Abstract
Emerging evidence shows that microRNAs (miRNAs) play a critical role in diverse fundamental and important biological processes associated with human diseases. Inferring potential disease ...related miRNAs and employing them as the biomarkers or drug targets could contribute to the prevention, diagnosis and treatment of complex human diseases. In view of that traditional biological experiments cost much time and resources, computational models would serve as complementary means to uncover potential miRNA–disease associations. In this study, we proposed a new computational model named Neighborhood Constraint Matrix Completion for MiRNA–Disease Association prediction (NCMCMDA) to predict potential miRNA–disease associations. The main task of NCMCMDA was to recover the missing miRNA–disease associations based on the known miRNA–disease associations and integrated disease (miRNA) similarity. In this model, we innovatively integrated neighborhood constraint with matrix completion, which provided a novel idea of utilizing similarity information to assist the prediction. After the recovery task was transformed into an optimization problem, we solved it with a fast iterative shrinkage-thresholding algorithm. As a result, the AUCs of NCMCMDA in global and local leave-one-out cross validation were 0.9086 and 0.8453, respectively. In 5-fold cross validation, NCMCMDA achieved an average AUC of 0.8942 and standard deviation of 0.0015, which demonstrated NCMCMDA’s superior performance than many previous computational methods. Furthermore, NCMCMDA was applied to three different types of case studies to further evaluate its prediction reliability and accuracy. As a result, 84% (colon neoplasms), 98% (esophageal neoplasms) and 98% (breast neoplasms) of the top 50 predicted miRNAs were verified by recent literature.
Obtaining the reactivities (such as nucleophilicities and electrophilicities) of molecules is of fundamental importance in chemistry. Mayr and co‐workers have developed the Mayr equation, which has ...been widely used to quantify nucleophilicity and electrophilicity. Herein we propose a theoretical understanding of the Mayr equation based on frontier molecular orbital (FMO) theory and the Eyring equation of the transition state theory, showing that the nucleophilicity of a molecule is related to the energy of this molecule’s highest occupied molecular orbital (HOMO), while the electrophilicity is related to the energy of the lowest unoccupied molecular orbital (LUMO) of the electrophile. Consequently, we propose a new approach by combining the FMO theory and the Mayr equation to predict the reactivities of new molecules. Ab initio calculation results support these linear relationships between LUMO energies and the Mayr electrophilicities (E) and the HOMO energies and the Mayr nucleophilicities (N) for sets of electrophiles and nucleophiles, respectively. For each set of nucleophiles or electrophiles, their different reactivities are mainly controlled by the electronic effects of the substituents. If other effects, such as sterics, affect reactivity for a set of electrophiles or nucleophiles, the linear relationships between HOMO levels and N values and LUMO levels and E values cannot be secured. The present approach through combining Mayr equation and the quantitative FMO theory suggests that the Mayr nucleophilicity or electrophilicity of a new molecule, which could be an intermediate of a reaction, unstable reactant, or a hypothetical reactive species, can be obtained through ab initio calculations of the frontier molecular orbital energies, and this will greatly expand the data sets of Mayr nucleophilicities and electrophilicities.
Crystal ball? A theoretical investigation of the Mayr equation based on frontier molecular orbital (FMO) theory and the Eyring equation of transition‐state theory shows that the nucleophilicity of a given molecule is related to its HOMO energy, while the electrophilicity is related to its LUMO energy. Mayr nucleophilicities and electrophilicities can thus be predicted for new molecules if electronic effects dominate reactivity.
Asymmetric hydrogenation of quinolines catalyzed by chiral cationic η6-arene–N-tosylethylenediamine–Ru(II) complexes have been investigated. A wide range of quinoline derivatives, including ...2-alkylquinolines, 2-arylquinolines, and 2-functionalized and 2,3-disubstituted quinoline derivatives, were efficiently hydrogenated to give 1,2,3,4-tetrahydroquinolines with up to >99% ee and full conversions. This catalytic protocol is applicable to the gram-scale synthesis of some biologically active tetrahydroquinolines, such as (−)-angustureine, and 6-fluoro-2-methyl-1,2,3,4-tetrahydroquinoline, a key intermediate for the preparation of the antibacterial agent (S)-flumequine. The catalytic pathway of this reaction has been investigated in detail using a combination of stoichiometric reaction, intermediate characterization, and isotope labeling patterns. The evidence obtained from these experiments revealed that quinoline is reduced via an ionic and cascade reaction pathway, including 1,4-hydride addition, isomerization, and 1,2-hydride addition, and hydrogen addition undergoes a stepwise H+/H– transfer process outside the coordination sphere rather than a concerted mechanism. In addition, DFT calculations indicate that the enantioselectivity originates from the CH/π attraction between the η6-arene ligand in the Ru-complex and the fused phenyl ring of dihydroquinoline via a 10-membered ring transition state with the participation of TfO– anion.
•An automatic fundamental contour extraction of dugong chirps was presented.•Five categories of dugong chirps were identified.•A specific classification criterion was proposed for the automatic and ...effective identification of chirp types.•Our results enrich the known repertoire of dugong chirps, and may be useful in future passive acoustic monitoring studies.
A steady decrease in the Dugong (Dugong dugon) population has been notices worldwide. Considering the social function and utilization rate, dugong chirp classification has become an important bioacoustics research topic, which may help marine biologists monitor the change of their population, study their behavioral context in different environments and optimise the protection policy. However, the objective classification of dugong chirps has not been adequately addressed in the literature. In this paper, an automatic fundamental contour extraction using the tempo-frequency variables to describe the contours of the fundamental frequency of the chirps is presented. With the automatic fundamental contour extraction, the time–frequency information of dugong chirps can be effectively represented, which gives a good classification performance. Following the principles used for the classification of dolphin whistles, three variables were chosen and performed with hierarchical cluster analysis. Based on these results and further visual examination, five categories of chirps were identified. A simple classification criterion was proposed which could be used in the automatic and effective identification of chirp types. Our findings enrich the known repertoire of dugong chirps, and may be useful in future passive acoustic monitoring studies.
We report a novel strategy of integrating microbial fuel cell (MFC) with microbial immobilization technology (MIT) in a sequencing batch reactor (SBR) to test the performance of nitrate removal for ...the first time. Results showed that MFC could enhance nitrate removal in the novel integrated system, especially for wastewater with low carbon-to-nitrogen ratios, and the nitrate removal efficiency reached 91.35% in the lab-scale integrated system, including 12.25% nitrate consumption by MFC in one typical cycle. The anode of MFC recovered energy in the form of electricity, floating cathode of MFC prevented the loss of immobilized denitrifying bacteria particles and degraded a portion of nitrate, and the maximum voltage production of MFC was 0.246 V. The novel integrated system in this paper showed excellent nitrate removal performance and it will be a highly potential novel setup for efficient nitrate removal of wastewater treatment.
Weak ion diffusion and electron transport due to limited interlayer spacing and poor electrical conductivity have been identified as critical roadbacks for fast and abundant energy storage of both ...MoS
2
-based lithium ion batteries (LIBs) and sodium ion batteries (SIBs). In this work, MoS
2
porous-hollow nanorods (MoS
2
/m-C800) have been designed and synthesized via an annealing-followed chemistry-intercalated strategy to solve the two issues. They are uniformly assembled from ultrathin MoS
2
nanosheets, deviated to the rod-axis direction, with expanded interlayer spacing due to alternate intercalation of N-doped carbon monolayers between the adjacent MoS
2
monolayers. Electrochemical studies of the MoS
2
/m-C800 sample, as an anode of LIBs, demonstrate that the superstructure can deliver a reversible discharge capacity of 1,170 mAh•g
−1
after 100 cycles at 0.2 A•g
−1
and maintain a reversible capacity of 951 mAh•g
−1
at 1.25 A•g
−1
after 350 cycles. While for SIBs, the superstructure also delivers a reversible discharge capacity of 350 mAh•g
−1
at 0.5 A•g
−1
after 500 cycles and exhibits superior rate capacity of 238 mAh•g
−1
at 15 A•g
−1
.The excellent electrochemical performance is closely related with the hierarchical superstructures, including expanded interlayer spacing, alternate intercalation of carbon monolayers and mesoporous feature, which effectively reduce ion diffusion barrier, shorten ion diffusion paths and improve electrical conductivity.
•A method that can accomplish both detection and classification tasks of three marine mammal calls in one-step with Convolutional neural networks is proposed.•The proposed method can reach high ...identification precise and recall rate.•The identification process is fast and can be done in real-time.•The proposed method shows the potential to be applied in passive acoustic monitoring systems in the future.
Animal vocalization is one of the most important ways to identify the existence and occurrence of marine mammals. Accurately detecting and identifying marine mammal species in real time is significant in the field of marine mammal research. In this study, we developed a novel method based on convolutional neural networks (CNNs) to precisely identify the calls of bottlenose dolphins (Tursiops), dugongs (Dugong dugong), and the Indo-Pacific humpback dolphin (Sousa chinensis). Compared with traditional detection and classification techniques, the proposed method is a one-step algorithm that combines detection and classification. It can automatically learn the features of different marine mammal calls and position the target calls with bounding boxes in a spectrogram. Furthermore, the whole process can be conducted in real time. With this method, the raw data are cut into fixed lengths and spectrograms are created. Next, the annotated sound data are sent to the CNNs to train an identification model. Experimental results showed that the proposed method achieved >91% precision and >84% recall of test data with real-time speed. In the future, this method can be applied to passive acoustic observation equipment for quick, accurate pre-detection of marine mammal calls.
Despite high theoretical specific capacity and uniform interlayer channel for accommodation of ions, poor cycling stability and rate capacity have been identified as critical roadblocks to further ...development of MoS2-based lithium ion batteries (LIBs) or sodium ion batteries (SIBs). In this study, few-atomic-layered MoS2 hollow nanospheres with expanded interlayer spacing, due to alternate intercalation of N-doped monolayer carbon (m-C) between the adjacent MoS2 monolayers, have been designed and synthesized via an annealing-followed soft-template approach. As an anode of SIBs, the ultrathin-layered m-C/MoS2 superstructures electrode can deliver a reversible discharge capacity of 401 mA h g−1 at 200 mA g−1 after 150 cycles. It can maintain 262 mA h g−1 at 2000 mA g−1 after 600 cycles with a capacity retention of 105% in comparison with that of the 2nd cycle. For LIBs, the hollow nanospheres can also deliver a reversible discharge capacity of 1025 mA h g−1 at 1000 mA g−1 after 80 cycles. The excellent electrochemical performance can be attributed to the synergy effect of expanded interlayer spacing (improving ion diffusion mobility), ultrathin feature (shortening ion diffusion paths) and alternate intercalation of monolayer carbon (improving the electrical conductivity and maintaining the structural integrity), which ensures new opportunities for designing advanced two-dimensional hosts for energy storage devices.
An annealing-followed soft-template strategy was developed to prepare alternately intercalated m-C/MoS2 hollow nanospheres with few atomic layers, which shows expanded interlayer spacing and ideal atomic contact between N-doped porous carbon layers and MoS2 monolayers. These features can achieve fast ion/electron transport and structural integrity upon repeated ion insertion/extraction. As a consequence, the m-C/MoS2 superstructures electrode delivers high discharge capacity and long-life cycling stability. Display omitted
•An annealing-followed soft-template strategy was developed to prepare m-C/MoS2 hollow nanospheres with few atomic layers.•Alternate intercalation of carbon and MoS2 monolayers realizes expanded interlayer spacing and ideal atomic contact.•Synergetic effect solves the issues of fast ion/electron transport and structural integrity.•The m-C/MoS2 superstructures electrode exhibits high discharge capacity and cycling stability.
A novel Rh(I)-catalyzed (3 + 2) + 1 cycloaddition, which can be regarded as a homologous Pauson−Khand reaction, was developed to synthesize bicyclic cyclohexenones and cyclohexanones, enabling a new ...approach for synthesis of six-membered carbocycles ubiquitously found in natural products and pharmaceutics. The significance of the Rh-catalyzed (3 + 2) + 1 cycloaddition has been demonstrated by the total synthesis of a furanoid sesquiterpene natural product, α-agarofuran, in which the bicyclic skeleton was constructed by the (3 + 2) + 1 reaction of 1-yne-VCP and CO.
Phytoremediation provides substantial advantages, including eco-friendliness, cost-effectiveness, efficiency, and visual appeal. However, the current knowledge of the factors influencing ...phytoremediation in pesticide-contaminated environments remains limited. It is critical to understand phytoremediation and the factors affecting the variation in removal efficiency. In this study, we compiled 72 previous research articles to quantify plant-induced improvements in removal efficiency and identify factors that influence variations in phytoremediation behavior through meta-analysis. We observed a significant increase in the removal efficiency of phytoremediation compared to the control group which did not involve phytoremediation. Pesticides significantly affect removal efficiency in terms of their modes of action, substance group, and properties. Plants demonstrated higher efficiency in remediating environments contaminated with pesticides possessing lower molecular masses and log Kow values. Plant species emerged as a crucial determinant of variations in removal efficiency. Annual plants exhibited a 1.45-fold higher removal efficiency than perennial plants. The removal efficiencies of different plant types decreased in the following order: agri-food crops > aquatic macrophytes > turfgrasses > medicinal plants > forage crops > woody trees. The Gramineae family, which was the most prevalent, demonstrated a robust and consistent phytoremediation ability. This study offers a more comprehensive triangular relationship between removal efficiency, pesticides, and plants, expanding the traditional linear model. Our findings offer valuable insights into the behavior of phytoremediation in pesticide-contaminated environments and the factors determining its success, ultimately guiding further research toward developing strategies for higher removal efficiency in phytoremediation.
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•Annual plants are more effective in remediating pesticide-contaminated environments than perennial plants.•Plant species are the primary factors driving variation in removal efficiency in phytoremediation.•The translocation factor (TF) is positively correlated with removal efficiency in phytoremediation.
