Miracle-dz/UniFAR-FTUs huggingface dataset:
Importance of the Positive-Strand RNA Secondary Structure of a Murine Coronavirus Defective Interfering RNA Internal Replication Signal in Positive-Strand RNA Synthesis

ABSTRACT The RNA elements that are required for replication of defective interfering (DI) RNA of the JHM strain of mouse hepatitis virus (MHV) consist of three discontinuous genomic regions: about 0.46 to 0.47 kb from both terminal sequences and an internal 58-nucleotide (nt)-long sequence (58-nt region) present at about 0.9 kb from the 5′ end of the DI genome. The internal region is important for positive-strand DI RNA synthesis (Y. N. Kim and S. Makino, J. Virol. 69:4963–4971, 1995). We further characterized the 58-nt region in the present study and obtained the following results. (i) The positive-strand RNA structure in solution was comparable with that predicted by computer modeling. (ii) Positive-strand RNA secondary structure, but not negative-strand RNA structure, was important for the biological function of the region. (iii) The biological function had a sequence-specific requirement. We discuss possible mechanisms by which the internal cis-acting signal drives MHV positive-strand DI RNA synthesis.
The Longissimus and Semimembranosus Muscles Display Marked Differences in Their Gene Expression Profiles in Pig

Background Meat quality depends on skeletal muscle structure and metabolic properties. While most studies carried on pigs focus on the Longissimus muscle (LM) for fresh meat consumption, Semimembranosus (SM) is also of interest because of its importance for cooked ham production. Even if both muscles are classified as glycolytic muscles, they exhibit dissimilar myofiber composition and metabolic characteristics. The comparison of LM and SM transcriptome profiles undertaken in this study may thus clarify the biological events underlying their phenotypic differences which might influence several meat quality traits. Methodology/Principal Findings Muscular transcriptome analyses were performed using a custom pig muscle microarray: the 15 K Genmascqchip. A total of 3823 genes were differentially expressed between the two muscles (Benjamini-Hochberg adjusted P value ≤0.05), out of which 1690 and 2133 were overrepresented in LM and SM respectively. The microarray data were validated using the expression level of seven differentially expressed genes quantified by real-time RT-PCR. A set of 1047 differentially expressed genes with a muscle fold change ratio above 1.5 was used for functional characterization. Functional annotation emphasized five main clusters associated to transcriptome muscle differences. These five clusters were related to energy metabolism, cell cycle, gene expression, anatomical structure development and signal transduction/immune response. Conclusions/Significance This study revealed strong transcriptome differences between LM and SM. These results suggest that skeletal muscle discrepancies might arise essentially from different post-natal myogenic activities.
Affine Point Processes and Portfolio Credit Risk

This paper analyzes a family of multivariate point process models of correlated event timing whose arrival intensity is driven by an affine jump diffusion. The components of an affine point process are self- and cross-exciting and facilitate the description of complex event dependence structures. ODEs characterize the transform of an affine point process and the probability distribution of an integer-valued affine point process. The moments of an affine point process take a closed form. This guarantees a high degree of computational tractability in applications. We illustrate this in the context of portfolio credit risk, where the correlation of corporate defaults is the main issue. We consider the valuation of securities exposed to correlated default risk and demonstrate the significance of our results through market calibration experiments. We show that a simple model variant can capture the default clustering implied by index and tranche market prices during September 2008, a month that witnessed significant volatility.
Life cycle transcriptome of the malaria mosquito Anopheles gambiae and comparison with the fruitfly Drosophila melanogaster

The African mosquito Anopheles gambiae is the major vector of human malaria. We report a genome-wide survey of mosquito gene expression profiles clustered temporally into developmental programs and spatially into adult tissue-specific patterns. Global expression analysis shows that genes that belong to related functional categories or that encode the same or functionally linked protein domains are associated with characteristic developmental programs or tissue patterns. Comparative analysis of our data together with data published from Drosophila melanogaster reveal an overall strong and positive correlation of developmental expression between orthologous genes. The degree of correlation varies, depending on association of orthologs with certain developmental programs or functional groups. Interestingly, the similarity of gene expression is not correlated with the coding sequence similarity of orthologs, indicating that expression profiles and coding sequences evolve independently. In addition to providing a comprehensive view of temporal and spatial gene expression during the A. gambiae life cycle, this large-scale comparative transcriptomic analysis has detected important evolutionary features of insect transcriptomes.
Intelligent High-Interaction Web Honeypots Based on URL Conversion Scheme

Vulnerabilities in web applications expose computer networks to security threats. For example, attackers use a large number of normal user websites as hopping sites, which are illegally operated using malware distributed by abusing vulnerabilities in web applications on these websites, for attacking other websites and user terminals. Thus, the security threats, resulting from vulnerabilities in web applications prevent service providers from constructing secure networking environments. To protect websites from attacks based on the vulnerabilities of web applications, security vendors and service providers collect attack information using web honeypots, which masquerade as vulnerable systems. To collect all accesses resulting from attacks that include further network attacks by malware, such as downloaders, vendors and providers use high-interaction web honeypots, which are composed of vulnerable systems with surveillance functions. However, conventional high-interaction web honeypots can collect only limited information and malware from attacks, whose paths in the destination URLs do not match the path structure of the web honeypot since these attacks are failures. To solve this problem, we propose a scheme in which the destination URLs of these attacks are corrected by determining the correct path from the path structure of the web honeypot. Our Internet investigation revealed that 97% of attacks are failures. However, we confirmed that approximately 50% of these attacks will succeed with our proposed scheme. We can use much more information with this scheme to protect websites than with conventional high-interaction web honeypots because we can collect complete information and malware from these attacks.
Inverse kinematics solution based on fuzzy logic for redundant manipulators

An inverse kinematics solution that utilizes the differential relationship between the joint space and Cartesian space of redundant manipulators is proposed. Until now, this solution could be obtained using the pseudo inverse of the Jacobian matrix. However the computation of the pseudo inverse is complex so that it is not easy to implement it on a digital computer for online motion planning of the robot. As an alternative to the pseudo inverse solution, an inverse kinematics solution using fuzzy logic is derived. We find the rough solution based on the gradient method, and then refine it by introducing the fuzzy logic through the extension principle. As a result, a simple and fast inverse kinematics solution is obtained. The simulation results verify the efficiency of the proposed solution.
Molecular Design and Synthesis of Novel Salicyl Glycoconjugates as Elicitors against Plant Diseases

A new series of salicyl glycoconjugates containing hydrazide and hydrazone moieties were designed and synthesized. The bioassay indicated that the novel compounds had no in vitro fungicidal activity but showed significant in vivo antifungal activity against the tested fungal pathogens. Some compounds even had superior activity than the commercial fungicides in greenhouse trial. The results of RT-PCR analysis showed that the designed salicyl glycoconjugates could induce the expression of LOX1 and Cs-AOS2, which are the specific marker genes of jasmonate signaling pathway, to trigger the plant defense resistance.
Determining the Realization Risk of Network Structured Material Flows in Machine Building Industry Production Processes

In the paper are presented the results of the theoretical researches of the quantification of superposing flow rate periods of complex activity flows and occurrences in network structures for designs according to the PERT model in mechanical engineering. Expanding Clark’s researches we generalize the flow models of parallel and ordinal activities and events of preferentially their critical flows. The computer solving of the selected variants of activity flows models through the network in addition to the Clark’s equations. The numerical test is realized by Mathcad Professional program package. Index Term— Flow rate periods of production, Mathematical model, S imulation Monte Carlo
Incremental Delta-Sigma Structures for DC Measurement: an Overview

In this paper the theoretical operation of incremental (charge-balancing) delta-sigma (DeltaSigma) converters is reviewed, and the implementation of a 22-bit incremental A/D converter is described. Two different analyses of the first-order incremental converter are presented, and based on these results two extensions to higher-order modulators are proposed. Since line-frequency noise suppression is often important in measurement applications, modulators followed by sinck filters are also analyzed. Equations are derived for the estimation of the required number of cycles for a given resolution and architecture. Finally, the design and implementation of a third-order incremental converter with a fourth-order sine filter is briefly discussed
Glycyrrhizin treatment inhibits proliferation and invasive potential of lung cancer cells

The present study was aimed to investigate the effect of glycyrrhizin onosteopontin (OPN) expression, cell proliferation, invasion potential and cell cycle distribution inhuman lung carcinoma cell line, HCC827. The results revealed a significant inhibition in the expression of OPN protein on treatment with 100 μM doses of glycyrrhizin after 48 h in HCC827 cells. Glycyrrhizin treatment also inhibited the rate of cell proliferation and caused cell cycle arrest by preventing the cells from entering into the G2 phase. Exposure of HCC827 cells to glycyrrhizin at 100 μM concentration inhibited the invasion potential significantly compared to the control cells. In addition, glycyrrhizin treatment reduced the expression of MMP-2 and MMP-9 significantly after 48 h inHCC827 cells. Thus, glycyrrhizin treatment inhibits proliferation, invasion potential and arrests cell cycle in lung cancer cells through down-regulation of OPN expression. Therefore, glycyrrhizin can be of therapeutic importance for the treatment of lung cancer.
Massive Data Pre-Processing with a Cluster Based Approach

Data coming from complex simulation models reach easily dimensions much greater than available computational resources. Visualization of such data still represents the most intuitive and effective tool for scientific inspection of simulated phenomena. To ease this process several techniques have been adopted mainly concerning the use of hierarchical multi-resolution representations. In this paper we present the implementation of a hierarchical indexing schema for multiresolution data tailored to overwork the computational power of distributed environments.
Advances in Practical Well-Test Analysis

The 1980's produced important advances in well-test analysis. The large number of new and sometimes competitive methods, however, also produced confusion. The main objective of this paper is to consider the current state of practical well-test analysis methods. The storage log-log type curve was initially presented as a method to analyze short-time data. This was later found to be impossible. But the diagnostic value of log-log curves was far more important than short-time analysis. Later, the derivative was added to the type curve, leading to the conclusions that Horner curves were no longer necessary and that short-time analysis was now possible. Another major development was computer-aided interpretation. The computer was necessary to differentiate data and helped to prepare the large number of graphs required for modern interpretation. An important breakthrough resulted with the development of nonlinear regression for specific models and the ability to consider rate variation. Results of an interpretation could be used to simulate test data, and then simulated and field data could be compared.
Conceptual and Practical Steps in Event Coreference Analysis of Large-scale Data

A simple conceptual model is employed to investigate events, and break the task of coreference resolution into two steps: semantic class detection and similaritybased matching. With this perspective an algorithm is implemented to cluster event mentions in a large-scale corpus. Results on test data from AQUAINT TimeML, which we annotated manually with coreference links, reveal how semantic conventions vs. information available in the context of event mentions affect decisions in coreference analysis.
Plasmid Control of 6-Aminohexanoic Acid Cyclic Dimer Degradation Enzymes of Flavobacterium sp. K172

Flavobacterium sp. K172, which is able to grow on 6-aminohexanoic acid cyclic dimer as the sole source of carbon and nitrogen, and plasmid control of the responsible enzymes, 6-aminohexanoic acid cyclic dimer hydrolase and 6-aminohexanoic acid linear oligomer hydrolase, were studied. The wild strain of K172 harbors three kinds of plasmid, pOAD1 (26.2 megadaltons), pOAD2 (28.8 megadaltons), and pOAD3 (37.2 megadaltons). The wild strain K172 was readily cured of its ability to grow on the cyclic dimer by mitomycin C, and the cyclic dimer hydrolase could not be detected either as catalytic activity or by antibody precipitation. No reversion of the cured strains was detected. pOAD2 was not detected in every cured strain tested but was restored in a transformant. The transformant recovered both of the enzyme activities, and the cyclic dimer hydrolase of the transformant was immunologically identical with that of the wild strain. All of the strains tested, including the wild, cured, and transformant ones, possessed identical pOAD3 irrespective of the metabolizing activity. Some of the cured strains possessed pOAD1 identical with the wild strain, but the others harbored plasmids with partially altered structures which were likely to be derived from pOAD1 by genetic rearrangements such as deletion, insertion, or substitution. These results suggested that the genes of the enzymes were borne on pOAD2.
Linguistic Human Rights: Overcoming Linguistic Discrimination.

Only a few hundred of the world's 6,000-7,000 languages have any kind of official status, and it is only speakers of official languages (speakers of dominant majority languages) who enjoy all linguistic human rights. As many of the collected papers in this book document, most linguistic minorities are deprived of these rights. This book describes what linguistic human rights are, who has and who does not have them and why, and suggests which linguistic rights should be regarded as basic human rights. Linguistic Human Rights introduces a new area, combining sociolinguistics, educational, and minority concerns with human rights. Discrimination against language minorities is widespread, despite national and international law prohibiting this. The book analyzes language rights in many countries worldwide, including North and Latin America, several European states, the former USSR, India, Kurdistan, Australia and New Zealand.
Sustainability Assessment of Solid Waste Management in China: A Decoupling and Decomposition Analysis

As the largest solid waste (SW) generator in the world, China is facing serious pollution issues induced by increasing quantities of SW. The sustainability assessment of SW management is very important for designing relevant policy for further improving the overall efficiency of solid waste management (SWM). By focusing on industrial solid waste (ISW) and municipal solid waste (MSW), the paper investigated the sustainability performance of SWM by applying decoupling analysis, and further identified the main drivers of SW change in China by adopting Logarithmic Mean Divisia Index (LMDI) model. The results indicate that China has made a great achievement in SWM which was specifically expressed as the increase of ISW utilized amount and harmless disposal ratio of MSW, decrease of industrial solid waste discharged (ISWD), and absolute decoupling of ISWD from economic growth as well. However, China has a long way to go to achieve the goal of sustainable management of SW. The weak decoupling, even expansive negative decoupling of ISW generation and MSW disposal suggests that China needs timely technology innovation and rational institutional arrangement to reduce SW intensity from the source and promote classification and recycling. The factors of investment efficiency and technology are the main determinants of the decrease in SW, inversely, economic growth has increased SW discharge. The effects of investment intensity showed a volatile trend over time but eventually decreased SW discharged. Moreover, the factors of population and industrial structure slightly increased SW.
Feature topography and sound intensity level encoding in primary auditory cortex

ii Acknowledgments . iv List of Tables . ix List of Figures . x 1 General Introduction . 1 2 Experimental Methods . 5 2.1 A Computational Framework for Topographies of Cortical Areas. 6 2.1. 1 Self-Organizing Feature Map. 6 2.1. 2 Unit Grid Initialization . 8 2.1. 3 Metrics of Topographical Characteristics . 9 2.1. 4 Conditions Driving Dominance and Global Orthogonality . 18 2.2 Neuronal Responses to Sound Intensity Level.21 2.2.1 Electrophysiology . 21 2.2.2 Acoustic Stimuli . 23 2.2.3 Data Analysis.24 2.3 Neuronal Adaptation to Sound Intensity Level.30 2.3. 1 Acoustic Stimuli . 30 2.3. 2 Data Analysis.34 2.4 Time Course of Neuronal Adaptation to Sound Intensity Level.39 2.4. 1 Acoustic Stimuli . 39 2.4. 2 Data Analysis.44 3 A Computational Framework for Topographies of Cortical Areas . 64 3.
Teaching from a Multicultural Perspective

Once You Accept, Then You Can Teach - Juan C Gonzalez Diversity and Change on Campus - Helen R Roberts Teaching All Students Equally - Ray Lou Including Multicultural Content and Perspectives in Your Courses - Otis Scott Language and Culture in the Classroom - Ann Johns Equity in Classroom Assessment - Olita Harris On Becoming a Mensch or a Mentor - Delores Huff
Next generation simulation environments founded on open source software and XML-based standard interfaces

During the Winter Simulation Conference 2001 the OpenSML-project was presented and started. The OpenSML-project is based on the Simulation Modeling Language (SML/sup TM/) and is an open source, Web-based, multi-language simulation development project guided by a consortium of industrial, academic and government simulation consultants, practitioners and developers. For the simulation community, the open source movement represents an opportunity to improve the quality of common core simulation functions, improve the potential for creating reusable modeling components from those core functions, and improve the ability to merge those components using XML, HLA and other simulation community standards. This paper extends the OpenSML-project by using universal, language independent XML-descriptions and code generators for converting OpenSML-models to programs in Java, VisualBasic or C++. This would be the first time a simulation model could be transferred between different platforms without manual changes.
Pheromone trail initialization with local optimal solutions in ant colony optimization

This paper presents a method to improve the search rate of Max-Min Ant System for the traveling salesman problem. The proposed method gives deviations from the initial pheromone trails by using a set of local optimal solutions calculated in advance. Max-Min Ant System has demonstrated impressive performance, but the rate of search is relatively low. Considering the generic purpose of stochastic search algorithms, which is to find near optimal solutions subject to time constraints, the rate of search is important as well as the quality of the solution. The experimental results using benchmark problems with 51 to 318 cities suggested that the proposed method is better than the conventional method in both the quality of the solution and the rate of search.
Skeletal variability in the pelvis and limb skeleton of humans: Does stabilizing selection limit female pelvic variation?

This study tests the hypothesis, a correlate of the obstetric dilemma, that skeletal variability in the human female pelvic canal is limited owing to the action of stabilizing selection. Levels of variation in three skeletal regions (pelvic canal, noncanal pelvis, and limbs) of females and males are compared to each other and between sexes.
LoCaTe: Influence Quantification for Location Promotion in Location-based Social Networks

Location-based social networks (LBSNs) such as Foursquare offer a platform for users to share and be aware of each other’s physical movements. As a result of such a sharing of check-in information with each other, users can be influenced to visit (or check-in) at the locations visited by their friends. Quantifying such influences in these LBSNs is useful in various settings such as location promotion, personalized recommendations, mobility pattern prediction etc. In this paper, we focus on the problem of location promotion and develop a model to quantify the influence specific to a location between a pair of users. Specifically, we develop a joint model called LoCaTe, consisting of (i) user mobility model estimated using kernel density estimates; (ii) a model of the semantics of the location using topic models; and (iii) a model of time-gap between check-ins using exponential distribution. We validate our model on a long-term crawl of Foursquare data collected between Jan 2015 Feb 2016, as well as on publicly available LBSN datasets. Our experiments demonstrate that LoCaTe significantly outperforms state-of-the-art models for the same task.