Transferable E(3) equivariant parameterization for Hamiltonian of molecules and solids

Using the message-passing mechanism in machine learning (ML) instead of self-consistent iterations to directly build the mapping from structures to electronic Hamiltonian matrices will greatly improve the efficiency of density functional theory (DFT) calculations. In this work, we proposed a general analytic Hamiltonian representation in an E(3) equivariant framework, which can fit the ab initio Hamiltonian of molecules and solids by a complete data-driven method and are equivariant under rotation, space inversion, and time reversal operations. Our model reached state-of-the-art precision in the benchmark test and accurately predicted the electronic Hamiltonian matrices and related properties of various periodic and aperiodic systems, showing high transferability and generalization ability. This framework provides a general transferable model that can be used to accelerate the electronic structure calculations on different large systems with the same network weights trained on small structures.Comment: 33 pages, 6 figure

Comparison of [11C]TZ1964B and [18F]MNI659 for PET imaging brain PDE10A in nonhuman primates

Phosphodiesterase 10A (PDE10A) inhibitors show therapeutic effects for diseases with striatal pathology. PET radiotracers have been developed to quantify in vivo PDE10A levels and target engagement for therapeutic interventions. The aim of this study was to compare two potent and selective PDE10A radiotracers, [(11)C]TZ1964B and [(18)F]MNI659 in the nonhuman primate (NHP) brain. Double scans in the same cynomolgus monkey on the same day were performed after injection of [(11)C]TZ1964B and [(18)F]MNI659. Specific uptake was determined in two ways: nondisplaceable binding potential (BP(ND)) was calculated using cerebellum as the reference region and the PDE‐10A enriched striatum as the target region of interest (ROI); the area under the time–activity curve (AUC) for the striatum to cerebellum ratio was also calculated. High‐performance liquid chromatography (HPLC) analysis of solvent‐extracted NHP plasma identified the percentage of intact tracer versus radiolabeled metabolites samples post injection of each radiotracer. Both radiotracers showed high specific accumulation in NHP striatum. [(11)C]TZ1964B has higher striatal retention and lower specific striatal uptake than [(18)F]MNI659. The BP(ND) estimates of [(11)C]TZ1964B were 3.72 by Logan Reference model (LoganREF) and 4.39 by simplified reference tissue model (SRTM); the BP(ND) estimates for [(18)F]MNI659 were 5.08 (LoganREF) and 5.33 (SRTM). AUC ratios were 5.87 for [(11)C]TZ1964B and 7.60 for [(18)F]MNI659. Based on BP(ND) values in NHP striatum, coefficients of variation were ~10% for [(11)C]TZ1964B and ~30% for [(18)F]MNI659. Moreover, the metabolism study showed the percentage of parent compounds were ~70% for [(11)C]TZ1964B and ~50% for [(18)F]MNI659 60 min post injection. These data indicate that either [(11)C]TZ1964B or [(18)F]MNI659 could serve as suitable PDE10A PET radiotracers with distinguishing features for particular clinical application

Ordered Semiconducting Nitrogen-Graphene Alloys

The interaction between substitutional nitrogen atoms in graphene is studied by performing first principles calculations. The nearest neighbor interaction between nitrogen dopants is highly repulsive because of the strong electrostatic repulsion between nitrogen atoms, which prevents the full phase separation in nitrogen doped graphene. Interestingly, there are two relatively stable nitrogen-nitrogen pairs due to the anisotropy charge redistribution induced by nitrogen doping. We reveal two stable semiconducting ordered N doped graphene structures C3N and C12N through the cluster expansion technique and particle swarm optimization method. In particular, C12N has a direct band gap of 0.98 eV. The heterojunctions between C12N and graphene nanoribbons might be promising organic solar cells

Tet3 regulates synaptic transmission and homeostatic plasticity via DNA oxidation and repair.

Contrary to the long-held belief that DNA methylation of terminally differentiated cells is permanent and essentially immutable, post-mitotic neurons exhibit extensive DNA demethylation. The cellular function of active DNA demethylation in neurons, however, remains largely unknown. Tet family proteins oxidize 5-methylcytosine to initiate active DNA demethylation through the base-excision repair (BER) pathway. We found that synaptic activity bi-directionally regulates neuronal Tet3 expression. Functionally, knockdown of Tet or inhibition of BER in hippocampal neurons elevated excitatory glutamatergic synaptic transmission, whereas overexpressing Tet3 or Tet1 catalytic domain decreased it. Furthermore, dysregulation of Tet3 signaling prevented homeostatic synaptic plasticity. Mechanistically, Tet3 dictated neuronal surface GluR1 levels. RNA-seq analyses further revealed a pivotal role of Tet3 in regulating gene expression in response to global synaptic activity changes. Thus, Tet3 serves as a synaptic activity sensor to epigenetically regulate fundamental properties and meta-plasticity of neurons via active DNA demethylation

Revisiting the annihilation decay Bˉs→π+π−\bar{B}_{s}\to\pi^{+}\pi^{-}

It is very important to know the strength of annihilation contribution in B charmless nonleptonic decays. $\bar{B}_{s}\to \pi^{+}\pi^{-}$ process could serve a good probe of the strength. We have studied the process in QCD factorization framework. Using a gluon mass scale indicted by the studies of infrared behavior of gluon propagators to avoid enhancements in the soft end point regions, we find that the CP averaged branching ratio is about $1.24\times 10^{-7}$, the direct CP asymmetry $C_{\pi\pi}$ is about -0.05, while the mixing-induced CP asymmetry quite large with the value $S_{\pi\pi}$=0.18. The process could be measured at LHC-b experiments in the near future and would deepen our understanding of dynamics of B charmless decays.Comment: 9 pages, 3 eps figures. To appear in EPJ

Micronutrients and risks of three main urologic cancers: A mendelian randomization study

BackgroundThe effect of micronutrients on urologic cancers has been explored in observational studies. We conducted the two-sample mendelian randomization (TSMR) study to investigate whether micronutrients could causally influence the risk of urologic cancers.MethodsSummary statistics for four micronutrients and three main urologic cancers outcomes were obtained from genome-wide association studies (GWAS). MR analyses were applied to explore the potential causal association between them. Sensitivity analyses using multiple methods were also conducted.ResultsGenetically predicted one SD increase in serum copper and iron concentrations was causally associated with increased risks of renal cell carcinoma (RCC) (OR = 3.021, 95%CI = 2.204–4.687, P < 0.001, male; OR = 2.231, 95%CI = 1.524-3.953, P < 0.001, female; OR = 1.595, 95%CI = 1.310–1.758, P = 0.0238, male; OR = 1.484, 95%CI = 1.197–2.337, P = 0.0210, female, respectively) and per SD increase in serum zinc levels was related to decreased risks of RCC (OR = 0.131, 95%CI = 0.0159–0.208, P < 0.001, male; OR = 0.124, 95%CI = 0.0434–0.356, P < 0.001, female). No significant results were observed between micronutrients and the risk of bladder cancer after Bonferroni correction. Additionally, per SD increase in serum zinc level was associated with a 5.8% higher risk of prostate cancer (PCa) [OR = 1.058, 95%CI = 1.002–1.116, P = 0.0403, inverse-variance weight (IVW)].ConclusionsMicronutrients play a vital role in the development of urological tumors. Future studies are required to replicate the findings, explore the underlying mechanisms, and examine the preventive or therapeutic role of micronutrients in clinical settings

Deletion of 1.8-kb mRNA of Marek's disease virus decreases its replication ability but not oncogenicity

<p>Abstract</p> <p>Background</p> <p>The 1.8-kb mRNA was reported as one of the oncogenesis-related genes of Marek's disease virus (MDV). In this study, the bacterial artificial chromosome (BAC) clone of a MDV field strain GX0101 was used as the platform to generate mutant MDV to examine the functional roles of 1.8-kb mRNA.</p> <p>Results</p> <p>Based on the BAC clone of GX0101, the 1.8-kb mRNA deletion mutant GX0101Δ(A+C) was constructed. The present experiments indicated that GX0101Δ(A+C) retained a low level of oncogenicity, and it showed a decreased replication capacity in vitro and in vivo when compared with its parent virus, GX0101. Further studies in vitro demonstrated that deletion of 1.8-kb mRNA significantly decreased the transcriptional activity of the bi-directional promoter between 1.8-kb mRNA and pp38 genes of MDV.</p> <p>Conclusion</p> <p>These results suggested that the 1.8-kb mRNA did not directly influence the oncogenesis but related to the replication ability of MDV.</p

Pyrolysis gas as a carbon source for biogas production via anaerobic digestion

Carbon is an important resource for anaerobes to enhance biogas production. In this study, the possibility of using simulated pyrolysis gas (SPG) as a carbon source for biogas production was investigated. The effects of stirring speed (SS), gas holding time (GHT), and H2 addition on biomethanation of SPG were evaluated. The diversity and structure of microbial communities were also analyzed under an illumina MiSeq platform. Results indicated that at a GHT of 14 h and an SS at 400 rpm, SPG with up to 64.7% CH4could be bio-upgraded to biogas. Gas–liquid mass transfer is the limitation for SPG biomethanation. For the first time, it has been noticed that the addition of H2 can bioupgrade SPG to high quality biogas (with 91.1% CH4). Methanobacterium was considered as a key factor in all reactors. This study provides an idea and alternative way to convert lignocellulosic biomass and solid organic waste into energy (e.g., pyrolysis was used as a pretreatment to produce pyrolysis gas from biomass, and then, pyrolysis gas was bioupgraded to higher quality biogas via anaerobic digestion)

Prediction of Drug Positioning for Quan-Du-Zhong Capsules Against Hypertensive Nephropathy Based on the Robustness of Disease Network

Hypertensive nephropathy (HN) is a medical condition in which chronic high blood pressure causes different kidney damage, including vascular, glomerular and tubulointerstitial lesions. For HN patients, glomerular and tubulointerstitial lesions occur in different renal structure with distinct mechanisms in the progression of renal damage. As an extraction of Eucommia ulmoides, Quan-du-zhong capsule (QDZJN) has the potential to treat HN due to antihypertensive and renal protective activities. Complicated mechanism of HN underlying various renal lesions and the “multi-component and multi-target” characteristics of QDZJN make identifying drug positioning for various renal lesions of HN complex. Here, we proposed an approach based on drug perturbation of disease network robustness, that is used to assess QDZJN positioning for various HN lesions. Topological characteristics of drug-attacked nodes in disease network were used to evaluated nodes importance to network. To evaluate drug attack on the whole disease network of various HN lesions, the robustness of disease networks before/after drug attack were assessed and compared with null models generated from random networks. We found that potential targets of QDZJN were specifically expressed in the kidneys and tended to participate in the “inflammatory response,” “regulation of blood pressure,” and “response to LPS and hypoxia,” and they were also key factors of HN. Based on network robustness assessment, QDZJN may specifically target glomeruli account to the stronger influence on glomerular network after removal of its potential targets. This prediction strategy of drug positioning is suitable for multi-component drugs based on drug perturbation of disease network robustness for two renal compartments, glomeruli and tubules. A stronger influence on the disease network of glomeruli than of tubules indicated that QDZJN may specifically target glomerular lesion of HN patients and will provide more evidence for precise clinical application of QDZJN against HN. Drug positioning approach we proposed also provides a new strategy for predicting precise clinical use of multi-target drugs