Inverse Temperature Dependence of Nuclear Quantum Effects in DNA Base Pairs

Despite the inherently quantum mechanical nature of hydrogen bonding, it is unclear how nuclear quantum effects (NQEs) alter the strengths of hydrogen bonds. With this in mind, we use ab initio path integral molecular dynamics to determine the absolute contribution of NQEs to the binding in DNA base pair complexes, arguably the most important hydrogen-bonded systems of all. We find that depending on the temperature, NQEs can either strengthen or weaken the binding within the hydrogen-bonded complexes. As a somewhat counterintuitive consequence, NQEs can have a smaller impact on hydrogen bond strengths at cryogenic temperatures than at room temperature. We rationalize this in terms of a competition of NQEs between low-frequency and high-frequency vibrational modes. Extending this idea, we also propose a simple model to predict the temperature dependence of NQEs on hydrogen bond strengths in general

The quantum nature of hydrogen

Hydrogen is the most abundant element in the universe. It is also the lightest and as such the most quantum of the elements, in the sense that quantum tunnelling, quantum delocalisation, and zero-point motion can be important. For practical reasons most computer simulations of materials have not taken such effects into account, rather they have treated atomic nuclei as classical point-like particles. However, it is an exciting time for the theory and simulation of materials and thanks to significant methodological developments over the last few decades, nuclear quantum effects can now be accurately treated in complex materials. In this brief review we discuss our recent studies on the role nuclear quantum effects play in hydrogen containing systems. We give examples of how the quantum nature of the nuclei has a significant impact on the location of the boundaries between phases in high pressure condensed hydrogen, including a dramatic lowering of the solid to liquid melting line. We show how nuclear quantum effects facilitate the dissociative adsorption of molecular hydrogen on solid surfaces and the diffusion of atomic hydrogen across surfaces; effects that are of relevance to the catalytic performance of the surfaces. Finally, we discuss how nuclear quantum effects alter the strength and structure of hydrogen bonds, including the hydrogen bonds in DNA. Overall these studies demonstrate that nuclear quantum effects can manifest in many different, interesting, and at times non-intuitive ways. Whilst historically it has been difficult to know in advance what influence nuclear quantum effects will have, some of the important conceptual foundations have now started to emerge

CityNet: A Multi-city Multi-modal Dataset for Smart City Applications

Data-driven approaches have been applied to many problems in urban computing. However, in the research community, such approaches are commonly studied under data from limited sources, and are thus unable to characterize the complexity of urban data coming from multiple entities and the correlations among them. Consequently, an inclusive and multifaceted dataset is necessary to facilitate more extensive studies on urban computing. In this paper, we present CityNet, a multi-modal urban dataset containing data from 7 cities, each of which coming from 3 data sources. We first present the generation process of CityNet as well as its basic properties. In addition, to facilitate the use of CityNet, we carry out extensive machine learning experiments, including spatio-temporal predictions, transfer learning, and reinforcement learning. The experimental results not only provide benchmarks for a wide range of tasks and methods, but also uncover internal correlations among cities and tasks within CityNet that, with adequate leverage, can improve performances on various tasks. With the benchmarking results and the correlations uncovered, we believe that CityNet can contribute to the field of urban computing by supporting research on many advanced topics

Structural water as an essential comonomer in supramolecular polymerization

Water is an essential comonomer in a supramolecular polymer that is used as a recyclable, water-activated glue.</jats:p

CivRealm: A Learning and Reasoning Odyssey in Civilization for Decision-Making Agents

The generalization of decision-making agents encompasses two fundamental elements: learning from past experiences and reasoning in novel contexts. However, the predominant emphasis in most interactive environments is on learning, often at the expense of complexity in reasoning. In this paper, we introduce CivRealm, an environment inspired by the Civilization game. Civilization's profound alignment with human history and society necessitates sophisticated learning, while its ever-changing situations demand strong reasoning to generalize. Particularly, CivRealm sets up an imperfect-information general-sum game with a changing number of players; it presents a plethora of complex features, challenging the agent to deal with open-ended stochastic environments that require diplomacy and negotiation skills. Within CivRealm, we provide interfaces for two typical agent types: tensor-based agents that focus on learning, and language-based agents that emphasize reasoning. To catalyze further research, we present initial results for both paradigms. The canonical RL-based agents exhibit reasonable performance in mini-games, whereas both RL- and LLM-based agents struggle to make substantial progress in the full game. Overall, CivRealm stands as a unique learning and reasoning challenge for decision-making agents. The code is available at https://github.com/bigai-ai/civrealm

Quantitative analysis of the developmental potential of cells and tissues based on evolutionary conservation of genes and regulatory regions

Objective·To study the relationship between evolution and the developmental process from the perspective of DNA sequence conservation, and explore their inherent principles.Methods·First, conservation rate (CR) was established by analyzing the conservation of amino acid sequences of coding genes in 100 species to quantify the evolutionary conservation of genes. The relationship between CR and developmental potential was verified by using the feature genes involved in embryonic stem cells pathways. Secondly, cell type-specific genes and their characteristics in conservation were studied by analyzing the RNA sequencing (RNA-seq) data of the three early germ layers (ectoderm, mesoderm and endoderm) and their corresponding mature organs (brain, heart, liver, etc). Then, chromatin immunoprecipitation sequencing (ChIP-seq) data of enhancer histone H3 acetylated at lysine 27 (H3K27ac) from early germ layers and mature organs were collected to search for enhancer sites and identify super enhancers in various cells and tissues by using the ROSE procedure. Functional enrichment and signaling pathway analysis of genes was used to examine the identity correlation between SEs-regulated genes and the corresponding cell characteristics, to clarify whether the SEs identified in this study were consistent with the characteristics reported in previous studies. Finally, PhastCons program was used to calculate the DNA conservation score (CS) of non-coding regulatory regions to study their relationship with developmental potential.Results·In the coding region of DNA, CR was successfully established to quantify the conservation of genes. The gene expression data of early germ layers and mature organs showed that the genes with higher conservation rate were more relevant to the stemness and early developmental process, and the differences between the tissues from early and late development could be distinguished by using CR. In the non-coding regions of DNA, it was found that the conservation of regulatory regions was also correlated with development. The CS of the SE sequences in the early developmental germ layers was significantly higher than that of the SE sequences in the corresponding mature organs. However, cell-specific typical enhancers (TEs) did not show such a trend.Conclusion·During the developmental process, CR of genes expressed in the coding region decreases, and CS of super-enhancer DNA in the non-coding region decreases

Prediction of ESRD in IgA Nephropathy Patients from an Asian Cohort: A Random Forest Model

Background/Aims: There is an increasing risk of end-stage renal disease (ESRD) among Asian people with immunoglobulin A nephropathy (IgAN). A computer-aided system for ESRD prediction in Asian IgAN patients has not been well studied. Methods: We retrospectively reviewed biopsy-proven IgAN patients treated at the Department of Nephrology of the Second Xiangya Hospital from January 2009 to November 2013. Demographic and clinicopathological data were obtained within 1 month of renal biopsy. A random forest (RF) model was employed to predict the ESRD status in IgAN patients. All cases were initially trained and validated, taking advantage of the out-of-bagging(OOB) error. Predictors used in the model were selected according to the Gini impurity index in the RF model and verified by logistic regression analysis. The area under the receiver operating characteristic(ROC) curve (AUC) and F-measure were used to evaluate the RF model. Results: A total of 262 IgAN patients were enrolled in this study with a median follow-up time of 4.66 years. The importance rankings of predictors of ESRD in the RF model were first obtained, indicating some of the most important predictors. Logistic regression also showed that these factors were statistically associated with ESRD status. We first trained an initial RF model using gender, age, hypertension, serum creatinine, 24-hour proteinuria and histological grading suggested by the Clinical Decision Support System for IgAN (CDSS, www.IgAN.net). This 6-predictor model achieved a F-measure of 0.8 and an AUC of 92.57%. By adding Oxford-MEST scores, this model outperformed the initial model with an improved AUC (96.1%) and F-measure (0.823). When C3 staining was incorporated, the AUC was 97.29% and F-measure increased to 0.83. Adding the estimated glomerular filtration rate (eGFR) improved the AUC to 95.45%. We also observed improved performance of the model with additional inputs of blood urea nitrogen (BUN), uric acid, hemoglobin and albumin. Conclusion: In addition to the predictors in the CDSS, Oxford-MEST scores, C3 staining and eGFR conveyed additional information for ESRD prediction in Chinese IgAN patients using a RF model

Highly efficient cash sterilization with ultrafast and flexible Joule‐heating strategy by laser patterning

Since ancient times, humans have learned to use fire and other heating methods to fight against dangerous pathogens, like cooking raw food, sterilizing surgical tools, and disinfecting other pathogen transmission media. However, it remains difficult for current heating methods to achieve extremely fast and highly efficient sterilization simultaneously. Herein, an ultrafast and uniform heating‐based strategy with outstanding bactericidal performance is proposed. Ultra‐precise laser manufacturing is used to fabricate the Joule heater which can be rapidly heated to 90 °C in 5 s with less than 1 °C fluctuation in a large area by real‐time temperature feedback control. An over 98% bactericidal efficiency on S. aureus for 30 s and on E. coli for merely 5 s is shown. The heating strategy shows a 360 times faster acceleration compared to the commonly used steam sterilization from the suggested guidelines by the Centers for Disease Control and Prevention (CDC), indicating that high temperatures with short duration can effectively disinfect microorganisms. As a proof of concept, this heating strategy can be widely applied to sterilizing cash and various objects to help protect the public from bacteria in daily life

The Asian Arowana (Scleropages formosus) Genome Provides New Insights into the Evolution of an Early Lineage of Teleosts

The Asian arowana (Scleropages formosus), one of the world’s most expensive cultivated ornamental fishes, is an endangered species. It represents an ancient lineage of teleosts: the Osteoglossomorpha. Here, we provide a high-quality chromosome-level reference genome of a female golden-variety arowana using a combination of deep shotgun sequencing and high-resolution linkage mapping. In addition, we have also generated two draft genome assemblies for the red and green varieties. Phylogenomic analysis supports a sister group relationship between Osteoglossomorpha (bonytongues) and Elopomorpha (eels and relatives), with the two clades together forming a sister group of Clupeocephala which includes all the remaining teleosts. The arowana genome retains the full complement of eight Hox clusters unlike the African butterfly fish (Pantodon buchholzi), another bonytongue fish, which possess only five Hox clusters. Differential gene expression among three varieties provides insights into the genetic basis of colour variation. A potential heterogametic sex chromosome is identified in the female arowana karyotype, suggesting that the sex is determined by a ZW/ZZ sex chromosomal system. The high-quality reference genome of the golden arowana and the draft assemblies of the red and green varieties are valuable resources for understanding the biology, adaptation and behaviour of Asian arowanas