gebhart/patrepeval huggingface dataset:
Deformation due to the 17 August 1999 Izmit, Turkey, earthquake measured from SPOT images (2002)

The geometry of the ruptured areas and the coseismic slip distribution data are key to highlighting the behavior of seismic faults. This information is generally retrieved from field investigations and geodetic measurements or synthetic aperture radar (SAR) interferometry. Here we show that SPOT images can also be used to accurately map the fault zone and to determine the slip distribution by subpixel correlation of images acquired before and after an earthquake. The measured slip includes the contribution of possible distributed shear that might not be clearly expressed in surface ruptures and smoothes out possible along‐strike variability due to near‐surface fault complexities. We apply the technique to the M s = 7.4, 1999, Izmit earthquake. Our results reveal a &lt;100‐m‐wide and very linear fault zone that can be traced for 70 km from Gölcük to Akyazi, along which supershear rupture has been inferred. The obtained slip distribution compares well with the field measurements and is consistent with ground deformation measured at some distance from the fault zone using SAR images. Very little deformation was accommodated off the main fault plane. Maximum slip is observed near Sapanca lake at a small fault jog that has probably influenced rupture propagation.
Role of I Bα Ubiquitination in Signal-induced Activation of NF- B in Vivo (1996)

In unstimulated cells, the transcription factor NF-kappaB is held in the cytoplasm in an inactive state by the inhibitor protein IkappaBalpha. Stimulation of cells results in rapid phosphorylation and degradation of IkappaBalpha, thus releasing NF-kappaB, which translocates to the nucleus and activates transcription of responsive genes. Here we demonstrate that in cells where proteasomal degradation is inhibited, signal induction by tumor necrosis factor alpha results in the rapid accumulation of higher molecular weight forms of IkappaBalpha that dissociate from NF-kappaB and are consistent with ubiquitin conjugation. Removal of the high molecular weight forms of IkappaBalpha by a recombinant ubiquitin carboxyl-terminal hydrolase and reactivity of the immunopurified material with a monoclonal antibody specific for ubiquitin indicated that IkappaBalpha was conjugated to multiple copies of ubiquitin. Western blot analysis of immunopurified IkappaBalpha from cells expressing epitope-tagged versions of IkappaBalpha and ubiquitin revealed the presence of multiple copies of covalently bound tagged ubiquitin. An S32A/S36A mutant of IkappaBalpha that is neither phosphorylated nor degraded in response to signal induction fails to undergo inducible ubiquitination in vivo. Thus signal-induced activation of NF-kappaB involves phosphorylation-dependent ubiquitination of IkappaBalpha, which targets the protein for rapid degradation by the proteasome and releases NF-kappaB for translocation to the nucleus.
Interference with brome mosaic virus replication by targeting the minus strand promoter (1993)

Sense and antisense strategies for interfering with the replication of brome mosaic virus (BMV) were examined. The effects of 200 nucleotide-long sense and antisense transcripts, corresponding to the viral 3' end (-) strand promoter, on the accumulation of progeny viral RNAs were studied by co-inoculation with wildtype BMV RNAs. Progeny accumulation in barley protoplasts transfected with either sense or antisense transcripts of the (-) strand promoter and BMV RNAs-1 and -2 was decreased by more than 90%, and by 60 to 80% when RNA-3 was also present. This trans interference was concentration-dependent, and reduced both (+) and (-) strand progeny accumulation to a similar extent. The appearance of complementary (-) strands indicated that sense interfering transcripts could serve as templates for (-) strand synthesis, and the use of deletion mutants revealed that the observed interference was in part mediated by this template activity. The reproducibility of the protoplast assay used here allows rapid evaluation of interference strategies and comparisons to be made of alternative approaches to engineered resistance. The results presented here suggest that targeting viral (-) strand promoters with sense and antisense transcripts may be an effective method for engineering plant resistance to viral infection.
Cytokine expression increases in nonmyocytes from rats with postinfarction heart failure (1998)

Growing evidence suggests that cardiac nonmyocyte cells may play an important regulatory role in the response to myocardial overload and injury via altered expression of paracrine products, such as cytokines and growth factors, but information concerning the cell-specific changes in the expression of these substances in heart-failure models is limited. Therefore, cardiac nonmyocytes were isolated from rats 1 day and 1 and 6 wk after left coronary artery ligation with resulting hemodynamic evidence of heart failure and in sham-operated control animals. mRNAs for tumor necrosis factor-alpha (TNF-alpha), interleukin (IL)-1beta, IL-6, transforming growth factors (TGF)-beta1 and TGF-beta3, and type I and type III collagen were measured by Northern analyses. The temporal and quantitative relationships between the expression of these cytokines and collagen and myocyte hypertrophy were determined. mRNA expression of IL-1beta was increased by 1.3-fold at 1 day and 1 wk, and expression of TNF-alpha, IL-1beta, IL-6, TGF-beta1, and TGF-beta3 were increased by 1.4- to 2.1-fold at the 1-wk time point before returning toward baseline at 6 wk. There were significant correlations between the expression of these cytokines and the expression of types I and III collagen, which also peaked at 1 wk. Myocyte hypertrophy was seen first at 6 wk. These observations are consistent with a hypothesis that nonmyocyte cells play a regulatory role in the extracellular matrix changes during postinfarction remodeling and highlight the importance of examining cell-specific changes in gene expression and elucidating the role of cell-to-cell interactions within the myocardium.
Male infertility: nutritional and environmental considerations. (2000)

Studies confirm that male sperm counts are declining, and environmental factors, such as pesticides, exogenous estrogens, and heavy metals may negatively impact spermatogenesis. A number of nutritional therapies have been shown to improve sperm counts and sperm motility, including carnitine, arginine, zinc, selenium, and vitamin B-12. Numerous antioxidants have also proven beneficial in treating male infertility, such as vitamin C, vitamin E, glutathione, and coenzyme Q10. Acupuncture, as well as specific botanical medicines, have been documented in several studies as having a positive effect on sperm parameters. A multi-faceted therapeutic approach to improving male fertility involves identifying harmful environmental and occupational risk factors, while correcting underlying nutritional imbalances to encourage optimal sperm production and function.
Role of glutathione in the metabolism-dependent toxicity and chemotherapy of cyclophosphamide. (1981)

The role of glutathione in the biological effects of cyclophosphamide (CP) was evaluated by investigating the following: effect of CP on hepatic glutathione levels; relationship between hepatic glutathione depletion (repletion) and the binding of [chloroethyl-3H]CP and [4-14C]CP to hepatic macromolecules; effects of interaction between CP (or acrolein) and diethyl maleate (a classical glutathione depletor), and/or between CP and cysteine on the binding of labeled CP to hepatic macromolecules, on the induction of hematuria, on the content of hepatic cytochrome P-450, on weight gain in rats, on survival in mice, and on the chemotherapeutic efficacy of CP against Walker 256 carcinoma in rats. CP and acrolein produced dose-dependent depletion of hepatic glutathione in mice, whereas phosphoramide mustard was at least one order of magnitude less effective. Acrolein caused death in mice; CP became covalently bound to hepatic macromolecules, prevented weight gain in rats, and produced hematuria and depression of hepatic cytochrome P-450 in vivo. These effects of CP (or acrolein) were enhanced by diethyl maleate but partially blocked by cysteine. On the other hand, reduction in the volume of Walker 256 carcinoma in rats by CP was not antagonized by cysteine. All these investigations point to the following conclusions: (a) acrolein produced during the metabolism of CP binds to proteins and, by doing so may denature these proteins; and (b) acrolein in vivo preferentially reacts with glutathione, and sulfhydryl-containing compounds may protect against acrolein toxicity and at the same time not interfere with the chemotherapeutic activity of CP.
Direct Proinflammatory Effect of C-Reactive Protein on Human Endothelial Cells (2000)

CRP induces adhesion molecule expression in human endothelial cells in the presence of serum. These findings support the hypothesis that CRP may play a direct role in promoting the inflammatory component of atherosclerosis and present a potential target for the treatment of atherosclerosis.
SMUG: Scientific Music Generator (2015)

Music is based on the real world. Composers use their day-to-day lives as inspiration to create rhythm and lyrics. Procedural music generators are capable of creating good quality pieces, and while some already use the world as inspiration, there is still much to be explored in this. We describe a system to generate lyrics and melodies from real-world data, in particular from academic papers. Through this we want to create a playful experience and establish a novel way of generating content (textual and musical) that could be applied to other domains, in particular to games. For melody generation, we present an approach to Markov chains evolution and briefly discuss the advantages and disadvantages of this approach.
Transfer of the CFTR Gene to the Lung of Nonhuman Primates with E1-Deleted, E2a-Defective Recombinant Adenoviruses: A Preclinical Toxicology Study (1995)

This paper describes a preclinical toxicology study designed to investigate the biological efficacy and safety profile of second-generation adenovirus for CFTR gene transfer into the baboon lung. This second-generation virus is deleted of E1 and contains a temperature-sensitive mutation in the E2a gene, which encodes a defective DNA-binding protein. Two distinct projects were undertaken. Group A animals received a first-generation adenovirus (i.e., deleted of E1) in an upper lobe at the time a second-generation virus was instilled into the contralateral upper lobe. The goal of study A was to compare the biology of each construct directly and to determine if an immune response to the first-generation virus affected the performance of the second-generation virus. Group B animals received a lacZ second-generation virus in an upper lobe at the same time the CFTR second-generation virus was instilled in the other upper lobe. Necropsies were performed 4 or 21 days after gene transfer and tissues were evaluated for recombinant gene expression and histopathology. Using a second-generation adenovirus, recombinant gene stability was prolonged and associated with a diminished level of perivascular inflammation as compared to first-generation vectors. Markedly diminished levels of hexon protein were present in tissues infected with second-generation as compared to first-generation virus. No evidence of viral shedding was evident. Furthermore, coadministration of first- and second-generation adenovirus did not affect the stability of transgene expression from the second-generation virus. These data suggest that second-generation adenoviral vectors provide an improved gene delivery vehicle, and thus may be useful in gene therapy for cystic fibrosis.
Nucleofugality effects in the pyridine promoted formation of esters from 2-substituted ethanesulfonyl chlorides (1988)

The products of reaction of a series of 10 2-substituted ethanesulfonyl chlorides, X—CH 2 CH 2 SO 2 Cl (1), with neopentyl alcohol and pyridine-d 5 in nitromethane-d 3 showed three reaction pathways depending on the nucleofugality of the substituent, X. These routes lead, respectively, to (i) the corresponding neopentyl ester (4), via the sulfene (3) (low substituent nucleofugality); (ii) a mixture of ester 4 and neopentyl ethenesulfonate (5), by the same route except for a partial loss of the 2-substituent during trapping of the sulfene (3) (intermediate nucleofugality); and (iii) a mixture of the ethenesulfonate (5) and the pyridino-betylate (4g) esters, arising from initial elimination of HX to form ethenesulfonyl chloride (2) followed by its further reaction (high substituent nucleofugality). A set of nucleofugality values closely related to, and partly complementing, those derived by Stirling and co-workers can be estimated from the product ratios in those reactions proceeding (at least in part) by route (ii) above. Old reports of anomalous products from 1,2-ethanedisulfonyl chloride (1i) and 2-chloroethanesulfonyl chloride (1j) are simply accounted for on the basis of the initial conversion to ethenesulfonyl chloride (2).
Optimization of Small Molecule Drugs Binding to Highly Polar Target Sites: Lessons from the Discovery and Development of Neuraminidase Inhibitors (2006)

Binding affinity optimization of small molecules interacting with polar binding sites on target proteins is a formidable, but not uncommon challenge in drug discovery. The challenge relates to the difficulty of integrating favourable and unfavourable polar, non-polar and conformation contributions into overall favourable binding energies. This review describes the surprising breakthrough findings leading to the development of Tamiflu, a clinically efficacious orally bioavailable drug targeting the active site of influenza neuraminidase (NA). The NA active site is highly polar and formed mostly by arginine, aspartate and glutamate residues. This active site structure evolved for efficient interaction with charged sialic acid moieties on glycoproteins and stabilization of an oxocarbonium ion in the transition state of the neuraminidase reaction. The initial strategy of optimizing polar interactions in transition state analogs led to NA inhibitors (NAIs) with sub-nanomolar binding affinities, but such compounds were highly polar and lacked oral bioavailability. The realization of the possibility to achieve high affinity binding in a highly polar active site through optimization of non-polar and van-der-Waals interactions initially appeared counterintuitive and required a few serendipitous findings, but was key to reduce the polarity of drug candidates, avoid large desolvation penalties and achieve oral bioavailability.
Hydroxyurea for Patients with Essential Thrombocythemia and a High Risk of Thrombosis (1995)

Hydroxyurea is effective in preventing thrombosis in high-risk patients with essential thrombocythemia.
Studies on vitamin B6 metabolism in microorganisms. XVII. Bacterial distribution of glycolaldehyde dehydrogenase in relation to vitamin B6 biosynthesis. (1979)

A number of aldehyde dehydrogenase from mamma
Stable trimerization of recombinant rabies virus glycoprotein ectodomain is required for interaction with the p75NTR receptor (2005)

Native rabies virus glycoprotein (RVGvir) is a trimeric, membrane-anchored protein that has been shown to interact with the p75NTR neurotrophin receptor. In order to determine if the RVG trimeric oligomerization state is required for its binding with p75NTR, different soluble recombinant molecules containing the entire RVG ectodomain (RVGect) were expressed alone or fused at its C terminus to the trimerization domain of the bacteriophage T4 fibritin, termed 'foldon'. The oligomerization status of recombinant RVG was investigated using sedimentation in sucrose gradient and p75NTR binding assays. It was found that, in the absence of the fibritin foldon, recombinant RVGect forms unstable trimers that dissociate into monomers in a concentration-dependent manner. C-terminal fusion with the foldon induces stable RVG trimerization, which is concentration-independent. Furthermore, the fibritin foldon maintains the native antigenic structure of the carboxy part of RVGect. Cell binding experiments showed that RVG trimerization is required for efficient interaction with p75NTR. However, the exact mode of trimerization appears unimportant, as trimeric recombinant RVGect (fused to the fibritin foldon) and RVGvir both recognize p75NTR with similar nanomolar affinities, as shown by surface plasmon resonance experiments. Altogether, these results show that the C-terminal fusion of the RVG ectodomain with the fibritin foldon is a powerful way to obtain a recombinant trimeric native-like structure of the p75NTR binding domain of RVG.
Flexible camera calibration by viewing a plane from unknown orientations (1999)

Proposes a flexible new technique to easily calibrate a camera. It only requires the camera to observe a planar pattern shown at a few (at least two) different orientations. Either the camera or the planar pattern can be freely moved. The motion need not be known. Radial lens distortion is modeled. The proposed procedure consists of a closed-form solution followed by a nonlinear refinement based on the maximum likelihood criterion. Both computer simulation and real data have been used to test the proposed technique, and very good results have been obtained. Compared with classical techniques which use expensive equipment, such as two or three orthogonal planes, the proposed technique is easy to use and flexible. It advances 3D computer vision one step from laboratory environments to real-world use. The corresponding software is available from the author's Web page (<http://research.microsoft.com//spl sim/zhang>).
Energy and the U.S. Economy: A Biophysical Perspective (1984)

A series of hypotheses is presented about the relation of national energy use to national economic activity (both time series and cross-sectional) which offer a different perspective from standard economics for the assessment of historical and current economic events. The analysis incorporates nearly 100 years of time series data and 3 years of cross-sectional data on 87 sectors of the United States economy. Gross national product, labor productivity, and price levels are all correlated closely with various aspects of energy use, and these correlations are improved when corrections are made for energy quality. A large portion of the apparent increase in U.S. energy efficiency has been due to our ability to expand the relative use of high-quality fuels such as petroleum and electricity, and also to relative shifts in fuel use between sectors of the economy. The concept of energy return on investment is introduced as a major driving force in our economy, and data are provided which show a marked decline in energy return on investment for all our principal fuels in recent decades. Future economic growth will depend largely on the net energy yield of alternative fuel sources, and some standard economic models may need to be modified to account for the biophysical constraints on human economic activity.
Enzyme-catalyzed Free Radical Reactions with Nicotinamide Adenine Nucleotides (1974)

Abstract The superoxide radical produced by xanthine oxidase can be coupled to oxidation of NADH in the presence of lactate dehydrogenase. The oxidized product has been identified as the enzymatically active NAD+. If the superoxide radical is determined quantitatively by its interaction with ferricytochrome c under similar conditions, it can be estimated that for each superoxide radical produced in the xanthine oxidase system an average of 6.2 molecules of NADH can be oxidized, which indicates a chain reaction in the oxidation process. The lactate dehydrogenase-catalyzed oxidation activity can be inhibited by either superoxide dismutase or oxamate.
AN6520 Ag: An antigen purified from liver with non‐A, non‐B hepatitis (1985)

An extract prepared from the liver of patient with chronic non-A, non-B (NANB) hepatitis was found to produce a precipitin line in immunodiffusion with a serum from a multiply transfused patient and those from patients convalescent from NANB hepatitis. The antigen was purified by gel filtration and density gradient centrifugation. The antigen had a buoyant density of 1.16-1.20 g/cm3 in cesium chloride, a sedimentation coefficient (S20,w) of 51.5, and a molecular weight of larger than 1.5 X 10(6) daltons. Electron microscopic examination revealed particles 29-34 nm in diameter (average 31.5 nm), which could be agglutinated by the specific antiserum. We developed a reverse passive hemagglutination (R-PHA) and a passive hemagglutination (PHA) technique for detection of the new antigen and antibody, respectively, and applied these to human sera. Antibody to the antigen was detected in 19/28 (67.9%) convalescent sera of NANB hepatitis. This prevalence was significantly higher than those found in convalescent sera of type A hepatitis patients (2/17 = 11.8%), type B hepatitis patients (2/15 = 13.3%), and normal blood donors (9/129 = 7.0%) (p less than 0.01); and the prevalence in hepatitis A and B patients did not differ significantly from that of normal donors. Furthermore, most (66.7%) of the cases of NANB hepatitis endemic in Shimizu City, Japan, showed clear seroconversion with respect to this antibody. These results suggest that the new antigen/antibody system is associated with NANB hepatitis.
Substrate-Adsorbate Coupling in CO-Adsorbed Copper (1996)

The vibrational properties of carbon monoxide adsorbed to the copper (100) surface are explored within density-functional theory. Atoms of the substrate and adsorbate are treated on an equal footing in order to examine the effect of substrate--adsorbate coupling. This coupling is found to have a significant effect on the vibrational modes, particularly the in-plane frustrated translation, which mixes strongly with substrate phonons and broadens into a resonance. The predicted lifetime due to this harmonic decay mechanism is in excellent quantitative agreement with experiment.
Chemical analysis of acetylated bovine growth hormone, a growth-hormone inhibitor (1967)

Purified bovine growth hormone was acetylated with acetic anhydride under various conditions. Acetylated bovine growth hormone prepared in anhydrous acetic anhydride at 43 degrees for 5min. inhibited the growth-promoting response of unmodified bovine growth hormone in hypophysectomized rats. This acetylated bovine growth hormone contained 18 total acetyl groups/mol., which included 12 N(in)-acetyl and 6-8 hydroxylamine-reactive acetyl groups (acetylated aliphatic hydroxy amino acids and 2-3 O-acetyltyrosine residues). Deacetylation of acetylated bovine growth hormone with hydroxylamine at pH9.5 destroyed its ability to inhibit the growth-promoting activity of bovine growth hormone.
Genetic Control of Susceptibility to Mycobacterial Infections (1989)

Susceptibility of mice to the establishment of infection after exposure to mycobacteria is controlled by a single, dominant, autosomal gene: the Bcg gene. It is located on the centromeric portion of chromosome 1 within a linkage group that shows structural homology with a conserved region of human chromosome 2. The Bcg gene regulates directly the process of T cell-independent macrophage activation for antimycobacterial function and, indirectly, the magnitude and the quality of specific immune response to mycobacterial antigens.