Miracle-dz/UniFAR-FTUs huggingface dataset:
DNA Sequences Involved in the Regulation of Human c-myc Gene Expression by Herpes Simplex Virus Type 1 (HSV-1)

An abstract of the thesis of Shanli Ye for the Master of Science in Biology presented November 29, 1995. Title: DNA Sequences Involved in The Regulation of Human c-myc Gene Expression by Herpes Simplex Virus Type 1 (HSV-1). The human c-myc gene is a cellular proto-oncogene composed of three exons and two introns. Transcription of c-myc is controlled by two promoters, Pl and P2. The activity of these promoters is regulated by many factors, such as cellular transcription factors E2F, YYl, and HSV-1 immediate-early proteins, ICPO, ICP4. Many regulatory elements located both upstream of and between P 1 and P2 have been identified, and some of these are required for optimum expression of c-myc. In this thesis research, a region downstream from P2 in the c-myc exon 1 was identified by its response to transactivation by HSV-1 immediate-early proteins, ICPO and ICP4. The purpose of this research was to examine this region for regulatory sites that respond to HSV-1 infection. I hypothesized that after HSV-1 infection, ICPO and ICP4 activate c-myc expression, in part, through regulatory sequences present in exon 1. To test for this hypothesis, reporter plasmids containing (I) the c-myc promoter (from 101 bp relative to Pl) and exon 1 coupled to the bacterial CAT gene were constructed. (ii) The c-myc exon sequences used were either intact (wild-type) or they were constructed with various deletions. The activities of these plasmids were examined in transient expression assays. To analyze protein binding, electrophoretic mobility shift assay (EMSA) . --·------·--·-"" . ,, ____________________ _ and completion EMSAs were carried out. The results from these experiments lead to the following conclusions: (i) ICP4 and ICPO serve as activators, whereas ICP27 inhibits c-myc gene expression. (ii) The region from +332 to +513 within the c-myc exon 1 contains an important element required for transactivation of the c-myc gene by HSV-1 proteins. (iii) Cellular proteins, including factor YYl, bind to the region from +332 to +513 in the c-myc exon 1. Although the exact mechanism by which HSV-1 immediate-early proteins regulate cmyc gene expression is still not clear, it gives rise to a possibility that this regulation is caused by turning on or activation of the cellular regulatory proteins by ICP4 and ICPO. The cellular proteins in turn activate the c-myc gene expression by interacting with the ciselement downstream from P2.
The Effect of R&D Intensity on Relationship between Corporate Social Responsibility and Real Earnings Management: Evidence from U.S. Firms

Prior studies indicate that R&D intensity and corporate social responsibility (CSR) have a positive relationship, meaning that firms investing more in R&D can promote more CSR related activities and develop more innovative products. However, R&D investment is also a tool for firms to smooth their earnings, or firms may enhance their earnings by reducing R&D expenses. Prior literature suggests a negative relationship between CSR and earnings management. Firms involved in more CSR activities are relatively ethical and less likely to manipulate earnings. Sustainable innovation and development play an important role for firms to establish competitive advantages. The main purpose of this paper is not only to discuss the relationship between CSR and real earnings management (RM) activities in U.S. firms from 2000 to 2014, but also to examine whether R&D intensity and the global financial crisis of 2007 – 2008 will affect the relation between CSR and earnings management. To avoid the endogeneity issue, we adopt a Two-Stage Regression to test the relationship between CSR and earnings management, and incorporate the effects of R&D intensity and the financial crisis. We find that the relation between CSR and earnings management is negative for the entire sample and for those firms with high R&D intensity or after the financial crisis. Those firms with high R&D intensity are more likely to participate in CSR activities and less likely to manipulate earnings. Nevertheless, our results show that the negative relation between CSR and earnings management does not exist in low R&D intensive firms. In addition, our results show that high R&D intensive firms with larger size, higher leverage, or lower profitability are more likely to engage in earnings management activities.
My title

A random geometric irrigation graph Γn(rn, ξ) has n vertices identified by n independent uniformly distributed points X1, . , Xn in the unit square [0, 1]. Each point Xi selects ξi neighbors at random, without replacement, among those points Xj (j 6= i) for which ‖Xi − Xj‖ < rn, and the selected vertices are connected to Xi by an edge. The number ξi of the neighbors is an integer-valued random variable, chosen independently with identical distribution for each Xi such that ξi satisfies 1 ≤ ξi ≤ κ for a constant κ > 1. We prove that when rn = γn √ log n/n for γn → ∞ with γn = o(n/ log n), then the random geometric irrigation graph experiences explosive percolation in the sense that when Eξi = 1, then the largest connected component has size o(n) but if Eξi > 1, then the size of the largest connected component is with high probability n− o(n). This offers a natural non-centralized sparsification of a random geometric graph that is mostly connected.
Locally linear constraint based optimization model for material decomposition

Dual spectral computed tomography (DSCT) has a superior material distinguishability than the conventional single spectral computed tomography (SSCT). However, the decomposition process is an illposed problem, which is sensitive to noise. Thus, the decomposed image quality is degraded, and the corresponding signal-to-noise ratio (SNR) is much lower than that of directly reconstructed image of SSCT. In this work, we establish a locally linear relationship between the decomposed results of DSCT and SSCT. Based on this constraint, we propose an optimization model for DSCT and develop an iterative method with image guided filtering. To further improve the image quality, we employ a preprocessing method based on the relative total variation regularization. Both numerical simulations and real experiments are performed, and the results confirm the effectiveness of our proposed approach.
SERIES ( Statistics # 2011-03 ) A partition model for analyzing categorical data subject to non-ignorable non-response

In many surveys, the goal is to estimate the proportion of the population within different domains with a certain characteristic of interest. This estimation problem is often complicated by survey nonresponse and the difficulty in modeling the non-response mechanism. In this paper we develop a new method for analyzing categorical data with non-response when there is uncertainty about ignorability, which incorporates the idea that there are many a priori plausible ignorable and non-ignorable models. We consider saturated submodels of the full model, which may have a mixture of ignorable and nonignorable components, and use Bayesian averaging to incorporate model uncertainty. This method is illustrated using data from the 2000 Accuracy and Coverage Evaluation Survey. A simulation study is used to evaluate the performance of the model and to compare the partition model to other popular non-ignorable Bayesian models.
PERFORMANCE BASED DESIGN SYSTEM FOR CONCRETE MIXTURE WITH MULTI-OPTIMIZING GENETIC ALGORITHM

This paper presents a method for optimizing concrete mixture proportions according to the required performance and also presents several case studies. Since various qualities are usually required of concrete, we characterize the proportioning problems as multi-criteria optimization problems. We dealt with the notion of Pareto optimality to derive the optimum solution and applied it to a genetic algorithm. In this contribution, two proportioning problems are solved by the genetic algorithm: a request of cost-performance at 60 MPa in strength as a simple problem, and a concrete mix for mass concrete in cold weather at the coast.
Ju l 2 01 2 ROBUST MAXIMIZATION OF ASYMPTOTIC GROWTH UNDER COVARIANCE

This paper resolves a question proposed in Kardaras and Robertson (2012): how to invest in a robust growth-optimal way in a market where precise knowledge of the covariance structure of the underlying assets is unavailable. Among an appropriate class of admissible covariance structures, we characterize the optimal trading strategy in terms of a generalized version of the principal eigenvalue of a fully nonlinear elliptic operator and its associated eigenfunction, by slightly restricting the collection of non-dominated probability measures.
ST ] 1 4 Fe b 20 11 STATISTICAL ANALYSIS OF THE HIRSCH INDEX By

The Hirsch index (commonly referred to as h-index) is a bibliometric indicator which is widely recognized as effective for measuring the scientific production of a scholar since it summarizes size and impact of the research output. In a formal setting, the h-index is actually an empirical functional of the distribution of the citation counts received by the scholar. Under this approach, the asymptotic theory for the empirical hindex has been recently exploited when the citation counts follow a continuous distribution and, in particular, variance estimation has been considered for the Pareto-type and the Weibull-type distribution families. However, in bibliometric applications, citation counts display a distribution supported by the integers. Thus, we provide general properties for the empirical h-index under the smalland large-sample settings. In addition, we also introduce consistent nonparametric variance estimation, which allows for the implemention of large-sample set estimation for the theoretical h-index.
Chemical modelling of dust–gas chemistry within AGB outflows – I. Effect on the gas-phase chemistry

Chemical modelling of asymptotic giant branch (AGB) outflows is typically focused on either non-thermodynamic equilibrium chemistry in the inner region or photon-driven chemistry in the outer region. We include, for the first time, a comprehensive dust–gas chemistry in our AGB outflow chemical kinetics model, including both dust–gas interactions and grain-surface chemistry. The dust is assumed to have formed in the inner region, and follows an interstellar-like dust-size distribution. Using radiative transfer modelling, we obtain dust temperature profiles for different dust types in an O-rich and a C-rich outflow. We calculate a grid of models, sampling different outflow densities, drift velocities between the dust and gas, and dust types. Dust–gas chemistry can significantly affect the gas-phase composition, depleting parent and daughter species and increasing the abundance of certain daughter species via grain-surface formation followed by desorption/sputtering. Its influence depends on four factors: outflow density, dust temperature, initial composition, and drift velocity. The largest effects are for higher density outflows with cold dust and O-rich parent species, as these species generally have a larger binding energy. At drift velocities larger than ∼10 km s−1, ice mantles undergo sputtering; however, they are not fully destroyed. Models with dust–gas chemistry can better reproduce the observed depletion of species in O-rich outflows. When including colder dust in the C-rich outflows and adjusting the binding energy of CS, the depletion in C-rich outflows is also better reproduced. To best interpret high-resolution molecular line observations from AGB outflows, dust–gas interactions are needed in chemical kinetics models.
Emergence of Genetic Diversity and Multi-Drug Resistant Campylobacter jejuni From Wild Birds in Beijing, China

Campylobacter jejuni (C. jejuni) is considered as an opportunistic zoonotic pathogen that may cause gastroenteritis in humans and other animals. Wild birds may be as potential vectors of C. jejuni around urban and suburban areas. Here, 520 samples were collected from 33 wild bird species in urban and suburban areas, Beijing. In total 57 C. jejuni were isolated from seven species. It was found that Nineteen (33.33%, 19/57) isolates were resistant to at least one of 11 antibiotics, especially streptomycin (36.84%) and four isolates resistant to all. Nineteen (33.33%, 19/57) isolates were multi-drug resistance. Multilocus sequence typing (MLST) analysis of the isolates showed that 36 different sequence types (STs) belonged to four Clonal complexes and unassigned. Twenty STs (55.56%) and six alleles among them were first detected. Virulence genes including flaA, cadF, and the cytolethal distending toxin (CDT) gene cluster, were detected in all isolates, but truncated cdt gene clusters only detected in the isolates from the crow, daurian jackdaw and silver pheasant. In conclusion, it was the first detection of C. jejuni involved truncated cdt gene clusters from the silver pheasant. These wild birds around urban and suburban areas may pose potential public health problems as reservoir vectors of C. jejuni.
Network Representations of Facial and Bodily Expressions: Evidence From Multivariate Connectivity Pattern Classification

Emotions can be perceived from both facial and bodily expressions. Our previous study has found the successful decoding of facial expressions based on the functional connectivity (FC) patterns. However, the role of the FC patterns in the recognition of bodily expressions remained unclear, and no neuroimaging studies have adequately addressed the question of whether emotions perceiving from facial and bodily expressions are processed rely upon common or different neural networks. To address this, the present study collected functional magnetic resonance imaging (fMRI) data from a block design experiment with facial and bodily expression videos as stimuli (three emotions: anger, fear, and joy), and conducted multivariate pattern classification analysis based on the estimated FC patterns. We found that in addition to the facial expressions, bodily expressions could also be successfully decoded based on the large-scale FC patterns. The emotion classification accuracies for the facial expressions were higher than that for the bodily expressions. Further contributive FC analysis showed that emotion-discriminative networks were widely distributed in both hemispheres, containing regions that ranged from primary visual areas to higher-level cognitive areas. Moreover, for a particular emotion, discriminative FCs for facial and bodily expressions were distinct. Together, our findings highlight the key role of the FC patterns in the emotion processing, indicating how large-scale FC patterns reconfigure in processing of facial and bodily expressions, and suggest the distributed neural representation for the emotion recognition. Furthermore, our results also suggest that the human brain employs separate network representations for facial and bodily expressions of the same emotions. This study provides new evidence for the network representations for emotion perception and may further our understanding of the potential mechanisms underlying body language emotion recognition.
Progress on Implementing Ecosystem-Based Fisheries Management in the United States Through the Use of Ecosystem Models and Analysis

Worldwide fisheries management has been undergoing a paradigm shift from a single-species approach to ecosystem approaches. In the U.S., NOAA has adopted a policy statement and Road Map to guide the development and implementation of ecosystem-based fisheries management (EBFM). NOAA’s EBFM policy supports addressing the ecosystem interconnections to help maintain resilient and productive ecosystems, even as they respond to climate, habitat, ecological, and social and economic changes. Managing natural marine resources while taking into account their interactions with their environment and our human interactions with our resources and environment requires the support of ecosystem science, modeling, and analysis. Implementing EBFM will require using existing mandates and approaches that fit regional management structures and cultures. The primary mandate for managing marine fisheries in the U.S. is the Magnuson-Stevens Fishery Conservation and Management Act. Many tenets of the Act align well with the EBFM policy; however, incorporating ecosystem analysis and models into fisheries management processes has faced procedural challenges in many jurisdictions. In this paper, we review example cases where scientists have had success in using ecosystem analysis and modeling to inform management priorities, and identify practices that help bring new ecosystem science information into existing policy processes.
MiR-29 Regulates de novo Lipogenesis in the Liver and Circulating Triglyceride Levels in a Sirt1-Dependent Manner

MicroRNAs (miRNAs) are known regulators of lipid homeostasis. We recently demonstrated that miR-29 controls the levels of circulating cholesterol and triglycerides, but the mechanisms remained unknown. In the present study, we demonstrated that systemic delivery of locked nucleic acid inhibitor of miR-29 (LNA29) through subcutaneous injection effectively suppresses hepatic expression of miR-29 and dampens de novo lipogenesis (DNL) in the liver of chow-fed mice. Next, we used mice with liver-specific deletion of Sirtuin 1 (L-Sirt1 KO), a validated target of miR-29, and demonstrated that the LNA29-induced reduction of circulating triglycerides, but not cholesterol, is dependent on hepatic Sirt1. Moreover, lipidomics analysis revealed that LNA29 suppresses hepatic triglyceride levels in a liver-Sirt1 dependent manner. A comparative transcriptomic study of liver tissue from LNA29-treated wild-type/floxed and L-Sirt1 KO mice identified the top candidate lipogenic genes and hepatokines through which LNA29 may confer its effects on triglyceride levels. The transcriptomic analysis also showed that fatty acid oxidation (FAO) genes respond differently to LNA29 depending on the presence of hepatic Sirt1. Overall, this study demonstrates the beneficial effects of LNA29 on DNL and circulating lipid levels. In addition, it provides mechanistic insight that decouples the effect of LNA29 on circulating triglycerides from that of circulating cholesterol.
Advances in Nutrition Science and Integrative Physiology: Insights From Controlled Feeding Studies

Nutrition science is a highly impactful but contentious area of biomedical science. Establishing cause and effect relationships between the nutrients and/or diets we consume and the avoidance of or risk of disease is extremely challenging. As such, evidence-based nutrition is best served by considering the totality of evidence across multiple study types including nutritional epidemiological studies, randomized controlled trials of behavioral interventions, and controlled feeding studies. The purpose of the present review is to provide an overview for those conducting research outside of clinical nutrition on how controlled feeding studies can be used to gain insight into integrative physiology/metabolism as well as to inform dietary guidelines. We discuss the rationale, basic elements, and complexities of conducting controlled feeding studies and provide examples of contributions of controlled feeding studies to advances in nutrition science and integrative physiology. Our goal is to provide a resource for those wishing to leverage the experimental advantage provided by controlled feeding studies in their own research programs.
A CRISPR RNA Is Closely Related With the Size of the Cascade Nucleoprotein Complex

The currently known prokaryotic adaptive immune system against mobile genetic elements is based on clustered regularly interspaced short palindromic repeats (CRISPR). CRISPR-associated (Cas) proteins and the transcribed short CRISPR RNA (crRNA) molecule form a heterologous ribonucleoprotein complex that neutralizes invading foreign nucleic acids, wherein the crRNA molecule base-pairs with the exogenous genetic elements. In the ribonucleoprotein complexes of the type I CRISPR system, a helical backbone of six identical subunits is commonly found. However, it is not clear how this ribonucleoprotein complex is assembled and what is the determinant factor for its size. We elucidated the crystal structure of the Csy3 subunit of the type I-F ribonucleoprotein complex from Zymomonas mobilis (ZmCsy3), in which seven ZmCsy3 protomers in the asymmetric unit form a molecular helix that is part of a filamentous structure in the entire crystal system. This ZmCsy3 helical structure is remarkably similar to the crRNA-bound hexameric Csy3 backbone from Pseudomonas aeruginosa, with conserved interactions between neighboring subunits. The monomeric ZmCsy3 in solution is transformed into different oligomeric states depending on the added crRNAs. These results suggest that a crRNA and Csy3 subunit play a determinant role in the stepwise formation of the functional Cascade ribonucleoprotein complex and the recruitment of other subunits, and crRNA functions as a molecular ruler for determining the size of the Cascade silencing complex.
. s of t ] 1 9 O ct 2 00 0 Stability Puzzles in Phage λ

In the absence of RecA-mediated cleavage of the repressor, the λ prophage is exceptionally stable. In fact, the repressed state is then more stable than the gene encoding the repressor. We develop a mathematical treatment that predicts the stability of such epigenetic states from affinities of the molecular components. We apply the model to the behavior of recently published mutants of OR and find that their observed stability indicates that the current view of the OR switch is incomplete. The approach described here should be generally applicable to the stability of expressed states.
Exosome-Transmitted miR-25 Induced by H. pylori Promotes Vascular Endothelial Cell Injury by Targeting KLF2

Background: Increasing evidence has shown that Helicobacter pylori is associated with coronary heart disease (CHD); however, the underlying mechanism remains unclear. Methods: The expression of miR-25 and mRNAs was measured using qRT-PCR. Protein levels were detected using western blotting and exosomes were assessed with an electron microscope. The target gene of miR-25 was identified using the luciferase report system. Results: H. pylori infection increased the expression of miR-25 in gastric epithelial cells and was associated with increased levels of exosome-transmitted miR-25 in human peripheral blood. Mechanistic investigation showed the Kruppel-like factor 2 (KLF2) was a direct target of exosome-transmitted miR-25 in vascular endothelial cells. In addition, the miR-25/KLF2 axis regulated the NF-κB signaling pathway, resulting in increased expression of interleukin 6 (IL6), monocyte chemoattractant protein-1 (MCP-1), vascular cell adhesion molecule-1 (VCAM-1), and intercellular adhesion molecule-1 (ICAM-1). Conclusion: Our findings suggest that the miR-25/KLF2 axis may be a potential therapeutic target for H. pylori-associated CHD. Furthermore, high levels of exosome-transmitted miR-25 in peripheral blood may pose a potential risk for CHD.