Miracle-dz/UniFAR-FTUs huggingface dataset:
Role of reactive oxygen species in the transforming growth factor-β1-induced collagen production and differentiation of cardiac fibroblasts into myofibroblasts

The aim of the present study was to determine whether transforming growth factor-β1 (TGF-β1)-induced collagen production in cardiac fibroblasts is affected by reactive oxygen species (ROS). Cardiac fibroblasts (passage 2) from normal male adult rats were cultured to confluency and incubated in serum-free Dulbecco’s modified Eagle’s medium for 24 h. The cells were then preincubated with(out) the tested inhibitors for 1 h and further incubated with(out) TGF-β1 at various concentrations and for 1, 2, 4, 24 or 48 h. TGF-β1 induced a dose-dependent increase in the soluble collagen production in cardiac fibroblasts after 48 h of incubation. No significant effect of TGF-β1 (600 pmol/l) on collagen production and on α-smooth muscle actin (α-SMA) protein expression was found after 1, 2 and 4 h of incubation. After 24 and 48 h, TGF-β1 stimulated collagen production and α-SMA protein expression in cardiac fibroblasts. Intracellular ROS were not affected by TGF-β1 after 0.5 and 1 h of incubation, began to rise after 2 h, and reached a maximal increase after 4 h. The TGF-β1-stimulated ROS and collagen production is reduced by the ROS inhibitor diphenyleneiodonium chloride (DPI). DPI also decreased the TGF-β1-stimulated α-SMA protein expression in rat cardiac fibroblasts. Our data indicate that the TGF-β1-induced increase in ROS preceded the rise in collagen production and α-SMA protein expression and that ROS inhibition diminished the conversion of fibroblasts into myofibroblasts.
Problems and Pitfalls in Evaluating Adaptive Systems 1

Empirical studies with adaptive systems offer many advantages and opportunities. Nevertheless, there is still a lack of evaluation studies. This paper lists several problems and pitfalls that arise when evaluating an adaptive system and provides guidelines and recommendations for workarounds or even avoidance of these problems. Among other things the following issues are covered: relating evaluation studies to the development cycle; saving resources; specifying control conditions, sample and criteria; asking users for adaptivity effects; reporting results. An overview of existing evaluation frameworks shows which of these problems have been addressed in which way. 1. Introduction Empirical evaluation of adaptive learning systems is a very important task, as the lack of strong theories, models and laws requires that we do evaluative experiments that check our intuition and imagination. Researchers from various fields have made experiments and published a considerable amount of experimental data. Many of these data sets can be valuable form adaptive learning systems. Still, most of the results are given in a textual form, while structure of these results is not standardized. This limits the practical value of the results. Therefore, if we want to improve the usefulness of the experimental results, it is important to make more formal descriptions of them. The first step toward this goal is creation of the metamodel of empirical evaluation that should identify concepts such as evaluation style, methods and evaluation approaches. This metamodel serves as a conceptual basis form various applications, such as metadescription of experimental data, and creation of experimental data warehouses. Based on this metamodel various tools can work together on creation and processing and comparative analysis of these experimental data.
Explicit robustness margin for contractive piecewise affine control laws

This paper deals with the class of discrete-time linear dynamics affected by polytopic uncertainty in closed loop with contractive piecewise affine (PWA) control law. Starting from the hypothesis that the synthesis ensures a λ-contractive PWA control law for the nominal model, the objective is to calculate the robustness margin guaranteeing the contractivity (and consequently the asymptotic stability) of the closed loop dynamics. The robustness margin is represented as a subset of parameters within the set describing the polytopic uncertainty. For all these parameters, the λ-contractive behavior of the trajectories can be certified. This set of parameters is then compared to the set assuring the invariance of the contraction property of the considered closed-loop PWA dynamics which represents a limit case of the robustness study presented here.
Insights into the mechanism of X-ray-induced disulfide-bond cleavage in lysozyme crystals based on EPR, optical absorption and X-ray diffraction studies

Electron paramagnetic resonance (EPR) and online UV–visible absorption microspectrophotometry with X-ray crystallography have been used in a complementary manner to follow X-ray-induced disulfide-bond cleavage, to confirm a multi-track radiation-damage process and to develop a model of that process.
Thin edge detector

Most edge detectors are based on detecting points in the image with a high gradient value. However, in general, they omit the idea that the edge must be a connected line of pixels. Instead of that, these techniques normally use a global threshold value, to control the quantity of edge points detected. Due to this, many other edge points are detected, but some of them do not really belong to an edge. In this paper we propose a new edge detector, that detects entire pieces of 1-pixel-thick lines. This algorithm is more robust concerning the choice of the threshold value, because it works with the average gradient value of each piece of line. Two previous filters are needed: a contrast process, to enhance the edges, and a morphological denoising to remove noise but without blurring the edges in the image. The proposed algorithm starts from pixels with a high gradient value, and follows neighbor pixels connecting new points.
Record-breaking ozone loss in the Arctic winter 2010/2011: comparison with 1996/1997

We present a detailed discussion of the chemical and dynamical processes in the Arctic winters 1996/1997 and 2010/2011 with high resolution chemical transport model (CTM) simulations and space-based observations. In the Arctic winter 2010/2011, the lower stratospheric minimum temperatures were below 195 K for a record period of time, from December to mid-April, and a strong and stable vortex was present during that period. Simulations with the Mimosa-Chim CTM show that the chemical ozone loss started in early January and progressed slowly to 1 ppmv (parts per million by volume) by late February. The loss intensified by early March and reached a record maximum of ~2.4 ppmv in the late March–early April period over a broad altitude range of 450–550 K. This coincides with elevated ozone loss rates of 2–4 ppbv sh^(−1) (parts per billion by volume/sunlit hour) and a contribution of about 30–55% and 30–35% from the ClO-ClO and ClO-BrO cycles, respectively, in late February and March. In addition, a contribution of 30–50% from the HO_x cycle is also estimated in April. We also estimate a loss of about 0.7–1.2 ppmv contributed (75%) by the NO_x cycle at 550–700 K. The ozone loss estimated in the partial column range of 350–550 K exhibits a record value of ~148 DU (Dobson Unit). This is the largest ozone loss ever estimated in the Arctic and is consistent with the remarkable chlorine activation and strong denitrification (40–50%) during the winter, as the modeled ClO shows ~1.8 ppbv in early January and ~1 ppbv in March at 450–550 K. These model results are in excellent agreement with those found from the Aura Microwave Limb Sounder observations. Our analyses also show that the ozone loss in 2010/2011 is close to that found in some Antarctic winters, for the first time in the observed history. Though the winter 1996/1997 was also very cold in March–April, the temperatures were higher in December–February, and, therefore, chlorine activation was moderate and ozone loss was average with about 1.2 ppmv at 475–550 K or 42 DU at 350–550 K, as diagnosed from the model simulations and measurements.
Computing betweenness centrality in external memory

Betweenness centrality is one of the most well-known measures of the importance of nodes in a social-network graph. In this paper we describe the first known external-memory and cache-oblivious algorithms for computing betweenness centrality. We present four different external-memory algorithms exhibiting various tradeoffs with respect to performance. Two of the algorithms are cache-oblivious. We describe general algorithms for networks with weighted and unweighted edges and a specialized algorithm for networks with small diameters, as is common in social networks exhibiting the “small worlds” phenomenon.
Chlamydia Species-Dependent Differences in the Growth Requirement for Lysosomes

Genome reduction is a hallmark of obligate intracellular pathogens such as Chlamydia, where adaptation to intracellular growth has resulted in the elimination of genes encoding biosynthetic enzymes. Accordingly, chlamydiae rely heavily on the host cell for nutrients yet their specific source is unclear. Interestingly, chlamydiae grow within a pathogen-defined vacuole that is in close apposition to lysosomes. Metabolically-labeled uninfected host cell proteins were provided as an exogenous nutrient source to chlamydiae-infected cells, and uptake and subsequent labeling of chlamydiae suggested lysosomal degradation as a source of amino acids for the pathogen. Indeed, Bafilomycin A1 (BafA1), an inhibitor of the vacuolar H+/ATPase that blocks lysosomal acidification and functions, impairs the growth of C. trachomatis and C. pneumoniae, and these effects are especially profound in C. pneumoniae. BafA1 induced the marked accumulation of material within the lysosomal lumen, which was due to the inhibition of proteolytic activities, and this response inhibits chlamydiae rather than changes in lysosomal acidification per se, as cathepsin inhibitors also inhibit the growth of chlamydiae. Finally, the addition of cycloheximide, an inhibitor of eukaryotic protein synthesis, compromises the ability of lysosomal inhibitors to block chlamydial growth, suggesting chlamydiae directly access free amino acids in the host cytosol as a preferred source of these nutrients. Thus, chlamydiae co-opt the functions of lysosomes to acquire essential amino acids.
The Study of Video Frame Tracking Based on the New Scale Invariant Algorithm and the Feature Classification Tree

For the difficult question of how to track moving object accurately during the augment reality without sign identification process. This paper suggests a comprehensive video frame tracking theory model. Using the new scale invariant algorithm to optimize the process of the feature extraction and the forming characteristics description. Meanwhile, Using the Feature classification tree algorithm to transform the image feature point identification matching problem into the characteristic pattern recognition classification problem¡£Finally, apply SIFT-RT model to the process of video tracking and get a good experimental results. The model owns the advantages such as the small time complexity, the precise characteristics tracking. Experiments demonstrate that SIFT-RT model can satisfy the requirements of special tracking of the augment reality without the sign.
Changes in the regulation of the Notch signaling pathway are temporally correlated with regenerative failure in the mouse cochlea

Sensorineural hearing loss is most commonly caused by the death of hair cells in the organ of Corti, and once lost, mammalian hair cells do not regenerate. In contrast, other vertebrates such as birds can regenerate hair cells by stimulating division and differentiation of neighboring supporting cells. We currently know little of the genetic networks which become active in supporting cells when hair cells die and that are activated in experimental models of hair cell regeneration. Several studies have shown that neonatal mammalian cochlear supporting cells are able to trans-differentiate into hair cells when cultured in conditions in which the Notch signaling pathway is blocked. We now show that the ability of cochlear supporting cells to trans-differentiate declines precipitously after birth, such that supporting cells from six-day-old mouse cochlea are entirely unresponsive to a blockade of the Notch pathway. We show that this trend is seen regardless of whether the Notch pathway is blocked with gamma secretase inhibitors, or by antibodies against the Notch1 receptor, suggesting that the action of gamma secretase inhibitors on neonatal supporting cells is likely to be by inhibiting Notch receptor cleavage. The loss of responsiveness to inhibition of the Notch pathway in the first postnatal week is due in part to a down-regulation of Notch receptors and ligands, and we show that this down-regulation persists in the adult animal, even under conditions of noise damage. Our data suggest that the Notch pathway is used to establish the repeating pattern of hair cells and supporting cells in the organ of Corti, but is not required to maintain this cellular mosaic once the production of hair cells and supporting cells is completed. Our results have implications for the proposed used of Notch pathway inhibitors in hearing restoration therapies.
Encoding context likelihood functions as classifiers in particle filters for target tracking

In this work we address the problem of multilevel context representation and exploitation for target tracking. Specifically, we present an approach for encoding different types of contextual information (CI) as likelihood functions via classifiers in particle filters. The proposed solution is sufficiently versatile as to be able to couch different types of CI. Promising results have been obtained from our simulations on synthetic data.
Using CBR to Estimate Development Effort for Web Hypermedia Applications

Good estimates of development effort play an important role in the successful management of larger software development projects. This paper compares the prediction accuracy of three CBR techniques to estimate the effort to develop Web hypermedia applications. Most comparative studies have used one CBR technique. We beli eve this may bias the results, as there are several CBR techniques that may also be used for effort prediction. This paper shows that a weighted Euclidian similarity measure was the most accurate of the CBR techniques tested.
Exercise and Intermittent Claudication: I. Effect of Repetition and Intensity of Exercise

Four men with arteriosclerosis obliterans (ASO) were exercised on a treadmill on 4 different days to determine their maximal walking time (MWT) and the point at which their claudication pain (CPT) began. Each subject was exercised at 60%, 75%, and 90% of his MWT to determine the effect of work intensity on the systolic blood pressure at the ankle (AP). To measure the effect of exercise repeated on the same day, each subject walked five times each day on 4 different days at each of the three workloads. After each subject completed the required number of walks, his MWT was again measured on 4 separate days (one subject was retested only once) to determine whether it had changed.In every case the greatest reduction in AP occurred after the initial maximal walk but the submaximal intensities caused different responses in the different subjects. With repetition of exercise each subject displayed a progressive increase in either the AP level taken 2 minutes postexercise or the rate of recovery of AP to the pre-exercise level. There were significant increases in MWT, in CPT, and in the resting and postexercise AP levels in some of these subjects. This was most probably due to increased collateral circulation before, during, and after exercise.
Jack: scalable accumulator-based nymble system

Anonymous blacklisting schemes enable online service providers to block future accesses from abusive users behind anonymizing networks, such as Tor, while preserving the privacy of all users, both abusive and non-abusive. Several such schemes exist in the literature, but all suffer from one of several faults: they rely on trusted parties that can collude to de-anonymize users, they scale poorly with the number of blacklisted users, or they place a very high computational load on the trusted parties. We introduce Jack, an efficient, scalable anonymous blacklisting scheme based on cryptographic accumulators. Compared to the previous efficient schemes, Jack significantly reduces the communication and computation costs required of trusted parties while also weakening the trust placed in these parties. Compared with schemes with no trusted parties, Jack enjoys constant scaling with respect to the number of blacklisted users, imposing dramatically reduced computation and communication costs for service providers. Jack is provably secure in the random oracle model, and we demonstrate its efficiency both analytically and experimentally.
Go!Poly: A gene‐oriented polymorphism database

Human genome polymorphisms play a key role in defining the molecular basis of phenotypic differences between individuals in aspects such as disease susceptibility and drug responses. The database requirements for supporting the study of human genetic variation have been well recognized. In order to meet these needs, several generalized databases have been built. However, it is still hard for users to find gene‐related variation data from these huge and sophisticated databases. In its role as a gene‐oriented directory of polymorphism data, Go! Poly (Gene Oriented Polymorphism Database; http://61.139.84.5/gopoly/) utilizes two new highly curated and non‐redundant resources, LocusLink (http://www.ncbi.nlm.nih.gov/LocusLink/) and RefSeq (http://www.ncbi.nlm.nih.gov/LocusLink/refseq.html), as the standard for identifying and positioning nucleotide variations. As a generalized polymorphism database, Go! Poly extracts human gene‐linked sequence variations of all common types (SNP, insertion‐deletion, simple tandem repeat, and complex nucleotides variations) from various public resources including scientific journals and internet resources, such as HGBASE (http://hgbase.cgr.ki.se) and dbSNP (http://www.ncbi.nlm.nih.gov/SNP/). The polymorphism data are then categorized into different gene loci, and the reference sequences given by LocusLink are used as positioning references. Through close integration with LocusLink, Go! Poly also provides facilitated connections among sequence data, gene name, and related biological information. This feature also makes Go! Poly easy to search and navigate. Future automated annotations and internal consistency checking may also benefit from this. Extensive efforts are being taken to make the polymorphism information generated by the Chinese scientific community available from this resource. Hum Mutat 18:382–387, 2001. © 2001 Wiley‐Liss, Inc.
Control of Plasma Membrane Permeability by ABC Transporters

ABSTRACT ATP-binding cassette transporters Pdr5 and Yor1 from Saccharomyces cerevisiae control the asymmetric distribution of phospholipids across the plasma membrane as well as serving as ATP-dependent drug efflux pumps. Mutant strains lacking these transporter proteins were found to exhibit very different resistance phenotypes to two inhibitors of sphingolipid biosynthesis that act either late (aureobasidin A [AbA]) or early (myriocin [Myr]) in the pathway leading to production of these important plasma membrane lipids. These pdr5Δ yor1 strains were highly AbA resistant but extremely sensitive to Myr. We provide evidence that these phenotypic changes are likely due to modulation of the plasma membrane flippase complexes, Dnf1/Lem3 and Dnf2/Lem3. Flippases act to move phospholipids from the outer to the inner leaflet of the plasma membrane. Genetic analyses indicate that lem3Δ mutant strains are highly AbA sensitive and Myr resistant. These phenotypes are fully epistatic to those seen in pdr5Δ yor1 strains. Direct analysis of AbA-induced signaling demonstrated that loss of Pdr5 and Yor1 inhibited the AbA-triggered phosphorylation of the AGC kinase Ypk1 and its substrate Orm1. Microarray experiments found that a pdr5Δ yor1 strain induced a Pdr1-dependent induction of the entire Pdr regulon. Our data support the view that Pdr5/Yor1 negatively regulate flippase function and activity of the nuclear Pdr1 transcription factor. Together, these data argue that the interaction of the ABC transporters Pdr5 and Yor1 with the Lem3-dependent flippases regulates permeability of AbA via control of plasma membrane protein function as seen for the high-affinity tryptophan permease Tat2.
A New Framework for Nonlinear Cointegration Analysis and Its Application to Finance

With the purpose of analyzing non-stationary time series, this paper innovates the nonlinear cointegration dis- criminate analysis by introducing support vector machine and innovated feature-weighting model to overcome existing limitations of two methods, that is, the statistical approach and the neural network used by the nonlinear cointegration theory. Then, the application of the innovated method for the investigation of the connection between financial markets is explored. The empirical analysis demonstrates that the support vector machine is effective in analyzing the money de- mand function and its stability and has advantages in dealing with nonlinear cointegration relations and estimating nonlin- ear functions over the two methods above.
Recording and modeling of cultural heritage objects with coded structured light projection systems

Active sensors (Blais 2004), based on coherent (laser) and non-coherent light, are nowadays used for many kinds of 3D reconstruction tasks and recently very much for the recording and 3D documentation of cultural heritage objects. They have become a very common source of documentation data, in particular for non-expert users, as they easily provide range data of surfaces in high resolution and with high accuracy. Compared to passive image-based approaches (Remondino and ElHakim, 2006), active sensors provide directly and quickly 3D information of the surveyed object in form of range data (point clouds). Active sensors are suitable for different scales and objects. While the recording devices are still relatively expensive, important progress has been made in recent years towards an efficient processing and analysis of range data.
Parametric Generalized Linear System Based on the Notion of the T-Norm

By using the triangular norm, we propose two methods for the construction of generalized linear systems, and show new insights into the relationship between typical systems. Using the Hamacher and Frank t-norm, we propose a parametric log-ratio model, which is a generalization of the log-ratio model and is more flexible in algorithmic development. We develop a generalized linear contrast enhancement algorithm based on the proposed parametric log-ratio model. We show that the performance of the proposed algorithm is effective and robust for different types of images.