery model). We found that the extent to which the leaf area–length allometry deviates from the principle of similarity depends upon the extent of variation of the ratio of leaf width to length. Estimates of the parameter of the Montgomery model ranged between 1/2, which corresponds to a triangular leaf with leaf length as its height and leaf width as its base, and π/4, which corresponds to an elliptical leaf with leaf length as its major axis and leaf width as its minor axis, for the six classes of plants. The narrow range in practice of the Montgomery parameter implies an evolutionary stability for the leaf area of large-leaved plants despite the fact that leaf shapes of these plants are rather different.
Keywords: A1 Journal article; Sustainable Energy, Air and Water Technology (DuEL)
DOI: 10.1007/S00468-019-01843-4
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“Proportional relationship between leaf area and the product of leaf length and width of four types of special leaf shapes”. Shi P, Liu M, Yu X, Gielis J, Ratkowsky DA, Forests (19994907) 10, 178 (2019). http://doi.org/10.3390/F10020178
Abstract: The leaf area, as an important leaf functional trait, is thought to be related to leaf length and width. Our recent study showed that the Montgomery equation, which assumes that leaf area is proportional to the product of leaf length and width, applied to different leaf shapes, and the coefficient of proportionality (namely the Montgomery parameter) range from 1/2 to π/4. However, no relevant geometrical evidence has previously been provided to support the above findings. Here, four types of representative leaf shapes (the elliptical, sectorial, linear, and triangular shapes) were studied. We derived the range of the estimate of the Montgomery parameter for every type. For the elliptical and triangular leaf shapes, the estimates are π/4 and 1/2, respectively; for the linear leaf shape, especially for the plants of Poaceae that can be described by the simplified Gielis equation, the estimate ranges from 0.6795 to π/4; for the sectorial leaf shape, the estimate ranges from 1/2 to π/4. The estimates based on the observations of actual leaves support the above theoretical results. The results obtained here show that the coefficient of proportionality of leaf area versus the product of leaf length and width only varies in a small range, maintaining the allometric relationship for leaf area and thereby suggesting that the proportional relationship between leaf area and the product of leaf length and width broadly remains stable during leaf evolution.
Keywords: A1 Journal article; Engineering sciences. Technology; Sustainable Energy, Air and Water Technology (DuEL)
DOI: 10.3390/F10020178
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“A general leaf area geometric formula exists for plants evidence from the simplified Gielis equation”. Shi P, Ratkowsky DA, Li Y, Zhang L, Lin S, Gielis J, Forests (19994907) 9, 714 (2018). http://doi.org/10.3390/F9110714
Abstract: Plant leaves exhibit diverse shapes that enable them to utilize a light resource maximally. If there were a general parametric model that could be used to calculate leaf area for different leaf shapes, it would help to elucidate the adaptive evolutional link among plants with the same or similar leaf shapes. We propose a simplified version of the original Gielis equation (SGE), which was developed to describe a variety of object shapes ranging from a droplet to an arbitrary polygon. We used this equation to fit the leaf profiles of 53 species (among which, 48 bamboo plants, 5 woody plants, and 10 geographical populations of a woody plant), totaling 3310 leaves. A third parameter (namely, the floating ratio c in leaf length) was introduced to account for the case when the theoretical leaf length deviates from the observed leaf length. For most datasets, the estimates of c were greater than zero but less than 10%, indicating that the leaf length predicted by the SGE was usually smaller than the actual length. However, the predicted leaf areas approximated their actual values after considering the floating ratios in leaf length. For most datasets, the mean percent errors of leaf areas were lower than 6%, except for a pooled dataset with 42 bamboo species. For the elliptical, lanceolate, linear, obovate, and ovate shapes, although the SGE did not fit the leaf edge perfectly, after adjusting the parameter c, there were small deviations of the predicted leaf areas from the actual values. This illustrates that leaves with different shapes might have similar functional features for photosynthesis, since the leaf areas can be described by the same equation. The anisotropy expressed as a difference in leaf shape for some plants might be an adaptive response to enable them to adapt to different habitats.
Keywords: A1 Journal article; Sustainable Energy, Air and Water Technology (DuEL)
DOI: 10.3390/F9110714
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“A new program to estimate the parameters of Preston's equation, a general formula for describing the egg shape of birds”. Shi P, Wang L, Quinn BKK, Gielis J, Symmetry 15, 231 (2023). http://doi.org/10.3390/SYM15010231
Abstract: Preston's equation is a general model describing the egg shape of birds. The parameters of Preston's equation are usually estimated after re-expressing it as the Todd-Smart equation and scaling the egg's actual length to two. This method assumes that the straight line through the two points on an egg's profile separated by the maximum distance (i.e., the longest axis of an egg's profile) is the mid-line. It hypothesizes that the photographed egg's profile is perfectly bilaterally symmetrical, which seldom holds true because of photographic errors and placement errors. The existing parameter estimation method for Preston's equation considers an angle of deviation for the longest axis of an egg's profile from the mid-line, which decreases prediction errors to a certain degree. Nevertheless, this method cannot provide an accurate estimate of the coordinates of the egg's center, and it leads to sub-optimal parameter estimation. Thus, it is better to account for the possible asymmetry between the two sides of an egg's profile along its mid-line when fitting egg-shape data. In this paper, we propose a method based on the optimization algorithm (optimPE) to fit egg-shape data and better estimate the parameters of Preston's equation by automatically searching for the optimal mid-line of an egg's profile and testing its validity using profiles of 59 bird eggs spanning a wide range of existing egg shapes. We further compared this method with the existing one based on multiple linear regression (lmPE). This study demonstrated the ability of the optimPE method to estimate numerical values of the parameters of Preston's equation and provide the theoretical egg length (i.e., the distance between two ends of the mid-line of an egg's profile) and the egg's maximum breadth. This provides a valuable approach for comparing egg shapes among conspecifics or across different species, or even different classes (e.g., birds and reptiles), in future investigations.
Keywords: A1 Journal article; Engineering sciences. Technology; Sustainable Energy, Air and Water Technology (DuEL)
Impact Factor: 2.7
DOI: 10.3390/SYM15010231
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