Given a compound, can we predict which anatomical therapeutic chemical (ATC) class/classes it belongs to? It is a challenging problem since the information thus obtained can be used to deduce its ...possible active ingredients, as well as its therapeutic, pharmacological and chemical properties. And hence the pace of drug development could be substantially expedited. But this problem is by no means an easy one. Particularly, some drugs or compounds may belong to two or more ATC classes.
To address it, a multi-label classifier, called iATC-mISF, was developed by incorporating the information of chemical–chemical interaction, the information of the structural similarity, and the information of the fingerprintal similarity. Rigorous cross-validations showed that the proposed predictor achieved remarkably higher prediction quality than its cohorts for the same purpose, particularly in the absolute true rate, the most important and harsh metrics for the multi-label systems.
The web-server for iATC-mISF is accessible at http://www.jci-bioinfo.cn/iATC-mISF. Furthermore, to maximize the convenience for most experimental scientists, a step-by-step guide was provided, by which users can easily get their desired results without needing to go through the complicated mathematical equations. Their inclusion in this article is just for the integrity of the new method and stimulating more powerful methods to deal with various multi-label systems in biology.
xxiao@gordonlifescience.org
Supplementary data are available at Bioinformatics online.
Compared to bulk metal–organic framework (MOF), 2D MOF nanosheets have gained intensive research attention due to their ultrathin thickness and large surface area with highly accessible active sites. ...However, structural deterioration and morphological damage have impeded producing high‐quality MOF nanosheets during exfoliation. Here, first a new layered bulk MOF ZSB‐1 is synthesized and several solvents such as isopropanol, methanol, n‐hexyl alcohol, and N,N‐dimethylformamide are surveyed to examine their performance for the exfoliation of layered ZSB‐1. As a result, a highly solvent‐stable metal–organic framework rectangular nanosheet retaining undamaged morphology is obtained by the soft‐physical method in n‐hexyl alcohol. Theoretical simulations reveal that the strong interaction energy between n‐hexyl alcohol and MOF layers is responsible for the best exfoliation performance of making the bulk MOF into nanosheets. In addition, ZSB‐1 shows a tunable fluorescence peak position, fluorescent lifetime, and quantum yield by simply changing the solvent and morphology. Besides, the ZSB‐1 was selected as a fluorescence sensor to detect metal ions, and ZSB‐1 nanosheet exhibits excellent sensing ability for Fe3+. It is worth noting that the ZSB‐1 nanosheet has better detection limit performance of 0.054 × 10−6
m than that of its bulk counterpart.
A highly solvent‐stable metal–organic framework (MOF) nanosheet retaining undamaged morphology and structural integrity is obtained. Theoretical simulations reveal that the strong interaction energy between solvent and MOF layers is responsible to the best exfoliation performance of making bulk MOF into nanosheets. This work provides a 2D MOF fluorescence sensor with tunable luminescent property by simply changing the solvent and morphology.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
Facile activation and conversion of small molecules (e.g., H
O, CO
, N
, CH
, and C
H
) into solar fuels or value-added chemicals under mild conditions is an attractive pathway in dealing with the ...worldwide appeal of energy consumption and the growing demand of industrial feedstocks. Compared with conventional thermo- or electro-catalytic approaches, the protocol of photocatalysis shines light on green and low-cost storage of sunlight in chemical bonds. For instance, artificial photosynthesis is an effective way to split H
O into molecular O
and H
, thereby storing solar energy in the form of hydrogen fuel. Because of rational tunability in band gaps, charge-carrier dynamics, exposed active sites and catalytic redox activities by tailoring size, composition, morphology, surface, and/or interface property, semiconductor nanocrystals (NCs) emerge as very promising candidates for photo-induced small molecule activation, including H
O splitting, CO
reduction, N
fixation, CH
conversion and chemical bond formation (e.g., S-S, C-C, C-N, C-P, C-O). In this review, we summarize the recent advances in small molecule activation via artificial photosynthesis using semiconductor NCs, especially those consisting of II-VI and III-V elements. Moreover, we highlight the intrinsic advantages of semiconductor NCs in this field and look into the fabrication of prototype devices for large-scale and sustainable small molecule activation to store solar energy in chemical bonds.
•The sensitivities can reach to 79.2nm/°C and −69.9nm/°C as the temperature is 23°C.•The high sensitivities are 77,000nm/RIU and −106,000nm/RIU as the RI of the liquid is 1.409.•The sensitivity ...increases infinitely near the special wavelength related with zero-point group birefringence Bg.•The wavelength of zero-point group birefringence Bg can be changed by adjusting the corresponding parameters.
We propose a high-sensitivity temperature sensor based on Sagnac interferometer with a PCF. The diameter of the central hole of the PCF is decreased to form defect core which supports fiber mode. All the air holes are injected with liquid which is sensitive to temperature. The simulation result demonstrates that the birefringence of the PCF is low. The loss, the overlap between fiber mode and the liquid in the central hole increases as the wavelength increases. The sensitivity has a great relation with group birefringence Bg. Therefore, we analyze the influences of the structural parameters d1, d2, d3 and the RI of the liquid on the group birefringence Bg. By adjusting the corresponding parameters, we can change the wavelength of zero-point group birefringence Bg. The high sensitivity can be obtained near the special wavelength. The sensitivities can reach to 79.2nm/°C and −69.9nm/°C as the temperature is 23°C. The average sensitivities are 26.4nm/°C, −17.9nm/°C as the temperature changes from 27°C to 35°C, and the linear fitting degrees are 0.99489 and 0.98832. The RI sensitivity is also studied as RI changes from 1.404 to 1.409. The average sensitivities are 43,400nm/RIU and −73,743nm/RIU respectively. The high sensitivities are 77,000nm/RIU and −106,000nm/RIU as the RI of the liquid is 1.409.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK, ZRSKP
Recommended by the World Health Organization (WHO), drug compounds have been classified into 14 main ATC (Anatomical Therapeutic Chemical) classes according to their therapeutic and chemical ...characteristics. Given an uncharacterized compound, can we develop a computational method to fast identify which ATC class or classes it belongs to? The information thus obtained will timely help adjusting our focus and selection, significantly speeding up the drug development process. But this problem is by no means an easy one since some drug compounds may belong to two or more than two ATC classes. To address this problem, using the DO (Drug Ontology) approach based on the ChEBI (Chemical Entities of Biological Interest) database, we developed a predictor called iATC-mDO. Subsequently, hybridizing it with an existing drug ATC classifier, we constructed a predictor called iATC-mHyb. It has been demonstrated by the rigorous cross-validation and from five different measuring angles that iATC-mHyb is remarkably superior to the best existing predictor in identifying the ATC classes for drug compounds. To convenience most experimental scientists, a user-friendly web-server for iATC-mHyd has been established at http://www.jci-bioinfo.cn/iATC-mHyb, by which users can easily get their desired results without the need to go through the complicated mathematical equations involved.
Cells are deemed the basic unit of life. However, many important functions of cells as well as their growth and reproduction are performed via the protein molecules located at their different ...organelles or locations. Facing explosive growth of protein sequences, we are challenged to develop fast and effective method to annotate their subcellular localization. However, this is by no means an easy task. Particularly, mounting evidences have indicated proteins have multi-label feature meaning that they may simultaneously exist at, or move between, two or more different subcellular location sites. Unfortunately, most of the existing computational methods can only be used to deal with the single-label proteins. Although the 'iLoc-Animal' predictor developed recently is quite powerful that can be used to deal with the animal proteins with multiple locations as well, its prediction quality needs to be improved, particularly in enhancing the absolute true rate and reducing the absolute false rate.
Here we propose a new predictor called 'pLoc-mAnimal', which is superior to iLoc-Animal as shown by the compelling facts. When tested by the most rigorous cross-validation on the same high-quality benchmark dataset, the absolute true success rate achieved by the new predictor is 37% higher and the absolute false rate is four times lower in comparison with the state-of-the-art predictor.
To maximize the convenience of most experimental scientists, a user-friendly web-server for the new predictor has been established at http://www.jci-bioinfo.cn/pLoc-mAnimal/, by which users can easily get their desired results without the need to go through the complicated mathematics involved.
xxiao@gordonlifescience.org or kcchou@gordonlifescience.org.
Supplementary data are available at Bioinformatics online.
•Different green DESs were used in the extraction of flavonoids from liquorice.•The major factors influencing DES-UAE was optimized using RSM.•The proposed extraction method is highly efficient for ...GLA and ISL extraction.•The possible mechanism of DES-UAE for efficient extraction was illustrated.•The excellent pharmacological activities of enriched extracts were demonstrated.
Licorice (Glycyrrhiza glabra) is extensively used owing to the superior pharmacological effects. However, its maximum application potential has not been fully exploited due to the limitation of currently available extraction solvent and methods. In this study, an eco-friendly deep eutectic solvent (NADESs) based ultrasound-assisted extraction (DES-UAE) method was applied to prepare licorice extracts. The DES-UAE using choline chloride and lactic acid as solvent was optimized and modeled by using response surface methodology to maximize the extraction yields of glabridin (GLA) and isoliquiritigenin (ISL). The optimized extracts possessed higher contents of GLA and ISL than available extraction methods, and the enriched products showed superior pharmacological activities in vitro. Furthermore, scanning electron microscopy (SEM) and molecular dynamic simulation analyses were performed to deeply investigate the interaction between solvent and targeted compounds. This study not only provides an eco-friendly method for high-efficient extraction of GLA and ISL from licorice but also illustrates the mechanism of the increased extraction efficacy, which may contribute to the application of licorice and deep insight into extraction mechanism using DES.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Residual stress in selective laser melting (SLM) is one of the key challenges in terms of precision control, success rate and the performance of deposited components. Ti6Al4V belongs to α+β titanium ...alloy, the residual stress of selective laser melted (SLMed) Ti6Al4V component maybe affected by solid-state phase transformation result from complex thermal history of SLM. In the present study, effect of solid-state phase transformation on residual stress of SLM Ti6Al4V was investigated. A coupled modeling method of thermo-metallurgical-mechanical considering solid-state phase transition is provided and validated by microstructure observation and residual stress measurements. Then the solid-state phase transformation strain was neglected in the validated model, the computed residual stress is used to investigate the effect of solid-state phase transformation strain on residual stress by comparing with experimental measurements. In addition, the influence of the difference in yield strength and thermal expansion coefficient between the original phase and the transition phase on the residual stress is discussed. It has been found that the residual stress of SLMed Ti6Al4V is related to the direction, the longitudinal residual stress is about twice transverse, and they are all tensile stresses. The microstructure and residual stress predicted by the simulation are in good agreement with the experimental measurements. The microstructure of SLM Ti6Al4V is mainly composed of martensite α', and the average error between the predicted longitudinal stress and measurement is 2.1%. The solid-state phase transformation has a stress relaxation effect during the SLM Ti6Al4V, predicted longitudinal and transverse residual stress exceeds the experimental measurement by up to 80.7% and 53.9%, when neglecting the solid-state phase transformation strain. The influence of the solid-state phase transformation of SLM Ti6Al4V on the residual stress is mainly determined by the volume change between the solid-state phases.
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GEOZS, IMTLJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Cadmium (Cd) is a widely distributed soil contaminant which induces oxidative damage and is therefore toxic to plants. Although selenium oxyanions such as selenite (SeO32-) and selenate (SeO42-) can ...alleviate Cd stress to plants, it is not known whether selenium nanoparticles (SeNPs) are able to do the same. The present study demonstrated the positive impact of both SeNPs and SeO32- on Brassica napus L. growth under conditions of Cd stress. Underlying mechanisms were elucidated using an oxidative stress detection assay, whole-genome RNA sequencing, and RT-qPCR. Application of selenium, especially in the form of SeNPs, decreased Cd-induced reactive oxygen species production by inhibiting the expression of NADPH oxidases (BnaRBOHC, BnaRBOHD1, and BnaRBOHF1) and glycolate oxidase (BnaGLO), thereby decreasing oxidative protein and membrane lipid damage. In addition, SeNPs improved resistance to Cd stress by decreasing Cd accumulation, maintaining intracellular calcium homeostasis, promoting disulfide bond formation, and restoring the waxy outer layer of the leaf surface. Although both forms of selenium decreased Cd toxicity, the beneficial concentration range was more extensive for SeNPs than for SeO32-.
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•SeNPs alleviated the toxic effects of Cd and improved the plant growth in B. napus.•SeNPs demonstrated superior roles in inhibiting ROS production and scavenging ROS.•SeNPs improved the basal metabolism and maintained calcium homeostasis.•SeNP is an environmental-friendly Se supplement for alleviating Cd stress.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Catalytic conversion of carbon dioxide (CO
2
) to value-added chemicals under mild conditions is highly desired, albeit with significant challenges. Here, in terms of exposure of abundant active ...sites and excellent photo-to-thermal conversion properties, flower-like Co
2
C has been firstly used for effectively catalysing the cycloaddition of CO
2
with epoxides to produce cyclic carbonates with yields of up to 95% under solar light. Density functional theory (DFT) calculations reveal that Lewis acid sites of the surface Co atoms can activate both CO
2
and epoxide, thus opening up the possibility of a CO
2
-epoxide cycloaddition reaction.
Flower-like Co
2
C enables photothermal catalytic CO
2
-epoxide cycloaddition with yields of up to ∼95% under solar light.
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