Artykuły w czasopismach: „PDE template”

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Fu, Haibin, Shaojun Bian, Ehtzaz Chaudhry, Shuangbu Wang, Lihua You i Jian Jun Zhang. "PDE Surface-Represented Facial Blendshapes". Mathematics 9, nr 22 (15.11.2021): 2905. http://dx.doi.org/10.3390/math9222905.

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Partial differential equation (PDE)-based geometric modelling and computer animation has been extensively investigated in the last three decades. However, the PDE surface-represented facial blendshapes have not been investigated. In this paper, we propose a new method of facial blendshapes by using curve-defined and Fourier series-represented PDE surfaces. In order to develop this new method, first, we design a curve template and use it to extract curves from polygon facial models. Then, we propose a second-order partial differential equation and combine it with the constraints of the extracted curves as boundary curves to develop a mathematical model of curve-defined PDE surfaces. After that, we introduce a generalized Fourier series representation to solve the second-order partial differential equation subjected to the constraints of the extracted boundary curves and obtain an analytical mathematical expression of curve-defined and Fourier series-represented PDE surfaces. The mathematical expression is used to develop a new PDE surface-based interpolation method of creating new facial models from one source facial model and one target facial model and a new PDE surface-based blending method of creating more new facial models from one source facial model and many target facial models. Some examples are presented to demonstrate the effectiveness and applications of the proposed method in 3D facial blendshapes.

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Pawlowski, Roger P., Eric T. Phipps, Andrew G. Salinger, Steven J. Owen, Christopher M. Siefert i Matthew L. Staten. "Automating Embedded Analysis Capabilities and Managing Software Complexity in Multiphysics Simulation, Part II: Application to Partial Differential Equations". Scientific Programming 20, nr 3 (2012): 327–45. http://dx.doi.org/10.1155/2012/818262.

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A template-based generic programming approach was presented in Part I of this series of papers [Sci. Program. 20 (2012), 197–219] that separates the development effort of programming a physical model from that of computing additional quantities, such as derivatives, needed for embedded analysis algorithms. In this paper, we describe the implementation details for using the template-based generic programming approach for simulation and analysis of partial differential equations (PDEs). We detail several of the hurdles that we have encountered, and some of the software infrastructure developed to overcome them. We end with a demonstration where we present shape optimization and uncertainty quantification results for a 3D PDE application.

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CORINTO, FERNANDO, i MARCO GILLI. "ON STABILITY OF CELLULAR NEURAL NETWORKS WITH POLYNOMIAL INTERACTIONS". International Journal of Neural Systems 13, nr 06 (grudzień 2003): 379–85. http://dx.doi.org/10.1142/s0129065703001704.

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Cellular neural/nonlinear networks (CNNs) are analog dynamic processor arrays, that present local interconnections. CNN models with polynomial interactions among the cells (Polynomial type CNNs) have been recently introduced. They are useful for solving some complex computational problems and for real-time implementation of PDE-based algorithms. This manuscript provides some simple and rigorous sufficient conditions for stability of polynomial type CNNs. A particular emphasis is given to conditions that can be expressed in terms of template elements, since they can be exploited for design purposes.

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Sun, Jinyang, Fangjun Luan i Hanhui Wu. "Optic Disc Segmentation by Balloon Snake with Texture from Color Fundus Image". International Journal of Biomedical Imaging 2015 (2015): 1–14. http://dx.doi.org/10.1155/2015/528626.

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A well-established method for diagnosis of glaucoma is the examination of the optic nerve head based on fundus image as glaucomatous patients tend to have larger cup-to-disc ratios. The difficulty of optic segmentation is due to the fuzzy boundaries and peripapillary atrophy (PPA). In this paper a novel method for optic nerve head segmentation is proposed. It uses template matching to find the region of interest (ROI). The method of vessel erasing in the ROI is based on PDE inpainting which will make the boundary smoother. A novel optic disc segmentation approach using image texture is explored in this paper. A cluster method based on image texture is employed before the optic disc segmentation step to remove the edge noise such as cup boundary and vessels. We replace image force in the snake with image texture and the initial contour of the balloon snake is inside the optic disc to avoid the PPA. The experimental results show the superior performance of the proposed method when compared to some traditional segmentation approaches. An average segmentation dice coefficient of 94% has been obtained.

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Jones, Susan, i Janet M. Thornton. "Protein–DNA Interactions: The Story so Far and a New Method for Prediction". Comparative and Functional Genomics 4, nr 4 (2003): 428–31. http://dx.doi.org/10.1002/cfg.303.

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This review describes methods for the prediction of DNA binding function, and specifically summarizes a new method using 3D structural templates. The new method features the HTH motif that is found in approximately one-third of DNAbinding protein families. A library of 3D structural templates of HTH motifs was derived from proteins in the PDB. Templates were scanned against complete protein structures and the optimal superposition of a template on a structure calculated. Significance thresholds in terms of a minimum root mean squared deviation (rmsd) of an optimal superposition, and a minimum motif accessible surface area (ASA), have been calculated. In this way, it is possible to scan the template library against proteins of unknown function to make predictions about DNA-binding functionality.

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Sun, Jie, i Ke Chen. "NSiteMatch: Prediction of Binding Sites of Nucleotides by Identifying the Structure Similarity of Local Surface Patches". Computational and Mathematical Methods in Medicine 2017 (2017): 1–16. http://dx.doi.org/10.1155/2017/5471607.

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Nucleotides play a central role in life-form metabolism, by interacting with proteins and mediating the function of proteins. It is estimated that nucleotides constitute about 15% of the biologically relevant ligands included in PDB. Prediction of binding sites of nucleotides is useful in understanding the function of proteins and can facilitate the in silico design of drugs. In this study, we propose a nucleotide-binding site predictor, namely, NSiteMatch. The NSiteMatch algorithm integrates three different strategies: geometrical analysis, energy calculation, and template comparison. Unlike a traditional template-based predictor, which identifies global similarity between target structure and template, NSiteMatch concerns the local similarity between a surface patch of the target protein and the binding sites of template. To this end, NSiteMatch identifies more templates than traditional template-based predictors. The NSiteMatch predictor is compared with three representative methods, Findsite, Q-SiteFinder, and MetaPocket. An extensive evaluation demonstrates that NSiteMatch achieves higher success rates than Findsite, Q-SiteFinder, and MetaPocket, in prediction of binding sites of ATP, ADP, and AMP.

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Byun, Hyeran, i Byoungchul Ko. "Robust Face Detection and Tracking for Real-Life Applications". International Journal of Pattern Recognition and Artificial Intelligence 17, nr 06 (wrzesień 2003): 1035–55. http://dx.doi.org/10.1142/s0218001403002721.

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In this paper, we propose a new face detection and tracking algorithm for real-life telecommunication applications, such as video conferencing, cellular phone and PDA. We combine template-based face detection and tracking method with color information to track a face regardless of various lighting conditions and complex backgrounds as well as the race. Based on our experiments, we generate robust face templates from wavelet-transformed lowpass and two highpass subimages at the second level low-resolution. However, since template matching is generally sensitive to the change of illumination conditions, we propose a new type of preprocessing method. Tracking method is applied to reduce the computation time and predict precise face candidate region even though the movement is not uniform. Facial components are also detected using k-means clustering and their geometrical properties. Finally, from the relative distance of two eyes, we verify the real face and estimate the size of facial ellipse. To validate face detection and tracking performance of our algorithm, we test our method using six different video categories of QCIF size which are recorded in dynamic environments.

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Sheng, Nan, Jing-shu Xiong, Yi-hua Wang, Hao Chen i Jian-fang Sun. "Infiltrative Plaques on the Temple". Pediatric Dermatology 32, nr 2 (marzec 2015): 283–84. http://dx.doi.org/10.1111/pde.12465.

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Wu, Tong, Yu Li, Hailin Xiao i Mingli Fu. "Molecular Modifications and Control of Processes to Facilitate the Synergistic Degradation of Polybrominated Diphenyl Ethers in Soil by Plants and Microorganisms Based on Queuing Scoring Method". Molecules 26, nr 13 (26.06.2021): 3911. http://dx.doi.org/10.3390/molecules26133911.

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In this paper, a combination of modification of the source and regulation of the process was used to control the degradation of PBDEs by plants and microorganisms. First, the key proteins that can degrade PBDEs in plants and microorganisms were searched in the PDB (Protein Data Bank), and a molecular docking method was used to characterize the binding ability of PBDEs to two key proteins. Next, the synergistic binding ability of PBDEs to the two key proteins was evaluated based on the queuing integral method. Based on this, three groups of three-dimensional quantitative structure-activity relationship (3D-QSAR) models of plant-microbial synergistic degradation were constructed. A total of 30 PBDE derivatives were designed using BDE-3 as the template molecule. Among them, the effect on the synergistic degradation of six PBDE derivatives, including BDE-3-4, was significantly improved (increased by more than 20%) and the environment-friendly and functional evaluation parameters were improved. Subsequently, studies on the synergistic degradation of PBDEs and their derivatives by plants and microorganisms, based on the molecular docking method, found that the addition of lipophilic groups by modification is beneficial to enhance the efficiency of synergistic degradation of PBDEs by plants and microorganisms. Further, while docking PBDEs, the number of amino acids was increased and the binding bond length was decreased compared to the template molecules, i.e., PBDE derivatives could be naturally degraded more efficiently. Finally, molecular dynamics simulation by the Taguchi orthogonal experiment and a full factorial experimental design were used to simulate the effects of various regulatory schemes on the synergistic degradation of PBDEs by plants and microorganisms. It was found that optimal regulation occurred when the appropriate amount of carbon dioxide was supplied to the plant and microbial systems. This paper aims to provide theoretical support for enhancing the synergistic degradation of PBDEs by plants and microorganisms in e-waste dismantling sites and their surrounding polluted areas, as well as, realize the research and development of green alternatives to PBDE flame retardants.

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Suprianto, Made Budiarsa i Fatmah Dhafir. "3D Structure of VP1 Structural Protein on Enterovirus A71 Using Swiss-Model". BIOEDUSCIENCE: Jurnal Pendidikan Biologi dan Sains 4, nr 1 (30.06.2020): 37–47. http://dx.doi.org/10.29405/j.bes/4137-474353.

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Background: VP1 structural protein plays a role as a key player in the pathogenesis, has a uniqueness that is interesting enough to be studied by studying the nature and function of structural proteins VP1. This study aims to predict the three-dimensional structure of proteins VP1 on EV-A71. Methods: The target protein is obtained from UniProt server with an access code A0A097EV89using templates 4cey.1.A (PDB ID) were analyzed in silico by homology method using SWISS-MODEL server. Results: Analysis showed the target protein and the template has 95.29% identity and is composed of 297 amino acids with a value of -2.15 QMEAN. Structural protein VP1 in Ramachandran Plots have a stable structure, non-glycine residue in the outlier regions only around 0.34% (A53 ALA) Rated rotamer outliers 1.61%. Conclusion: The three-dimensional structure model of the protein studied has a stable structure and the information obtained is useful for further research in developing vaccines for diseases caused by EV-A71.

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Oh, Sanghyun, Yoo S. Hong, Jihwan Lee i Yong Se Kim. "AN EVALUATION METHOD FOR BUSINESS MODELS IN PRODUCT-SERVICE SYSTEMS DESIGN". Proceedings of the Design Society 1 (27.07.2021): 427–36. http://dx.doi.org/10.1017/pds.2021.43.

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AbstractTo pursue business innovation with PSS, many different PSS concepts are designed and evaluated. Various business models of a PSS design concept are devised and evaluated as well. Evaluation of the economic sustainability of PSS business models is critical. This paper presents a systematic method to evaluate the economic sustainability of PSS business models using a system dynamics modelling template. System dynamics modelling task is challenging for practitioners due to the variety of variables comprising business model strategies and their complex interrelationships. To enable the modelling task, a system dynamics modelling template composed of six modules of customer acquisition, channel acquisition, profit creation, resource acquisition, PSS provision, and partnership pattern has been devised. The PSS business model evaluation method has been illustrated using a smart study experience management service system design case to demonstrate the proposed system dynamics modelling template can reflect the case-specific business model which consists of the particular business model strategies.

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Stein, Norman. "CHAINSAW: a program for mutating pdb files used as templates in molecular replacement". Journal of Applied Crystallography 41, nr 3 (8.04.2008): 641–43. http://dx.doi.org/10.1107/s0021889808006985.

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CHAINSAWis a model editing program for use in molecular replacement. Given a sequence alignment between template and target, it modifies the template structure on a residue-by-residue basis by pruning nonconserved residues while leaving conserved residues unchanged. Three degrees of pruning are possible. An internal alignment algorithm is used to cope with any residues that may be missing from the X-ray structure.CHAINSAWhas been successfully used as a tool to assist in solving a number of protein structures.

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Nukunudompanich, Methawee, Surawut Chuangchote, Jatuporn Wootthikanokkhan i Yoshikazu Suzuki. "TiO₂ Nanorods Prepared from Anodic Aluminum Oxide Template and their Applications in Dye-Sensitized Solar Cells". International Letters of Chemistry, Physics and Astronomy 46 (styczeń 2015): 30–36. http://dx.doi.org/10.18052/www.scipress.com/ilcpa.46.30.

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Anodic aluminum oxide (AAO) was used as a template coupled with liquid process for synthesis of TiO2 nanorods. Immersion setting (IS) was carried out to insert a TiO2 precursor solution into AAO pore. With the calcination and NaOH treatment to remove AAO, SEM characterization revealed that TiO2 nanorods with diameter around 100-200 nm were successfully fabricated from AAO commercial templates. The synthesized nanorods mixed with commercial TiO2 nanoparticles (P-25) with a mixing ratio of 5:95 (by mass) were used as an electrode in a dye-sensitized solar cell (DSSC), The photoelectrodes made with nanorods showed a better performance than the cells used of only pristine TiO2 nanoparticles. The results from current density-voltage (J-V) characteristics of DSSCs showed that short-circuit current density (JSC), open-circuit voltage (VOC), fill factor (FF), and power conversion efficiency (PCE) are 11.78 mA/cm2, 0.72 V, 0.55, and 4.68%, respectively. Due to the effects of one-dimensional (1-D) nanostructure, the electron expressway concept was achieved in this research.

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Nukunudompanich, Methawee, Surawut Chuangchote, Jatuporn Wootthikanokkhan i Yoshikazu Suzuki. "TiO<sub>2</sub> Nanorods Prepared from Anodic Aluminum Oxide Template and their Applications in Dye-Sensitized Solar Cells". International Letters of Chemistry, Physics and Astronomy 46 (26.01.2015): 30–36. http://dx.doi.org/10.56431/p-p1r32g.

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Anodic aluminum oxide (AAO) was used as a template coupled with liquid process for synthesis of TiO2 nanorods. Immersion setting (IS) was carried out to insert a TiO2 precursor solution into AAO pore. With the calcination and NaOH treatment to remove AAO, SEM characterization revealed that TiO2 nanorods with diameter around 100-200 nm were successfully fabricated from AAO commercial templates. The synthesized nanorods mixed with commercial TiO2 nanoparticles (P-25) with a mixing ratio of 5:95 (by mass) were used as an electrode in a dye-sensitized solar cell (DSSC), The photoelectrodes made with nanorods showed a better performance than the cells used of only pristine TiO2 nanoparticles. The results from current density-voltage (J-V) characteristics of DSSCs showed that short-circuit current density (JSC), open-circuit voltage (VOC), fill factor (FF), and power conversion efficiency (PCE) are 11.78 mA/cm2, 0.72 V, 0.55, and 4.68%, respectively. Due to the effects of one-dimensional (1-D) nanostructure, the electron expressway concept was achieved in this research.

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Fang, Qunling, Yuhang Sun, Jinyu Duan, Linfeng Bai, Kezhu Xu, Qinshan Xiong, Huajian Xu, Ken Cham-Fai Leung, Ailing Hui i Shouhu Xuan. "ZIF-8 self-etching method for Au/polydopamine hybrid cubic microcapsules with modulated nanostructures". CrystEngComm 21, nr 45 (2019): 6935–44. http://dx.doi.org/10.1039/c9ce01426h.

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Parry, Christian S., Andrey Ivanov, Guelaguetza Vazquez-meves, Fatemah A. Alhakami, Jessika Agyepong, Kyungreem Han, Bernard R. Brooks i Sergei Nekhai. "4096 Refined structure of human ferroportin using restraints from mass spectrometry". Journal of Clinical and Translational Science 4, s1 (czerwiec 2020): 101–2. http://dx.doi.org/10.1017/cts.2020.314.

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OBJECTIVES/GOALS: Mammals require iron for hemoglobin, respiration, immunity and as cofactor in enzymes. But free iron is toxic from the production of reactive oxygen species. Ferroportin is the sole exporter of cellular iron and it crucially determines cellular and systemic iron levels. Labile iron must be tightly regulated. This requires structural understanding. METHODS/STUDY POPULATION: We built structure of human ferroportin (FPN1) using the ab ignition prediction approaches of Rosetta/Robetta and by comparative modeling with distance restraints in MODELLER. Templates selected were from solute carrier protein families of distantly related orthologs and homologs including a proton coupled peptide transporter (PDB ID: 4IKV) and the bacterial iron transporter in outward-open and inward-open states, (PDB ID: 5AYM, 5AYO). Each model was validated by experimental mass spectrometry data. The energy minimized structural model was inserted into a lipid bilayer, placed in a rectangular simulation box, covered with TIP3P water solvent balanced with counterions and conditioned. Finally, we carried out 350 nanoseconds molecular dynamics simulations. RESULTS/ANTICIPATED RESULTS: Our first model of FPN1 (571aa), using Rosetta/Robetta ab initio approach, resembles the structure of the proton-dependent transporter, POT and consists of 12 transmembrane helices. The membrane spanning helices veer away from the orientation in the structure of 4IKV. The alternate model using MODELLER and the method of satisfaction of constraints, returned one template, the structure of Bdellovibrio bacteriovorus iron (Fe2+) transporter homolog (5AYN, 440aa) with sequence identity of 19%. Aligning FPN1 on the template sequence incorporating structural information revealed better conservation (29%). This model also comprises 12 transmembrane helices in two bundles separated by a large intracellular loop. The iron binding site predicted in both models match the structures of distant bacterial homologs. DISCUSSION/SIGNIFICANCE OF IMPACT: We are using these experimentally verified structures and functional data to answer questions about the mechanism of ferroportin iron transport, structural dynamics and the significance of mutations in ferroportin seen in different populations, especially the Q248H mutation found in Africans and black Americans with moderate to high prevalence.

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Singha, Soumen, Bhaskar Khanra, Somen Goswami, Rituparna Mondal, Rajkumar Jana, Arka Dey, Sanjoy Kumar Dey i in. "Structural, optical, dielectric and electrical transport properties of a [Mg(H₂O)₆]²⁺-templated proton conducting, semiconducting and photoresponsive 3D hydrogen bonded supramolecular framework". New Journal of Chemistry 45, nr 44 (2021): 20596–611. http://dx.doi.org/10.1039/d1nj04237h.

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{[Co(2,5-Pdc)2,(H2O)2]2−·[Mg(H2O)6]2+·4(H2O)} (where 2,5-pdc = 2,5-pyridinedicarboxylate): a proton conducting semiconducting photoresponsive [Mg(H2O)6]2+ templated 3D hydrogen bonded supramolecular framework (HSF).

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Wang, Yanhu, Huihui Shi, Jiantao Sun, Jianjian Xu, Mengchun Yang i Jinghua Yu. "Hollow-Channel Paper Analytical Devices Supported Biofuel Cell-Based Self-Powered Molecularly Imprinted Polymer Sensor for Pesticide Detection". Biosensors 12, nr 11 (5.11.2022): 974. http://dx.doi.org/10.3390/bios12110974.

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Herein, a paper-based glucose/air biofuel cell (BFC) was constructed and implemented for self-powered pesticide detection. Our developed paper-based chip relies on a hollow-channel to transport fluids rather than capillarity, which reduces analysis times as well as physical absorption. The gold nanoparticles (Au NPs) and carbon nanotubes (CNTs) were adapted to modify the paper fibers to fabricate the flexible conductive paper anode/cathode electrode (Au–PAE/CNT–PCE). Molecularly imprinted polymers (MIPs) using 2,4-dichlorophenoxyacetic acid (2,4-D) as a template were synthesized on Au–PAE for signal control. In the cathode, bilirubin oxidase (BOD) was used for the oxygen reduction reaction. Based on a competitive reaction between 2,4-D and glucose-oxidase-labeled 2,4-D (GOx-2,4-D), the amount of GOx immobilized on the bioanode can be simply tailored, thus a signal-off self-powered sensing platform was achieved for 2,4-D determination. Meanwhile, the coupling of the paper supercapacitor (PS) with the paper-based chip provides a simple route for signal amplification. Combined with a portable digital multi-meter detector, the amplified signal can be sensitively readout. Through rational design of the paper analytical device, the combination of BFC and PS provides a new prototype for constructing a low-cost, simple, portable, and sensitive self-powered biosensor lab-on-paper, which could be easily expanded in the field of clinical analysis and drug delivery.

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Zhang, Bowei, Hongwei Ni, Rongsheng Chen, Tongcun Zhang, Xi Li, Weiting Zhan, Zhenyu Wang i Yao Xu. "Cytotoxicity effects of three-dimensional graphene in NIH-3T3 fibroblasts". RSC Advances 6, nr 51 (2016): 45093–102. http://dx.doi.org/10.1039/c6ra04018g.

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We present an evaluation of the in vitro cytotoxicity of 3D graphene sheets fabricated by carbonization of polydopamine (PDA) films on a template of aligned nanopore arrays (NPAs) on a stainless steel surface.

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Komari, Noer, Samsul Hadi i Eko Suhartono. "Pemodelan Protein dengan Homology Modeling menggunakan SWISS-MODEL". Jurnal Jejaring Matematika dan Sains 2, nr 2 (30.12.2020): 65–70. http://dx.doi.org/10.36873/jjms.2020.v2.i2.408.

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The three-dimensional (3D) structure of proteins is necessary to understand the properties and functions of proteins. Determining protein structure by laboratory equipment is quite complicated and expensive. An alternative method to predict the 3D structure of proteins in the in silico method. One of the in silico methods is homology modeling. Homology modeling is done using the SWISS-MODEL server. Proteins that will be modeled in the 3D structure are proteins that do not yet have a structure in the RCSB PDB database. Protein sequences were obtained from the UniProt database with code A0A0B6VWS2. The results showed that there were two models selected, namely model-1 with the PDB code template 1q0e and model-2 with the PDB code template 3gtv. The results of sequence alignment and model visualization show that model-1 and model-2 are identical. The evaluation and assessment of model-1 on the Ramachandran Plot have a Favored area of ??97.36%, a MolProbity score of 0.79, and a QMEAN value is 1.13. Model-1 is a good 3D protein structure model.

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Zhu, Qiuhong, Hua Jiao, Xiaoliang Zhao, Yufei Tang, Kang Zhao i Xingchun Gou. "Hydroxyapatite formation in biomimetic synthesis with the interface of a pDA@SIS membrane". RSC Advances 12, nr 21 (2022): 13209–19. http://dx.doi.org/10.1039/d2ra00910b.

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Porcine decellularized small intestine submucosa (SIS) is a collagen membrane, which offers great potential as an organic substrate template in mineralization processes due to its good biodegradability and biocompatibility.

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Sun, Qiang, Huaili Zheng, Xuebin Hu, Jun Li, Rui Zhao, Chun Zhao i Wei Ding. "Magnetic Template Anion Polyacrylamide–Polydopamine-Fe3O4 Combined with Ultraviolet/H2O2 for the Rapid Enrichment and Degradation of Diclofenac Sodium from Aqueous Environment". Polymers 12, nr 1 (2.01.2020): 72. http://dx.doi.org/10.3390/polym12010072.

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In this study, a novel system was set up by preparing a magnetic flocculant combining with ultraviolet/H2O2 to realize the rapid enrichment and degradation of diclofenac sodium (DCFS). For the magnetic flocculant, template anion polyacrylamide (TAPAM) with anion micro-block structure was prepared. Thereafter, polydopamine was used to modify TAPAM, Fe3O4 nanoparticles was grafted to the modified TAPAM by chelation, named template anion polyacrylamide-polydopamine-Fe3O4 (TAPAM-PDA-Fe3O4). Furthermore, the TAPAM-PDA-Fe3O4 preparation protocol was optimized by the response surface method (RSM). In the DCFS enrichment section, the rapid separation of flocs from water was realized by an external magnetic field and it indicated that the π–π stacking effect was dominant in neutral/alkaline condition, whereas charge neutralization was favored in acidic conditions. Meanwhile, a DCFS enrichment kinetic curve was much fitted by the pseudo-second-order kinetic model and DCFS enrichment isothermal curve was close to the Freundlich isothermal model, indicating the dependence of DCFS quantity enriched by TAPAM-PDA-Fe3O4 and a multilayer heterogeneous enrichment process. The degradation experiment confirmed that DCFS was effectively degraded by ultraviolet/H2O2/TAPAM-PDA-Fe3O4 and the maximum value of DCFS degradation efficiency reached 98.1%. Furthermore, the regeneration experiment showed that the enrichment and degradation efficiency of DCFS could maintain a relatively high level in the initial three recycles.

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Gao, Qiqian, Liying Wang, Xueyu Zhang, Lianfeng Duan, Xuesong Li, Xijia Yang i Wei Lü. "Carbon nanoparticle template assisted formation of mesoporous TiO2 photoanodes for quantum dot-sensitized solar cells". New Journal of Chemistry 43, nr 14 (2019): 5374–81. http://dx.doi.org/10.1039/c8nj05617j.

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While the power conversion efficiency (PCE) of quantum dot-sensitized solar cells (QDSSCs) is still far below their theoretical efficiency, we herein provide a method to improve the solar cell performance by using carbon nanoparticles as a template to construct TiO₂ mesoporous photoanodes.

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Zallio, M., i P. J. Clarkson. "The Inclusive Design Canvas. A Strategic Design Template for Architectural Design Professionals". Proceedings of the Design Society 2 (maj 2022): 81–90. http://dx.doi.org/10.1017/pds.2022.9.

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AbstractDesigning accessible and inclusive buildings is essential if they are to provide enjoyable and inspiring experiences for all their occupants. Research revealed that many architectural design professionals perceive a lack of awareness of the aspects to consider when designing to be a limiting factor in the uptake of Inclusive Design. By involving expert stakeholders this study provides evidence for the demand to create an Inclusive Design Canvas, a strategic design template offering an educational springboard for building industry professionals to embed Inclusive Design in the design process.

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Cui, Xinyu, Yuanyuan Yin, Zuo Ma, Yongkui Yin, Yue Guan, Shengzhong Rong, Jinxia Gao, Yingying Niu i Miaojing Li. "Polydopamine used as Hollow Capsule and Core–Shell Structures for Multiple Applications". Nano 10, nr 05 (lipiec 2015): 1530003. http://dx.doi.org/10.1142/s1793292015300030.

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Polydopamine (PDA) capsule and core–shell structures with tailored structures and properties are of particular interests due to their multifunctions and potential applications as new colloidal structures in diverse fields. Among the available fabrication methods, PDA film onto colloidal particles followed by selective template removal has attracted extensive attention due to its advantages of precise control over the size, wall thickness and functions of the obtained capsules. The past several years has witnessed a rapid increase of research concerning the new fabrication strategies, functionalization and applications of this kind of capsules and core–shell structures, particularly in many fields such as drug delivery, catalysis, antibacterial, etc. In this review, the very recent progress of the capsule and core–shell structures based on PDA are summarized. There are basically two sections, including the fabrication process of PDA capsules, core–shell structures, and the various applications based on PDA.

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Brylinski, Michal. "Is the growth rate of Protein Data Bank sufficient to solve the protein structure prediction problem using template-based modeling?" Bio-Algorithms and Med-Systems 11, nr 1 (31.01.2015): 1–7. http://dx.doi.org/10.1515/bams-2014-0024.

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AbstractThe Protein Data Bank (PDB) undergoes an exponential expansion in terms of the number of macromolecular structures deposited every year. A pivotal question is how this rapid growth of structural information improves the quality of three-dimensional models constructed by contemporary bioinformatics approaches. To address this problem, we performed a retrospective analysis of the structural coverage of a representative set of proteins using remote homology detected by COMPASS and HHpred. We show that the number of proteins whose structures can be confidently predicted increased during a 9-year period between 2005 and 2014 on account of the PDB growth alone. Nevertheless, this encouraging trend slowed down noticeably around the year 2008 and has yielded insignificant improvements ever since. At the current pace, it is unlikely that the protein structure prediction problem will be solved in the near future using existing template-based modeling techniques. Therefore, further advances in experimental structure determination, qualitatively better approaches in fold recognition, and more accurate template-free structure prediction methods are desperately needed.

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Mirloup, A., Q. Huaulmé, N. Leclerc, P. Lévêque, T. Heiser, P. Retailleau i R. Ziessel. "Thienyl-BOPHY dyes as promising templates for bulk heterojunction solar cells". Chemical Communications 51, nr 79 (2015): 14742–45. http://dx.doi.org/10.1039/c5cc05095b.

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Li, Guochang, Jian Li, Ziwei Zhou, Congling Li, Chao Cai, Bingkun Guo, Rodney D. Priestley, Lei Han i Rui Liu. "Silica-polydopamine core–shell self-confined templates for ultra-stable hollow Pt anchored N-doped carbon electrocatalysts". Dalton Transactions 46, nr 47 (2017): 16419–25. http://dx.doi.org/10.1039/c7dt03021e.

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We present the use of silica-polydopamine (SiO₂@PDA) core–shell nanoparticles (NPs) as self-confined templates for the fabrication of ultra-stable hollow Pt anchored N-doped carbon nanospheres (Pt/HN-C).

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Zhang, Wen, Juanjuan Wang, Xue Han, Lele Li, Enping Liu i Conghua Lu. "Carbon Nanotubes and Polydopamine Modified Poly(dimethylsiloxane) Sponges for Efficient Oil–Water Separation". Materials 14, nr 9 (7.05.2021): 2431. http://dx.doi.org/10.3390/ma14092431.

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In this paper, effective separation of oil from both immiscible oil–water mixtures and oil-in-water (O/W) emulsions are achieved by using poly(dimethylsiloxane)-based (PDMS-based) composite sponges. A modified hard template method using citric acid monohydrate as the hard template and dissolving it in ethanol is proposed to prepare PDMS sponge composited with carbon nanotubes (CNTs) both in the matrix and the surface. The introduction of CNTs endows the composite sponge with enhanced comprehensive properties including hydrophobicity, absorption capacity, and mechanical strength than the pure PDMS. We demonstrate the successful application of CNT-PDMS composite in efficient removal of oil from immiscible oil–water mixtures within not only a bath absorption, but also continuous separation for both static and turbulent flow conditions. This notable characteristic of the CNT-PDMS sponge enables it as a potential candidate for large-scale industrial oil–water separation. Furthermore, a polydopamine (PDA) modified CNT-PDMS is developed here, which firstly realizes the separation of O/W emulsion without continuous squeezing of the sponge. The combined superhydrophilic and superoleophilic property of PDA/CNT-PDMS is assumed to be critical in the spontaneously demulsification process.

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LEMAN, K., G. ANKIT i T. TAN. "PDA BASED HUMAN MOTION RECOGNITION SYSTEM". International Journal of Software Engineering and Knowledge Engineering 15, nr 02 (kwiecień 2005): 199–204. http://dx.doi.org/10.1142/s021819400500218x.

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This paper describes the design and implementation of autonomous real-time motion recognition on a Personal Digital Assistant. All previous such applications have been non real-time and required user interaction. The motivation to use a PDA is to test the viability of performing complex video processing on an embedded platform. The application was constructed using a representation and recognition technique for identifying patterns using Hu Moments. The approach is based upon temporal templates (Motion Energy and History Images) and their matching in time. The implementation was done using Intel Integrated Performance Primitives functions in order to reduce the complexity of the application. Tests were conducted using 5 different motion actions like arm waving, walking from left and right of the camera, head tilting and bending forward. Suggestions were also made on how to improve the performance of the system and possible applications.

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YANG, ZHIWEI, FEI WU, JUNXING LIU, SHUQIU WANG i XIAOHUI YUAN. "SUSCEPTIBILITY OF COMMERCIAL NEURAMINIDASE INHIBITORS AGAINST 2013 A/H7N9 INFLUENZA VIRUS: A DOCKING AND MOLECULAR DYNAMICS STUDY". Journal of Theoretical and Computational Chemistry 12, nr 07 (listopad 2013): 1350069. http://dx.doi.org/10.1142/s0219633613500697.

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The latest influenza A ( H 7 N 9) virus attracted a worldwide attention due to the first report of human infections and the continuing reported cases in China. In this work, homology modeling, docking and molecular dynamics simulations were combined to study the interactions between neuraminidase ( N 9_2013, from novel A/ H 7 N 9 virus) and agents zanamivir, oseltamivir, peramivir. It was found that N 9_2013 protein is structurally close to the template (PDB code: 1F8B), especially the active site. The binding properties of N 9_2013 protein were nearly identical to those of template. As a result, the three available drugs should be still efficacious for the new emerging A ( H 7 N 9) virus. However, the stabilities of docked complexes and binding affinities (Eint) were slightly reduced, in contrast to the corresponding inhibitor-template complexes, with the values of -82.27 (-84.30), -78.84 (-80.28) and -77.52 (-81.94) kcal mol-1, respectively. Besides, R292K mutation might induce the resistance of the novel virus to the commercial inhibitors. Thus, it arouses the need for continuous monitoring of antiviral drug susceptibilities.

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Deng, Kui Lin, Tao Yi Zhang, Xiao Jing Zhang, Ping Xie i Rong Ben Zhang. "H-bonding template-directed synthesis of a complete m-PDA-bridged ladder polyhydrosiloxane (OLPHS)". Chinese Chemical Letters 18, nr 7 (lipiec 2007): 779–82. http://dx.doi.org/10.1016/j.cclet.2007.05.037.

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Frogel, Michael, Avram Flamm, Mayer Sagy, Katharine Uraneck, Edward Conway, Michael Ushay, Bruce M. Greenwald i in. "Utilizing a Pediatric Disaster Coalition Model to Increase Pediatric Critical Care Surge Capacity in New York City". Disaster Medicine and Public Health Preparedness 11, nr 4 (13.06.2017): 473–78. http://dx.doi.org/10.1017/dmp.2016.152.

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AbstractA mass casualty event can result in an overwhelming number of critically injured pediatric victims that exceeds the available capacity of pediatric critical care (PCC) units, both locally and regionally. To address these gaps, the New York City (NYC) Pediatric Disaster Coalition (PDC) was established. The PDC includes experts in emergency preparedness, critical care, surgery, and emergency medicine from 18 of 25 major NYC PCC-capable hospitals. A PCC surge committee created recommendations for making additional PCC beds available with an emphasis on space, staff, stuff (equipment), and systems. The PDC assisted 15 hospitals in creating PCC surge plans by utilizing template plans and site visits. These plans created an additional 153 potential PCC surge beds. Seven hospitals tested their plans through drills. The purpose of this article was to demonstrate the need for planning for disasters involving children and to provide a stepwise, replicable model for establishing a PDC, with one of its primary goals focused on facilitating PCC surge planning. The process we describe for developing a PDC can be replicated to communities of any size, setting, or location. We offer our model as an example for other cities. (Disaster Med Public Health Preparedness. 2017;11:473–478)

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Wang, Jianping, Min Zhang, Teng Miao, Yang Ling, Qiong Wen, Jing Zheng, Jingli Xu, Tasawar Hayat i Njud S. Alharbi. "A facile self-template and carbonization strategy to fabricate nickel nanoparticle supporting N-doped carbon microtubes". Inorganic Chemistry Frontiers 5, nr 4 (2018): 844–52. http://dx.doi.org/10.1039/c8qi00039e.

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A facile one-pot approach is utilized to construct nickel-ion–PDA complex thin coatings on MoO₃@PPy microtubes, which can be carbonized under an inert atmosphere to obtain nickel/N-doped carbon microtubes (Ni/NCMTs).

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Damberga, Daina, Viktoriia Fedorenko, Kārlis Grundšteins, Şahin Altundal, Andris Šutka, Arunas Ramanavičius, Emerson Coy, Radosław Mrówczyński, Igor Iatsunskyi i Roman Viter. "Influence of PDA Coating on the Structural, Optical and Surface Properties of ZnO Nanostructures". Nanomaterials 10, nr 12 (6.12.2020): 2438. http://dx.doi.org/10.3390/nano10122438.

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Polydopamine (PDA) is a new biocompatible material, which has prospects in biomedical and sensor applications. Due to functional groups, it can host wide range of biomolecules. ZnO nanostructures are well known templates for optical sensors and biosensors. The combination of ZnO and PDA results in a change of optical properties of ZnO–PDA composites as a shift of photoluminescence (PL) peaks and PL quenching. However, to date, the effect of the PDA layer on fundamental properties of ZnO–PDA nanostructures has not been studied. The presented paper reports on optical and surface properties of novel ZnO–PDA nanocomposites. PDA layers were chemically synthesized on ZnO nanostructures from different solution concentrations of 0.3, 0.4, 0.5 and 0.7 mg/mL. Structure, electronic and optical properties were studied by SEM, Raman, FTIR, diffuse reflectance and photoluminescence methods. The Z-potential of the samples was evaluated in neutral pH (pH = 7.2). The response of the samples towards poly-l-lysine adsorption, as a model molecule, was studied by PL spectroscopy to evaluate the correlation between optical and surface properties. The role of the PDA concentration on fundamental properties was discussed.

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Chin, Hsien-Kuo, Pei-Ying Lin, Jyunde Chen, Rajendranath Kirankumar, Zhi-Hong Wen i Shuchen Hsieh. "Polydopamine-Mediated Ag and ZnO as an Active and Recyclable SERS Substrate for Rhodamine B with Significantly Improved Enhancement Factor and Efficient Photocatalytic Degradation". Applied Sciences 11, nr 11 (27.05.2021): 4914. http://dx.doi.org/10.3390/app11114914.

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We demonstrate the development of an active multicomponent Ag/PDA/ZnO@GMF surface-enhanced Raman scattering (SERS) substrate via introducing bio-inspired polydopamine (PDA) in between a noble metal (AgNPs) and ZnO nanorods. The insertion of PDA enabled efficient charge redistribution between metal and semiconductor through their aromatic cores. The substrate exhibited a high enhancement factor (EF) of 1010 for the organic pollutant dye Rhodamine B (RhB). Subsequent exposure of a RhB-loaded substrate to an external UV light source developed an efficient pathway for RhB degradation and replenished the substrate for multiple usage cycles with remarkable photostability. Thus, enhanced performance of the substrate in terms of light-harvesting capability and high charge-separation efficiency was observed. In addition, the much larger surface area of the branched ZnO nanostructures served as a template for PDA assisted synthesis and controlled deposition of AgNPs, which further improved the SERS effect. Our work seeks to understand the contributions of the noble metal and semiconductor components and the synergistic effects of combining them with a facile charge transport medium to enable the fabrication of highly efficient SERS substrates for use in industrial and environmental applications.

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Siddiqi, Abdul Rauf, Pierre Nioche, Abdul Basit Siddiqui, Sadaf Abdul Rauf, Amir Waseem i Bruno O. Villoutreix. "EFFICIENCY OF A HIERARCHICAL DOCKING PROTOCOL FOR COMPUTATIONAL LIGAND SCREENING AGAINST HOMOLOGY MODELS". Biomedical Engineering: Applications, Basis and Communications 26, nr 02 (12.03.2014): 1450024. http://dx.doi.org/10.4015/s1016237214500240.

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We assessed the efficiency of a hierarchical docking protocol against homology models in virtual ligand screening (VLS) studies. A low resolution model of factor X (FX) was built on a template of Trypsin molecule (PDB ID:1EB2). Afterward VLS was performed involving a hierarchical protocol, rigid body followed by flexible docking, both against model as well as an X-ray structure of FX (PDB ID:1FJS) using a smart library of 50,000 chemical compounds seeded with 9 known inhibitors of FX. The percentage enrichments of screened chemical compounds obtained both from the crystal structure and homology model of FX were compared to analyze the efficiency of the protocol. In the first 5% of the finally ranked database of the screened compounds, both against model and the X-ray structure, 67% of the inhibitors were retrieved.

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Jiang, Binbin, Ranhong Li, Xu He, Yunlong Chai, Yuxin Chai i Yan Wang. "Fabrication PDA-polyurea microcapsules with anti-photolysis and sustained-release performances via Pickering emulsion template". Colloid and Polymer Science 300, nr 1 (13.11.2021): 1–10. http://dx.doi.org/10.1007/s00396-021-04922-6.

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Jiang, Wenwen, Xinyue Zhang, Yafei Luan, Rensheng Wang, Hanzhou Liu, Dan Li i Liang Hu. "Using γ-Ray Polymerization-Induced Assemblies to Synthesize Polydopamine Nanocapsules". Polymers 11, nr 11 (25.10.2019): 1754. http://dx.doi.org/10.3390/polym11111754.

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This work reports a simple and robust strategy for synthesis of polydopamine nanocapsules (PDA NCs). First, polymer assemblies were synthesized by a γ-ray-induced liquid–liquid (H2O–acrylate) interface polymerization strategy, in the absence of any surfactants. 1H nuclear magnetic resonance analysis and molecular dynamics simulation reveal that the generation of polymer assemblies largely depends on the hydrophilicity of acrylate and gravity of the oligomers at the interface. By virtue of the spherical structure and mechanic stability of the polymer assemblies, PDA NCs are next prepared by the interfacial polymerization of dopamine onto the assemblies, followed by the removal of templates by using ethanol. The polydopamine nanocapsules are shown to load and release ciprofloxacin (CIP, a model drug), such that the CIP-loaded PDA NCs are able to inhibit the growth of Escherichia coli.

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40

Jia, Hanzhong, Cheng Gu, Hui Li, Xiaoyun Fan, Shouzhu Li i Chuanyi Wang. "Effect of groundwater geochemistry on pentachlorophenol remediation by smectite-templated nanosized Pd0/Fe0". Environmental Science and Pollution Research 19, nr 8 (17.04.2012): 3498–505. http://dx.doi.org/10.1007/s11356-012-0895-z.

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Augustin, Laura, Sabrina Pfrang, Andrea Wolffram i Christiane Beyer. "THE VALUE OF THE NON-USER: DEVELOPING (NON-)USER PROFILES FOR THE DEVELOPMENT OF A ROBOT VACUUM WITH THE USE OF THE (NON-)PERSONA". Proceedings of the Design Society 1 (27.07.2021): 3131–40. http://dx.doi.org/10.1017/pds.2021.574.

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AbstractThis contribution explores non-user integration in a product development context of the development of a vacuum robot in order to analyse users as well as non-users of a product. While user profiles like the persona have been part of product development and product design for years, the non-user has not been widely explored.Within this contribution the known concept of the persona is extended and further developed to the non-persona, a profile that describes non-users and why they do not use a certain product, in this case the vacuum robot. Including the non-user in product development offers the chance of addressing yet unidentified product requirements and therefore opening the product up to a bigger audience. This template works for both users and non-users and can be used to include both sides in a development project.

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Zhang, Chengxin, Wei Zheng, S. M. Mortuza, Yang Li i Yang Zhang. "DeepMSA: constructing deep multiple sequence alignment to improve contact prediction and fold-recognition for distant-homology proteins". Bioinformatics 36, nr 7 (18.11.2019): 2105–12. http://dx.doi.org/10.1093/bioinformatics/btz863.

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Abstract Motivation The success of genome sequencing techniques has resulted in rapid explosion of protein sequences. Collections of multiple homologous sequences can provide critical information to the modeling of structure and function of unknown proteins. There are however no standard and efficient pipeline available for sensitive multiple sequence alignment (MSA) collection. This is particularly challenging when large whole-genome and metagenome databases are involved. Results We developed DeepMSA, a new open-source method for sensitive MSA construction, which has homologous sequences and alignments created from multi-sources of whole-genome and metagenome databases through complementary hidden Markov model algorithms. The practical usefulness of the pipeline was examined in three large-scale benchmark experiments based on 614 non-redundant proteins. First, DeepMSA was utilized to generate MSAs for residue-level contact prediction by six coevolution and deep learning-based programs, which resulted in an accuracy increase in long-range contacts by up to 24.4% compared to the default programs. Next, multiple threading programs are performed for homologous structure identification, where the average TM-score of the template alignments has over 7.5% increases with the use of the new DeepMSA profiles. Finally, DeepMSA was used for secondary structure prediction and resulted in statistically significant improvements in the Q3 accuracy. It is noted that all these improvements were achieved without re-training the parameters and neural-network models, demonstrating the robustness and general usefulness of the DeepMSA in protein structural bioinformatics applications, especially for targets without homologous templates in the PDB library. Availability and implementation https://zhanglab.ccmb.med.umich.edu/DeepMSA/. Supplementary information Supplementary data are available at Bioinformatics online.

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Löffler, Frank E., Qing Sun, Jieran Li i James M. Tiedje. "16S rRNA Gene-Based Detection of Tetrachloroethene-Dechlorinating Desulfuromonas andDehalococcoides Species". Applied and Environmental Microbiology 66, nr 4 (1.04.2000): 1369–74. http://dx.doi.org/10.1128/aem.66.4.1369-1374.2000.

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ABSTRACT Members of the genera Desulfuromonas andDehalococcoides reductively dechlorinate tetrachloroethene (PCE) and trichloroethene. Two primer pairs specific to hypervariable regions of the 16S rRNA genes of the Dehalococcoides group (comprising Dehalococcoides ethenogenes andDehalococcoides sp. strain FL2) and the acetate-oxidizing, PCE-dechlorinating Desulfuromonas group (comprisingDesulfuromonas sp. strain BB1 and Desulfuromonas chloroethenica) were designed. The detection threshold of a nested PCR approach using universal bacterial primers followed by a second PCR with the Desulfuromonas dechlorinator-targeted primer pair was 1 × 103 BB1 cells added per gram (wet weight) of sandy aquifer material. Total community DNA isolated from sediments of three Michigan rivers and six different chloroethene-contaminated aquifer samples was used as template in nested PCR. All river sediment samples yielded positive signals with the BB1- and the Dehalococcoides-targeted primers. One chloroethene-contaminated aquifer tested positive with theDehalococcoides-targeted primers, and another contaminated aquifer tested positive with the Desulfuromonasdechlorinator-targeted primer pair. Restriction fragment analysis of the amplicons could discriminate strain BB1 from other knownDesulfuromonas species. Microcosm studies confirmed the presence of PCE-dechlorinating, acetate-oxidizingDesulfuromonas and hydrogenotrophicDehalococcoides species in samples yielding positive PCR signals with the specific primers.

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Szczesny, Pawel, Grzegorz Wieczorek i Piotr Zielenkiewicz. "MOFOID--not only the protein modeling server." Acta Biochimica Polonica 52, nr 1 (31.03.2005): 267–69. http://dx.doi.org/10.18388/abp.2005_3518.

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MOFOID is a new server developed mainly for automated modeling of protein structures by their homology to the structures deposited in the PDB database. Selection of a template and calculation of the alignment is performed with the Smith-Waterman or Needleman-Wunsch algorithms implemented in the EMBOSS package. The final model is built and optimised with programs from the JACKAL package. The wide spectrum of options in the web-based interface and the possibility of uploading user's own alignment make MOFOID a suitable platform for testing new approaches in the alignment building. The server is available at https:// valis.ibb.waw.pl/mofoid/.

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Hou, Yuemin, i Linhong Ji. "ON FORMATION OF STRUCTURES: DESIGN EXAMPLES AND DISCUSSION". Proceedings of the Design Society 1 (27.07.2021): 2287–96. http://dx.doi.org/10.1017/pds.2021.490.

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AbstractThis paper discusses the formation of structures by taking the process of gene transcription and translation as the template. The hypothesis of this paper is that the gene transcription and translation process can describe the formation of structures both in engineering design and in biology. The paper first presents design examples including integrated circuit (IC) chambers, flapping wings of bird robots, and typical mechanisms and formulate the formation patterns of the design process as four steps: information interpretation, selection of building blocks, the connection of building blocks, and formation of structures. The key step of the formation process is to assemble building blocks for structures both in engineering and in biology. Building blocks in biology are amino acids while they are structures in design. The autonomous degree of the formation process depends on the level of building blocks. The reuse degree of the building blocks depends on the level of building blocks too. In biology, structures of proteins are self-organized, so one way towards design automation is to use lower-level building blocks.

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Zhang, Shuangxia, Yan Liu i Bo Liu. "Highly Active Nano-Reactor for Responding Tumor Microenvironment and Antitumor Therapy". Technology in Cancer Research & Treatment 21 (styczeń 2022): 153303382210956. http://dx.doi.org/10.1177/15330338221095670.

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The tumor microenvironment is complex and changeable, so the design of a nano-delivery system for the tumor microenvironment has attracted wide attention. Based on this, we designed an intelligent nano-reactor for the characteristics of acidic pH and hypoxia in the tumor microenvironment. Firstly, the silver nano-balls were synthesized by the biological template method, which exhibited a good photothermal conversion efficiency and can realize the photothermal treatment of tumor sites. Subsequently, the hypoxic prodrug tirapazamine (TPZ) and polydopamine (PDA) for chemotherapy were self-assembled. After PDA arrived at the tumor site (pH 5.5) from the normal physiological environment (pH 7.4), the hypoxic prodrug TPZ was released in pH response by PDA. Subsequently, TPZ selectively induced obvious cell damage under tumor hypoxia stimulation but had no toxic effect on normal cells under normal oxygen. In addition, the nano-converter was loaded with iRGD on the surface, which enhanced the targeted delivery of the nano-reactor to achieve a highly effective antitumor effect. The nano-reactor was capable of combining photothermal/chemotherapy therapy. Importantly, it can selectively kill tumor cells without damaging normal cells based on the characteristics of the tumor microenvironment, with high bio-safety and clinical transformation potential.

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Reddy, Chinreddy Subramanyam. "Phylogenetic and modelling analysis of purple acid phosphatase 18 (SiPAP18) from Setaria italica". Bioinformation 17, nr 8 (31.08.2021): 727–30. http://dx.doi.org/10.6026/97320630017727.

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Purple acid phosphatases belong to metallo-phosphatase family. Intracellular phosphatases are crucial for phosphorus (P) distribution in the cell and are highly induced in phosphorus-deprived conditions in the soil. Disparate PAP isoforms exist within discrete subcellular compartments in Setaria italica and their expression in P deprived conditions fosters phosphorus amelioration. We isolated the SiPAP18 gene and developed the homology SiPAP18 protein model based on the crystal structure of the Kidney bean PvPAP (PDB ID: 2QFP) as template (sequence similarity 42.7%) using Modeller 9.12 with adequate validation. Structure model analysis shows the significance of five conserved signatures with seven metal-paired amino acid residues during P-deprivation induced phosphorus amelioration.

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Tao, Wei Ye, Lai You Wang, Guo Quan Huang i Man Luo. "Three-Dimensional Protein Structure Prediction for CD36". Advanced Materials Research 881-883 (styczeń 2014): 390–93. http://dx.doi.org/10.4028/www.scientific.net/amr.881-883.390.

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CD36 is a class B scavenger receptor, which is on the surface of many cells such as platelets, macrophages, endothelial and smooth muscle cells. CD36 has been shown to play a critical role in the development of atherosclerosis by its capacity to adhere oxidized low density lipoproteins (OxLDL). It’s very valuable to find out the antagonists for CD36, but the three-dimensional protein structure of CD36 has not been determined and there are no template structures in the PDB library, which greatly prevents the antagonist discovery from structure-based drug discovery. The aim of the present study is to predict the three-dimensional structure using computational methods by I-TASSER.

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Zhang, Lingzi, Jun Liu, Guowei Zhou i Zhiliang Zhang. "Controllable In-Situ Growth of Silver Nanoparticles on Filter Paper for Flexible and Highly Sensitive SERS Sensors for Malachite Green Residue Detection". Nanomaterials 10, nr 5 (26.04.2020): 826. http://dx.doi.org/10.3390/nano10050826.

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In this work, a series of highly flexible and sensitive surface-enhanced Raman scattering (SERS) substrates were fabricated by the in-situ growth of silver nanoparticles (AgNPs) on polydopamine (PDA) templated filter papers (FPs), based on mussel-inspired surface chemistry. The obtained FP@PDA@AgNPs strips exhibited high sensitivity and reproducibility with Rhodamine 6G (R6G) probe molecules, with a calculated detection limit of approximately 10−10 M. More critically, these FP@PDA@AgNPs strips could be used as outstanding flexible SERS sensors to quickly collect and detect malachite green (MG) residues on fish scales, crab shells and shrimp skins by a swabbing extraction method. The detection limits for MG residues were calculated to be approximately as low as 0.04635 pg/cm2, 0.06952 pg/cm2 and 0.09270 pg/cm2, respectively. This facile and efficient strategy could to be utilized as a universal approach to fabricating a variety of flexible, cheap and portable SERS sensors for surface contamination analysis, and has great potential in the environmental scientific analysis and food safety monitoring fields.

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Minter, Rebecca Manget, Mary Uan-Sian Feng, Mahmoud Al-Hawary, Jincheng Shen, Matthew J. Schipper, Filip Bednar, Erica Proctor, Susanne Gray Warner, Mark M. Zalupski i Diane M. Simeone. "Effect of neoadjuvant chemoradiotherapy (nCRT) on survival in patients with borderline resectable (BR) pancreatic adenocarcinoma (PDA) with acceptable peri-operative morbidity." Journal of Clinical Oncology 32, nr 3_suppl (20.01.2014): 288. http://dx.doi.org/10.1200/jco.2014.32.3_suppl.288.

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288 Background: The impact of nCRT for patients (pts) with BR PDA has been debated, with wide variation in practice. Most studies in pts undergoing nCRT have no or historic controls, rather than a direct comparison of BR pts treated in the same era. We aimed to assess the effect of nCRT on operative, pathologic, and survival endpoints in pts with BR PDA. Methods: 241 pts underwent pancreatectomy (177 without and 64 with nCRT) for PDA (2001-2011). CT scans at dx were re-reviewed by a pancreatic radiologist using a standardized template. Pts were categorized as resectable, BR, or unresectable according to 2012 NCCN criteria. BR pts (n=74) were extracted for analysis. Survival was compared using log-rank tests; pathologic features and peri-op factors were compared using Wilcoxon rank sum tests (continuous variables) or Fisher's exact test (binary variables). Results: Median follow up was 26 ±21 months. nCRT was associated with higher 1 and 3 yr OS, lower margin and node positivity, decreased pre-op CA19-9, and lower post-op pancreatic fistula (POPF), with higher operative time, vascular reconstructions, and transfusion (PRBCs). On univariate analysis, POPF negatively impacted survival (HR 2.34, 1.16-4.75, p=0.02) as did pre-op CA19-9>150 U/mL (HR 2.11, 1.16-3.87, p=0.015). Conclusions: Pts receiving nCRT for BR PDA had higher 1 and 3 yr OS, more negative margins, and fewer positive nodes, with minimal additional peri-op co-morbidity, compared with pts going directly to surgery. These data support consideration of enrolling all pts with BR PDA into a neoadjuvant program prior to resection. [Table: see text]

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