Gram matrix: an efficient representation of molecular conformation and learning objective for molecular pretraining.

Accurate prediction of molecular properties is fundamental in drug discovery and development, providing crucial guidance for effective drug design. A critical factor in achieving accurate molecular property prediction lies in the appropriate representation of molecular structures. Presently, prevalent deep learning-based molecular representations rely on 2D structure information as the primary molecular representation, often overlooking essential three-dimensional (3D) conformational information due to the inherent limitations of 2D structures in conveying atomic spatial relationships. In this study, we propose employing the Gram matrix as a condensed representation of 3D molecular structures and for efficient pretraining objectives. Subsequently, we leverage this matrix to construct a novel molecular representation model, Pre-GTM, which inherently encapsulates 3D information. The model accurately predicts the 3D structure of a molecule by estimating the Gram matrix. Our findings demonstrate that Pre-GTM model outperforms the baseline Graphormer model and other pretrained models in the QM9 and MoleculeNet quantitative property prediction task. The integration of the Gram matrix as a condensed representation of 3D molecular structure, incorporated into the Pre-GTM model, opens up promising avenues for its potential application across various domains of molecular research, including drug design, materials science, and chemical engineering.

Exploring and Predicting the Drivers of Ongoing HIV-1 Transmission in Guangyuan, Sichuan.

Purpose: Guangyuan was selected as the first pilot city of molecular transmission network in Sichuan Province to implement dynamic monitoring. This study aim to insight the characteristics of HIV-1 molecular epidemiology and explore the influencing factors of transmission dynamics. Furthermore, it predict the driving factors of network expansion by established a transmission risk prediction model. Patients and Methods: A longitudinal cohort study was conducted to obtain a total of 1434 plasma samples from newly diagnosed HIV-infected patients from 2010 to June 2022. Phylogenetic relationship and cluster analysis were performed using HIV-1 polymerase (pol) gene sequences to study the risk factors of clustering. We applied Logistic ML algorithms to establish a transmission risk prediction model, and model performance was checked using 10-fold cross-validation in the training set and receiver operating characteristic (ROC) curve analysis. Results: A total of 1360 pol sequences linked demographics obtained in this study cover approximately 94.8% of newly notified infections from 2010 to June 2022. The major epidemic genotypes were CRF07_BC, CRF01_AE, CRF08_BC and B subtypes, accounting for 93.82% of all. The differences of some clinical and demographic factors (eg, age, marital status) were statistically significant (P<0.05). We identified 136 clusters containing 654 HIV-1 pol sequences and observed that some characteristics (eg, over 50 years, married) were more likely to associated to the clusters (P<0.05). The predictive model showed excellent predictive ability to forecast cluster growth. Conclusion: The epidemic genotypes were relatively complex and diverse in Guangyuan. There was a potential transmission association caused widely spread in local area after the new strains entering. The transmission risk prediction model showed excellent predictive ability to forecast cluster growth which can predict the risk factors causing clusters expansion and provide a guidance for precise intervention strategies.

GPR15-mediated homing controls immune homeostasis in the large intestine mucosa.

Lymphocyte homing, which contributes to inflammation, has been studied extensively in the small intestine, but there is little known about homing to the large intestine, the site most commonly affected in inflammatory bowel disease. GPR15, an orphan heterotrimeric guanine nucleotide-binding protein (G protein)-coupled receptor, controlled the specific homing of T cells, particularly FOXP3(+) regulatory T cells (Tregs), to the large intestine lamina propria (LILP). GPR15 expression was modulated by gut microbiota and transforming growth factor-ß1, but not by retinoic acid. GPR15-deficient mice were prone to develop more severe large intestine inflammation, which was rescued by the transfer of GPR15-sufficient Tregs. Our findings thus describe a T cell-homing receptor for LILP and indicate that GPR15 plays a role in mucosal immune tolerance largely by regulating the influx of Tregs.

Role for CXCR6 in recruitment of activated CD8+ lymphocytes to inflamed liver.

Hepatic infiltration of activated CD8 lymphocytes is a major feature of graft-vs-host disease (GvHD). Chemoattractant cytokines and their receptors are key regulators of lymphocyte trafficking, but the involvement of chemoattractant receptors in the physiologic recruitment of cells into the inflamed liver has not been defined. The present study examines the role of the chemokine receptor CXCR6, which is highly expressed by liver-infiltrating CD8 T cells. Hepatic accumulation of donor CD8, but not donor CD4, lymphocytes was significantly reduced in GvHD induced by transfer of CXCR6(-/-), H-2D(b) lymphocytes into BDF(1), H-2D(bxd) recipients. To determine whether altered recruitment contributes to the reduced accumulation, CXCR6(-/-) or wild-type splenic lymphocytes participating in an active GvHD response were isolated and transferred i.v. into secondary recipients with active GvHD, and the short term (6-h) recruitment of transferred cells to the inflamed liver was assessed. CXCR6(-/-) CD8 (but not CD4) cells displayed a significant (33%) reduction in liver localization, whereas frequencies in blood of CXCR6(-/-) and wild-type CD8 cells were similar. Proliferation and apoptosis of liver-infiltrating donor CD8 cells were unaffected. We conclude that CXCR6 helps mediate the recruitment of activated CD8 lymphocytes in GvHD-induced hepatitis and may be a useful target to treat pathological inflammation in the liver.

Analysis of the cloverleaf element in a human rhinovirus type 14/poliovirus chimera: correlation of subdomain D structure, ternary protein complex formation and virus replication.

RNA genomes of enteroviruses and rhinoviruses contain a 5'-terminal structure, the cloverleaf (CL), which serves as signal in RNA synthesis. Substitution of the poliovirus [PV1(M)] CL with that of human rhinovirus type 2 (HRV2) was shown previously to produce a viable chimeric PV, whereas substitution with the HRV14 CL produced a null phenotype. Fittingly, the HRV14 CL failed to form a complex with PV-specific proteins 3CD(pro)-3AB or 3CD(pro)-PCBP2, considered essential for RNA synthesis. It was reported previously (Rohll et al., J Virol 68, 4384-4391, 1994) that the major determinant for the null phenotype of a PV/HRV14 chimera resides in subdomain Id of the HRV14 CL. Using a chimeric PV/HRV14 CL in the context of the PV genome, stem-loop Id of HRV14 CL was genetically dissected. It contains the sequence C(57)UAU(60)-G, the underlined nucleotides forming the loop that is shorter by 1 nt when compared to the corresponding PV structure (UUGC(60)GG). Insertion of a G nucleotide to form a tetra loop (C(57)UAU(60)GG(61)) did not rescue replication of the chimera. However, an additional mutation at position 60 (C(57)UAC(60)GG(61)) yielded a replicating genome. Only the mutant PV/HRV14 CL with the UAC(60)G tetra loop formed ternary complexes efficiently with either PV proteins 3CD(pro)-3AB or 3CD(pro)-PCBP2. Thus, in the context of PV RNA synthesis, the presence of a tetra loop in subdomain D of the CL per se is not sufficient for function. The sequence and, consequently, the structure of the tetra loop plays an essential role. Biochemical assays demonstrated that the function of the CL element and the function of the cis-acting replication element in the 3D(pol)-3CD(pro)-dependent uridylylation of VPg are not linked.