Miracle-dz/UniFAR-FTUs huggingface dataset:
Probabilistic Models for Gene Silencing Data (Probabilistische Modelle für RNA-Interferenz-Daten)

Title Page, Preface, Contents 1\. Introduction 1.1 Signal transduction and gene regulation 1.2 Gene silencing by RNA interference 1.3 Thesis organization 2\. Statistical models of cellular networks 2.1 Conditional independence models 2.2 Bayesian networks 2.3 Score based structure learning 2.4 Benchmarking 2.5 A roadmap to network reconstruction 3\. Inferring transcriptional regulatory networks 3.1 Graphical models for interventional data 3.2 Ideal interventions and mechanism changes 3.3 Pushing interventions at single nodes 3.4 Pushing in conditional Gaussian networks 4\. Inferring signal transduction pathways 4.1 Non-transcriptional modules in sigaling pathways 4.2 Gene silencing with transcriptional phenotypes 4.3 Accuracy and sample size requirements 4.4 Application to Drosophila immune response 5\. Summary and outlook Bibliography Zusammenfassung
Article-Level Metrics and the Evolution of Scientific Impact

Formally published papers that have been through a traditional prepublication peer review process remain the most important means of communicating science today. Researchers depend on them to learn about the latest advances in their fields and to report their own findings. The intentions of traditional peer review are certainly noble: to ensure methodological integrity and to comment on potential significance of experimental studies through examination by a panel of objective, expert colleagues. In principle, this system enables science to move forward on the collective confidence of previously published work. Unfortunately, the traditional system has inspired methods of measuring impact that are suboptimal for their intended uses.
Research on knowledge innovation system of university science parks based on the SECI model

Based on analyzing the theory of knowledge innovation system of Nonaka I. and Takeuchi H. , the article takes example from it and gives the definitions of knowledge assets, micro Ba and macro Ba in the university science parks. On this basis, the article constructs a new knowledge innovation system for the university science parks based on Nonaka's SECI model. It also analyzes the contents of the input subsystem, the catalytic subsystem, the output subsystem and the feedback subsystem in the new system and discusses how the four subsystems interact and influence the new system. As a result, all the effort hopes to drive forward the development of University Science Parks.
Wind erosion in the Qaidam basin, central Asia: Implications for tectonics, paleoclimate, and the source of the Loess Plateau

Liquid water and ice are the dominant agents of erosion and sediment transport in most actively growing mountain belts. An exception is in the western Qaidam basin along the northeastern margin of the Tibetan Plateau, where wind and windblown sand have sculpted enormous yardang fields in actively folding sedimentary strata. Here, we present observations suggesting that since the late Pliocene, wind episodically (during glacial and stadial periods) removed strata from the western Qaidam basin at high rates (>0.12–1.1 mm/yr) and may have accelerated rates of tectonic folding. Severe wind erosion likely occurred during glacial and stadial periods when central Asia was drier and the main axis of the polar jet stream was located ~10° closer to the equator (over the Qaidam basin), as predicted by global climate models. Reconstructed wind patterns, the estimated volume of Qaidam basin material removed by wind, and numerical models of dust transport all support the hypothesis that the Qaidam basin was a major source of dust to the Loess Plateau.
Vacuum polarization and the black hole singularity

In order to investigate the effects of vacuum polarization on mass inflation singularities, the authors study a simple toy model of a charged black hole with cross flowing radial null dust which is homogeneous in the black hole interior. In the region r2<<e2 they find an approximate analytic solution to the classical field equations. The renormalized stress-energy tensor, for conformally coupled fields, is evaluated on this background and they find the vacuum polarization backreaction corrections to the mass function m(r). Asymptotic analysis of the semiclassical mass function shows that the mass inflation singularity is much stronger in the presence of vacuum polarization than in the classical case.
Paeoniflorin Attenuated Oxidative Stress in Rat COPD Model Induced by Cigarette Smoke

Paeoniflorin (PF), a monoterpene glucoside, might have an effect on the oxidative stress. However, the mechanism is still unknown. In this study, we made the COPD model in Sprague-Dawley (SD) rats by exposing them to the smoke of 20 cigarettes for 1 hour/day and 6 days/week, for 12 weeks, 24 weeks, or 36 weeks. Our findings suggested that smoke inhalation can trigger the oxidative stress from the very beginning. A 24-week treatment of PF especially in the dosage of 40 mg/kg·d can attenuate oxygen stress by partially quenching reactive oxygen species (ROS) and upregulating antioxidant enzymes via an Nrf2-dependent mechanism.
Iontophoresis: A Potential Emergence of a Transdermal Drug Delivery System

The delivery of drugs into systemic circulation via skin has generated much attention during the last decade. Transdermal therapeutic systems propound controlled release of active ingredients through the skin and into the systemic circulation in a predictive manner. Drugs administered through these systems escape first-pass metabolism and maintain a steady state scenario similar to a continuous intravenous infusion for up to several days. However, the excellent impervious nature of the skin offers the greatest challenge for successful delivery of drug molecules by utilizing the concepts of iontophoresis. The present review deals with the principles and the recent innovations in the field of iontophoretic drug delivery system together with factors affecting the system. This delivery system utilizes electric current as a driving force for permeation of ionic and non-ionic medications. The rationale behind using this technique is to reversibly alter the barrier properties of skin, which could possibly improve the penetration of drugs such as proteins, peptides and other macromolecules to increase the systemic delivery of high molecular weight compounds with controlled input kinetics and minimum inter-subject variability. Although iontophoresis seems to be an ideal candidate to overcome the limitations associated with the delivery of ionic drugs, further extrapolation of this technique is imperative for translational utility and mass human application.
Intestinal Epithelial Cell Regulation of Adaptive Immune Dysfunction in Human Type 1 Diabetes

Environmental factors contribute to the initiation, progression, and maintenance of type 1 diabetes (T1D), although a single environmental trigger for disease has not been identified. Studies have documented the contribution of immunity within the gastrointestinal tract (GI) to the expression of autoimmunity at distal sites. Intestinal epithelial cells (IECs) regulate local and systemic immunologic homeostasis through physical and biochemical interactions with innate and adaptive immune populations. We hypothesize that a loss in the tolerance-inducing nature of the GI tract occurs within T1D and is due to altered IECs’ innate immune function. As a first step in addressing this hypothesis, we contrasted the global immune microenvironment within the GI tract of individuals with T1D as well as evaluated the IEC-specific effects on adaptive immune cell phenotypes. The soluble and cellular immune microenvironment within the duodenum, the soluble mediator profile of primary IECs derived from the same duodenal tissues, and the effect of the primary IECs’ soluble mediator profile on T-cell expansion and polarization were evaluated. Higher levels of IL-17C and beta-defensin 2 (BD-2) mRNA in the T1D-duodenum were observed. Higher frequencies of type 1 innate lymphoid cells (ILC1) and CD8+CXCR3+ T-cells (Tc1) were also observed in T1D-duodenal tissues, concomitant with lower frequencies of type 3 ILC (ILC3) and CD8+CCR6+ T-cells (Tc17). Higher levels of proinflammatory mediators (IL-17C and BD-2) in the absence of similar changes in mediators associated with homeostasis (interleukin 10 and thymic stromal lymphopoietin) were also observed in T1D-derived primary IEC cultures. T1D-derived IEC culture supernatants induced more robust CD8+ T-cell proliferation along with enhanced polarization of Tc1 populations, at the expense of Tc17 polarization, as well as the expansion of CXCR3+CCR6+/− Tregs, indicative of a Th1-like and less regulatory phenotype. These data demonstrate a proinflammatory microenvironment of the T1D-duodenum, whereby IECs have the potential to contribute to the expansion and polarization of innate and adaptive immune cells. Although these data do not discern whether these observations are not simply a consequence of T1D, the data indicate that the T1D-GI tract has the capacity to foster a permissive environment under which autoreactive T-cells could be expanded and polarized.
Friend Recommendation Based on the Similarity of Micro-blog User Model

Online social network has obtained a significant increase in recent years. Making friends is an ordinary way of establishing social relationships with others in online social network. Therefore friend recommendation is becoming a very important aspect and attracting extensive attention in visual communities and social network. Among various online social networks, micro-blog has become increasingly popular. The rapid growth of micro-blog data provides a rich resource for social community mining. In this paper, we present a friend recommendation approach based on the similarity of micro-blog user model. The proposed approach constructs the user model by considering four aspects: user profile, the content information that user posted, the link relationship and the interaction relationship between users. The interaction information such as users' comments and forwards are considered while calculate the link strength between users. The micro-blog content is divided into different topics which are obtained from an existing topic hierarchy. After we obtained the micro-blog user model, we calculate the interaction based similarity and content based similarity separately. After that, we mix the two kind of similarity together to calculate the similarity of micro-blog user model. At last, we recommend friend to users by this similarity. Experiments show that the friend recommendation approach based on the similarity of micro-blog user model has a higher precision than traditional approaches.
Vertical integration and communication

Among the many possible motives for vertical integration, the one emphasized here is uncertainty in the supply of the upstream good and the consequent need for information by downstream firms. The basic conclusion is that, even when the initial conditions are of the type usually thought of as competitive, the upshot will be a tendency to imperfect competition.
DIFFERENTIAL TAXATION AND TAX EVASION BY SMALL BUSINESS

This paper examines the compliance pattern of small businesses, using pooled 1985 and 1988 Taxpayer Compliance Measurement Program (TCMP) data. Specifically, we focus on the voluntary reporting compliance of income from proprietorship, farm, and rental real estate activities. We find that differential taxation due to selfemployment taxes (SECA) plays an important role in explaining the observed disparity in voluntary reporting compliance among sources of selfemployment income.
Author manuscript, published in "EGOS 2013 Sub-theme 09: (SWG) Identity in Art, Design and Organization, Montréal: Canada (2013)" EGOS 2013 Montreal

EGOS 2013 Montreal Sub-theme 09: (SWG) Identity in Art, Design and Organization " Three cases of identity (re)construction through art interventions: the dialogical and the " sensible ". " Authors : Warning: What follows is a classical paper format, while our presentation will use a more creative setting, and let the audience experience a participative and artistic performance where to discuss the proposed hypothesis.
Reconfigurable complex digital Delta-Sigma modulator synthesis for digital wireless transmitters

Digital generation of radio-frequency signals is a key concept of software defined radio. One of the main difficulties for multi-standard transmitter design based on delta-sigma (DeltaSigma) modulators is to respect the different specifications in terms of out-of-band spurious emission. Focusing on the TX path of a UMTS/DCS1800 mobile phone, we propose hereinafter an efficient method aiming at synthesizing a complex 5th-order DeltaSigma modulator which respects the targeted standards spurious specifications. The use of a complex noise transfer function allows a better optimization of noise shaping. In addition, this approach eases the reconfiguration of the modulator, and, it is a powerful tool for all order (real and complex) DeltaSigma modulators synthesis, as it will be illustrated.
Simian Virus Large T Antigen Interacts with the N-Terminal Domain of the 70 kD Subunit of Replication Protein A in the Same Mode as Multiple DNA Damage Response Factors

Simian virus 40 (SV40) serves as an important model organism for studying eukaryotic DNA replication. Its helicase, Large T-antigen (Tag), is a multi-functional protein that interacts with multiple host proteins, including the ubiquitous ssDNA binding protein Replication Protein A (RPA). Tag recruits RPA, actively loads it onto the unwound DNA, and together they promote priming of the template. Although interactions of Tag with RPA have been mapped, no interaction between Tag and the N-terminal protein interaction domain of the RPA 70kDa subunit (RPA70N) has been reported. Here we provide evidence of direct physical interaction of Tag with RPA70N and map the binding sites using a series of pull-down and mutational experiments. In addition, a monoclonal anti-Tag antibody, the epitope of which overlaps with the binding site, blocks the binding of Tag to RPA70N. We use NMR chemical shift perturbation analysis to show that Tag uses the same basic cleft in RPA70N as multiple of DNA damage response proteins. Mutations in the binding sites of both RPA70N and Tag demonstrate that specific charge reversal substitutions in either binding partner strongly diminish the interaction. These results expand the known repertoire of contacts between Tag and RPA, which mediate the many critical roles of Tag in viral replication.
Clinical research informatics: a conceptual perspective

Clinical research informatics is the rapidly evolving sub-discipline within biomedical informatics that focuses on developing new informatics theories, tools, and solutions to accelerate the full translational continuum: basic research to clinical trials (T1), clinical trials to academic health center practice (T2), diffusion and implementation to community practice (T3), and ‘real world’ outcomes (T4). We present a conceptual model based on an informatics-enabled clinical research workflow, integration across heterogeneous data sources, and core informatics tools and platforms. We use this conceptual model to highlight 18 new articles in the JAMIA special issue on clinical research informatics.
Deleterious effects of chronic clenbuterol treatment on endurance and sprint exercise performance in rats.

The beta(2)-adrenergic agonist, clenbuterol, has powerful muscle anabolic and lipolytic effects and is used by athletes to improve exercise performance; however, its use in conjunction with different forms of exercise training has received limited attention. Since previous studies have reported that chronic use of other beta(2)-adrenergic agonists has deleterious effects on cardiac muscle structure and function, the aim of the present study was to determine whether chronic clenbuterol administration would reduce the exercise capabilities of rats subjected to long-term treadmill sprint running, endurance swimming or voluntary wheel running training. The effect of clenbuterol treatment on exercise performance in rats was evaluated in three separate studies. Different groups of male rats were assigned to an endurance swimming (2 h/day, 5/7 days, 18 weeks) group, a treadmill sprint running (8x1 min bouts, 1.05 m/s, 20 weeks) group, or a voluntary wheel running (16 weeks) group. In each study, rats were allocated into either a treated group that received clenbuterol (2 mg.kg(-1). day(-1)) in their drinking water or an untreated control group. In each of the three studies, treated rats exhibited a reduction in exercise performance compared with untreated rats. Treated rats ran approximately 57% less total distance than untreated rats in the voluntary running programme and were unable to complete the swimming and sprinting protocols performed by the untreated rats. In each of the studies, the treated rats exhibited cardiac hypertrophy, with absolute heart mass increased by approximately 19% and heart mass relative to body mass increased by approximately 20%. The hearts of sedentary rats treated with clenbuterol exhibited extensive collagen infiltration surrounding blood vessels and in the wall of the left ventricle. The results indicate strongly that chronic clenbuterol administration deleteriously affects exercise performance in rats, potentially due to alterations in cardiac muscle structure and function.
Optimization of File Allocation for Video Sharing Servers

This paper focuses on one of the most used short video servers on the Internet, it is YouTube. YouTube has the third rank of the internet sites related to its traffic transactions. In this work, firstly, we study the effect of the huge numbers of viewers, hits, users and files on the video sharing servers' behaviours by analyzing some recent statistics about YouTube. Then, we propose an optimization for file allocation procedures in general and then we apply the algorithm to some examples of YouTube videos. This solution improves the number of hits related to those kinds of servers over the Internet. Finally, we try to optimize the revenue from the file allocation and propose a hybrid solution for the file hosting or server caching systems.
Wps 2 L-2 0

The Current State of the Debate privatization of infrastructure in many developing countries has spawned new critiques of Mary Shirley privatization. How do theory Patrick Walsh and empirical evidence answer the much-debated questions, Which is more important to performance, competition or private ownership? Are state enterprises more subject to welfare-reducing interventions by government than orivate firms are? Do state enterprises uffer more from problems of corporate governance?
Normative power and democracy promotion in the European Neighbourhood Policy – A comparative case study of Azerbaijan and Egypt

The European Neighbourhood Policy (ENP) is deemed to be the EU’s most ambitious initiative to date. The EU is often considered to have normative power over partner countries and therefore the concept of Normative Power Europe has been investigated. In order to narrow the scope, democracy promotion was chosen as the primary channel for normative power. The purpose is to investigate how the ENP uses normative power for democracy promotion. The study was conducted by firstly creating an analytical framework on normative power and democracy promotion. The chosen countries for analysis are Azerbaijan and Egypt. The framework was then applied to the ENP Action Plans and Progress Reports on Azerbaijan and Egypt. The results show that the ENP mainly uses its normative power to promote democracy through political dialogue, support to democratic actors and by creating incentives for democratic change. Additionally, the ENP strives for increasing commitment from the partner country as well to issue standards and norms.
Title High expression of Twist is associated with tumor aggressiveness and poorprognosis in patients with renal cell carcinoma

Aims: Twist has been reported to play crucial roles for malignant aggressiveness; however, detailed pathological significance of Twist in renal cell carcinoma (RCC) is not fully understood. The present study was to clarify clinical significance and molecular functions of Twist in patients with RCC. Methods: Twist expression was examined by immunohistochemical techniques in 156 formalin-fixed specimens. Cell proliferation, angiogenesis, and apoptosis were measured as the percentage of Ki-67-positive cells (proliferation index, PI), CD31-stained vessels (microvessel density, MVD), and TUNEL-positive cells (apoptotic index, AI). In addition, semi-quantification of matrix metalloproteinase (MMP)-2 was performed. Macrophages were identified with anti-CD68 antibody, and the tumor associated macrophage (TAM) density was calculated as CD68-positive cells per high-power field. Results: Twist expression was positively associated with grade, pT stage, and metastasis (p<0.001). We also noticed that its expression was considerably higher in cancer cells of sarcomatoid RCC and in those at the edge of the tumors. Twist expression was positively correlated with PI, MVD, MMP2 expression, and TAM density (P<0.001), but not with AI, and MMP-2 expression and TAM density were independently correlate by multi-variate analyses. Kaplan-Meir survival curves showed high Twist expression was a worse predictor for cause-specific survival (P<0.001). Conclusions: Twist plays important roles in tumor growth, progression, and survival in patients with RCC patients. Such pathological mechanisms are significantly associated with increased cancer cell proliferation, angiogenesis, MMP2 expression, and macrophage recruitment. These findings are important information for discussion of treatment and observation strategies in these patients.