Miracle-dz/UniFAR-FTUs huggingface dataset:
Systematically deriving domain-specific transformation languages

Model transformations are helpful to evolve, refactor, refine and maintain models. While domain-specific languages are normally intuitive for modelers, common model transformation approaches (regardless of whether they transform graphical or textual models) are based on the modeling language's abstract syntax requiring the modeler to learn the internal representation of the model to describe transformations. This paper presents a process that allows to systematically derive a textual domain-specific transformation language from the grammar of a given textual modeling language. As example, we apply this systematic derivation to UML class diagrams to obtain a domain-specific transformation language called CDTrans. CDTrans incorporates the concrete syntax of class diagrams which is already familiar to the modeler and extends it with a few transformation operators. To demonstrate the usefulness of the derived transformation language, we describe several refactoring transformations.
Trend Analysis of the Slow-Speed and Heavy-Load Equipment with Acoustic Emission

The application of AE measurement for condition monitoring of the slow-speed and heavy-load equipment is gaining ground. However, different AE features are sensitive to fault in varying degrees when they are employed in the trend analysis. Therefore, in this paper the focus is on the selection of the appropriate AE features for the trend analysis. First the AE features are ranked by Laplacian Score method according to their importance, and then a new feature index is obtained by the fusion of the features with their ranking scores, which serve as weight coefficient in this condition. The degradation data of the bearings in the belt conveyor are used to prove that the proposed method is effective.
PerC and GrlA independently regulate Ler expression in enteropathogenic Escherichia coli

Ler, encoded by the locus of enterocyte effacement (LEE) of attaching and effacing (A/E) pathogens, induces the expression of LEE genes by counteracting the silencing exerted by H‐NS. Ler expression is modulated by several global regulators, and is activated by GrlA, which is also LEE‐encoded. Typical enteropathogenic Escherichia coli (EPEC) strains contain the EAF plasmid, which carries the perABC locus encoding PerC. The precise role of PerC in EPEC virulence gene regulation has remained unclear, mainly because EPEC strains lacking the pEAF still express the LEE genes and because PerC is not present in other A/E pathogens such as Citrobacter rodentium. Here, we describe that either PerC or GrlA can independently activate ler expression and, in consequence, of LEE genes depending on the growth conditions. Both PerC and GrlA, with the aid of IHF, counteract the repression exerted by H‐NS on ler and can also further increase its activity. Our results substantiate the role of PerC and GrlA in EPEC virulence gene regulation and suggest that these convergent regulatory mechanisms may have represented an evolutionary adaptation in EPEC to co‐ordinate the expression of plasmid‐ and chromosome‐encoded virulence factors needed to successfully colonize its intestinal niche.
Endothelial Function, Oxidative Stress and Inflammatory Studies in Chronic Coronary Slow Flow Phenomenon Patients

The coronary slow flow phenomenon (CSFP) is associated with coronary microvascular dysfunction although the responsible mechanisms are unknown. This study compared endothelial function assessed by changes in augmentation index (AIx) following endothelium-independent (glyceryl trinitrate, GTN) and endothelium-dependent vasodilators (salbutamol), in 40 stable CSFP patients and 23 age-matched healthy controls. Plasma concentrations of inflammatory proteins (myeloperoxidase and high-sensitivity C-reactive protein), oxidative stress biomarkers (malondialdehyde and homocysteine), and asymmetric dimethylarginine levels were also determined. There were no differences between CSFP and controls in response to salbutamol (AIx: –2.28 ± 0.88% vs. –3.22 ± 0.70%, p = 0.4) or GTN (AIx: –11.30 ± 0.75% vs. –13.30 ± 1.00%, p = 0.12). Similarly, there were no differences in the measured biomarkers. Thus, alternate mechanisms to the assessed endothelial function, inflammatory and oxidative stress processes should be explored to explain the microvascular dysfunction in CSFP patients.
Further Insights into the Mode of Action of the Lipoglycopeptide Telavancin through Global Gene Expression Studies

ABSTRACT Telavancin is a novel semisynthetic lipoglycopeptide derivative of vancomycin with a decylaminoethyl side chain that is active against Gram-positive bacteria, including Staphylococcus aureus strains resistant to methicillin or vancomycin. A dual mechanism of action has been proposed for telavancin involving inhibition of peptidoglycan biosynthesis and membrane depolarization. Here we report the results of genome-wide transcriptional profiling of the response of S. aureus to telavancin using microarrays. Short (15-min) challenge of S. aureus with telavancin revealed strong expression of the cell wall stress stimulon, a characteristic response to inhibition of cell wall biosynthesis. In the transcriptome obtained after 60-min telavancin challenge, in addition to induction of the cell wall stress stimulon, there was induction of various genes, including lrgA and lrgB, lysine biosynthesis operon (dap) genes, vraD and vraE, and hlgC, that have been reported to be induced by known membrane-depolarizing and active agents, including carbonyl cyanide m-chlorophenylhydrazone, daptomycin, bacitracin, and other antimicrobial peptides These genes were either not induced or only weakly induced by the parent molecule vancomycin. We suggest that expression of these genes is a response of the cell to mitigate and detoxify such molecules and is diagnostic of a membrane-depolarizing or membrane-active molecule. The results indicate that telavancin causes early and significant induction of the cell wall stress stimulon due to strong inhibition of peptidoglycan biosynthesis, with evidence in support of membrane depolarization and membrane activity that is expressed after a longer duration of drug treatment.
Fractal Analysis to Study the Structural Distribution of Wenchuan Earthquake in China

A comprehensive study of fractal property applied in earthquakes is analyzed based on the aftershock of 2008 Wenchuan earthquake. Different fractal parameters are analyzed to study the magnitude, epicenter and hypocenter structural distributions in time or space. The b-value is found to be 0.86 closed to which is usually 1.0 observed worldwide. This indicates there is a relative abundance of small magnitude events than large ones in the studied range. The spatial correlation is calculated using correlation integral technique, indicating that epicenters are approaching a two-dimensional region and the aftershocks are uniformly distributed along the trend of the aftershock zone. The rate of the fall of aftershock activity with time reflects the decrease of stress is modestly slow. Temporal correlation is 0.59 for aftershocks of M >4.0, indicating a non continuous aftershock activity. Geometrical probability dimension reflecting epicenter clustering degrees of the region was also analyzed. Also the volume fractal dimension of the aftershock region has been calculated using the box-counting technique to study the hypocenter distributions. From the assessment of slip on different faults it is inferred that 67.9% displacement is accommodated on the primary fault and the remainder on secondary faults.
Generating Subsequent Reference in Shared Visual Scenes: Computation vs Re-Use

Traditional computational approaches to referring expression generation operate in a deliberate manner, choosing the attributes to be included on the basis of their ability to distinguish the intended referent from its distractors. However, work in psycholinguistics suggests that speakers align their referring expressions with those used previously in the discourse, implying less deliberate choice and more subconscious reuse. This raises the question as to which is a more accurate characterisation of what people do. Using a corpus of dialogues containing 16,358 referring expressions, we explore this question via the generation of subsequent references in shared visual scenes. We use a machine learning approach to referring expression generation and demonstrate that incorporating features that correspond to the computational tradition does not match human referring behaviour as well as using features corresponding to the process of alignment. The results support the view that the traditional model of referring expression generation that is widely assumed in work on natural language generation may not in fact be correct; our analysis may also help explain the oft-observed redundancy found in human-produced referring expressions.
Two regulatory proteins that bind to the basic transcription element (BTE), a GC box sequence in the promoter region of the rat P‐4501A1 gene.

The cDNAs for two DNA binding proteins of BTE, a GC box sequence in the promoter region of the P‐450IA1(CYP1A1) gene, have been isolated from a rat liver cDNA library by using the BTE sequence as a binding probe. While one is for the rat equivalent to human Sp1, the other encodes a primary structure of 244 amino acids, a novel DNA binding protein designated BTEB. Both proteins contain a zinc finger domain of Cys‐Cys/His‐His motif that is repeated three times with sequence similarity of 72% to each other, otherwise they share little or no similarity. The function of BTEB was analysed by transfection of plasmids expressing BTEB and/or Sp1 with appropriate reporter plasmids into a monkey cell line CV‐1 and compared with Sp1. BTEB and Sp1 activated the expression of genes with repeated GC box sequences in promoters such as the simian virus 40 early promoter and the human immunodeficiency virus‐1 long terminal repeat promoter. In contrast, BTEB repressed the activity of a promoter containing BTE, a single GC box of the CYP1A1 gene that is stimulated by Sp1. When the BTE sequence was repeated five times, however, BTEB turned out to be an activator of the promoter. RNA blot analysis showed that mRNAs for BTEB and Sp1 were expressed in all tissues tested, but their concentrations varied independently in tissues. The former mRNA was rich in the brain, kidney, lung and testis, while the latter was relatively abundant in the thymus and spleen. (ABSTRACT TRUNCATED AT 250 WORDS)
DNA repair in bacteria and mammalian cells.

Since bacterial excision repair was last reviewed not only has the understanding of previously recognized mechanisms increased, but new mechanisms have been described which have broadened the concept of excision repair to include possible roles of glycosylases, insertases, and demethylases. In addition, the importance of interrelations between the inducible and constitutive responses to lesions in DNA has become evident. However, the relationships of biological end points, such as survival and mutagenesis, to the biochemical criteria of responses to DNA damage, remain obscure. This is a particularly serious problem in the case of mammalian cells, since the relevant biological end point may not be known. Survival and mutagenesis of cells in culture are not necessarily directly related to the function of cells in the organism. However, the colony-forming ability of irradiated XP cells does appear to correlate with the severity of the patients neurological symptoms, and the excision-repair capability of cultured human cells may correlate with mutation and survival after exposure to UV and chemical carcinogens. Further analysis of responses to DNA damage may clarify their role in abnormal differentiation and malignant transformation. 404 references.
Vitamin K prevents oxidative cell death by inhibiting activation of 12‐lipoxygenase in developing oligodendrocytes

Oxidative mechanisms of injury are important in many neurological disorders. Developing oligodendrocytes (pre‐OLs) are particularly sensitive to oxidative stress‐mediated injury. We previously demonstrated a novel function of phylloquinone (vitamin K1) and menaquinone 4 (MK‐4; a major form of vitamin K2) in protecting pre‐OLs and immature neurons against glutathione depletion‐induced oxidative damage (Li et al. [ 2003 ] J. Neurosci. 23:5816–5826). Here we report that vitamin K at nanomolar concentrations prevents arachidonic acid‐induced oxidative injury to pre‐OLs through blocking the activation of 12‐lipoxygenase (12‐LOX). Arachidonic acid metabolism is a potential source for reactive oxygen species (ROS) generation during ischemia and reperfusion. Exposure of pre‐OLs to arachidonic acid resulted in oxidative cell death in a concentration‐dependent manner. Administration of vitamin K (K1 and MK‐4) completely prevented the toxicity. Consistent with our previous findings, inhibitors of 12‐LOX abolished ROS production and cell death, indicating that activation of 12‐LOX is a key event in arachidonic acid‐induced pre‐OL death. Vitamin K1 and MK‐4 significantly blocked 12‐LOX activation and prevented ROS accumulation in pre‐OLs challenged with arachidonic acid. However, vitamin K itself did not directly inhibit 12‐LOX enzymatic activity when assayed with purified 12‐LOX in vitro. These results suggest that vitamin K, or likely its metabolites, acts upstream of activation of 12‐LOX in pre‐OLs. In summary, our data indicate that vitamin K prevents oxidative cell death by blocking activation of 12‐LOX and ROS generation. © 2009 Wiley‐Liss, Inc.
Evaluation of the failure progress in the static bending of GFRP laminates reinforced with a classic plain-woven fabric and a 3D fabric, by means of the vibrations analysis

The aim of the work is to evaluate the effectiveness of analysis of a failure progress of the glass fiber reinforced polymer laminate (classic and 3D), during static bending, with the use of high frequency vibration analysis (the order of kHz). During the tests, the instantaneous velocity of the samples' vibrations was recorded. The 3D laminate showed a more favorable course of failure (mostly fiber fracture) than the classic laminate (mostly delamination), but only in the direction transverse to the translaminar interweave strands. In the direction parallel to the interweave, it was also characterized mainly by delamination. It was stated that the vibration measurements significantly broaden and supplement the characteristics of bending, by way of revealing the local degradation changes in the examined material, especially before the initiation of the main stage of failure. The work also describes the frequency bands in which the symptoms of the occurring failures of particular laminate components were observed and where the values of the basic point parameters were estimated, which points to the occurrence of structure failure. The obtained results confirm the effectiveness of the vibration analysis as a tool for the evaluation of the course of composite material failure under static loads. POLYM. COMPOS. , 2015. © 2015 Society of Plastics Engineers
PVC‐clay nanocomposites: Preparation, thermal and mechanical properties

PVC‐clay nanocomposites were prepared by melt blending of the polymer with an organically modified clay, both in the presence and in the absence of di(2‐ethylhexyl) phthalate (DOP). The clay can serve as a plasticizer for PVC in the absence of DOP. The nanocomposites were characterized by using X‐ray diffraction and transmission electron microscopy, and the materials were found to be largely intercalated. Thermal properties were evaluated by using thermogravimetric analysis, and the thermal stability was determined to be variable, depending upon the amounts of clay and DOP that were present. The fraction of polymer that remained at 600°C was significantly reduced in the presence of the clay, a result indicating that the clay had an effect on the course of the degradation of the PVC. The tensile strength of the nanocomposites increased as the fraction of clay increased, and the addition of a small amount of clay increased the elongation, but when additional clay was added, the elongation decreased.
A Practical Verification Methodology for Concurrent Programs

We describe a methodology for reasoning about realistic concurrent programs. Our methodology allows two-state invariants that span multiple objects without sacrificing threador data-modularity, as well as the derived construction of first-class objects that capture knowledge about the system state. The methodology has been implemented in an automatic sound verifier for concurrent C programs being used to verify the code of the Microsoft Hypervisor, the virtualization kernel of Hyper-V.
Stroke Thrombolysis: Slow Progress

During the past decade, few topics have prompted as much controversy as stroke thrombolysis. Although there is general agreement that thrombolysis of stroke patients is effective, the major issue is case selection: Who should give what drug at what dose? Where, how, and to which patients? Like many potent treatments, there is great potential for effectiveness but also important risk of harm. In this issue of Circulation , Georgiadis and his Swiss colleagues1 analyze some aspects of potential harm. Article p 237 Stroke thrombolysis was jump-started during the summer of 1996, when the US Food and Drug Administration approved the use of tissue plasminogen activator (tPA) for treatment of patients with stroke when the drug was given within the first 3 hours. Approval was based on publication of the results of a National Institute for Neurological Disorders and Stroke (NINDS)–sponsored trial.2 Soon after that trial was reported, committees of the American Heart Association2 and the American Academy of Neurology3 published treatment protocols recommending intravenous tPA use according to the NINDS trial protocol. These guidelines (which have never been updated) recommend that patients be treated within 3 hours of symptom onset and that a computed tomography (CT) scan done before thrombolysis should not show major infarction, mass effect, edema, or hemorrhage. Treatment is not recommended in patients who wake up with a deficit, in those with minor signs, or those who are improving. The guidelines do not require or suggest magnetic resonance imaging (MRI) or vascular tests before treatment. Stroke neurologists were enthusiastic about the Food and Drug Administration approval. Before tPA, therapeutic nihilism prevailed. Approval of tPA was a wake-up call. Stroke can and should be treated. Patients with stroke should be hurried into medical centers, and doctors and hospitals must become prepared and able to …
B Lymphocytes: Development, Tolerance, and Their Role in Autoimmunity—Focus on Systemic Lupus Erythematosus

B lymphocytes are the effectors of humoral immunity, providing defense against pathogens through different functions including antibody production. B cells constitute approximately 15% of peripheral blood leukocytes and arise from hemopoietic stem cells in the bone marrow. It is here that their antigen receptors (surface immunoglobulin) are assembled. In the context of autoimmune diseases defined by B and/or T cell autoreactive that upon activation lead to chronic tissue inflammation and often irreversible structural and functional damage, B lymphocytes play an essential role by not only producing autoantibodies but also functioning as antigen-presenting cells (APC) and as a source of cytokines. In this paper, we describe B lymphocyte functions in autoimmunity and autoimmune diseases with a special focus on their abnormalities in systemic lupus erythematosus.
Investigations of Oxidative Stress, Antioxidant Response, and Protein Binding in Chlorpyrifos Exposed Rat Neuronal PC12 Cells

ABSTRACT Chlorpyrifos (CPF) is a widely used organophosphate insecticide. In addition to its known properties of cholinesterase inhibition, the production of reactive oxygen species (ROS) has been suggested as a possible toxic mechanism. To investigate CPF-generated ROS, rat neuronal PC12 cells were exposed to CPF concentrations of 0 to 5000 μg/mL in Krebs buffered media (KRH), KRH + 4% bovine serum albumin (BSA), and KRH + 25 μM of the antioxidant Trolox for 0 to 5 h. Paraquat served as a positive control for ROS. The fluorescent probe 2,7-dichlorodihydro-fluorescein and the MTS assay were used to measure ROS and cytotoxicity, respectively. Examinations into CPF-albumin binding were also conducted. CPF was not strongly cytotoxic to PC12 cells, causing only mild cytotoxicity at 5000 μg/ml. In KRH media, CPF-generated ROS was observed at 4 and 5 h at 500 and 1000 μg/mL, and at 1 to 5 h at 5000 μg/mL CPF. In KRH + 4% BSA, ROS was seen only at 5 h in 5000 μg/mL CPF. Trolox significantly reduced CPF- and paraquat-induced ROS. Calculated CPF-albumin binding at 1, 10, and 100 μg/mL CPF in 4% BSA was 96%, 75%, and 15%. These data show CPF at ≥500 μg/mL induced ROS in PC12 cells, but the addition of the antioxidant Trolox and 4% BSA dramatically reduced ROS levels.
Search for Interstellar Water in the Translucent Molecular Cloud toward HD 154368

We report an upper limit of 9 × 1012 cm-2 on the column density of water in the translucent cloud along the line of sight toward HD 154368. This result is based on a search for the C-X band of water near 1240 Å carried out using the Goddard High-Resolution Spectrograph (GHRS) of the Hubble Space Telescope. Our observational limit on the water abundance, together with detailed chemical models of translucent clouds and previous measurements of OH along the line of sight, constrains the branching ratio in the dissociative recombination of H3O+ to form water. We find at the 3 σ level that no more than 30% of dissociative recombinations of H3O+ can lead to H2O. The observed spectrum also yielded high-resolution observations of the Mg II doublet at 1239.9 Å and 1240.4 Å, allowing the velocity structure of the dominant ionization state of magnesium to be studied along the line of sight. The Mg II spectrum is consistent with GHRS observations at lower spectral resolution that were obtained previously but allow an additional velocity component to be identified.
Pediatric stimulant and selective serotonin reuptake inhibitor prescription trends: 1992 to 1998.

BACKGROUND Presciption trends have key implications for costs, outcomes, and research, yet few data exist on pediatric selective serotonin reuptake inhibitor (SSRI) trends and associations with stimulant trends. OBJECTIVE To describe prescription trends for stimulants, SSRIs, and combination prescriptions by age, sex, and race. METHODS Retrospective population-based analysis of North Carolina Medicaid prescription claims files. PARTICIPANTS North Carolina Medicaid recipients, 1992 through 1998, aged 1 to 19 years. The population ranged from 342 333 children in 1992 to 581 088 in 1998. MAIN OUTCOME MEASURES Annual number of prescriptions, patients filling a prescription claim, and prescription prevalence for stimulants and SSRIs. RESULTS The number of children and adolescents who received stimulants increased from 6407 (24 584 claims) in 1992 to 27 951 (135 057 claims) in 1998. The number of SSRI recipients increased from 510 children (1326 claims) in 1992 to 6984 children (25 392 claims) in 1998. Prescription prevalence in school-aged children 6 to 14 years increased from 4.4% to 9.5% for stimulants during the study period, and from 0.2% to 1.5% for SSRIs. In 1998, stimulant prescription prevalence was highest for white school-aged males (18.3%) vs black females (3.4%) and SSRI prescription prevalence was highest for white school-aged males (2.8%) vs black females (0.6%). Combination pharmacotherapy also increased during 1992 through 1998. CONCLUSIONS Prevalence of stimulant and SSRI medications has increased during the 1990s, with prescription prevalence in North Carolina Medicaid youth higher than previously reported. Age, sex, and racial differences are apparent and call for further attention. Combination pharmacotherapy also has growing importance.