Miracle-dz/UniFAR-FTUs huggingface dataset:
Visfatin Is Regulated by Rosiglitazone in Type 2 Diabetes Mellitus and Influenced by NFκB and JNK in Human Abdominal Subcutaneous Adipocytes

Visfatin has been proposed as an insulin-mimicking adipocytokine, predominantly secreted from adipose tissue and correlated with obesity. However, recent studies suggest visfatin may act as a proinflammatory cytokine. Our studies sought to determine the significance of this adipocytokine and its potential role in the pathogenesis of T2DM. Firstly, we examined the effects of diabetic status on circulating visfatin levels, and several other adipocytokines, demonstrating that diabetic status increased visfatin*, TNF-α*** and IL-6*** compared with non-diabetic subjects (*p<0.05, **p<0.01, ***p<0.001, respectively). We then assessed the effects of an insulin sensitizer, rosiglitazone (RSG), in treatment naïve T2DM subjects, on circulating visfatin levels. Our findings showed that visfatin was reduced post-RSG treatment [vs. pre-treatment (*p<0.05)] accompanied by a reduction in HOMA-IR**, thus implicating a role for insulin in visfatin regulation. Further studies addressed the intracellular mechanisms by which visfatin may be regulated, and may exert pro-inflammatory effects, in human abdominal subcutaneous (Abd Sc) adipocytes. Following insulin (Ins) and RSG treatment, our in vitro findings highlighted that insulin (100 nM), alone, upregulated visfatin protein expression whereas, in combination with RSG (10 nM), it reduced visfatin*, IKKβ** and p-JNK1/2*. Furthermore, inhibition of JNK protein exacted a significant reduction in visfatin expression (**p<0.01), whilst NF-κB blockade increased visfatin (*p<0.05), thus identifying JNK as the more influential factor in visfatin regulation. Additional in vitro analysis on adipokines regulating visfatin showed that only Abd Sc adipocytes treated with recombinant human (rh)IL-6 increased visfatin protein (*p<0.05), whilst rh visfatin treatment, itself, had no influence on TNF-α, IL-6 or resistin secretion from Sc adipocytes. These data highlight visfatin's regulation by insulin and RSG, potentially acting through NF-κB and JNK mechanisms, with only rh IL-6 modestly affecting visfatin regulation. Taken together, these findings suggest that visfatin may represent a pro-inflammatory cytokine that is influenced by insulin/insulin sensitivity via the NF-κB and JNK pathways.
Differential effects of the cyclin-dependent kinase inhibitors p27(Kip1), p21(Cip1), and p16(Ink4) on vascular smooth muscle cell proliferation.

BACKGROUND The cyclin-dependent kinase inhibitors (CKIs) have different patterns of expression in vascular diseases. The Kip/Cip CKIs, p27(Kip1) and p21(Cip1), are upregulated during arterial repair and negatively regulate the growth of vascular smooth muscle cells (VSMCs). In contrast, the Ink CKI, p16(Ink4), is not expressed in vascular lesions. We hypothesized that a variation in the inactivation of cdk2 and cdk4 during the G(1) phase of the cell cycle by p27(Kip1), p21(Cip1), and p16(Ink4) leads to different effects on VSMC growth in vitro and in vivo. METHODS AND RESULTS The expression of p27(Kip1) and p21(Cip1) in serum-stimulated VSMCs inactivated cdk2 and cdk4, leading to G(1) growth arrest. p16(Ink4) inhibited cdk4, but not cdk2, kinase activity, producing partial inhibition of VSMC growth in vitro. In an in vivo model of vascular injury, overexpression of p27(Kip1) reduced intimal VSMC proliferation by 52% (P<0.01) and the intima/media area ratio by 51% (P<0.005) after vascular injury and gene transfer to pig arteries, when compared with control arteries. p16(Ink4) was a weak inhibitor of intimal VSMC proliferation in injured arteries (P=NS), and it did not significantly reduce intima/media area ratios (P=NS), which is consistent with its minor effects on VSMC growth in vitro. CONCLUSIONS p27(Kip1) and p21(Cip1) are potent inhibitors of VSMC growth compared with p16(Ink4) because of their different molecular mechanisms of cyclin-dependent kinase inhibition in the G(1) phase of the cell cycle. These findings have important implications for our understanding of the pathophysiology of vascular proliferative diseases and for the development of molecular therapies.
Status of 4 D Treatment Planning Implementations for TRiP 98

TRiP98 is a treatment planning program for radiotherapy with scanned ion beams. It was developed at GSI and has been successfully used in clinical routine from 1997-2008 for over 400 patients, predominantly with head and neck tumors [1,2]. The treatment of tumors within moving organs, such as lung tumors, with scanned ion beams involves additional complexity of the beam delivery and the treatment planning process. Therefore, new implementations for 4D treatment planning in TRiP98 were needed and carried out at different stages of development [3-5]. This report gives an overview of recent developments of the 4D treatment planning version of TRiP98 (TRiP4D).
Online social network measurements and search privacy protection

This dissertation investigates the following issues within the context of online social networks (OSNs). (1) How to collect data from OSNs; (2) How to estimate OSN properties; (3) How to measure OSN behavior. First a case study is conducted with real OSN data to analyze the data collection process. The following problems are answered by evaluating various factors including the choice of seeds, node selection algorithms, and sample sizes. (1) Efficiency: How fast different crawlers discover nodes/links; (2) Sensitivity: How different OSN graphs and protected users affect crawlers; (3) Bias: How major graph properties are skewed. Secondly, to estimate the size of an OSN, this dissertation introduces two estimators using widely available OSN functionalities/services. An O(logn) algorithm is proposed to replace the original O(n) solution for the MLE estimator. The RW estimator is generalized to estimate other graph properties. In-depth evaluations are performed to show the bias and variance of these estimators. Furthermore, to measure information propagation and social influence, two important but not well defined types of social behavior, we present a measurement study of 58M messages collected from 700K Twitter users. First, we employ three methods to trace message propagation and examine their applicabilities on Twitter. Besides analyzing the propagation patterns of general messages, we show how breaking news (Michael Jackson's death) spread through Twitter. Finally, we evaluate different social influences and their stabilities, assessments, and correlations. With real OSN data, we address the complications and challenges to crawl, estimate and measure OSNs. We believe that our analysis here provides valuable insights for future OSN research. The second part of this dissertation proposes a noise injection model for search privacy protection. We model the search privacy threat as an information inference problem and show how to inject noise into user queries to minimize privacy breaches. We give the lower bound for the amount of noise queries required by a perfect privacy protection and provide the optimal protection given the number of noise queries. This work presents the first theoretical analysis on user side noise injection for search privacy protection.
Geo-consistency for wide multi-camera stereo

This paper presents a new model to overcome the occlusion problems coming from wide baseline multiple camera stereo. Rather than explicitly modeling occlusions in the matching cost function, it detects occlusions in the depth map obtained from regular efficient stereo matching algorithms. Occlusions are detected as inconsistencies of the depth map by computing the visibility of the map as it is reprojected into each camera. Our approach has the particularity of not discriminating between occluders and occludees. The matching cost function is modified according to the detected occlusions by removing the offending cameras from the computation of the matching cost. The algorithm gradually modifies the matching cost function according to the history of inconsistencies in the depth map, until convergence. While two graph-theoretic stereo algorithms are used in our experiments, our framework is general enough to be applied to many others. The validity of our framework is demonstrated using real imagery with different baselines.
An efficient switch for fat tree Network-on-Chip interconnection architecture

This paper describes a fat tree based Network-on-Chip (NOC) system. The fat tree includes processing nodes and communication switches. IP node has a message generator unit which randomly generates messages to different destinations with different packet lengths and buffering. Switches use wormhole routing with virtual channel mechanism. The switch consists of the following units: router, input/output link controllers and arbitration units. A simulator has been developed in C++ to analyze the proposed architecture. Moreover, a VHDL model for the employed algorithms has been simulated and prototyped (partially) in FPGA technology.
The Concurrency Column Causal-consistent Reversibility *

Reversible computing allows one to execute programs both in the standard, forward direction, and backward, going back to past states. In a concurrent scenario, the correct notion of reversibility is causal-consistent reversibility: any action can be undone, provided that all its consequences (if any) are undone beforehand. In this paper we present an overview of the main approaches, results, and applications of causal-consistent reversibility.
Controlling Energy-Level Alignments at Carbon Nanotube/Au Contacts

The properties of the contacts between single-walled carbon nanotubes (SWNTs) and Au electrodes are studied using scanning Kelvin probe and electrostatic force microscopies. Contact potential differences and local dipoles at the SWNT/Au interface are determined under various conditions involving gas adsorption and surface passivation. In particular, the effects of the coadsorption of alkanethiol, S, and O2 are explored in detail. We find that the coadsorbates alter the energy-level line-up at the contacts and induce significant shifts of the SWNT bands relative to the metal Fermi level. This behavior is explained by considering the response of the local Au work function to the presence of the nanotube and of the coadsorbates as well as the effects of the adsorbate dipoles near the contacts. Finally, we use coadsorption to control the Schottky barrier height at the nanotube−Au contacts.
Ganciclovir ophthalmic gel, 0.15%: a valuable tool for treating ocular herpes

Ocular herpes simplex virus (HSV) infection remains a major cause of corneal blindness. Several topical and oral antiviral medications have been used to treat herpetic keratitis. Advances in topical ophthalmic antivirals have been made over the past several decades. The first antivirals that were discovered were cytotoxic, while the antivirals developed more recently, such as acyclovir and ganciclovir, have exceeded these drugs in both efficacy and tolerability. Commercially available outside of the US since 1996, ganciclovir ophthalmic gel, 0.15% (GCV 0.15%, European tradename: Virgan®) is sold in more than 30 countries and has become the standard of care in treating acute herpetic keratitis. GCV 0.15% has been studied in animal models of ocular herpes, in healthy volunteers, and in several clinical studies. It has been found to be safe and effective at treating acute superficial herpetic keratitis. Previous preclinical studies of ganciclovir have shown activity against several common adenovirus strains and one recent clinical study demonstrated clinical effect against adenoviral conjunctivitis. This review is intended to provide a comprehensive overview of the GCV 0.15%, including a brief summary of the etiology and available treatments for ocular HSV, an explanation of GCV 0.15% mechanism of action, a compendium of preclinical and clinical GCV 0.15% studies, and an introduction into new areas of interest involving this drug.
Decentralised Solutions to the Cooperative Multi-Platform Navigation Problem

The problem of cooperative navigation for a team of platforms employing inter-platform observations is investigated. A decentralised solution in the framework of an information filter with delayed states is presented. In this structure, each platform first estimates its motion using only local sensor data, then shares its information across the network using an algorithm that employs a distributed Cholesky modification. The decentralised solution permits each platform to act in the same modular manner, providing robustness to individual platform failure. The solution yields linear minimum mean-square error estimation performance. As such the estimates generated are optimal; it generates exactly the same estimates as would a conventional extended Kalman filter (EKF), if given the same data. Efficient sparse implementation is accomplished without resorting to approximate methods. Simulation experiments employing a team of ten mobile platforms are described and used to evaluate the decentralised estimation performance. The robustness, flexibility, and cost of the decentralised approach are analyzed and compared with an existing distributed solution.
incompatibilities and sexually dimorphic gene expression-regulation in the evolution of regulatory trans-and cis The roles of Material Supplemental

Material Supplemental http://genome.cshlp. org/content/suppl/2013/11/04/gr.156414. 113.DC1. html References http://genome.cshlp. org/content/24/1/84.full. html#ref-list-1 This article cites 84 articles, 38 of which can be accessed free at: Open Access Open Access option. Genome Research Freely available online through the License Commons Creative . http://creativecommons.org/licenses/by-nc/3.0/ License (Attribution-NonCommercial 3.0 Unported), as described at , is available under a Creative Commons Genome Research This article, published in
Reconsidering the Origin of the 21 Micron Feature: Oxides in Carbon-rich Protoplanetary Nebulae?

The origin of the so-called 21 μm feature that is especially prominent in the spectra of some carbon-rich protoplanetary nebulae (PPNs) is the matter of a lively debate. A large number of potential band carriers have been presented and discarded within the past decade. This paper gives an overview of the problems related to the hitherto proposed feature identifications, including the recently suggested candidate carrier silicon carbide. We also discuss the case for spectroscopically promising oxides. SiC is shown to produce a strong resonance band at 20-21 μm if coated by a layer of silicon dioxide. At low temperatures, core-mantle particles composed of SiC and amorphous SiO2 indeed have their strongest spectral signature at a position of 20.1 μm, which coincides with the position of the 21 μm emission band. The optical constants of another candidate carrier that has been relatively neglected so far—iron monoxide—are proven to permit a fairly accurate reproduction of the 21 μm feature profile as well, especially when low-temperature measurements of the infrared properties of FeO are taken into account. As candidate carrier of the 21 μm emission band, FeO has the advantage of being stable against further oxidation and reduction only in a narrow range of chemical and physical conditions, coinciding with the fact that this feature, too, is detected in a small group of objects only. However, it is unclear how FeO would form or survive, particularly in carbon-rich PPNs.
Authenticity

Authenticity is generally believed to play an important role in our daily lives. Empirical research thus far has made progress in understanding the nature of this important construct. We identify four broad conclusions about authenticity based on this research: (a) People value authenticity in their own behavior and other domains (e.g., life experiences, consumer products), (b) Self-reports of personal authenticity are linked to psychological well-being, (c) People generally believe authentic, or “true,” selves are morally good, and (d) Authenticity judgments are guided by cognitive tendencies related to psychological essentialism. Despite this progress, many basic questions about authenticity remain unresolved including (a) What is the best way to define the construct? (b) Why do people care so much about whether something or someone is authentic? and (c) Why is personal authenticity so strongly related to psychological well-being? This special issue presents articles aimed to shed light on some of these basic questions. Although each of the articles offers a unique perspective to understanding authenticity, these collections of articles provide a generative framework to help researchers continue to explore this elusive construct.
Source distinguishability under corrupted training

We study a new variant of the source identification game with training data in which part of the training data is corrupted by an adversary. In such a scenario, the defender wants to decide whether a test sequence ξn has been drawn from the same source which generated a training sequence tN, part of which has been corrupted by the adversary. By adopting a game theoretical formulation, we derive the unique rationalizable equilibrium of the game in the asymptotic setup. Moreover, by mimicking Stein's lemma, we derive the best achievable performance for the defender, permitting us to analyze the ultimate distinguishability of the two sources.We conclude the paper by comparing the performance of the test with corrupted training to the simpler case in which the adversary can not modify the training sequence, and by deriving the percentage of samples that the adversary needs to modify to make source identification impossible.
A Novel Chimeric Gene, siren, With Retroposed Promoter Sequence in the Drosophila bipectinata Complex

Retrotransposons often produce a copy of host genes by their reverse transcriptase activity operating on host gene transcripts. Since transcripts normally do not contain promoter, a retroposed gene copy usually becomes a retropseudogene. However, in Drosophila bipectinata and a closely related species we found a new chimeric gene, whose promoter was likely produced by retroposition. This chimeric gene, named siren, consists of a tandem duplicate of Adh and a retroposed fragment of CG11779 containing the promoter and a partial intron in addition to the first exon. We found that this unusual structure of a retroposed fragment was obtained by retroposition of nanos, which overlaps with CG11779 on the complementary strand. The potential of retroposition to produce a copy of promoter and intron sequences in the context of gene overlapping was demonstrated.
Mu killer-Mediated and Spontaneous Silencing of Zea mays Mutator Family Transposable Elements Define Distinctive Paths of Epigenetic Inactivation

Mu killer contains a partial inverted duplication of the mudrA transposase gene and two copies of the terminal inverted repeat A (TIRA) region of the master MuDR element of maize. Mu killer can effectively silence single copy MuDR/Mu lines, and it is proposed that a ∼4 kb hairpin RNA is generated by read through transcription from a flanking gene and that this transcript serves as a substrate for siRNA production. Mu killer was sequenced, except for a recalcitrant portion in the center of the locus, and shown to be co-linear with mudrA as originally proposed. The ability of the dominant Mu killer locus to silence a standard high copy number MuDR/Mu transposon line was evaluated. After two generations of exposure, about three quarters of individuals were silenced indicating reasonable effectiveness as measured by the absence of mudrA transposase transcripts. Mu killer individuals that effectively silenced MuDR expressed two short antisense transcripts. In contrast, Mu killer individuals that failed to silence MuDR expressed multiple sense transcripts, derived from read through transcription initiating in a flanking gene, but no antisense transcripts were detected.
Polyreactive Monoclonal Autoantibodies in Multiple Sclerosis: Functional Selection from Phage Display Library and Characterization by Deep Sequencing Analysis

Multiple Sclerosis (MS) is a chronic inflammatory demyelinating disease of the central nervous system that primarily affects young and middle-aged people. It is widely accepted that B lymphocyte activation is required for MS progression. Despite the fact that the exact triggering mechanisms of MS remain enigmatic, one may suggest that MS can be induced by viral or bacterial infection in combination with specific genetic and environmental factors. Using deep sequencing and functional selection methodologies we characterized clones of poly- and cross-reactive antibodies that are capable of simultaneous recognition of viral proteins and autoantigens. The latter, in turn, possibly may trigger MS progression through molecular mimicry. It was identified that two cross-reactive antigens are probably recognized by light or heavy chains individually. According to the high structural homology between selected autoantibodies and a number of various antiviral IgGs, we suggest that a wide range of pathogens, instead of a single virus, be regarded as possible triggers of MS.
Social Learning and Coordination Conventions in Inter-Generational Games: An Experiment in Lamarckian Evolutionary Dynamics

This is a paper on the creation and evolution of conventions of behavior in "inter-generational games". In these games a sequence of nonoverlapping "generations" of players play a stage game for a finite number of periods and are then replaced by other agents who continue the game in their role for an identical length of time. Players in generation t are allowed to see the history of the game played by all (or some subset) of the generations who played it before them and can communicate with their successors in generation t+1 and advise them on how they should behave. What we find is that word-of-mouth social learning (in the form of advice from parents to children) can be a strong force in the creation of social conventions, far stronger than the type of learning subjects seem capable of doing simply by learning the lessons of history without the guidance offered by such advice.
The Economics of Recycling In France: Institutional Framework And Technological Adoption

The aim of this paper is to explore the main features of the new regime for packaging waste management established in France in 1992. A description of the institutional organisation is provided. Then, the paper analyses how the packaging tax implemented in France may allow the optimal application of recycling techniques, combined with waste-to-energy facilities. Nevertheless, this optimal utilisation is lessened by weak or even negative incentives which may lead to a sub-optimal equilibrium. The conclusion is that institutional conditions are directly affecting the investment behaviour of municipalities. The consequence will be the development of recycling at levels well below the objectives of policy makers.
Positional markedness as a by-product of the learning situation

0. Introduction This paper presents a simulation where a “learner” attempts to acquire a positionally unrestricted phonological contrast (plain vs. palatalized labial stops in a variety of contexts) without any a priori knowledge of the relevant positional hierarchies. The results show that an acquisition model that includes human-like perceptual limitations can give rise to cross-linguistically attested phonotactic grammars without positing this a priori knowledge.