Fractional Denoising for 3D Molecular Pre-training

Coordinate denoising is a promising 3D molecular pre-training method, which has achieved remarkable performance in various downstream drug discovery tasks. Theoretically, the objective is equivalent to learning the force field, which is revealed helpful for downstream tasks. Nevertheless, there are two challenges for coordinate denoising to learn an effective force field, i.e. low coverage samples and isotropic force field. The underlying reason is that molecular distributions assumed by existing denoising methods fail to capture the anisotropic characteristic of molecules. To tackle these challenges, we propose a novel hybrid noise strategy, including noises on both dihedral angel and coordinate. However, denoising such hybrid noise in a traditional way is no more equivalent to learning the force field. Through theoretical deductions, we find that the problem is caused by the dependency of the input conformation for covariance. To this end, we propose to decouple the two types of noise and design a novel fractional denoising method (Frad), which only denoises the latter coordinate part. In this way, Frad enjoys both the merits of sampling more low-energy structures and the force field equivalence. Extensive experiments show the effectiveness of Frad in molecular representation, with a new state-of-the-art on 9 out of 12 tasks of QM9 and on 7 out of 8 targets of MD17

Encapsulation of hydrophobic phthalocyanine with poly(N-isopropylacrylamide)/lipid composite microspheres for thermo-responsive release and photodynamic therapy

Phthalocyanine (Pc) is a type of promising sensitizer molecules for photodynamic therapy (PDT), but its hydrophobicity substantially prevents its applications. In this study, we efficiently encapsulate Pc into poly(N-isopropylacrylamide) (pNIPAM) microgel particles, without or with lipid decoration (i.e., Pc@pNIPAM or Pc@pNIPAM/lipid), to improve its water solubility and prevent aggregation in aqueous medium. The incorporation of lipid molecules significantly enhances the Pc loading efficiency of pNIPAM. These Pc@pNIPAM and Pc@pNIPAM/lipid composite microspheres show thermo-triggered release of Pc and/or lipid due to the phase transition of pNIPAM. Furthermore, in the in vitro experiments, these composite particles work as drug carriers for the hydrophobic Pc to be internalized into HeLa cells. After internalization, the particles show efficient fluorescent imaging and PDT effect. Our work demonstrates promising candidates in promoting the use of hydrophobic drugs including photosensitizers in tumor therapies

Comprehensive comparison of flavor and metabolomic profiles in kiwi wine fermented by kiwifruit flesh with different colors

The objective of the study was to comprehensively assess flavor and metabolomic disparities in the aroma and taste profiles of kiwi wine (KW) derived from kiwifruits with green (Hayward), red (Donghong), and yellow (Jinshi) flesh. The findings revealed that Hayward wine exhibited the most “floral, fruity and pleasant” aromas, while Donghong wine demonstrated the most “sweet, fullness and balanced” tastes. In KW, a total of 106 compounds were characterized using a flavor-directed research strategy and metabolomics. PCA and PLS-DA effectively differentiated the three types of KW based on their aroma and taste characteristics. Ten volatile compounds (ethyl isovalerate, ethyl hexanoate, isoamyl acetate-D, acetone, hexyl acetate-M, hexyl acetate-D, ethyl isobutyrate, 2-butylfuran, 2-pentylfuran and 2-methylbutanal) and ten non-volatile compounds (malate, lactate, hydroxyacetone, pyroglutamate, succinate, 2-oxoglutarate, galactarate, acetoin, pyruvate and proline) were identified through multivariate analysis as key discriminators of flavor and metabolomic differences among the three types of KW. Furthermore, several metabolic pathways were investigated to distinguish the KW fermented with the three flesh-colored kiwifruits, mainly pertaining to glycerolipid, amino acid, sucrose, butanoate and pyruvate metabolism. This study could offer valuable insights into the effect of flesh colors on the flavor and metabolomic characteristics of KW

The uppermost monoterpenes improving Cinnamomum camphora thermotolerance by serving signaling functions

Terpenes serve important functions in enhancing plant thermotolerance. Cinnamomum camphora mainly has eucalyptol (EuL), camphor (CmR), linalool (LnL) and borneol (BeL) chemotypes basing on the uppermost monoterpenes. To reveal the thermotolerance mechanisms of these uppermost monoterpenes (eucalyptol, camphor, linalool, and borneol) in C. camphora, we surveyed the ROS metabolism and photosynthesis in the 4 chemotypes fumigated with the corresponding uppermost monoterpene after fosmidomycin (Fos) inhibiting monoterpene synthesis under high temperature at 38°C (Fos+38°C+monoterpene), and investigated the related gene expression in EuL and CmR. Meanwhile, the thermotolerance differences among the 4 uppermost monoterpenes were analyzed. In contrast to normal temperature (28°C), ROS levels and antioxidant enzyme activities in the 4 chemotypes increased under 38°C, and further increased in the treatment with Fos inhibiting monoterpene synthesis at 38°C (Fos+38°C), which may be caused by the alterations in expression of the genes related with non-enzymatic and enzymatic antioxidant formation according to the analyses in EuL and CmR. Compared with Fos+38°C treatment, Fos+38°C+monoterpene treatments lowered ROS levels and antioxidant enzyme activities for the increased non-enzymatic antioxidant gene expression and decreased enzymatic antioxidant gene expression, respectively. High temperature at 38°C reduced the chlorophyll and carotenoid content as well as photosynthetic abilities, which may result from the declined expression of the genes associated with photosynthetic pigment biosynthesis, light reaction, and carbon fixation. Fos+38°C treatment aggravated the reduction. In contrast to Fos+38°C treatment, Fos+38°C+monoterpene treatments increased photosynthetic pigment content and improved photosynthetic abilities by up-regulating related gene expression. Among the 4 uppermost monoterpenes, camphor showed strong abilities in lowering ROS and maintaining photosynthesis, while eucalyptol showed weak abilities. This was consistent with the recovery effects of the gene expression in the treatments with camphor and eucalyptol fumigation. Therefore, the uppermost monoterpenes can enhance C. camphora thermotolerance as signaling molecules, and may have differences in the signaling functions

Peach allergen Pru p 1 content is generally low in fruit but with large variation in different varieties

Background: Pru p 1 is a major allergen in peach and nectarine, and the different content in varieties may affect the degree of allergic reactions. This study aimed to quantify Pru p 1 levels in representative peach varieties and select hypoallergenic Pru p 1 varieties. Methods: To obtain monoclonal and polyclonal antibodies, mice and rabbits, respectively, were immunized with recombinant Pru p 1.01 and Pru p 1.02. The Pru p 1 levels in fruits from 83 representative peach varieties was quantified by sandwich enzyme‐linked immunosorbent assay (sELISA). nPru p 1 was obtained through specific monoclonal antibody affinity purification and confirmed by Western blot and mass spectrometry. The variable Pru p 1 content of selected varieties was evaluated by Western blot and the expression level of encoding Pru p 1 genes by quantitative polymerase chain reaction. Results: A sELISA method with monoclonal and polyclonal antibodies was built for quantifying Pru p 1 levels in peach. Pru p 1 was mainly concentrated in the peel (0.20–73.44 μg/g, fresh weight), being very low in the pulp (0.05–9.62 μg/g) and not detected in wild peach. For the 78 peach and nectarine varieties, Pru p 1 content varied widely from 0.12 to 6.45 μg/g in whole fruit. We verified that natural Pru p 1 is composed of 1.01 and 1.02 isoallergens, and the Pru p 1 expression level and Pru p 1 band intensity in the immunoblots were in agreement with protein quantity determined by ELISA for some tested varieties. In some cases, the reduced levels of Pru p 1 did not coincide with low Pru p 3 in the same variety in whole fruit, while some ancient wild peach and nectarines contained low levels of both allergens, and late‐ripening yellow flesh varieties were usually highly allergenic. Conclusion: Pru p 1 content is generally low in peach compared to Pru p 3. Several hypoallergenic Pru p 1 and Pru p 3 varieties, “Zi Xue Tao,” “Wu Yue Xian,” and “May Fire,” were identified, which could be useful in trials for peach allergy patients.info:eu-repo/semantics/publishedVersio

Magnetic Domain Structure in Ferromagnetic Kagome Metal DyMn6Sn6

Two types of magnetic domains, that is, type-I domain belt domain and type-II new stripe domain, are observed in a kagome metal DyMn6Sn6 by microscopic magneto-optic Kerr imaging technique. From 255 to 235 K, the spin reorientation is observed directly in DyMn6Sn6. We analyze the structure of two types of domains through brightness distribution of the images. The type-II domain exists from 235 to 160 K by zero-field cooling (ZFC). At the same time, type-I domain and type-II domain coexist and transform into each other with variation of temperature. Type-II domains can easily transform into type-I domains when the temperature and magnetic field changes, and this process is irreversible. These results demonstrate that the type-I domain is more stable than the type-II domain. The phase diagram of magnetic domains in DyMn6Sn6 is obtained

Single Endemic Genotype of Measles Virus Continuously Circulating in China for at Least 16 Years

The incidence of measles in China from 1991 to 2008 was reviewed, and the nucleotide sequences from 1507 measles viruses (MeV) isolated during 1993 to 2008 were phylogenetically analyzed. The results showed that measles epidemics peaked approximately every 3 to 5 years with the range of measles cases detected between 56,850 and 140,048 per year. The Chinese MeV strains represented three genotypes; 1501 H1, 1 H2 and 5 A. Genotype H1 was the predominant genotype throughout China continuously circulating for at least 16 years. Genotype H1 sequences could be divided into two distinct clusters, H1a and H1b. A 4.2% average nucleotide divergence was found between the H1a and H1b clusters, and the nucleotide sequence and predicted amino acid homologies of H1a viruses were 92.3%–100% and 84.7%–100%, H1b were 97.1%–100% and 95.3%–100%, respectively. Viruses from both clusters were distributed throughout China with no apparent geographic restriction and multiple co-circulating lineages were present in many provinces. Cluster H1a and H1b viruses were co-circulating during 1993 to 2005, while no H1b viruses were detected after 2005 and the transmission of that cluster has presumably been interrupted. Analysis of the nucleotide and predicted amino acid changes in the N proteins of H1a and H1b viruses showed no evidence of selective pressure. This study investigated the genotype and cluster distribution of MeV in China over a 16-year period to establish a genetic baseline before MeV elimination in Western Pacific Region (WPR). Continuous and extensive MeV surveillance and the ability to quickly identify imported cases of measles will become more critical as measles elimination goals are achieved in China in the near future. This is the first report that a single endemic genotype of measles virus has been found to be continuously circulating in one country for at least 16 years

Nicotine Dependence among Rural-Urban Migrants in China

<p>Abstract</p> <p>Background</p> <p>The complex mechanism of nicotine dependency makes it challenging to evaluate dependence or progress towards dependence. The aim of this study was to estimate nicotine dependence levels and identify determinants of dependence among Chinese rural-urban migrants.</p> <p>Methods</p> <p>Multi-stage systematic sampling was used to select 4,198 rural-urban migrants aged 18 years or older from three metropolises in China. A structured questionnaire was administered during face-to-face interviews. Nicotine dependence among participants was assessed by means of the six-item Mandarin Chinese Version of the Fagerström Test for Nicotine Dependence (CFTND). Determinants of dependence were analyzed using multivariate analysis of variance (MANOVA).</p> <p>Results</p> <p>Among 4,198 participants, estimated current, daily, and occasional smoking rates were 28.3%, 21.2%, and 7.1%, respectively. The CTFND score for the 894 daily smokers was 3.39(SD: 2.32). MANOVA showed that work type, age at first migration, length of migration, and number of cities ever lived were associated with nicotine dependence.</p> <p>Conclusion</p> <p>A migratory lifestyle is associated with nicotine dependence. Results could inform the design of tobacco control programs that target Chinese rural-urban migrant workers as a special at-risk population.</p