69 research outputs found

    Modeling spontaneous three-dimensional polymerization

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    For human beings, the origin of life has always been an interesting and mysterious matter, particularly how life arose from inorganic matter through natural processes. Polymerization is always involved in such processes. In this paper we built what we refer to as ideal and physical models to simulate spontaneous polymerization based on certain physical principles. As the modeling confirms, without taking external energy, small and simple inorganic molecules formed bigger and more complicated molecules, which are necessary ingredients of all living organisms. In our simulations, we utilized actual ranges of parameters according to their experimentally observed values. The results from the simulations led to a good agreement with the nature of polymerization. After sorting out through all the models that were built, we arrived at a final model that, it is hoped, can be used to simply and efficiently describe spontaneous polymerization using only three parameters: the dipole moment, the distance between molecules, and the temperature

    UniColor: A Unified Framework for Multi-Modal Colorization with Transformer

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    We propose the first unified framework UniColor to support colorization in multiple modalities, including both unconditional and conditional ones, such as stroke, exemplar, text, and even a mix of them. Rather than learning a separate model for each type of condition, we introduce a two-stage colorization framework for incorporating various conditions into a single model. In the first stage, multi-modal conditions are converted into a common representation of hint points. Particularly, we propose a novel CLIP-based method to convert the text to hint points. In the second stage, we propose a Transformer-based network composed of Chroma-VQGAN and Hybrid-Transformer to generate diverse and high-quality colorization results conditioned on hint points. Both qualitative and quantitative comparisons demonstrate that our method outperforms state-of-the-art methods in every control modality and further enables multi-modal colorization that was not feasible before. Moreover, we design an interactive interface showing the effectiveness of our unified framework in practical usage, including automatic colorization, hybrid-control colorization, local recolorization, and iterative color editing. Our code and models are available at https://luckyhzt.github.io/unicolor.Comment: Accepted by SIGGRAPH Asia 2022. Project page: https://luckyhzt.github.io/unicolo

    Large-scale Multi-view Subspace Clustering in Linear Time

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    A plethora of multi-view subspace clustering (MVSC) methods have been proposed over the past few years. Researchers manage to boost clustering accuracy from different points of view. However, many state-of-the-art MVSC algorithms, typically have a quadratic or even cubic complexity, are inefficient and inherently difficult to apply at large scales. In the era of big data, the computational issue becomes critical. To fill this gap, we propose a large-scale MVSC (LMVSC) algorithm with linear order complexity. Inspired by the idea of anchor graph, we first learn a smaller graph for each view. Then, a novel approach is designed to integrate those graphs so that we can implement spectral clustering on a smaller graph. Interestingly, it turns out that our model also applies to single-view scenario. Extensive experiments on various large-scale benchmark data sets validate the effectiveness and efficiency of our approach with respect to state-of-the-art clustering methods.Comment: Accepted by AAAI 202

    Estimating Soil Parameters from DESIS Images using Deep Learning

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    There are several soil parameters that play a significant role in soil health and thus, crop production. Compared with traditional fieldwork by collecting soil samples, digital soil mapping by remote sensing data has many advantages, such as estimating soil properties efficiently in large areas. Multispectral and hyperspectral data have been used already widely for soil parameter retrieval using spectral soil models. Mostly, hyperspectral data have largely outperformed the model and prediction of soil parameters. However, the accuracy and uncertainty of both model results depend largely on the density of calibration points, which is especially problematic for large areas such as regions and countries. Therefore, new methods are needed that take into account the sparsity of calibration data during the training of the model. This work focuses on the SOC content for the whole Bavarian region in Germany (~70.000 km²). The soil data source is LFU (Bayerisches Landesamt fur Umwelt) and LUCAS 2018 (Land Use and Coverage Area Frame Survey). After data selection, we use 1171 soil samples. As for the hyperspectral images, we use DESIS data in Bavaria, whose spectral range is 400-1000 nm. We use 603 hyperspectral images in experiments. To get spectral reflectance for bare soils, we build temporal reflectance composites surrounding each soil sample from the original images. Specifically, We compute the NDVI value for each pixel and then filter pixels by NDVI threshold to filter out vegetated pixels. Temporal composites are then generated by the pixel-based averaging of the filtered images. These composites are fed into the deep learning model. The model would output the SOC value. Regarding the model framework, it consists of CNN layers followed by fully connected layers. To solve the sparsity of data availability, data augmentation, and transfer learning methodology are investigated in this work. During our experiments, we use cross-validation to evaluate the performance. Root Mean Square Error and R Square are used as the evaluation metrics

    Hydroxyapatite nanoparticles-cell interaction: New approaches to disclose the fate of membrane-bound and internalised nanoparticles

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    Hydroxyapatite nanoparticles are popular tools in bone regeneration, but they have also been used for gene delivery and as anticancer drugs. Understanding their mechanism of action, particularly for the latter application, is crucial to predict their toxicity. To this end, we aimed to elucidate the importance of nanoparticle membrane interactions in the cytotoxicity of MG-63 cells using two different types of nanoparticles. In addition, conventional techniques for studying nanoparticle internalisation were evaluated and compared with newer and less exploited approaches. Hydroxyapatite and magnesium-doped hydroxyapatite nanoparticles were used as suspensions or compacted as specular discs. Comparison between cells seeded on the discs and those supplemented with the nanoparticles allowed direct interaction of the cell membrane with the material to be ruled out as the main mechanism of toxicity. In addition, standard techniques such as flow cytometry were inconclusive when used to assess nanoparticles toxicity. Interestingly, the use of intracellular calcium fluorescent probes revealed the presence of a high number of calcium-rich vesicles after nanoparticle supplementation in cell culture. These structures could not be detected by transmission electron microscopy due to their liquid content. However, by using cryo-soft X-ray imaging, which was used to visualise the cellular ultrastructure without further treatment other than vitrification and to quantify the linear absorption coefficient of each organelle, it was possible to identify them as multivesicular bodies, potentially acting as calcium stores. In the study, an advanced state of degradation of the hydroxyapatite and magnesium-doped hydroxyapatite nanoparticles within MG-63 cells was observed. Overall, we demonstrate that the combination of fluorescent calcium probes together with cryo-SXT is an excellent approach to investigate intracellular calcium, especially when found in its soluble form.Peer ReviewedPostprint (published version

    SN 2022vqz: A Peculiar SN 2002es-like Type Ia Supernova with Prominent Early Excess Emission

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    We present extensive photometric and spectroscopic observations of a peculiar type Ia supernova (SN Ia) 2022vqz. It shares many similarities with the SN 2002es-like SNe Ia, such as low luminosity (i.e., MB,max=‚ąí18.11¬Ī0.16M_{B,\rm max}=-18.11\pm0.16 mag) and moderate post-peak decline rate (i.e., őĒm15,B=1.33¬Ī0.11\Delta m_{15,B}=1.33\pm0.11 mag). The nickel mass synthesized in the explosion is estimated as 0.20¬Ī0.04¬†M‚äô0.20\pm0.04~{\rm M}_\odot from the bolometric light curve, which is obviously lower than normal SNe Ia. SN 2022vqz is also characterized by a slow expanding ejecta, with Si II velocities persisting around 7000 km s‚ąí1^{-1} since 16 days before the peak, which is unique among all known SNe Ia. While all these properties imply a less energetic thermonuclear explosion that should leave considerable amount of unburnt materials, however, absent signature of unburnt carbon in the spectra of SN 2022vqz is puzzling. A prominent early peak is clearly detected in the cc- and oo-band light curves of ATLAS and in the grgr-band data of ZTF within days after the explosion. Possible mechanisms for the early peak are discussed, including sub-Chandrasekhar mass double detonation model and interaction of SN ejecta with circumstellar material (CSM). We found both models face some difficulties in replicating all aspects of the observed data. As an alternative, we propose a hybrid CONe white dwarf as progenitor of SN 2022vqz which can simultaneously reconcile the tension between low ejecta velocity and absence of carbon. We further discuss the diversity of 02es-like objects and possible origins of different scenarios.Comment: 24 pages, 12 figures, submitted to MNRA

    Effect of doping ions and organic molecules on the precipitation and biological interactions of nanostructured calcium phosphates

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    From a chemical and structural point of view, hydroxyapatite (HA) is a strong candidate in biomedical applications owing to its similarity to the inorganic components of bones and teeth. HA nanoparticles (NPs) as colloidal suspensions are becoming a popular tool in biomedical applications such as gene/drug delivery, bio-imaging etc. Although it is widely acknowledged that ionic substitutions on bulk HA substrates have a strong impact on their biological performance, little is known of their effect on NPs with potential use in gene transfection or drug delivery. In the third chapter carbonate (CO3) and magnesium (Mg) ions, which are the major substitutions in biological apatite, have been explored in the synthesis of ion-doped HA NPs under similar reaction conditions to allow comparison of results. CO3 and Mg ion were incorporated in the crystal lattice of HA and caused various changes mainly in the morphology and solubility of the different nanoparticles. In addition, the impact of ion doping on the interaction of HA NPs with cells was also evaluated under various cell culture conditions: 1) performing the cell culture study on citrate-dispersed NPs and on agglomerated NPs, 2) adding/excluding 10 % of foetal bovine serum (FBS) in the cell culture media and 3) using different types of cells, i.e. osteosarcoma MG-63 cells versus rat mesenchymal stem cells (rMSCs). The in vitro results indicated that Mg-doped HA NPs induced a profound impact on MG63 cells and, in the absence of citrate and FBS these nanoparticles were clearly cytotoxic. However, Mg-doped HA NPs did not alter cell viability in rMSCs under the same conditions. In the fourth chapter, Sr, Zn, Si and Fe(III) ions, which are minor ionic substitutions in biological apatite, were introduced to synthesize additional ion-doped HA NPs. Physicochemical characterization demonstrated that as-synthesized NPs were phase pure and doped ions had little influence on the morphology of NPs as in all cases they kept needle-like structure. Cytotoxicity studies performed using MG63 and rMSCs cells under the conditions of serum-containing and serum-free indicated that all NPs were non-cytotoxic if FBS was present. Interestingly, Zn-doped and Fe-doped HA NPs clearly stimulated MG63 cell proliferation in the absence of FBS. In addition to exploring the effect of ion-doped HA NPs on cell behaviour, it was also the interest of this thesis to investigate calcium phosphate (CaP) mineralization in the presence of organic molecules and also doping ions. In the fifth chapter of this thesis the effect of various organic molecules on CaP precipitation is provided. As shown by transmission electron microscopic studies (TEM) neuron-like CaP structures could be created using organic molecules of diverse nature such as non-ionic surfactant (Tween 80), anionic polymers (sodium polyacrylate) and cationic polymers (polydiallyldimethylammonium chloride). TEM studies through EELS, EFTEM and SAED proved that the neuron-like structures consisting of a dense core and thin filaments surrounding it had calcium, phosphorous and oxygen evenly distributed throughout the dense core as well as the filaments, and were amorphous in nature. Additionally, the co-effect of inorganic additives (i.e. Mg and Sr) together with organic molecules on CaP was also evaluated. It was proved that the addition of small amounts of ions had diverse impact on the stability of the neuron-like structures Mg clearly disrupting them but not Sr. All the findings with organic molecules provide much inspiration not only for the synthesis of more advanced CaP materials with novel structures and useful properties, but also for a better understanding of biomineralization process in nature.Desde el punto de vista qu√≠mico y estructural la hidroxiapatita (HA) se considera un gran candidato para aplicaciones biom√©dicas por su similitud con la fase mineral del hueso y los dientes. Aunque el efecto del dopaje se ha investigado con detalle en la fabricaci√≥n de implantes vi√©ndose que su presencia tiene un gran impacto en el comportamiento celular, poco se sabe de su efecto en nanopart√≠culas para su uso en terapia g√©nica y liberaci√≥n de f√°rmacos. En concreto, el tercer cap√≠tulo se centra en el dopaje de la apatita con iones carbonato (CO3) y magnesio (Mg) por ser √©stas las sustituciones m√°s importantes en la apatita biol√≥gica. Para ello todas las reacciones de s√≠ntesis se realizan bajo las mismas condiciones con la finalidad de poder comparar resultados. Los resultados muestran que ambas sustituciones acaban incorporando los iones dentro de la estructura del cristal causando diferentes impactos principalmente a nivel de morfolog√≠a y solubilidad. Con respecto al impacto del dopaje en la caracterizaci√≥n celular, se llevaron a cabo diferentes ensayos: 1) utilizando suspensiones dispersadas con citrato o sin √©l, 2) en medio de cultivo con o sin 10 % v/v de suero fetal bovino y 3) utilizando dos tipos de c√©lulas diferentes, c√©lulas de osteosarcoma (MG63) y c√©lulas de rata mesenquimales (rMSCs). Los resultados in vitro mostraron que las nanopart√≠culas dopadas con Mg eran claramente citot√≥xicas a las c√©lulas MG63 en ausencia de FBS. Sin embargo, las mismas NPs no alteraron la viabilidad celular en rMSCs bajo las mismas condiciones. El cap√≠tulo cuarto se centra en la s√≠ntesis y caracterizaci√≥n de NPs dopadas con iones Sr, Zn, Si y Fe(III), que representan sustituciones minoritarias en la apatita biol√≥gica. Su caracterizaci√≥n fisicoqu√≠mica mostr√≥ que todas las NPs eran puras con morfolog√≠a acicular. Los estudios de citotoxicidad con c√©lulas MG63 y rMSCs, con y sin FBS, mostraron viabilidad en presencia de FBS para todas las NPs. Adem√°s, para las NPs dopadas con Zn y Fe se observ√≥ un aumento notable en la proliferaci√≥n celular para las MG63 cultivadas sin FBS. Adem√°s de explorar el efecto del dopaje de iones en NP de HA, otro campo de inter√©s en esta tesis ha sido investigar la mineralizaci√≥n de fosfatos de calcio (CaP) en presencia de mol√©culas org√°nicas y de diferentes iones. A trav√©s de estudios recientes en el grupo de investigaci√≥n se ha visto que es posible formar fosfatos de calcio con estructura neuronal con la ayuda de simples mol√©culas org√°nicas. En el quinto cap√≠tulo de esta tesis se estudia el efecto de varias mol√©culas org√°nicas en la precipitaci√≥n de CaP. Estudios por microscopia electr√≥nica de transmisi√≥n (TEM) revelaron la presencia de estas estructuras neuronales formadas con la ayuda de mol√©culas org√°nicas de diferente naturaleza: surfactante no i√≥nicos (Tween 80), pol√≠meros ani√≥nicos (poliacrilato s√≥dico) y pol√≠remos cati√≥nicos (cloruro de polidialildimetilamonio). Varios estudios por TEM como son EELS, EFTEM y SAED permitieron establecer que las estructuras neuronales consist√≠an de un n√ļcleo denso del cual se extend√≠a una red de filamentos, que en estas estructuras el calcio, f√≥sforo y ox√≠geno estaba homog√©neamente distribuido y que eran de naturaleza amorfa. Adem√°s se investig√≥ el efecto simult√°neo de a√Īadir aditivos inorg√°nicos (iones Mg i Sr) junto con mol√©culas org√°nicas. Se observ√≥ que la adici√≥n de peque√Īas cantidades de iones afectaba la estabilidad de las estructuras neuronales. Con Mg las estructuras no eran estables pero s√≠ con Sr. Estos estudios pueden ser fuente no s√≥lo de inspiraci√≥n en la s√≠ntesis de estructuras m√°s avanzadas y con propiedades notablemente diferentes, sino que adem√°s proporcionan un mejor conocimiento de los procesos de biomineralizaci√≥n.Postprint (published version

    A Bacillus licheniformis Glycoside Hydrolase 43 Protein Is Recognized as a MAMP

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    Glycoside hydrolases from pathogens have often been reported as inducers of immune responses. However, the roles of glycoside hydrolase from plant-growth-promoting rhizobacteria (PGPR) in the resistance of plants against pathogens is not well studied. In this study, we identified a glycoside hydrolase 43 protein, H1AD43, produced by Bacillus licheniformis BL06 that can trigger defense responses, including cell death. Ion-exchange and size-exclusion chromatography were used for separation, and the amino acid sequence was identified by mass spectrometry. The recombinant protein generated by prokaryotic expression was able to elicit a hypersensitive response (HR) in Nicotiana benthamiana and trigger early defense responses, including reactive oxygen species (ROS) burst, callose accumulation, and the induction of defense genes. In addition, the protein could induce resistance in N. benthamiana, in which it inhibited infection by Phytophthora capsici Leonian and tobacco mosaic virus-green fluorescent protein (TMV-GFP) expression. H1AD43 thus represents a microbe-associated molecular pattern (MAMP) of PGPR that induces plant disease resistance and may provide a new method for the biological control of plant disease

    Cryogelation of human hair keratins

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    Human hair keratins (HHK) are known for their biocompatibility and potential to regulate cell response, possibly due to the presence of the leucine-aspartic-valine cell adhesion and signaling motifs. Together with the abundance of cysteine residues in HHK, 3D HHK scaffolds are fabricated through cryogelation based on spontaneous disulfide crosslinks and noncovalent interactions. Herein, the molecular mechanism of HHK self-assembly during cryogelation is interrogated and the influence of cryogelation parameters on the properties of the resultant scaffolds is studied. With successive freeze-thaw cycles, the storage modulus (G') of HHK cryogels substantially improves from 116.4 Pa at freeze-thaw cycle 3 (FT3) to 1908.7 Pa at freeze-thaw cycle 10 (FT10). Meanwhile, it is found that complete thiol-capping of HHK samples significantly inhibits cryogel formation as compared to partially or uncapped HHK samples, suggesting the dominant role of disulfide stabilization in cryogelation. Finally, uniaxial compression tests on HHK sponges demonstrate that FT cycling, from 0 to 10, is able to improve the compression modulus of sponges by ‚Čą12-folds. These findings show that macroscale properties of HHK cryogels can be conveniently modulated by physical parameters of cryogelation and that disulfide bonding is the main stabilizing force in HHK cryogels.Agency for Science, Technology and Research (A*STAR)Accepted versionThis research is supported by the Agency for Science, Technology and Research (A*STAR) under its Wound Care Innovation for the Tropics IAF-PP (H17/01/a0/0L9). The authors would like to acknowledge the Facility for Analysis, Characterization, Testing and Simulation, Nanyang Technological University, Singapore, for their technical support in scanning electron microscopy analysis
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