Miracle-dz/UniFAR-FTUs huggingface dataset:
TGF‐β signaling and the fibrotic response

The cause of fibrotic diseases, pathologies characterized by excessive production, deposition, and contraction of extracellular matrix, is unknown. To understand the molecular basis of fibrotic disease, it is essential to appreciate how matrix deposition is normally controlled and how this process is dysregulated in fibrogenesis. This review discusses the current state of knowledge concerning interactions among the profibrotic proteins transforming growth factor‐β (TGF‐β), connective tissue growth factor (CTGF, CCN2), and ED‐A fibronectin (ED‐A FN) and the antifibrotic proteins tumor necrosis factor‐α (TNF‐α) and γ‐interferon (IFN‐γ). —Leask, A. , Abraham, D. J. TGF‐β signaling and the fibrotic response. FASEB J. 18, 816–827 (2004)
Instance-based question answering

During recent years, question answering (QA) has grown from simple passage retrieval and information extraction to very complex approaches that incorporate deep question and document analysis, reasoning, planning, and sophisticated uses of knowledge resources. Most existing QA systems combine rule-based, knowledge-based and statistical components, and are highly optimized for a particular style of questions in a given language. Typical question answering approaches depend on specific ontologies, resources, processing tools, document sources, and very often rely on expert knowledge and rule-based components. Furthermore, such systems are very difficult to re-train and optimize for different domains and languages, requiring considerable time and human effort. We present a fully statistical, data-driven, instance-based approach to question answering (IBQA) that learns how to answer new questions from similar training questions and their known correct answers. We represent training questions as points in a multi-dimensional space and cluster them according to different granularity, scatter, and similarity metrics. From each individual cluster we automatically learn an answering strategy for finding answers to questions. When answering a new question that is covered by several clusters, multiple answering strategies are simultaneously employed. The resulting answer confidence combines elements such as each strategy's estimated probability of success, cluster similarity to the new question, cluster size, and cluster granularity. The IBQA approach obtains good performance on factoid and definitional questions, comparable to the performance of top systems participating in official question answering evaluations. Each answering strategy is cluster-specific and consists of an expected answer model, a query content model, and an answer extraction model. The expected answer model is derived from all training questions in its cluster and takes the form of a distribution over all possible answer types. The query content model for document retrieval is constructed using content from queries that are successful on training questions in that cluster. Finally, we train cluster-specific answer extractors on training data and use them to find answers to new questions. The IBQA approach is resource non-intensive, but can easily be extended to incorporate knowledge resources or rule-based components. Since it does not rely on hand-written rules, expert knowledge, and manually tuned parameters, it is less dependent on a particular language or domain, allowing for fast re-training with minimum human effort. Under limited data, our implementation of an IBQA system achieves good performance, improves with additional training instances, and is easily trainable and adaptable to new types of data. The IBQA approach provides a principled, robust, and easy to implement base system which constitutes a robust and well performing platform for further domain-specific adaptation.
Predictors and Prognostic Value of Myocardial Injury During Transcatheter Aortic Valve Implantation

Background— Myocardial injury is a common complication during cardiac surgery and percutaneous coronary intervention and is associated with postprocedural cardiovascular morbidity and mortality. Limited data have been reported about the occurrence of myocardial damage associated with transcatheter aortic valve implantation (TAVI). Therefore, our purpose was to investigate the incidence, predictors, and prognostic value of myocardial injury during TAVI. Methods and Results— We studied 119 patients (aged 81±8 years; 47 male) who had undergone a TAVI with the Medtronic-CoreValve bioprosthesis. Serum creatine kinase-MB (CK-MB) and cardiac troponin T (cTnT) levels were measured before and after the procedure. Myocardial injury was defined as a postprocedural increase of CK-MB and/or cTnT level >5 times the upper reference limit. After TAVI, the incidence of myocardial injury was 17%, which was independently predicted by procedural duration (in minutes) (odds ratio [OR], 1.04; 95% CI, 1.01–1.06), preprocedural &bgr;-blocker use (OR, 0.12; 95% CI, 0.03–0.45), peripheral arterial disease (OR, 6.36; 95% CI, 1.56–25.87), and prosthesis depth (in millimeters) (OR, 1.31; 95% CI, 1.08–1.59). The 30-day mortality after TAVI was 13% and was independently predicted by myocardial injury (OR, 8.54; 95% CI, 2.17–33.52), preprocedural hospitalization (OR, 9.36; 95% CI, 2.55–34.38), and left ventricular mass index (in g/m2) (OR, 1.02; 95% CI, 1.00–1.03). Conclusions— After transcatheter aortic valve implantation, serum levels of both CK-MB and cTnT increase, reflecting the occurrence of periprocedural myocardial injury. A longer procedural duration, the absence of &bgr;-blocker use, peripheral arterial disease, and a deeper prosthesis insertion are associated with myocardial injury. Together with preprocedural hospitalization and left ventricular mass, myocardial injury is an independent predictor for 30-day mortality after TAVI.
How Well Do Adverse Selection Components Measure Adverse Selection?

The performance of five adverse selection models are examined by comparing their component estimates to other measures of information asymmetry and informed trading. The models produce mixed results. Adverse selection components correlate with various volatility measures, but appear unrelated to measures of uncertainty. Only three of the five models have the expected relation with informed trader proxies, suggesting that the adverse selection models measure adverse selection weakly at best. Spread also relates to many of the volatility measures, suggesting that some adverse selection components might be measuring some other cost of trading. One of the significant recent advancements in the market microstructure literature is the development of models that decompose the bid-ask spread into various components. In these models, the spread generally has three cost components: order processing, inventory holding, and adverse selection (or asymmetric information). Even though these microstructure models provide an important development in empirical finance, we know little about how well these models measure adverse selection and perform relative to each other. In the corporate finance literature, variables such as market-to-book, volatility, and institutional ownership are often used to measure the asymmetric information present in a stock. Recent papers also use adverse selection components as a direct measure of information problems. 1 However, little is known about how well adverse selection components measure information asymmetries. In this paper, we test the performance of five commonly used methods of computing adverse selection components. To determine the usefulness of the adverse selection models in measuring information problems, the relation between adverse selection components and measures of information asymmetries and various proxies for the presence of informed traders are examined. As a benchmark for the analysis, we also examine the performance of spread as a measure of information asymmetry. Using a three-stage simultaneous equation framework, adverse selection models are found to relate inconsistently to the various information variables. The major determinant of adverse selection appears to be volatility. Other measures of information asymmetries, such as analyst forecast errors and market-to-book, are not related to adverse selection. The proxies for informed traders produce mixed results. Overall, the relation for four of the five models are similar to those
The Effects of an Early Galactic Wind on the Evolution of D,3He, and Z

The predictions of the abundances of D and 3He from big bang nucleosynthesis (BBN) and recent observations of these two isotopes suggest the need to develop new chemical evolution models. In particular, we examine the role of an early episode of massive star formation that would induce a strong destruction of D and a galactic wind. We discuss the ability of these models to match the observed local properties of the solar neighborhood such as the gas mass fraction, oxygen abundance, the age-metallicity relation, and the present-day mass function. We also examine in detail the ability of the chemical evolution models discussed to reproduce the apparent lack of low-mass, low-metallicity stars in the solar neighborhood, namely the G-dwarf distribution. Indeed, we find models which satisfy the above constraints while at the same time allowing for a large primordial D/H ratio as is reportedly measured in some quasar absorption systems at high z, without the overproduction of heavy elements. The latter constraint is achieved by employing a simple dynamical model for a galactic wind.
Reinforced Earth Retaining Structures - Failure Surface Shape

As an alternative to classical retaining solutions, as gravity or flexible retaining walls, the reinforced earth retaining structures are successfully used. The interaction between the reinforcement and the soil fill and their failure mode as well, are important issues to take into account for the design of these types of structures and the corresponding calculation methods used for their design. From this point of view, an important element is the shape of the failure surface, considered in the design calculation as: plane, circular, etc., which has an important influence on the tensile forces values within reinforcements. This paper presents a new theoretical method for the calculations of the reinforced earth retaining structures and the corresponding results for failure surface shape and for tensile forces in the reinforcements. Considering the similarities between the theoretical results presented in this paper and the experimental results presented in the specialty bibliography, this method creates the possibilities to design in a more economical way, only by taking into consideration the correct interaction mechanism between the soil and the reinforcements
Robust Finite-Time Parameter Estimation Using a Hybrid Systems Framework

This technical note investigates the problem of parameter estimation for a class of nonlinear systems. We show that by placing a member of this class of systems into a hybrid dynamical system, we can identify its parameter exactly and in finite time. Furthermore, by using tools developed for hybrid systems, we show that the estimation has robust properties. In particular, the hybrid system contains a compact globally asymptotically stable set where the stability is robust to small perturbations. We also present conditions that ensure convergence of the parameter estimate.
Tissue-Specific Methylation of Human Insulin Gene and PCR Assay for Monitoring Beta Cell Death

The onset of metabolic dysregulation in type 1 diabetes (T1D) occurs after autoimmune destruction of the majority of pancreatic insulin-producing beta cells. We previously demonstrated that the DNA encoding the insulin gene is uniquely unmethylated in these cells and then developed a methylation-specific PCR (MSP) assay to identify circulating beta cell DNA in streptozotocin-treated mice prior to the rise in blood glucose. The current study extends to autoimmune non-obese diabetic (NOD) mice and humans, showing in NOD mice that beta cell death occurs six weeks before the rise in blood sugar and coincides with the onset of islet infiltration by immune cells, demonstrating the utility of MSP for monitoring T1D. We previously reported unique patterns of methylation of the human insulin gene, and now extend this to other human tissues. The methylation patterns of the human insulin promoter, intron 1, exon 2, and intron 2 were determined in several normal human tissues. Similar to our previous report, the human insulin promoter was unmethylated in beta cells, but methylated in all other tissues tested. In contrast, intron 1, exon 2 and intron 2 did not exhibit any tissue-specific DNA methylation pattern. Subsequently, a human MSP assay was developed based on the methylation pattern of the insulin promoter and human islet DNA was successfully detected in circulation of T1D patients after islet transplantation therapy. Signal levels of normal controls and pre-transplant samples were shown to be similar, but increased dramatically after islet transplantation. In plasma the signal declines with time but in whole blood remains elevated for at least two weeks, indicating that association of beta cell DNA with blood cells prolongs the signal. This assay provides an effective method to monitor beta cell destruction in early T1D and in islet transplantation therapy.
A linear time algorithm for finding tree-decompositions of small treewidth

In this paper, we give for constant $k$ a linear-time algorithm that, given a graph $G=(V,E)$, determines whether the treewidth of $G$ is at most $k$ and, if so, finds a tree-decomposition of $G$ with treewidth at most $k$. A consequence is that every minor-closed class of graphs that does not contain all planar graphs has a linear-time recognition algorithm. Another consequence is that a similar result holds when we look instead for path-decompositions with pathwidth at most some constant $k$.
Modification of a Rapid Method for the Identification of Gene-Specific Polymorphisms inCryptosporidiumparvum and Its Application to Clinical and Epidemiological Investigations

ABSTRACT The application of genotyping to clinical isolates ofCryptosporidium has increased significantly our knowledge and understanding of the distribution and epidemiology of this parasite. However, some methods can be laborious and demand specialist technical expertise. PCR-restriction fragment length polymorphism (RFLP) techniques represent a more rapid and simple method of genotyping to support epidemiological and clinical investigations than conventional DNA analytical techniques. We describe a nested PCR-RFLP technique that identifies polymorphisms in theC. parvum thrombospondin-related adhesive protein gene locus; this method offers a sensitive and specific tool for the confirmation and investigation of disease associated withC. parvum. The potential of this enhanced method is demonstrated by its application to the confirmation and epidemiological investigation of an outbreak of cryptosporidiosis associated with a school visit to an open farm.
Simulations and Measurements of Wave Propagations in Curved Road Tunnels for Signals From GSM Base Stations

This paper presents a ray-tube tracing method to simulate waves propagating in curved road tunnels from base stations for mobile communications. Ray tubes are traced by including multiple reflections in the curved tunnels and diffractions from wedges of the tunnel structures, together with the direct path. To verify this ray-tube tracing approach, field measurements of 900 MHz signals in two curved road tunnels from GSM base stations were performed for comparisons with the ray-tube tracing simulations. By tracing ray tubes reflected and diffracted from the curved structures of the tunnels, the effects of the curvature on wave propagations in large guiding structures can be evaluated. Good agreement between simulations and measurements has been obtained. A parametric study of the influence of the tunnel geometry and the signal frequency on the path loss is also presented by applying this ray-tube tracing method. Curved tunnels for different radii of curvature in the tunnel cross-section and horizontal plane and also lengths of the curved part are compared, together with rectangular tunnels. Simulations of the field distribution over the cross-section of the curved tunnel away from the transmitting antenna are demonstrated as well. The ray-tube tracing program can be applied to determine the deployment of the base-station antennas for improving signal coverage in tunnels, which may have curved structures
Identification of Mixing Effects in Stratified Chilled-Water Storage Tanks by Analysis of Time Series Temperature Data

Several one-dimensional models of mixing in stratified chilled-water thermal energy storage tanks have been proposed. In the simplest models, mixing is assumed to be uniform throughout the tank. Other models permit spatial variation of mixing intensity. Published models were developed by adjusting model parameters to achieve qualitative agreement with measured profiles. The literature does not describe quantitative criteria for evaluating the performance of mixing models. This paper describes a method that can be used to determine the relative spatial distribution of mixing effects directly from experimental data. It also illustrates a method for quantitative comparison of experimental and modeled temperature profiles. The mixing calculation procedure may be applied to instantaneous spatial temperature data if temperature sensor spacing is sufficiently small. When sensors are widely spaced, time series data taken at individual sensors provide better accuracy. A criterion for maximum sensor spacing is proposed. The application of these procedures to time series charge-cycle operating data from a full-scale chilledwater thermal storage system serving a large medical center is described. Results of this analysis indicate that mixing is localized near the inlet diffuser and that one-dimensional flow with streamwise conduction predominates in most of the tank.
Rigid Graph Compression: Motif-Based Rigidity Analysis for Disordered Fiber Networks

Using particle-scale models to accurately describe property enhancements and phase transitions in macroscopic behavior is a major engineering challenge in composite materials science. To address some of these challenges, we use the graph theoretic property of rigidity to model mechanical reinforcement in composites with stiff rod-like particles. We develop an efficient algorithmic approach called rigid graph compression (RGC) to describe the transition from floppy to rigid in disordered fiber networks ("rod-hinge systems"), which form the reinforcing phase in many composite systems. To establish RGC on a firm theoretical foundation, we adapt rigidity matroid theory to identify primitive topological network motifs that serve as rules for composing interacting rigid particles into larger rigid components. This approach is computationally efficient and stable, because RGC requires only topological information about rod interactions (encoded by a sparse unweighted network) rather than geometrical details such as rod locations or pairwise distances (as required in rigidity matroid theory). We conduct numerical experiments on simulated two-dimensional rod-hinge systems to demonstrate that RGC closely approximates the rigidity percolation threshold for such systems, through comparison with the pebble game algorithm (which is exact in two dimensions). Importantly, whereas the pebble game is derived from Laman's condition and is only valid in two dimensions, the RGC approach naturally extends to higher dimensions.
Uptake of extracellular DNA: Competence induced pili in natural transformation of Streptococcus pneumoniae

Transport of DNA across bacterial membranes involves complex DNA uptake systems. In Gram-positive bacteria, the DNA uptake machinery shares fundamental similarities with type IV pili and type II secretion systems. Although dedicated pilus structures, such as type IV pili in Gram-negative bacteria, are necessary for efficient DNA uptake, the role of similar structures in Gram-positive bacteria is just beginning to emerge. Recently two essentially very different pilus structures composed of the same major pilin protein ComGC were proposed to be involved in transformation of the Gram-positive bacterium Streptococcus pneumoniae – one is a long, thin, type IV pilus-like fiber with DNA binding capacity and the other one is a pilus structure that was thicker, much shorter and not able to bind DNA. Here we discuss how competence induced pili, either by pilus retraction or by a transient pilus-related opening in the cell wall, may mediate DNA uptake in S. pneumoniae.
Prevalence of Preoperative Corneal Astigmatism in Patients Undergoing Cataract Surgery at Mettapracharak Hospital, Thailand.

OBJECTIVE To describe and analyze the demography and distribution of preoperative corneal astigmatism in patients undergoing cataract surgery at Mettapracharak Hospital. MATERIAL AND METHOD The medical records of consecutive patients who had cataract surgery between October 1, 2010 and September 30, 2011 at Mettapracharak Hospital were retrospectively reviewed and analyzed. Patient demographic and keratometric data were collected and analyzed. RESULTS The present study evaluated the keratometric data in 2,688 eyes of 2,671 patients who had cataract surgery with the mean age of 66.23±10.79 years. The mean corneal astigmatism was 1.09 D (range 0.00-8.50 D). Corneal astigmatism was higher than 1.00 D in 36.6%, between 0.51 D and 1.00 D in 37.9% and 0.50 D or less in 25.5% of eyes. The mean steep keratometry and flat keratometry values were 44.89±1.52 D and 43.81±1.57 D respectively. The magnitude of corneal astigmatism was positively correlated with age (p<0. 001) and there was a tendency for corneal astigmatism to increase with age above 50 years. Female had significantly steeper corneas than male. Corneal astigmatism was mainly against-the-rule (the steepest meridian at 180±30 degrees). The type of corneal astigmatism was strongly correlated with age. Against-the-rule astigmatism increased with older age. While aging decreased with-the-rule astigmatism. CONCLUSION The present report showed the pattern of corneal astigmatism before cataract surgery in Thai governmental hospital, approximately one third of cataract patients had more than 1.00 D of astigmatism. This finding provide the important normative reference and help ophthalmologists to plan and manage the cost-effective correction of preexisting corneal astigmatism in cataract patients to achieve the best visual outcome.