Learning Joint 2D & 3D Diffusion Models for Complete Molecule Generation

Designing new molecules is essential for drug discovery and material science. Recently, deep generative models that aim to model molecule distribution have made promising progress in narrowing down the chemical research space and generating high-fidelity molecules. However, current generative models only focus on modeling either 2D bonding graphs or 3D geometries, which are two complementary descriptors for molecules. The lack of ability to jointly model both limits the improvement of generation quality and further downstream applications. In this paper, we propose a new joint 2D and 3D diffusion model (JODO) that generates complete molecules with atom types, formal charges, bond information, and 3D coordinates. To capture the correlation between molecular graphs and geometries in the diffusion process, we develop a Diffusion Graph Transformer to parameterize the data prediction model that recovers the original data from noisy data. The Diffusion Graph Transformer interacts node and edge representations based on our relational attention mechanism, while simultaneously propagating and updating scalar features and geometric vectors. Our model can also be extended for inverse molecular design targeting single or multiple quantum properties. In our comprehensive evaluation pipeline for unconditional joint generation, the results of the experiment show that JODO remarkably outperforms the baselines on the QM9 and GEOM-Drugs datasets. Furthermore, our model excels in few-step fast sampling, as well as in inverse molecule design and molecular graph generation. Our code is provided in https://github.com/GRAPH-0/JODO

Regions are Who Walk Them: a Large Pre-trained Spatiotemporal Model Based on Human Mobility for Ubiquitous Urban Sensing

User profiling and region analysis are two tasks of significant commercial value. However, in practical applications, modeling different features typically involves four main steps: data preparation, data processing, model establishment, evaluation, and optimization. This process is time-consuming and labor-intensive. Repeating this workflow for each feature results in abundant development time for tasks and a reduced overall volume of task development. Indeed, human mobility data contains a wealth of information. Several successful cases suggest that conducting in-depth analysis of population movement data could potentially yield meaningful profiles about users and areas. Nonetheless, most related works have not thoroughly utilized the semantic information within human mobility data and trained on a fixed number of the regions. To tap into the rich information within population movement, based on the perspective that Regions Are Who walk them, we propose a large spatiotemporal model based on trajectories (RAW). It possesses the following characteristics: 1) Tailored for trajectory data, introducing a GPT-like structure with a parameter count of up to 1B; 2) Introducing a spatiotemporal fine-tuning module, interpreting trajectories as collection of users to derive arbitrary region embedding. This framework allows rapid task development based on the large spatiotemporal model. We conducted extensive experiments to validate the effectiveness of our proposed large spatiotemporal model. It's evident that our proposed method, relying solely on human mobility data without additional features, exhibits a certain level of relevance in user profiling and region analysis. Moreover, our model showcases promising predictive capabilities in trajectory generation tasks based on the current state, offering the potential for further innovative work utilizing this large spatiotemporal model.Comment: 8 page

Moderate increase of precipitation stimulates CO2 production by regulating soil organic carbon in a saltmarsh

Saltmarsh is widely recognized as a blue carbon ecosystem with great carbon storage potential. Yet soil respiration with a major contributor of atmospheric CO2 can offset its carbon sink function. Up to date, mechanisms ruling CO2 emissions from saltmarsh soil remain unclear. In particular, the effect of precipitation on soil CO2 emissions is unclear in coastal wetlands, due the lack of outdoor data in real situations. We conducted a 7-year field manipulation experiment in a saltmarsh in the Yellow River Delta, China. Soil respiration in five treatments (−60%, −40%, +0%, +40%, and + 60% of precipitation) was measured in the field. Topsoils from the last 3 years (2019–2021) were analyzed for CO2 production potential by microcosm experiments. Furthermore, quality and quantity of soil organic carbon and microbial function were tested. Results show that only the moderate precipitation rise of +40% induced a 66.2% increase of CO2 production potential for the microcosm experiments, whereas other data showed a weak impact. Consistently, soil respiration was also found to be strongest at +40%. The CO2 production potential is positively correlated with soil organic carbon, including carbon quantity and quality. But microbial diversity did not show any positive response to precipitation sizes. r-/K-strategy seemed to be a plausible explanation for biological factors. Overall, our finding reveal that a moderate precipitation increase, not decrease or a robust increase, in a saltmarsh is likely to improve soil organic carbon quality and quantity, and bacterial oligotroph:copiotroph ratio, ultimately leading to an enhanced CO2 production

Association of gamma-tocopherol serum concentrations and blood pressure among adults in the United States: a cross-sectional study

Backgroundhypertension is one of the major preventable risk factors for numerous diseases. The role of vitamin E in blood pressure (BP) has been controversial. We aimed to investigate the relationship between gamma-tocopherol serum concentration (GTSC) and BPMethodsData from 15,687 US adults from the National Health and Nutrition Examination Survey (NHANES) were analyzed. The correlations of GTSC with systolic BP (SBP), diastolic BP (DBP), and prevalence of hypertension were investigated by multivariate logistic regression models, generalized summation models, and fitted smoothing curves. Subgroup analyses were performed to investigate possible effect modifiers between them.ResultsWith each natural log increase in GTSC, SBP, and DBP increased by 1.28 mmHg (β 1.28, 95% CI 0.71–1.84) and 1.15 mmHg (β 1.15, 95% CI 0.72–1.57), respectively, both P for trend < 0.001; the prevalence of hypertension increased by 12% (OR 1.12, 95% CI 1.03–1.22), P for trend 0.008. In subgroup analysis, in drinkers, with each natural log increase in GTSC, SBP, and DBP increased by 1.77 mmHg (β 1.77,95% CI 1.13–2.41) and 1.37 mmHg (β 1.37,95% CI 0.9–1.85), respectively, whereas they were not correlated in non-drinkers.ConclusionGTSC was linearly and positively associated with SBP, DBP, and the prevalence of hypertension, and alcohol consumption may modify the relationship of GTSC with SBP and DBP

A molecular framework for lc controlled locule development of the floral meristem in tomato

Malformed tomato fruit with multiple locules is a common physiological disorder that significantly affects the quality of tomatoes. Research has shown that the occurrence of malformed fruit in tomatoes is closely linked to the number of locules, and two key QTLs, lc and fas, are involved in controlling this trait. It has been observed that lc has a relatively weaker effect on increasing locule number, which is associated with two SNPs in the CArG repressor element downstream of the SlWUS. However, the precise molecular mechanism underlying lc is not yet fully understood. In this study, we investigated the role of lc in tomato locule development. We found that the number of floral organs and fruit locules significantly increased in tomato lc knockout mutants. Additionally, these mutants showed higher expression levels of the SlWUS during carpel formation. Through cDNA library construction and yeast one-hybrid screening, we identified the MADS-box transcription factor SlSEP3, which was found to bind to lc. Furthermore, we observed an increase in floral organs and fruit locules similar to the lcCR plant on SlSEP3 silencing plants. However, it should be noted that the lc site is located after the 3′ untranslated region (UTR) of SlWUS in the tomato genome. As a result, SlSEP3 may not be able to exert regulatory functions on the promoter of the gene like other transcription factors. In the yeast two-hybrid assay, we found that several histone deacetylases (SlHDA1, SlHDA3, SlHDA4, SlHDA5, SlHDA6, SlHDA7, and SlHDA8) can interact with SlSEP3. This indicated that SlSEP3 can recruit these proteins to repress nucleosome relaxation, thereby inhibiting SlWUS transcription and affecting the number of locules in tomato fruit. Therefore, our findings reveal a new mechanism for lc playing a significant role in the genetic pathway regulating tomato locule development

Involvement in bullying and sleep disorders in Chinese early adolescents

BackgroundSchool bullying may cause sleep disorders in early adolescents. Here, we determined the relationship between school bullying (considering all the features of bullying involvement) and sleep disorders, which are the common problems in Chinese early adolescents.Materials and methodsWe conducted a questionnaire survey among 5,724 middle school students from Xuancheng, Hefei, and Huaibei cities in Anhui province, China. The self-report questionnaires included the Olweus Bully/Victim Questionnaire and Pittsburgh Sleep Quality Index. We used latent class analysis to identify the potential subgroups of bullying behavior. Logistic regression analysis was used to investigate the association between school bullying and sleep disorders.ResultsActive participants in bullying interactions, including the bullies and victims, reported higher levels of sleep disorders compared with the non-active participants [Bully: physical (aOR = 2.62), verbal (aOR = 1.73), relational (aOR = 1.80), and cyber (aOR = 2.08); Victim: physical (aOR = 2.42), verbal (aOR = 2.59), relational (aOR = 2.61), and cyber (aOR = 2.81)]. A dose–response relationship was observed between the number of school bullying types and sleep disorders. In the context of bullying roles, bully-victims had the highest risk of reporting sleep disorders (aOR = 3.07, 95% CI: 2.55–3.69). We identified four potential categories of school bullying behaviors: low involvement in bullying, verbal and relational victims, medium bully-victims, and high bully-victims, and the highest frequency of sleep disorders was observed in the high bully-victims group (aOR = 4.12, 95% CI: 2.94–5.76).ConclusionOur findings indicate a positive correlation between bullying roles and sleep disorders in early adolescents. Therefore, targeted intervention for sleep disorders should include an evaluation of bullying experiences

Reactive Oxygen Species Released from Hypoxic Hepatocytes Regulates MMP-2 Expression in Hepatic Stellate Cells

Hypoxia is a common environmental stress factor and is associated with fibrogenesis. Matrix metalloproteinase-2 (MMP-2), produced by hepatic stellate cells (HSCs), plays an important role in liver fibrogenesis. However, inconsistent results have been reported on the impact of hypoxia on MMP-2 expression and activity in HSCs. We speculated that cell–cell interaction is involved in the regulation of MMP-2 expression and activity at low oxygen level in vivo. Therefore, in this report we investigated the mechanism by which hypoxic hepatocytes regulates MMP-2 expression in HSCs. Our results showed that the conditioned medium from hypoxia-treated rat hepatocytes strongly induced the expression of MMP-2 mRNA and protein in rat HSC-T6 cells. Reduced glutathione neutralized ROS released from hypoxic hepatocytes, leading to reduced MMP-2 expression in HSC-T6 cells. In addition, phospho-IκB-α protein level was increased in HSC-T6 cells treated with hypoxia conditioned medium, and NF-κB signaling inhibitor inhibited MMP-2 expression in HSC-T6 cells. Taken together, our data suggest that ROS is an important factor released by hypoxic hepatocytes to regulate MMP-2 expression in HSCs, and NF-κB signaling is crucially involved in ROS-induced MMP-2 expression in HSCs. Our findings suggest that strategies aimed at antagonizing the generation of ROS in hypoxic hepatocytes and inhibiting NF-κB signaling in HSCs may represent novel therapeutic options for liver fibrosis

Associations of B Vitamin-Related Dietary Pattern during Pregnancy with Birth Outcomes: A Population-Based Study in Northwest China

This study aimed to derive a maternal dietary pattern to explain the variation in B vitamins during pregnancy and to investigate this pattern in relation to birth outcomes. A total of 7347 women who gave birth to live newborns less than one year were included. Their dietary pattern during pregnancy was derived using the reduced-rank regression method with six B vitamins as response variables. Associations between dietary pattern score and birth weight, gestational age at delivery, birth weight Z score, low birth weight, preterm, and small-for-gestational-age (SGA) were estimated using generalised linear mixed models. We identified a high B-vitamin dietary pattern characterised by high intakes of animal foods, vegetables, fungi and algae, legumes, and low intakes of oils and cereals. Women in the highest quartile of this pattern score had newborns with a 44.5 g (95% CI: 13.8, 75.2 g) higher birth weight, 0.101 (95% CI: 0.029, 0.172) higher birth weight Z score, and 27.2% (OR: 0.728; 95% CI: 0.582, 0.910) lower risk of SGA than those in the lowest quartile. Our study suggested that adherence to the high B-vitamin dietary pattern during pregnancy was associated with a higher birth weight and a lower risk of SGA