bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular Dynamics Simulations of Phosphorylated Intrinsically Disordered Proteins: A Force Field Comparison
Authors: Rieloff Ellen , Skepö Marie
Published: September 2021

Phosphorylation is a common post-translational modification among intrinsically disordered proteins and regions, which helps regulate function by changing the protein conformations, dynamics, and interactions with binding partners. To fully comprehend the effects of phosphorylation, computer simulations are a helpful tool, although they are dependent on the accuracy of the force field used. Here, we compared the conformational ensembles produced by Amber ff99SB-ILDN+TIP4P-D and CHARMM36m, for four phosphorylated disordered peptides ranging in length from 14–43 residues. CHARMM36m consistently produced more compact conformations with a higher content of bends, mainly due to more stable salt bridges. Based on comparisons with experimental size estimates for the shortest and longest peptide, CHARMM36m appeared to overestimate the compactness. The difference between the force fields was largest for the peptide showing the greatest separation between positively charged and phosphorylated residues, in line with the importance of charge distribution. For this peptide, the conformational ensemble did not change significantly upon increasing the ionic strength from 0 mM to 150 mM, despite a reduction of the salt-bridging probability in the CHARMM36m simulations, implying that salt concentration has negligible effects in this study.
Novel Silver-Functionalized Poly(ε-Caprolactone)/Biphasic Calcium Phosphate Scaffolds Designed to Counteract Post-Surgical Infections in Orthopedic Applications
Authors: Comini Sara , Sparti Rosaria , Coppola Bartolomeo , Mohammadi Mehdi , Scutera Sara , Menotti Francesca , Banche Giuliana , Cuffini Anna Maria , Palmero Paola , Allizond Valeria
Published: September 2021

In this study, we designed and developed novel poly(ε-caprolactone) (PCL)-based biomaterials, for use as bone scaffolds, through modification with both biphasic calcium phosphate (BCP), to impart bioactive/bioresorbable properties, and with silver nitrate, to provide antibacterial protection against Staphylococcus aureus, a microorganism involved in prosthetic joint infections (PJIs). Field emission scanning electron microscopy (FESEM) showed that the samples were characterized by square-shaped macropores, and energy dispersive X-ray spectroscopy analysis confirmed the presence of PCL and BCP phases, while inductively coupled plasma–mass spectrometry (ICP–MS) established the release of Ag+ in the medium (~0.15–0.8 wt% of initial Ag content). Adhesion assays revealed a significant (p < 0.0001) reduction in both adherent and planktonic staphylococci on the Ag-functionalized biomaterials, and the presence of an inhibition halo confirmed Ag release from enriched samples. To assess the potential outcome in promoting bone integration, preliminary tests on sarcoma osteogenic-2 (Saos-2) cells indicated PCL and BCP/PCL biocompatibility, but a reduction in viability was observed for Ag-added biomaterials. Due to their combined biodegrading and antimicrobial properties, the silver-enriched BCP/PCL-based scaffolds showed good potential for engineering of bone tissue and for reducing PJIs as a microbial anti-adhesive tool used in the delivery of targeted antimicrobial molecules, even if the amount of silver needs to be tuned to improve osteointegration.
How Wisdom Emerges from Intellectual Development: A Developmental/Historical Theory for Raising Mandelas
Authors: Demetriou Andreas , Liakos Antonis , Kizilyürek Niyazi
Published: September 2021

This paper invokes cognitive developmental theory as a means for preparing citizens to deal with and resolve conflicts within or across nations. We take the centuries-old Greek–Turkish dispute as an example. We first outline a theory of intellectual development postulating that mental changes emerge in response to changing developmental priorities in successive life periods, namely, interaction control in infancy, attention control and representational awareness in preschool, inferential control and cognitive management in primary school, and advanced forms of reasoning and self-evaluation in adolescence. Based on this model, we outline a control theory of wisdom postulating that different aspects of wisdom emerge during development as different levels of control of relations with others: trust and care for others in infancy, taking the other’s perspective, reflectivity, and empathy in preschool, rationality and understanding the rules underlying individual and group interactions in primary school, and understanding the general principles of societal operation explaining the differences in approach and interest between groups in adolescence and early adulthood. We also outline the educational implications of this theory for the education of citizens by capitalizing on intellectual strengths at successive developmental periods to comprehensively understand the world and to act prudently when dealing with interpersonal and social or national conflict. Finally, the paper discusses the political constraints and implications of this theory. This is the first attempt to derive wisdom from the development of cognitive and personality processes from infancy through early adulthood and to connect it to serious world problems.
Comparative Study of Ovule Development between Wild (Passiflora foetida L.) and Cultivated (P. edulis Sims) Species of Passiflora L. Provide Insights into Its Differential Developmental Patterns
Authors: Vijay Archa , Nizam Ashifa , Radhakrishnan Arun Madasseril , Anju Thattantavide , Kashyap Arun Kumar , Kumar Nitesh , Kumar Ajay
Published: September 2021

The ovules inside the ovary of a plant are the precursors of seeds and they are important for the perpetuation of the plants. The genus Passiflora L., produce fruits with numerous seeds and they have economic and medicinal value. The edible portion of the Passiflora are the seeds surrounded by pulp. Being the edible parts of a fruit, it is important to investigate the early development of ovules in Passiflora that lead to the formation of seeds after pollination. Wild relatives of the domesticated crops are increasingly being investigated for possible genetic resources that can be used for crop improvement programs. The present study was designed to investigate the comparative ovule development between a wild (Passiflora foetida L.) and a cultivated (Passiflora edulis Sims) species of Passiflora with an aim that it may provide important information about the common and diverging regulatory mechanisms during ovule development between the wild and the cultivated species. We also investigated the pollen morphology between the wild and cultivated species using light and scanning electron microscopy. Our results show that wild type P. foetida ovule growth is faster when compared with that of cultivated P. edulis. Furthermore, wild species harbour ovules of large size (0.14 mm2) but less in number (6) as compared to cultivated ones which show smaller size (0.05 mm2) of ovules but relatively more in number (21). The differences in ovary wall thickness were also stark between the two species. The ovary wall thickness was 0.10 mm in the wild type whereas it was 0.74 mm in cultivated species. Notable differences were also observed in diameter where the wild type (2.45 mm) reported smaller diameter than cultivated species (3.25 mm). We observed little difference in the pollen morphology between the two species.
Hydrogen-Bonding-Aided Fabrication of Wood Derived Cellulose Scaffold/Aramid Nanofiber into High-Performance Bulk Material
Authors: Han Xiaoshuai , Wu Weijie , Wang Jingwen , Tian Zhiwei , Jiang Shaohua
Published: September 2021

Preparing a lightweight yet high-strength bio-based structural material with sustainability and recyclability is highly desirable in advanced applications for architecture, new energy vehicles and spacecraft. In this study, we combined cellulose scaffold and aramid nanofiber (ANF) into a high-performance bulk material. Densification of cellulose microfibers containing ANF and hydrogen bonding between cellulose microfibers and ANF played a crucial role in enhanced physical and mechanical properties of the hybrid material. The prepared material showed excellent tensile strength (341.7 MPa vs. 57.0 MPa for natural wood), toughness (4.4 MJ/m3 vs. 0.4 MJ/m3 for natural wood) and Young’s modulus (24.7 GPa vs. 7.2 GPa for natural wood). Furthermore, due to low density, this material exhibited a superior specific strength of 285 MPa·cm3·g−1, which is remarkably higher than some traditional building materials, such as concrete, alloys. In addition, the cellulose scaffold was infiltrated with ANFs, which also improved the thermal stability of the hybrid material. The facile and top-down process is effective and scalable, and also allows one to fully utilize cellulose scaffolds to fabricate all kinds of advanced bio-based materials.
Dendritic Iron(III) Carbazole Complexes: Structural, Optical, and Magnetic Characteristics
Authors: Gruzdev Matvey , Chervonova Ulyana , Kolker Arkadiy , Fomina Nadezhda , Zueva Ekaterina , Vorobeva Valerya , Starichenko Denis , Korolev Alexander
Published: September 2021

This paper focuses on the synthesis, structural characterization, and study of the optical, magnetic, and thermal properties of novel architectures combining metal ions as magnetoactive centers and photoactive blocks formed by carbazole units. For this purpose, a series of azomethine complexes of the composition [Fe(L)2]X (L = 3,6-bis[(3′,6′-di-tert-butyl-9-carbazol)-9-carbazol]benzoyloxy-4-salicylidene-N′-ethyl-N-ethylenediamine, X = NO3−, Cl−, PF6−) were synthesized by the reaction of metal salts with Schiff bases in a mixture of solvents. The UV–Vis absorption properties were studied in dichloromethane and rationalized via time-dependent density functional theory (DFT) calculations. Upon excitation at 350 nm, the compounds exhibited an intense dual fluorescence with two emission bands centered at ~445 and ~485 nm, which were assigned to πcarb–π* intraligand and πcarb–dFe ligand-to-metal charge-transfer excited states. EPR spectroscopy and SQUID magnetometry revealed solid-state partial spin crossover in some compounds, and antiferromagnetic interactions between the neighboring Fe(III) ions.
Liquid Metal Embrittlement of Advanced High Strength Steel: Experiments and Damage Modeling
Authors: Prabitz Konstantin Manuel , Asadzadeh Mohammad Zhian , Pichler Marlies , Antretter Thomas , Beal Coline , Schubert Holger , Hilpert Benjamin , Gruber Martin , Sierlinger Robert , Ecker Werner
Published: September 2021

In the automotive industry, corrosion protected galvanized advanced high strength steels with high ductility (AHSS-HD) gain importance due to their good formability and their lightweight potential. Unfortunately, under specific thermomechanical loading conditions such as during resistance spot welding galvanized, AHSS-HD sheets tend to show liquid metal embrittlement (LME). LME is an intergranular decohesion phenomenon leading to a drastic loss of ductility of up to 95%. The occurrence of LME for a given galvanized material mainly depends on thermal and mechanical loading. These influences are investigated for a dual phase steel with an ultimate tensile strength of 1200 MPa, a fracture strain of 14% and high ductility (DP1200HD) by means of systematic isothermal hot tensile testing on a Gleeble® 3800 thermomechanical simulator. Based on the experimental findings, a machine learning procedure using symbolic regression is applied to calibrate an LME damage model that accounts for the governing quantities of temperature, plastic strain and strain rate. The finite element (FE) implementation of the damage model is validated based on the local damage distribution in the hot tensile tested samples and in an exemplary 2-sheet resistance spot weld. The developed LME damage model predicts the local position and the local intensity of liquid metal induced cracking in both cases very well.
Environmental and Economic Life Cycle Assessment of Recycled Coarse Aggregates: A Portuguese Case Study
Authors: Dias Adriana B. , Pacheco João N. , Silvestre José D. , Martins Isabel M. , de Brito Jorge
Published: September 2021

The incorporation of recycled aggregates in concrete not only reduces the extraction of natural resources, but also decreases landfill disposal of construction and demolition waste. Hence, environmental impacts and costs are reduced, promoting the use of recycled aggregates and circular economy. However, the impacts of transport depend on the distance between facilities and longer distances may result in recycled aggregates being more costly and having larger environmental impact than natural aggregates. This paper discusses this topic, presents a review on the use of life cycle assessment methodology on natural and recycled aggregates for concrete, and applies this methodology in a real context pertaining the procurement of coarse aggregates to ready-mix concrete plants. A case study of two Portuguese regions, Coimbra and Lisbon, is presented. For each region, a quarry, a construction and demolition waste plant, and a ready-mix concrete plant are chosen and a comparative life cycle assessment is made. Different scenarios for the supply of natural and recycled aggregates are studied and the scenarios for recycled aggregates procurement include different hypotheses for the installation (construction and demolition waste plant or quarry) processing the construction and demolition waste into recycled aggregates. For this case study and both regions, it was found that the supply of recycled aggregates produced at the construction and demolition waste plant has lower environmental impact and cost than all other scenarios, including the provision of natural aggregates, except when it is assumed that the quarry is licensed and equipped for receiving unsorted construction and demolition waste and processing it into recycled aggregates. The paper shows that transport distance is a determining factor in the comparison of the impacts of the procurement of natural and recycled aggregates. Moreover, in the Portuguese context, the environmental impacts of the procurement of recycled aggregates may be smaller than those of natural aggregates, but cost may be larger for recycled aggregates, preventing that the most sustainable option is chosen.
Synthesis of a CFD Benchmark Exercise: Examining Fluid Flow and Residence-Time Distribution in a Water Model of Tundish
Authors: Sheng Dong-Yuan
Published: September 2021

Computational Fluid Dynamics (CFD) has become an indispensable tool that can potentially predict many phenomena of practical interest in the tundish. Model verification and validation (V&V) are essential parts of a CFD model development process if the models are to be used with sufficient confidence in real industrial tundish applications. The crucial aspects of CFD simulations in the tundish are addressed in this study, such as the selection of the turbulence models, meshing, boundary conditions, and selection of discretization schemes. A series of CFD benchmarking exercises are presented serving as selected examples of appropriate modelling strategies. A tundish database, initiated by German Steel Institute VDEH working group “Fluid Mechanics and Fluid Simulation”, was revisited with the aim of establishing a comprehensive set of best practice guidelines (BPG) in CFD simulations for tundish applications. These CFD benchmark exercises yield important results for the sensible application of CFD models and contribute to further improving the reliability of CFD applications in metallurgical reactors.
Local Effects of a 1940 nm Thulium-Doped Fiber Laser and a 1470 nm Diode Laser on the Pulmonary Parenchyma: An Experimental Study in a Pig Model
Authors: Janeczek Maciej , Rybak Zbigniew , Lipińska Anna , Bujok Jolanta , Czerski Albert , Szymonowicz Maria , Dobrzyński Maciej , Świderski Jacek , Żywicka Bogusława
Published: September 2021

The lungs are a common site of metastases from malignant tumors. Their removal with a minimal but safe tissue margin is essential for the long-term survival of patients. The aim of this study was to evaluate the usefulness of a 1940 nm thulium-doped fiber laser (TDFL) and a 1470 nm diode laser (DL) in a pig model of lung surgery that involved the incision and excision of lung tissue. Histopathological analysis was performed on days 0 and 7 after surgery. Neither TDFL nor DL caused significant perioperative or postoperative bleeding. Histological analysis revealed the presence of carbonized necrotic tissue, mixed fibrin–cellular exudate in the superficial zone of thermal damage and bands of deeper thermal changes. The mean total width of thermal damage on day 0 was 499.46 ± 61.44 and 937.39 ± 109.65 µm for TDFL and DL, respectively. On day 7, cell activation and repair processes were visible. The total width of thermal damage was 2615.74 ± 487.17 µm for TDFL vs. 6500.34 ±1118.02 µm for DL. The superficial zone of thermal damage was narrower for TDFL on both days 0 and 7. The results confirm the effectiveness of both types of laser in cutting and providing hemostasis in the lungs. TDFL caused less thermal damage to the lung parenchyma than DL.
Heat-Treated Ni-CNT Nanocomposites Produced by Powder Metallurgy Route
Authors: Carneiro Íris , Simões Sónia
Published: September 2021

Nickel nanocomposites reinforced by carbon nanotubes (Ni-CNTs) are one of the possible candidates for applications in highly demanding industries such as the automotive and aerospace industries. As is well known, one of the limitations on the use of some materials in these applications is thermal stability. Some components in these industries are frequently subjected to high temperatures, which is crucial to understanding their microstructures and, consequently, their mechanical properties. For this reason, the main objective of this research is to understand the microstructural evolution of Ni-CNTs nanocomposites when subjected to heat treatment. The nanocomposites with varying levels of CNT content were produced by powder metallurgy, and unreinforced nickel was used for comparison purposes under the same conditions. The dispersion of CNTs, a critical aspect of nanocomposites production, was carried out by ultrasonication, which already proved its efficiency in previous research. The heat treatments were performed under high vacuum conditions at high temperatures (700 and 1100 °C for 30 and 120 min, respectively). Microhardness tests analyzed the mechanical properties while the extensive microstructural evaluation was conducted by combining advanced characterization techniques such as scanning electron microscopy (SEM) with electron backscatter diffraction (EBSD), transmission electron microscopy (TEM), and high-resolution TEM. The obtained results are promising and show that the presence of CNTs can contribute to the thermal stability of the Ni-CNT nanocomposites produced.
Ammonia Bioremediation from Aquaculture Wastewater Effluents Using Arthrospira platensis NIOF17/003: Impact of Biodiesel Residue and Potential of Ammonia-Loaded Biomass as Rotifer Feed
Authors: Ashour Mohamed , Alprol Ahmed E. , Heneash Ahmed M. M. , Saleh Hosam , Abualnaja Khamael M. , Alhashmialameer Dalal , Mansour Abdallah Tageldein
Published: September 2021

The present work evaluated the capability of Arthrospira platensis complete biomass (ACDW) and the lipid-free biomass (LFB) to remove ammonium ions (NH4+) from aquaculture wastewater discharge. Under controlled conditions in flasks filled with 100 mL of distilled water (synthetic aqueous solution), a batch process ion-exchange was conducted by changing the main parameters including contact times (15, 30, 45, 60, 120, and 180 min), initial ammonium ion concentrations (10, 20, 30, 40, 50, and 100 mg·L−1), and initial pH levels (2, 4, 6, 8, and 10) at various dosages of ACDW and LFB as adsorbents (0.02, 0.04, 0.06, 0.08, and 0.1 g). After lab optimization, ammonia removal from real aquaculture wastewater was also examined. The removal of ammonium using ACDW and LFB in the synthetic aqueous solution (64.24% and 89.68%, respectively) was higher than that of the real aquaculture effluents (25.70% and 37.80%, respectively). The data of IR and Raman spectroscopy confirmed the existence of various functional groups in the biomass of ACDW and LFB. The adsorption equilibrium isotherms were estimated using Freundlich, Langmuir, and Halsey models, providing an initial description of the ammonia elimination capacity of A. platensis. The experimental kinetic study was suitably fit by a pseudo-second-order equation. On the other hand, as a result of the treatment of real aquaculture wastewater (RAW) using LFB and ACDW, the bacterial counts of the LFB, ACDW, ACDW-RAW, and RAW groups were high (higher than 300 CFU), while the LFB-RAW group showed lower than 100 CFU. The current study is the first work reporting the potential of ammonia-loaded microalgae biomass as a feed source for the rotifer (Brachionus plicatilis). In general, our findings concluded that B. plicatilis was sensitive to A. platensis biomass loaded with ammonia concentrations. Overall, the results in this work showed that the biomass of A. platensis is a promising candidate for removing ammonia from aquaculture wastewater.
Activation of Porous Pt Electrodes Deposited on YSZ Electrolyte by Nitric Acid Treatment
Authors: Dunyushkina Liliya , Pavlovich Anastasiya , Khaliullina Adelya
Published: September 2021

The effect of nitric acid treatment on the electrochemical performance of porous Pt electrodes deposited on YSZ (abbreviation from yttria stabilized zirconia) electrolyte was investigated. Two identical symmetrical Pt/YSZ/Pt cells with porous Pt electrodes were fabricated, after which the electrodes of the first cell were kept as sintered, while those of the second cell were impregnated with HNO3 solution. The electrochemical behavior of the prepared electrodes was studied using impedance spectroscopy and cyclic voltammetry. Significant reduction of the polarization resistance of the HNO3-treated electrodes was revealed. The observed enhancement of the electrochemical performance of porous Pt electrodes was assumed to be caused by adsorption of NOx-species on YSZ and Pt surfaces, which promotes oxygen molecules dissociation and transport to the triple phase boundary by the “relay-race” mechanism. The obtained results allow for considering the nitric acid treatment of a porous Pt electrode as an effective way of electrode activation.
Study on the Synthesis of High-Purity γ-Phase Mesoporous Alumina with Excellent CO2 Adsorption Performance via a Simple Method Using Industrial Aluminum Oxide as Raw Material
Authors: Li Zhonglin , Wang Ding , Shen Jialong , Chen Junxue , Wu Chengzhi , Qu Zizheng , Luo Kun , Meng Zhengbing , Li Yibing
Published: September 2021

To mitigate the global greenhouse effect and the waste of carbon dioxide, a chemical raw material, high-purity γ-phase mesoporous alumina (MA) with excellent CO2 adsorption performance was synthesized by the direct aging method and ammonium salt substitution method. With this process, not only can energy consumption and time be shortened to a large extent but the final waste can also be recycled to the mother liquor by adding calcium hydroxide. Reaction conditions, i.e., pH value, calcination temperature, and desodium agent, were investigated in detail with the aid of X-ray fluorescence spectrum (XRF), X-ray diffraction (XRD), scanning electron microscopy (SEM), Brunauer–Emmett–Teller (BET) and Barret-Joyner-Hallender (BJH) methods, nonlocal density functional theory (NLDFT), transmission electron microscopy (TEM), temperature-programmed desorption of CO2 (CO2-TPD), and presented CO2 adsorption measurement. The results of this study are summarized as follows: the impurity content of the MA synthesized under optimal conditions is less than 0.01%, and its total removal rate of impurities is 99.299%. It was found that the MA adsorbent has a large specific surface area of 377.8 m2/g, pore volume of 0.55 cm3/g, and its average pore diameter is 3.1 nm. Under the condition of a gas flow rate of 20 cm3/min, its CO2 adsorption capacity is 1.58 mmol/g, and after 8 times of cyclic adsorption, the amount of CO2 adsorption remained basically unchanged, both of which indicate that the material has excellent adsorption properties and can be widely used for the adsorption of carbon dioxide.
Fixed-Bed Column Technique for the Removal of Phosphate from Water Using Leftover Coal
Authors: Mekonnen Dereje Tadesse , Alemayehu Esayas , Lennartz Bernd
Published: September 2021

The excessive discharge of phosphate from anthropogenic activities is a primary cause for the eutrophication of aquatic habitats. Several methodologies have been tested for the removal of phosphate from aqueous solutions, and adsorption in a flow-through reactor is an effective mechanism to reduce the nutrient loading of water. This research aimed to investigate the adsorption potential of leftover coal material to remove phosphate from a solution by using continuous flow fixed-bed column, and analyzes the obtained breakthrough curves. A series of column tests were performed to determine the phosphorus breakthrough characteristics by varying operational design parameters such as adsorbent bed height (5 to 8 cm), influent phosphate concentration (10–25 mg/L), and influent flow rate (1–2 mL/min). The amorphous and crystalline property of leftover coal material was studied using XRD technology. The FT-IR spectrum confirmed the interaction of adsorption sites with phosphate ions. Breakthrough time decreased with increasing flow rate and influent phosphate concentration, but increased with increasing adsorbent bed height. Breakthrough-curve analysis showed that phosphate adsorption onto the leftover coal material was most effective at a flow rate of 1 mL/min, influent phosphate concentration of 25 mg/L, and at a bed height of 8 cm. The maximal total phosphate adsorbed onto the coal material’s surface was 243 mg/kg adsorbent. The Adams–Bohart model depicted the experimental breakthrough curve well, and overall performed better than the Thomas and Yoon–Nelson models did, with correlation values (R2) ranging from 0.92 to 0.98. Lastly, leftover coal could be used in the purification of phosphorus-laden water, and the Adams–Bohart model can be employed to design filter units at a technical scale.
Effect of Composition on the Phase Structure and Magnetic Properties of Ball-Milled LaFe11.71-xMnxSi1.29H1.6 Magnetocaloric Powders
Authors: Brechtl Jamieson , Koehler Michael R. , Kesler Michael S. , Henderson Hunter B. , Baker Alexander A. , Li Kai , Kiggans James , Nawaz Kashif , Rios Orlando , Momen Ayyoub M.
Published: September 2021

Magnetocaloric alloys are an important class of materials that enable non-vapor compression cycles. One promising candidate for magnetocaloric systems is LaFeMnSi, thanks to a combination of factors including low-cost constituents and a useful curie temperature, although control of the constituents’ phase distribution can be challenging. In this paper, the effects of composition and high energy ball milling on the particle morphology and phase stability of LaFe11.71-xMnxSi1.29H1.6 magnetocaloric powders were investigated. The powders were characterized with optical microscopy, dynamic light scattering, X-ray diffraction (XRD), and differential scanning calorimetry (DSC). It was found that the powders retained most of their original magnetocaloric phase during milling, although milling reduced the degree of crystallinity in the powder. Furthermore, some oxide phases (<1 weight percent) were present in the as-received and milled powders, which indicates that no significant contamination of the powders occurred during milling. Finally, the results indicated that the Curie temperature drops as Fe content decreases (Mn content increases). In all of the powders, milling led to an increase in the Curie temperature of ~3–6 °C.
Sensitivity Analysis of In Silico Fluid Simulations to Predict Thrombus Formation after Left Atrial Appendage Occlusion
Authors: Mill Jordi , Agudelo Victor , Olivares Andy L. , Pons Maria Isabel , Silva Etelvino , Nuñez-Garcia Marta , Morales Xabier , Arzamendi Dabit , Freixa Xavier , Noailly Jérôme , Camara Oscar
Published: September 2021

Atrial fibrillation (AF) is nowadays the most common human arrhythmia and it is considered a marker of an increased risk of embolic stroke. It is known that 99% of AF-related thrombi are generated in the left atrial appendage (LAA), an anatomical structure located within the left atrium (LA). Left atrial appendage occlusion (LAAO) has become a good alternative for nonvalvular AF patients with contraindications to anticoagulants. However, there is a non-negligible number of device-related thrombus (DRT) events, created next to the device surface. In silico fluid simulations can be a powerful tool to better understand the relation between LA anatomy, haemodynamics, and the process of thrombus formation. Despite the increasing literature in LA fluid modelling, a consensus has not been reached yet in the community on the optimal modelling choices and boundary conditions for generating realistic simulations. In this line, we have performed a sensitivity analysis of several boundary conditions scenarios, varying inlet/outlet and LA wall movement configurations, using patient-specific imaging data of six LAAO patients (three of them with DRT at follow-up). Mesh and cardiac cycle convergence were also analysed. The boundary conditions scenario that better predicted DRT cases had echocardiography-based velocities at the mitral valve outlet, a generic pressure wave from an AF patient at the pulmonary vein inlets, and a dynamic mesh approach for LA wall deformation, emphasizing the need for patient-specific data for realistic simulations. The obtained promising results need to be further validated with larger cohorts, ideally with ground truth data, but they already offer unique insights on thrombogenic risk in the left atria.
A Massively Parallel Hybrid Finite Volume/Finite Element Scheme for Computational Fluid Dynamics
Authors: Río-Martín Laura , Busto Saray , Dumbser Michael
Published: September 2021

In this paper, we propose a novel family of semi-implicit hybrid finite volume/finite element schemes for computational fluid dynamics (CFD), in particular for the approximate solution of the incompressible and compressible Navier-Stokes equations, as well as for the shallow water equations on staggered unstructured meshes in two and three space dimensions. The key features of the method are the use of an edge-based/face-based staggered dual mesh for the discretization of the nonlinear convective terms at the aid of explicit high resolution Godunov-type finite volume schemes, while pressure terms are discretized implicitly using classical continuous Lagrange finite elements on the primal simplex mesh. The resulting pressure system is symmetric positive definite and can thus be very efficiently solved at the aid of classical Krylov subspace methods, such as a matrix-free conjugate gradient method. For the compressible Navier-Stokes equations, the schemes are by construction asymptotic preserving in the low Mach number limit of the equations, hence a consistent hybrid FV/FE method for the incompressible equations is retrieved. All parts of the algorithm can be efficiently parallelized, i.e., the explicit finite volume step as well as the matrix-vector product in the implicit pressure solver. Concerning parallel implementation, we employ the Message-Passing Interface (MPI) standard in combination with spatial domain decomposition based on the free software package METIS. To show the versatility of the proposed schemes, we present a wide range of applications, starting from environmental and geophysical flows, such as dambreak problems and natural convection, over direct numerical simulations of turbulent incompressible flows to high Mach number compressible flows with shock waves. An excellent agreement with exact analytical, numerical or experimental reference solutions is achieved in all cases. Most of the simulations are run with millions of degrees of freedom on thousands of CPU cores. We show strong scaling results for the hybrid FV/FE scheme applied to the 3D incompressible Navier-Stokes equations, using millions of degrees of freedom and up to 4096 CPU cores. The largest simulation shown in this paper is the well-known 3D Taylor-Green vortex benchmark run on 671 million tetrahedral elements on 32,768 CPU cores, showing clearly the suitability of the presented algorithm for the solution of large CFD problems on modern massively parallel distributed memory supercomputers.
Decision-Making with Fuzzy Soft Matrix Using a Revised Method: A Case of Medical Diagnosis of Diseases
Authors: Sangodapo Taiwo Olubunmi , Onasanya Babatunde Oluwaseun , Mayerova-Hoskova Sarka
Published: September 2021

In this paper, we study the matrix representation of fuzzy soft sets, complement of fuzzy soft sets, product of fuzzy soft matrices and the application of fuzzy soft matrices in medical diagnosis presented by Lavanya and Akila. Additionally, a new method (max-min average) based on fuzzy reference function is introduced instead of the max-product method by Lavanya and Akila to extend Sanchez’s technique for decision making problems in medical diagnosis. Using the same data by Lavanya and Akila, the result shows that the new method gives more information about the medical status of the patients being considered in relation to a set of diseases.
Flow towards a Stagnation Region of a Curved Surface in a Hybrid Nanofluid with Buoyancy Effects
Authors: Waini Iskandar , Ishak Anuar , Pop Ioan
Published: September 2021

This paper examines the impact of hybrid nanoparticles on the stagnation point flow towards a curved surface. Silica (SiO2) and alumina (Al2O3) nanoparticles are added into water to form SiO2-Al2O3/water hybrid nanofluid. Both buoyancy-opposing and -assisting flows are considered. The governing partial differential equations are reduced to a set of ordinary differential equations, before being coded in MATLAB software to obtain the numerical solutions. Findings show that the solutions are not unique, where two solutions are obtained, for both buoyancy-assisting and -opposing flow cases. The local Nusselt number increases in the presence of the hybrid nanoparticles. The temporal stability analysis shows that only one of the solutions is stable over time.
RHOASo: An Early Stop Hyper-Parameter Optimization Algorithm
Authors: Muñoz Castañeda Ángel Luis , DeCastro-García Noemí , Escudero García David
Published: September 2021

This work proposes a new algorithm for optimizing hyper-parameters of a machine learning algorithm, RHOASo, based on conditional optimization of concave asymptotic functions. A comparative analysis of the algorithm is presented, giving particular emphasis to two important properties: the capability of the algorithm to work efficiently with a small part of a dataset and to finish the tuning process automatically, that is, without making explicit, by the user, the number of iterations that the algorithm must perform. Statistical analyses over 16 public benchmark datasets comparing the performance of seven hyper-parameter optimization algorithms with RHOASo were carried out. The efficiency of RHOASo presents the positive statistically significant differences concerning the other hyper-parameter optimization algorithms considered in the experiments. Furthermore, it is shown that, on average, the algorithm needs around 70% of the iterations needed by other algorithms to achieve competitive performance. The results show that the algorithm presents significant stability regarding the size of the used dataset partition.
Cavitation Dynamics and Inertial Cavitation Threshold of Lipid Coated Microbubbles in Viscoelastic Media with Bubble–Bubble Interactions
Authors: Qin Dui , Zou Qingqin , Lei Shuang , Wang Wei , Li Zhangyong
Published: September 2021

Encapsulated microbubbles combined with ultrasound have been widely utilized in various biomedical applications; however, the bubble dynamics in viscoelastic medium have not been completely understood. It involves complex interactions of coated microbubbles with ultrasound, nearby microbubbles and surrounding medium. Here, a comprehensive model capable of simulating the complex bubble dynamics was developed via taking the nonlinear viscoelastic behaviors of the shells, the bubble–bubble interactions and the viscoelasticity of the surrounding medium into account simultaneously. For two interacting lipid-coated bubbles with different initial radii in viscoelastic media, it exemplified that the encapsulating shell, the inter-bubble interactions and the medium viscoelasticity would noticeably suppress bubble oscillations. The inter-bubble interactions exerted a much stronger suppressing effect on the small bubble within the parameters examined in this paper, which might result from a larger radiated pressure acting on the small bubble due to the inter-bubble interactions. The lipid shells make the microbubbles exhibit two typical asymmetric dynamic behaviors (i.e., compression or expansion dominated oscillations), which are determined by the initial surface tension of the bubbles. Accordingly, the inertial cavitation threshold decreases as the initial surface tension increases, but increases as the shell elasticity and viscosity increases. Moreover, with the distance between bubbles decreasing and/or the initial radius of the large bubble increasing, the oscillations of the small bubble decrease and the inertial cavitation threshold increases gradually due to the stronger suppression effects caused by the enhanced bubble–bubble interactions. Additionally, increasing the elasticity and/or viscosity of the surrounding medium would also dampen bubble oscillations and result in a significant increase in the inertial cavitation threshold. This study may contribute to both encapsulated microbubble-associated ultrasound diagnostic and emerging therapeutic applications.
Investigation on Design Theory and Performance Analysis of Vacuum Capacitive Micromachined Ultrasonic Transducer
Authors: Huang Xiao , Wang Hongliang , Yu Lijun
Published: September 2021

The capacitive micromachined ultrasonic transducer (CMUT), as a new acoustic-electric conversion element, has a promising application prospect. In this paper, the structure of the vacuum capacitive micromachined ultrasonic transducer is presented, and its performance-influencing factors are investigated. Firstly, the influencing factors of the performance parameters of the vacuum CMUT are analyzed theoretically based on the circular plate model and flat plate capacitance model, and the design principles of the structural parameters of the CMUT cell are proposed. Then, the finite element simulation software COMSOL Multiphysics is used to construct CMUT cell models with different membrane materials, membrane shapes, membrane radius thicknesses, and cavity heights for simulation verification. The results show that both the membrane parameters and the cavity heights affect the performance parameters of the Vacuum CMUT. In order to improve the efficiency of the CMUT, materials with low bending stiffness should be selected, and the filling factor of the membrane should be increased. In order to achieve high-transmission sound pressure, a smaller radius thickness and a larger cavity height should be selected. To achieve high reception sensitivity, a larger membrane radius thickness and a smaller cavity height should be selected. In order to obtain high fractional bandwidth, a larger membrane radius thickness should be selected. The results of this paper provide a basis for the design of Vacuum CMUT cell structure.
Anaerobic Fungal Mevalonate Pathway Genomic Biases Lead to Heterologous Toxicity Underpredicted by Codon Adaptation Indices
Authors: Hillman Ethan T. , Frazier Elizabeth M. , Shank Evan K. , Ortiz-Velez Adrian N. , Englaender Jacob A. , Solomon Kevin V.
Published: September 2021

Anaerobic fungi are emerging biotechnology platforms with genomes rich in biosynthetic potential. Yet, the heterologous expression of their biosynthetic pathways has had limited success in model hosts like E. coli. We find one reason for this is that the genome composition of anaerobic fungi like P. indianae are extremely AT-biased with a particular preference for rare and semi-rare AT-rich tRNAs in E coli, which are not explicitly predicted by standard codon adaptation indices (CAI). Native P. indianae genes with these extreme biases create drastic growth defects in E. coli (up to 69% reduction in growth), which is not seen in genes from other organisms with similar CAIs. However, codon optimization rescues growth, allowing for gene evaluation. In this manner, we demonstrate that anaerobic fungal homologs such as PI.atoB are more active than S. cerevisiae homologs in a hybrid pathway, increasing the production of mevalonate up to 2.5 g/L (more than two-fold) and reducing waste carbon to acetate by ~90% under the conditions tested. This work demonstrates the bioproduction potential of anaerobic fungal enzyme homologs and how the analysis of codon utilization enables the study of otherwise difficult to express genes that have applications in biocatalysis and natural product discovery.
Application of Fungus Enzymes in Spent Mushroom Composts from Edible Mushroom Cultivation for Phthalate Removal
Authors: Chang Bea-Ven , Yang Chiao-Po , Yang Chu-Wen
Published: September 2021

Spent mushroom composts (SMCs) are waste products of mushroom cultivation. The handling of large amounts of SMCs has become an important environmental issue. Phthalates are plasticizers which are widely distributed in the environment and urban wastewater, and cannot be effectively removed by conventional wastewater treatment methods. In this study, SMCs are tested for their ability to remove phthalates, including benzyl butyl phthalate (BBP), di-n-butyl phthalate (DBP), and diethyl phthalate (DEP). Batch experiments reveal that BBP, DBP, and DEP can be degraded by the SMC enzyme extracts of four edible mushrooms: Pleurotus eryngii, Pleurotus djamor, Pleurotus ostreatus, and Auricularia polytricha. Potential fungus enzymes associated with BBP, DBP, and DEP degradation in SMCs (i.e., esterases, oxygenases, and oxidases/dehydrogenases) are uncovered by metaproteomic analysis using mass spectrometry. Bioreactor experiments indicate that the direct application of SMCs can remove BBP, DBP, and DEP from wastewater, through adsorption and biodegradation. The results of this study extend the application of white-rot fungi without laccases (e.g., Auricularia sp.) for the removal of organic pollutants which are not degraded by laccases. The application of SMCs for phthalate removal can be developed into a mycoremediation-based green and sustainable technology.
Enhancing Teak (Tectona grandis) Seedling Growth by Rhizosphere Microbes: A Sustainable Way to Optimize Agroforestry
Authors: Chaiya Leardwiriyakool , Gavinlertvatana Paiboolya , Teaumroong Neung , Pathom-aree Wasu , Chaiyasen Amornrat , Sungthong Rungroch , Lumyong Saisamorn
Published: September 2021

With its premium wood quality and resistance to pests, teak is a valuable tree species remarkably required for timber trading and agroforestry. The nursery stage of teak plantation needs critical care to warrant its long-term productivity. This study aimed to search for beneficial teak rhizosphere microbes and assess their teak-growth-promoting potentials during nursery stock preparation. Three teak rhizosphere/root-associated microbes, including two teak rhizobacteria (a nitrogen-fixing teak root endophyte-Agrobacterium sp. CGC-5 and a teak rhizosphere actinobacterium-Kitasatospora sp. TCM1-050) and an arbuscular mycorrhizal fungus (Claroideoglomus sp. PBT03), were isolated and used in this study. Both teak rhizobacteria could produce in vitro phytohormones (auxins) and catalase. With the pot-scale assessments, applying these rhizosphere microbes in the form of consortia offered better teak-growth-promoting activities than the individual applications, supported by significantly increased teak seedling biomass. Moreover, teak-growth-promoting roles of the arbuscular mycorrhizal fungus were highly dependent upon the support by other teak rhizobacteria. Based on our findings, establishing the synergistic interactions between beneficial rhizosphere microbes and teak roots was a promising sustainable strategy to enhance teak growth and development at the nursery stage and reduce chemical inputs in agroforestry.
In Search of Embodied Conversational and Explainable Agents for Health Behaviour Change and Adherence
Authors: Abdulrahman Amal , Richards Deborah
Published: September 2021

Conversational agents offer promise to provide an alternative to costly and scarce access to human health providers. Particularly in the context of adherence to treatment advice and health behavior change, they can provide an ongoing coaching role to motivate and keep the health consumer on track. Due to the recognized importance of face-to-face communication and establishment of a therapist-patient working alliance as the biggest single predictor of adherence, our review focuses on embodied conversational agents (ECAs) and their use in health and well-being interventions. The article also introduces ECAs who provide explanations of their recommendations, known as explainable agents (XAs), as a way to build trust and enhance the working alliance towards improved behavior change. Of particular promise, is work in which XAs are able to engage in conversation to learn about their user and personalize their recommendations based on their knowledge of the user and then tailor their explanations to the beliefs and goals of the user to increase relevancy and motivation and address possible barriers to increase intention to perform the healthy behavior.
Chitosan-Coated PLGA Nanoparticles Loaded with Peganum harmala Alkaloids with Promising Antibacterial and Wound Healing Activities
Authors: Azzazy Hassan Mohamed El-Said , Fahmy Sherif Ashraf , Mahdy Noha Khalil , Meselhy Meselhy Ragab , Bakowsky Udo
Published: September 2021

Wound healing is a major healthcare concern, and complicated wounds may lead to severe outcomes such as septicemia and amputations. To date, management choices are limited, which warrants the search for new potent wound healing agents. Natural products loaded in poly (lactic-co-glycolic acid) (PLGA) coated with chitosan (CS) constitute a promising antibacterial wound healing formulation. In this work, harmala alkaloid-rich fraction (HARF) loaded into PLGA nanoparticles coated with chitosan (H/CS/PLGA NPs) were designed using the emulsion-solvent evaporation method. Optimization of the formulation variables (HARF: PLGA and CS: PLGA weight ratios, sonication time) was performed using the 33 Box–Behnken design (BBD). The optimal NPs were characterized using transmission electron microscopy (TEM) and Attenuated Total Reflection Fourier-Transformed Infrared Spectroscopy (ATR-FTIR). The prepared NPs had an average particle size of 202.27 ± 2.44 nm, a PDI of 0.23 ± 0.01, a zeta potential of 9.22 ± 0.94 mV, and an entrapment efficiency of 86.77 ± 4.18%. In vitro drug release experiments showed a biphasic pattern where an initial burst of 82.50 ± 0.20% took place in the first 2 h, which increased to 87.50 ± 0.50% over 72 h. The designed optimal H/CS/PLGA NPs exerted high antibacterial activity against Staphylococcus aureus and Escherichia coli (MIC of 0.125 and 0.06 mg/mL, respectively) compared to unloaded HARF (MIC of 0.50 mg/mL). The prepared nanoparticles were found to be biocompatible when tested on human skin fibroblasts. Moreover, the wound closure percentage after 24 h of applying H/CS/PLGA NPs was found to be 94.4 ± 8.0%, compared to free HARF and blank NPs (68.20 ± 5.10 and 50.50 ± 9.40%, respectively). In conclusion, the three components of the developed nanoformulation (PLGA, chitosan, and HARF) have synergistic antibacterial and wound healing properties for the management of infected wounds.