gebhart/patrepeval huggingface dataset:
Interferon γ Regulates Acute and Latent Murine Cytomegalovirus Infection and Chronic Disease of the Great Vessels (1998)

To define immune mechanisms that regulate chronic and latent herpesvirus infection, we analyzed the role of interferon gamma (IFN-gamma) during murine cytomegalovirus (MCMV) infection. Lethality studies demonstrated a net protective role for IFN-gamma, independent of IFN-alpha/beta, during acute MCMV infection. Mice lacking the IFN-gamma receptor (IFN-gammaR-/-) developed and maintained striking chronic aortic inflammation. Arteritis was associated with inclusion bodies and MCMV antigen in the aortic media. To understand how lack of IFN-gamma responses could lead to chronic vascular disease, we evaluated the role of IFN-gamma in MCMV latency. MCMV-infected IFN-gammaR-/- mice shed preformed infectious MCMV in spleen, peritoneal exudate cells, and salivary gland for up to 6 mo after infection, whereas the majority of congenic control animals cleared chronic productive infection. However, the IFN-gammaR was not required for establishment of latency. Using an in vitro explant reactivation model, we showed that IFN-gamma reversibly inhibited MCMV reactivation from latency. This was at least partly explained by IFN-gamma- mediated blockade of growth of low levels of MCMV in tissue explants. These in vivo and in vitro data suggest that IFN-gamma regulation of reactivation from latency contributes to control of chronic vascular disease caused by MCMV. These studies are the first to demonstrate that a component of the immune system (IFN-gamma) is necessary to regulate MCMV-associated elastic arteritis and latency in vivo and reactivation of a herpesvirus from latency in vitro. This provides a new model for analysis of the interrelationships among herpesvirus latency, the immune system, and chronic disease of the great vessels.
Comparison of the Effects of Nitrogen Poisoning on Molybdenum Oxycarbide and Pt/β-Zeolite Catalysts in the Isomerization of n-Heptane (1996)

The effect of nitrogen-containing compounds was studied over MoO3-carbon-modified and Pt(1.5 wt %)/β-zeolite catalysts using n-heptane isomerization as the test reaction and piperidine and pyridine as the poisoning molecules. n-Heptane isomerization performed over both catalysts under pure feed showed no deactivation as a function of time on stream. At a pressure of 6 bar the MoO3-carbon-modified catalyst exhibited a high resistance to deactivation up to 10 ppm of nitrogen, while the Pt-based catalyst was strongly deactivated down to 30% of its initial activity after 20 h. At higher concentrations of nitrogen (≥40 wt ppm) deactivation occurred over both catalysts as a function of time. Results obtained after different regeneration regimes on the MoO3-carbon-modified deactivated catalyst led to the conclusion that the deactivation observed was essentially due to coke formation. Finally, increasing the total pressure allowed a better resistance to deactivation by hydrogenating the coke residues over the MoO3-carbon-modified catalyst.
The centrosome protein NEDD1 as a potential pharmacological target to induce cell cycle arrest (2009)

We propose that NEDD1 may be a promising target for controlling cell proliferation, in particular if targeted in combination with Plk1 inhibitors.
Circulating levels of matrix metalloproteinases MMP-3 and MMP-1, tissue inhibitor of metalloproteinases 1 (TIMP-1), and MMP-1/TIMP-1 complex in rheumatic disease. Correlation with clinical activity of rheumatoid arthritis versus other surrogate markers. (1999)

Elevated MMP-3 and MMP-1 levels are not specific for RA or for erosive joint diseases in general. In contrast, elevated MT complex levels were observed in patients with RA. However, the correlation of MT-1 with clinical data was weaker than that of MMP-3. Elevated MMP-3 levels reflected disease activity of RA better than cytokine levels or markers of connective tissue turnover. However, MMP-3 levels do not exceed the association of CRP with clinical activity.
Desferrithiocin Analogue Based Hexacoordinate Iron(III) Chelators (2002)

Traditional thinking has been that hexacoordinate Fe(III) ligands are more effective at preventing iron's interactions with reactive oxygen species, most particularly the Fe(II)-mediated reduction of hydrogen peroxide to the hydroxyl radical (i.e., Fenton chemistry), than are ligands of lower denticity. Thus, a hexacoordinate derivative of the well-characterized tricoordinate ligand (S)-2-(2,4-dihydroxyphenyl)-4,5-dihydro-4-thiazolecarboxylic acid [4'-(HO)-DADMDFT], (S,S)-1,11-bis[5-(4-carboxy-4,5-dihydrothiazol-2-yl)-2,4-dihydroxyphenyl]-4,8-dioxaundecane, was designed with the aid of a molecular modeling program and synthesized. Evaluations both in vitro and in vivo were carried out to determine whether there is any advantage, at the level of prevention of Fenton chemistry, radical trapping, or iron clearance, to constructing a desferrithiocin-based hexacoordinate analogue. The hexacoordinate analogue was more effective at preventing the iron-mediated oxidation of ascorbate at low ligand/metal ratios than was its tricoordinate parent and can function as an excellent radical scavenger. At equivalent iron binding doses in the bile duct cannulated rodent, oral administration of the tricoordinate ligand was 3-fold more effective than was po administration of the hexacoordinate derivative. However, sc administration of the hexacoordinate derivative resulted in an efficiency that was 3 times greater than that of the tricoordinate chelator. Unfortunately, the rodent findings were not substantiated in the primates. The hexacoordinate ligand was only about one-half as efficient as its tricoordinate parent when administered sc. Owing to these results, po dosing was not attempted. Thus, there appears to be no overall advantage to coupling two molecules of 4'-(HO)-DADMDFT to afford a hexacoordinate derivative.
Integration of Existing Software Artifacts into a View- and Change-Driven Development Approach (2015)

For the description of complex software systems, a variety of different languages can be used, e.g., architecture diagrams, behavior models, source code, etc. Maintaining these artifacts is a complex task, if the contained information is not completely disjoint. There are approaches that keep such redundancies consistent by propagating changes. This is, however, only possible if change descriptions are recorded or provided. Therefore, these change-driven approaches cannot be used to maintain existing software projects, which did not record all changes during development. This results in the need of developing a possibility for the integration of said projects. We therefore propose two different strategies for integrating existing artifacts into a change-driven approach: Our first strategy creates change histories for models, while the second strategy builds correspondences from given trace links and their attached artifacts. Furthermore, we suggest a number of criteria, which determine which strategy is best used, and when. In this paper, we applied our strategies to architectural models and object-oriented source code and used a reverse engineering tool to create the necessary trace links. We evaluated the applicability of our approach with several case studies, containing five real world architectural models and five medium-sized Java projects.
Human Parvovirus B19 (2002)

Parvovirus B19 (B19) was discovered in 1974 and is the only member of the family Parvoviridae known to be pathogenic in humans. Despite the inability to propagate the virus in cell cultures, much has been learned about the pathophysiology of this virus, including the identification of the cellular receptor (P antigen), and the control of the virus by the immune system. B19 is widespread, and manifestations of infection vary with the immunologic and hematologic status of the host. In healthy immunocompetent individuals B19 is the cause of erythema infectiosum and, particularly in adults, acute symmetric polyarthropathy. Due to the tropism of B19 to erythroid progenitor cells, infection in individuals with an underlying hemolytic disorder causes transient aplastic crisis. In the immunocompromised host persistent B19 infection is manifested as pure red cell aplasia and chronic anemia. Likewise, the immature immune response of the fetus may render it susceptible to infection, leading to fetal death in utero, hydrops fetalis, or development of congenital anemia. B19 has also been suggested as the causative agent in a variety of clinical syndromes, but given the common nature, causality is often difficult to infer. Diagnosis is primarily based on detection of specific antibodies by enzyme-linked immunosorbent assay or detection of viral DNA by dot blot hybridization or PCR. Treatment of persistent infection with immunoglobulin reduces the viral load and results in a marked resolution of anemia. Vaccine phase I trials show promising results.
Production of a new aminoglycoside antibiotic by a mutant of Bacillus circulans. (1980)

A new aminoglycoside antibiotic, S-11-A, was isolated from the fermentation broth of the 2-deoxystreptamine negative (DOS-) mutant of Bacillus circulans S-11. The structure of S-11-A was elucidated as 1-deamino-1-hydroxyxylostasin, which contains an intermediate of DOS biosynthesis (S-11-P) and has resistance to some aminoglycoside-inactivating enzymes. This is the first finding of antibiotic production by a DOS- mutant without any supplementation of DOS or a DOS analog, and could be described as a novel method of getting a new aminoglycoside antibiotic.
Scalable Nearest Neighbor Algorithms for High Dimensional Data (2014)

For many computer vision and machine learning problems, large training sets are key for good performance. However, the most computationally expensive part of many computer vision and machine learning algorithms consists of finding nearest neighbor matches to high dimensional vectors that represent the training data. We propose new algorithms for approximate nearest neighbor matching and evaluate and compare them with previous algorithms. For matching high dimensional features, we find two algorithms to be the most efficient: the randomized k-d forest and a new algorithm proposed in this paper, the priority search k-means tree. We also propose a new algorithm for matching binary features by searching multiple hierarchical clustering trees and show it outperforms methods typically used in the literature. We show that the optimal nearest neighbor algorithm and its parameters depend on the data set characteristics and describe an automated configuration procedure for finding the best algorithm to search a particular data set. In order to scale to very large data sets that would otherwise not fit in the memory of a single machine, we propose a distributed nearest neighbor matching framework that can be used with any of the algorithms described in the paper. All this research has been released as an open source library called fast library for approximate nearest neighbors (FLANN), which has been incorporated into OpenCV and is now one of the most popular libraries for nearest neighbor matching.
Design and Synthesis of Inhibitors of Adenosine and AMP Deaminases (2001)

Nucleosides and nucleotides which are able to undergo covalent hydration in the aglycone ring system are potential inhibitors of the enzymes adenosine deaminase (ADA) and AMP deaminase, respectively. Calculations of the enthalpy of covalent hydration and of enzyme binding energy have been used to design new inhibitors of ADA. The ribosyl triazolotriazine 16, which was synthesized as a result of these calculations, exists predominantly as the covalent hydrate 18 in water and is a potent inhibitor of mammalian ADA (IC(50) 50 nM).
Non-invasive detection of thermal effects due to highly focused ultrasonic fields (1993)

A noninvasive technique for the localization and evaluation of thermal effects in tissue due to focused high intensity ultrasound beams is described. A combined therapy/imaging transducer assembly is used to deliver a specific dose (ultrasound time-intensity product) to a tissue sample and to gather A-mode data as a function of time. In-vitro experiments performed on calf liver and in-vivo experiments performed on rat brains and liver have shown the following: 1. Reflection coefficients calculated based on a low-order autoregressive (AR) tissue model assumption and signal entropy follow the temperature rise at the heating point; 2. Heated region size and position can be monitored with high accuracy. Such information could be used effectively for feedback purposes during a rapid heating hyperthermia or ultrasound surgery procedure
Removal of erythrocyte membrane iron in vivo ameliorates the pathobiology of murine thalassemia. (1997)

Abnormal deposits of free iron are found on the cytoplasmic surface of red blood cell (RBC) membranes in beta-thalassemia. To test the hypothesis that this is of importance to RBC pathobiology, we administered the iron chelator deferiprone (L1) intraperitoneally to beta-thalassemic mice for 4 wk and then studied RBC survival and membrane characteristics. L1 therapy decreased membrane free iron by 50% (P = 0.04) and concomitantly improved oxidation of membrane proteins (P = 0.007), the proportion of RBC gilded with immunoglobulin (P = 0.001), RBC potassium content (P < 0.001), and mean corpuscular volume (P < 0.001). Osmotic gradient ektacytometry confirmed a trend toward improvement of RBC hydration status. As determined by clearance of RBC biotinylated in vivo, RBC survival also was significantly improved in L1-treated mice compared with controls (P = 0.007). Thus, in vivo therapy with L1 removes pathologic free iron deposits from RBC membranes in murine thalassemia, and causes improvement in membrane function and RBC survival. This result provides in vivo confirmation that abnormal membrane free iron deposits contribute to the pathobiology of thalassemic RBC.
ALCAM/CD166: cancer-related issues. (2011)

Activated leucocyte adhesion molecule (ALCAM) was originally identified as a transmembrane receptor which is involved in T-cell activation and has other still unresolved functions in hematopoiesis, development, inflammation and transendothelial migration of neutrophils. ALCAM is a member of a subfamily of immunoglobulin receptors with five immunoglobulin-like domains (VVC2C2C2) in the extracellular domain and is expressed in many types of tumors. The tumor-type-dependent impact of its expression level with respect to prognosis points to a possible context-dependent function. Most functional investigations have focused on malignant melanoma, in which high ALCAM expression at the protein level correlates with a poor prognosis. ALCAM mediates low-affinity homophilic interactions and much stronger interactions with CD6. Modulation of ALCAM function with agents such as transfected dominant negative ALCAM and ligand-binding secreted ALCAM both lead to inhibition of matrix metalloproteinase-2 activation, but their impact with respect to invasion in vitro and metastasis in vivo are different. Single-chain Fv fragments directed against ALCAM are efficiently internalized, paving the way for exploration of immunoconjugates as therapeutic agents. Validation experiments of the target with modulatory agents for possible therapeutic application in oncology are discussed.
Ophthalmic Drug Delivery through Contact Lenses (2004)

Particle-laden hydrogels are promising candidates for ophthalmic drug delivery. They are transparent and can release drugs for extended periods. The drug delivery rates can be controlled by varying the loading of nanoparticles in the gel.
Detection of Altered Global DNA Methylation in Coronary Artery Disease Patients (2008)

Epigenetic modifications, especially alteration in DNA methylation, are increasingly being recognized as a key factor in the pathogenesis of complex disorders, including atherosclerosis. However, there are limited data on the epigenetic changes in the coronary artery disease (CAD) patients. In the present study we evaluated the methylation status of genomic DNA from peripheral lymphocytes in a cohort of 287 individuals: 137 angiographically confirmed CAD patients and 150 controls. The differential susceptibility of genomic DNA to methylation-sensitive restriction enzymes was utilized to assess the methylation status of the genome. We observed that the genomic DNA methylation in CAD patients is significantly higher than in controls (p < 0.05). Since elevated homocysteine levels are known to be an independent risk factor for CAD and a key modulator of macromolecular methylation, we investigated the probable correlation between plasma homocysteine levels and global DNA methylation. We observed a significant positive correlation of global DNA methylation with plasma homocysteine levels in CAD patients (p = 0.001). Further, within a higher range of serum homocysteine levels (>/=12-50 muM), global DNA methylation was significantly higher in CAD patients than in controls. The alteration in genomic DNA methylation associated with cardiovascular disease per se appears to be further accentuated by higher homocysteine levels.
Virus Neutralizing Activity Induced by Synthetic Peptides of Glycoprotein D of Herpes Simplex Virus Type 1, selected by their Reactivity with Hyperimmune Sera from Mice (1990)

Mice were immunized with synthetic peptides covering the first 56 amino acids of herpes simplex virus type 1 (HSV-1) glycoprotein D (gD) and a fusion protein, produced in Escherichia coli, containing the first 55 amino acid residues of gD. It was found that mice immunized with peptides composed of amino acid residues 1 to 13, 18 to 30. 22 to 38 and 38 to 56 of gD were not significantly protected against a lethal challenge with HSV-1. Immunization with peptide 9-21 and the gD fusion protein resulted in significant protection. Antisera, from mice immunized with HSV-1, were investigated for reactivity with a series of 57 overlapping gD peptides covering the entire amino acid sequence, except for the membrane-spanning region. All antisera reacted with peptides 9-21, 10-24, 151-165, 216-232, 282-301 and with peptide 340-354 located in the anchoring region of gD, and 15 other peptides were recognized by at least one antiserum. Twelve peptides (10-24, 151-165, 216-232, 244-267, 260-274, 270-284, 260-284, 282-301, 300-314, 340-354, 348-362 and 355-369) reacted most frequently with the hyperimmune sera from mice and were selected for further study. These were conjugated to bovine serum albumin and used to immunize rabbits. Only antisera against peptide 10-24, which covers the same epitope as peptide 9-21, neutralized HSV-1 in vitro.
Satellite cells are mitotically quiescent in mature mouse muscle: An EM and radioautographic study (1978)

Normal adult mouse tibialis anterior muscles were perfused continuously with 3H-thymidine for nine days. Quantitation of the satellite cell population in these muscles reveals that not only is the frequency of satellite cell nuclei low, but that those present are mitotically quiescent.
Homogeneous Chromium Catalysts for Olefin Polymerization (1998)

Chromium-based heterogeneous catalysts are used extensively for the polymerization of olefins. There are few homogeneous model systems that allow investigation of the reaction mechanisms and unique characteristics of chromium catalysts. Coordinatively unsaturated paramagnetic chromium alkyls containing a Cp*CrIIIR fragment (Cp* = η5-C5Me5, pentamethylcyclopentadienyl) catalyze the polymerization of ethylene and α-olefins. Correlations between molecular structure and catalytic activity are reviewed.
Recovery of cytopathogenic and noncytopathogenic bovine viral diarrhea viruses from cDNA constructs (1996)

After cDNA cloning of the genome of bovine viral diarrhea virus (BVDV) isolate CP7, a full-length cDNA clone was constructed. RNA transcribed in vitro from this construct was shown to direct the generation of infectious BVDV upon transfection into bovine cells. To confirm the de novo generation of infectious BVDV from cloned cDNA a genetically tagged virus was constructed. In comparison with parental BVDV, the recombinant virus was slightly retarded in growth. The NS2 coding region of the CP7 genome contains a duplication of 27 nucleotides which is not present in the genome of its noncytopathogenic counterpart, NCP7. Exchange of a small fragment harboring this insertion against the corresponding part of the NCP7 sequence led to recovery of noncytopathogenic BVDV. Alteration of the construct by introduction of a fragment derived from a cytopathogenic BVDV defective interfering particle resulted in a chimeric defective interfering particle which exhibits a cytopathogenic phenotype. These findings confirm the hypothesis that the recombination-induced alterations in the genomes of cytopathogenic BVDV are responsible for the induction of cell lysis.
Building a high-level dataflow system on top of Map-Reduce (2009)

Increasingly, organizations capture, transform and analyze enormous data sets. Prominent examples include internet companies and e-science. The Map-Reduce scalable dataflow paradigm has become popular for these applications. Its simple, explicit dataflow programming model is favored by some over the traditional high-level declarative approach: SQL. On the other hand, the extreme simplicity of Map-Reduce leads to much low-level hacking to deal with the many-step, branching dataflows that arise in practice. Moreover, users must repeatedly code standard operations such as join by hand. These practices waste time, introduce bugs, harm readability, and impede optimizations. Pig is a high-level dataflow system that aims at a sweet spot between SQL and Map-Reduce. Pig offers SQL-style high-level data manipulation constructs, which can be assembled in an explicit dataflow and interleaved with custom Map- and Reduce-style functions or executables. Pig programs are compiled into sequences of Map-Reduce jobs, and executed in the Hadoop Map-Reduce environment. Both Pig and Hadoop are open-source projects administered by the Apache Software Foundation. This paper describes the challenges we faced in developing Pig, and reports performance comparisons between Pig execution and raw Map-Reduce execution.
Clinically Related Protein–Peptide Interactions Monitored in Real Time on Novel Peptide Chips by Surface Plasmon Resonance Imaging (2005)

Because of its characteristics (easy preparation of the peptide chip; high-throughput, label-free, real-time detection; high specificity; and low background), this technology is suitable for screening biological samples and for large-scale studies.
Competitive antibody binding to soluble CD16B antigen and CD16B antigen on neutrophils in whole blood by flow cytometry (2001)

The competitive antibody binding assay for shed and cell-bound CD16b antigen can be applied to similar GPI-linked antigens, for which purified antibody and fluorescent antibody against the same antigenic receptor are available.