Protein Fold Recognition Using Adaboost Learning Strategy

Protein structure prediction is one of the most important and difficult problems in computational molecular biology. Unlike sequence-only comparison, protein fold recognition based on machine learning algorithms attempts to detect similarities between protein structures which might not be accompanied with any significant sequence similarity. It takes advantage of the information from structural and physic properties beyond sequence information. In this thesis, we present a novel classifier on protein fold recognition, using AdaBoost algorithm that hybrids to k Nearest Neighbor classifier. The experiment framework consists of two tasks: (i) carry out cross validation within the training dataset, and (ii) test on unseen validation dataset, in which 90% of the proteins have less than 25% sequence identity in training samples. Our result yields 64.7% successful rate in classifying independent validation dataset into 27 types of protein folds. Our experiments on the task of protein folding recognition prove the merit of this approach, as it shows that AdaBoost strategy coupling with weak learning classifiers lead to improved and robust performance of 64.7% accuracy versus 61.2% accuracy in published literatures using identical sample sets, feature representation, and class labels

Extended dissipaton equation of motion for electronic open quantum systems: Application to the Kondo impurity model

In this paper, we present an extended dissipaton equation of motion for studying the dynamics of electronic impurity systems. Compared with the original theoretical formalism, the quadratic couplings are introduced into the Hamiltonian accounting for the interaction between the impurity and its surrounding environment. By exploiting the quadratic dissipaton algebra, the proposed extended dissipaton equation of motion offers a powerful tool for studying the dynamical behaviors of electronic impurity systems, particularly in situations where nonequilibrium and strongly correlated effects play significant roles. Numerical demonstrations are carried out to investigate the temperature dependence of the Kondo resonance in the Kondo impurity model.Comment: 6 pages, 1 figur

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

The food retail revolution in China and its association with diet and health

The processed food sector in low- and middle-income countries has grown rapidly. Little is understood about its effect on obesity. Using data from 14,976 participants aged two and older in the 2011 China Health and Nutrition Survey, this paper examines patterns of processed food consumption and their impacts on obesity while considering the endogeneity of those who purchase processed foods. A major assumption of our analysis of the impact of processed foods on overweight and obesity was that the consumption of processed foods is endogenous due to their accessibility and urbanicity levels. The results show that 74.5% of participants consumed processed foods, excluding edible oils and other condiments; 28.5% of participants' total daily energy intake (EI) was from processed foods. Children and teenagers in megacities had the highest proportion of EI (40.2%) from processed foods. People who lived in megacities or highly urbanized neighborhoods with higher incomes and educational achievement consumed more processed foods. When controlling for endogeneity, only the body mass index (BMI) and risk of being overweight of children ages two to eighteen are adversely associated with processed foods (+4.97 BMI units, 95% confidence interval (CI): 1.66–8.28; odds ratio (OR) = 3.63, 95% CI: 1.45–9.13). Processed food purchases represent less than a third of current Chinese food purchases. However, processed food purchases are growing at the rate of 50% per year, and we must begin to understand the implications for the future

NF45/NF90-mediated rDNA transcription provides a novel target for immunosuppressant development

Herein, we demonstrate that NFAT, a key regulator of the immune response, translocates from cytoplasm to nucleolus and interacts with NF45/NF90 complex to collaboratively promote rDNA transcription via triggering the directly binding of NF45/NF90 to the ARRE2-like sequences in rDNA promoter upon T-cell activation in vitro. The elevated pre-rRNA level of T cells is also observed in both mouse heart or skin transplantation models and in kidney transplanted patients. Importantly, T-cell activation can be significantly suppressed by inhibiting NF45/NF90-dependent rDNA transcription. Amazingly, CX5461, a rDNA transcription-specific inhibitor, outperformed FK506, the most commonly used immunosuppressant, both in terms of potency and off-target activity (i.e., toxicity), as demonstrated by a series of skin and heart allograft models. Collectively, this reveals NF45/NF90-mediated rDNA transcription as a novel signaling pathway essential for T-cell activation and as a new target for the development of safe and effective immunosuppressants

Evidence That Descending Cortical Axons Are Essential for Thalamocortical Axons to Cross the Pallial-Subpallial Boundary in the Embryonic Forebrain

Developing thalamocortical axons traverse the subpallium to reach the cortex located in the pallium. We tested the hypothesis that descending corticofugal axons are important for guiding thalamocortical axons across the pallial-subpallial boundary, using conditional mutagenesis to assess the effects of blocking corticofugal axonal development without disrupting thalamus, subpallium or the pallial-subpallial boundary. We found that thalamic axons still traversed the subpallium in topographic order but did not cross the pallial-subpallial boundary. Co-culture experiments indicated that the inability of thalamic axons to cross the boundary was not explained by mutant cortex developing a long-range chemorepulsive action on thalamic axons. On the contrary, cortex from conditional mutants retained its thalamic axonal growth-promoting activity and continued to express Nrg-1, which is responsible for this stimulatory effect. When mutant cortex was replaced with control cortex, corticofugal efferents were restored and thalamic axons from conditional mutants associated with them and crossed the pallial-subpallial boundary. Our study provides the most compelling evidence to date that cortical efferents are required to guide thalamocortical axons across the pallial-subpallial boundary, which is otherwise hostile to thalamic axons. These results support the hypothesis that thalamic axons grow from subpallium to cortex guided by cortical efferents, with stimulation from diffusible cortical growth-promoting factors

Tourism Knowledge Domains of Chinese and International Research

Tourism knowledge domain has always been one of the appealing topics in tourism academic circle. This paper extracted author-selected keywords from 4788 articles published from 2012 to 2021 in four authoritative journals: Annals of Tourism Research, Tourism Management, Journal of Sustainable Tourism and Tourism Tribune. These keywords were coded according to “research areas”, “research objects”, “research methods”, and “research disciplines”, and a statistical analysis was carried out regarding the frequency, quantity, average frequency, and frequency variance of each category of the keywords. A total of 3459 Chinese keywords and 9128 English keywords formed the basis of this analysis. According to the findings, China is the most frequently studied geographical region in the international tourism research. The application of qualitative methods in the Chinese tourism research is less frequent than that in the international research, and the combination of qualitative and quantitative methods has become an important trend in tourism research. The international tourism research on certain topics is more in-depth and cutting-edge than the Chinese tourism research

Identification of Urban Functional Areas and Governance Measures Based on Point of Interest Data: A Case Study of the Shenyang Railway Station Area in Shenyang City

Inventory extraction and governance measures in urban land use have become important topics in urban regeneration research. This study aimed to inform design governance in urban regeneration through a point of interest (POI) data-based case study. An approximately 15 km2 rectangular development area was assessed for its characteristics and deficiencies. Frequency density analysis was conducted based on data identification of urban built environments and governance from an integrated planning perspective, using field research, spatial autocorrelation, Getis–Ord Gi* analysis, and SPSS. We (1) applied POI data to assess the frequency ratios of the function types for the 6008 buildings in the study area; (2) analysed layouts of POI densities in hotspots for different formats; and (3) applied an evidence-based approach and overlay analysis to identify the area’s functional morphological zones. Finally, the urban physical and morphological properties were identified and compared with the identification result of the urban functional areas to qualitatively evaluate the differences. Global Moran’s I of the POI density of Retail Business (B11), Restaurants (B13), Hotels (B14), Entertainment and Recreation (B3), and Residential Services (R22) were 0.35, 0.35, 0.06, 0.20, and 0.15, respectively, displaying a significant spatial clustering feature. However, for land types including Administrative Offices (A1), Finance and Insurance (B21), and Other Business Facilities (B29), the p-values between the POI density and the random pattern were 0.23, 0.71, 0.56, respectively, showing no significant difference. Our study provides recommendations for governance and integrated urban redevelopment planning to coordinate and guide further regeneration