gebhart/patrepeval huggingface dataset:
Human Immune Proteome in Experimental Colonization with <i>Staphylococcus aureus</i> (2009)

More than 20% of adults are persistently colonized with Staphylococcus aureus. When hospitalized, these carriers have increased risks of infection with their own strains. However, a recent study demonstrated a lower incidence of bacteremia-related death among carriers than among noncarriers, raising the question whether the adaptive immune system plays a protective role. In fact, S. aureus carriers mount a highly specific neutralizing antibody response against superantigens of their colonizing strains. We now used 2-dimensional immunoblotting to investigate the profiles of antibodies from healthy individuals against S. aureus extracellular proteins. Moreover, we tested whether symptom-free experimental colonization of these individuals with an S. aureus strain of low virulence, 8325-4, is sufficient to induce an antibody response. Sera obtained before and 4 weeks after colonization were screened for immunoglobulin G (IgG) antibody binding to extracellular staphylococcal proteins. At baseline, most volunteers harbored IgG directed against conserved virulence factors, including alpha-hemolysin (Hla), beta-hemolysin (Hlb), phospholipase C (Plc), staphylococcal serine protease (SspA), and cysteine protease (SspB). However, the variability of spot patterns and intensities was striking and could be important in case of infection. Experimental nasal colonization with S. aureus 8325-4 did not elicit new antibodies or boost the humoral response. Thus, the high antibody prevalence in humans is likely not induced by short-term nasal colonization, and presumably minor infections are required to trigger anti-S. aureus antibody responses.
ACCELERATED PAPER: Targeted disruption of the DNA repair methyltransferase gene renders mice hypersensitive to alkylating agent (1996)

Alkylation of DNA at the O(6)-position of guanine is one of the most critical events leading to induction of mutation as well as to cancer. The enzyme O(6)-methylguanine-DNA methyltransferase repairs this and related lesions in DNA. By means of gene targeting, we established mouse lines deficient in the methyltransferase gene and tissues from these mice contained no methyltransferase activity. Administration of methylnitrosourea to these gene-targeted mice led to early death, and normal mice treated in the same manner showed no untoward effects. In mice given methylnitrosourea treatment, the bone marrow became hypocellular and there was a drastic decrease in the number of leukocytes and platelets, thereby indicating an impaired reproductive capacity of hematopoietic stem cells. Methyltransferase apparently protected these mice from the pancytopenia caused by the alkylating agent.
Single stain normalization for IHC whole slide images (2018)

Performance of image analysis algorithms in digital pathology whole slide images (WSI) is usually hampered by the stain variations cross images. To overcome such difficulties, many stain normalization methods have been proposed where normalization is applied to all the stains in the image. However, for immunohistochemistry (IHC) images, there exist situations where not all the stains in the images are desired or feasible to be normalized, especially when the stain variations relate to certain biological indications. In contrast, the counter stain, usually hematoxylin (HTX), is always desired to be consistent cross images for robust nuclei detection. In this work, we present a framework to normalize the HTX stain in an IHC WSI through alignment to a template IHC WSI. For this purpose, we use the Hue-Saturation- Density (HSD) model and align the chromatic components distribution of the image to the template. Then we shift and scale density component to match the template. In order to retain the non-HTX stain, we differentiate the pixels which have pure HTX stain from those which are mixture of HTX and non-HTX stains, and different normalization strategy is applied accordingly. In the results, for a wide range of HTX stain variations, we show qualitatively the performance of the method. We also show algorithm performance dependence on the stain concentration can be much reduced by the proposed method.
Alphavirus cDNA‐based expression vectors: Effects of RNA transcription and nuclear export (2003)

The construction of layered DNA-RNA replicons has facilitated and expanded the use of alphavirus vectors to vaccine development, construction of packaging cell lines and long-term heterologous gene expression. In these vector systems, the alphavirus replicon is under the control of a strong RNA polymerase II promoter and replicon RNA is transcribed from DNA before transport to the cytoplasm. Efficient RNA amplification catalyzed by the viral replicase results in high levels of mRNA and the recombinant protein. Recently, we developed a temperature-regulated Sindbis replicon-based DNA expression system characterized by a linear increase of expression upon decrease of the temperature from 37 degrees C to 29 degrees C. Modifications known to affect transcription and nuclear export of RNA led to a 5-fold increase in expression in BHK cells and up to over 80-fold increase in CHO cells and BF fibroblasts in transient transfection experiments. Furthermore, reducing cell proliferation resulted in a further 2- to 3-fold higher expression. While increased expression per cell was responsible for some of the enhanced production, it was primarily the number of expressing cells that made the difference in most cell lines. Further experiments indicated that a threshold amount of replicon RNA had to reach the cytoplasm in order for replication to occur. Thus, alterations that improve transcription, nuclear export and stability of the RNA had a significant impact on protein production in the pCytTS expression system and probably in other layered DNA-based viral vectors. Furthermore the results indicate that RNA replication is differentially regulated in DNA layered RNA replicons versus viral infection.
A reduced CSI feedback approach for precoded MIMO-OFDM systems (2007)

To obtain the closed-loop capacity of a multiple-input and multiple-output (MlMO) orthogonal frequency division multiplexing (OFDM) system, channel state information (CSI) is required at the transmitter. To reduce the data rate of CSI feedback, preceding matrix approach has been proposed for MIMO systems in flat fading channels. In this paper, we develop a novel approach for MIMO-OFDM systems in frequency-selective fading channels. The proposed approach exploits the correlation of frequency responses at different subchannels in MIMO-OFDM systems to reduce CSI feedback. It is not only flexible to multiple data stream transmission but also has better performance than the existing approaches
Sintering of Ceramic Particulate Composites: Effect of Matrix Density (1991)

Composites consisting of a fine‐grained, polycrystalline zinc oxide matrix and <10 vol% coarse, rigid silicon carbide inclusions were prepared by the same mixing procedure and then compacted to produce samples with matrix densities of 0.45 and 0.68 of the theoretical. The samples were sintered under identical temperature profiles in separate experiments that employed either a constant rate of heating of 4°C/min or near isothermal heating at 735°C. The ratio of the densification rate of the composite matrix to the densification rate of the unreinforced zinc oxide was found to be independent of the initial matrix density. This ratio increased significantly with temperature in the constant‐heating‐rate experiments but was relatively constant in the isothermal experiments. The results indicate that microstructural coarsening may be an important mechanism for explaining the reduced sinterability of polycrystalline matrix composites.
Zirconium and Hafnium Separation by Liquid-liquid Extraction with Hexone (Methyl isobutyl ketone) (1969)

Reactor grade zirconium is required to keep hafnium content below 0.01%(as metal ratio).However, zircon (ZrSiO4), a major source of zirconium, contains about 2.5% hafnium (as metal ratio), and it is extremely difficult to remove 99.7% of hafnium for the material, because of similar chemical properties of zirconium and hafnium.From the authors experience on the industrial production of about 600 tons hafnium-free zirconium oxide (ZrO2) by the hexone extraction process, the following results were obtained.(1) In the step of feed preparation, the zirconium concentration of about lmol/l and ammoniumthiocyanate (NH4SCN) of 1.2-1.3mol/l revealed a good result for the extraction steps which follow.(2) In the step of hafnium extraction, the thiocyanic acid concentration in hexone is preferred at about 2mol/l. Flow ratio (solvent/feed) should be about 2, and 15 to 17 stages of extraction are required.(3) In the step of zirconium stripping, a desirable stripping solution is 4N hydrochloric acid. Flow ratio should be about 1/5 and 15 stages of stripping are required.(4) In the step of hafnium scrubbing, a scrubbing solution of 6N sulfuric acid, is preferred. Flow ratio should be about 1/4 and 6 stages of scrubbing are required.Control of impurities in the hexone after the scrubbing step is particularly important in order to limit the hafnium content to 0.01/0 or less. The content of impurities must, therefore, be reduced below 3mg/100ml.(at metal oxide).(5) The theoretical explanation for their separation was made by the equilibrium studies on the solvent extraction system and it was in good agreement with the results of practical operation.(6) For the separation of zirconium and hafnium, the prevention of decomposing thiocyanic acid is a factor of particular importance. Concerning this, the effects of extraction atmasphere, temperature, iron content were investigated which led to the prevention of the decomposition.(7) Special equipment is required for satisfying the extracting conditions, and it is to be adapted for the continuous counter-current extraction in thenon-oxidizing atomospher. The equipment should resist against the highly corrosive mixture of acid such as hydrochloric acid and thiocyanic acid. A new extraction equipm-ent of jet system which meets all these requirements was developed.
Calmodulin Binds to K-Ras, but Not to H- or N-Ras, and Modulates Its Downstream Signaling (2001)

Activation of Ras induces a variety of cellular responses depending on the specific effector activated and the intensity and amplitude of this activation. We have previously shown that calmodulin is an essential molecule in the down-regulation of the Ras/Raf/MEK/extracellularly regulated kinase (ERK) pathway in cultured fibroblasts and that this is due at least in part to an inhibitory effect of calmodulin on Ras activation. Here we show that inhibition of calmodulin synergizes with diverse stimuli (epidermal growth factor, platelet-derived growth factor, bombesin, or fetal bovine serum) to induce ERK activation. Moreover, even in the absence of any added stimuli, activation of Ras by calmodulin inhibition was observed. To identify the calmodulin-binding protein involved in this process, calmodulin affinity chromatography was performed. We show that Ras and Raf from cellular lysates were able to bind to calmodulin. Furthermore, Ras binding to calmodulin was favored in lysates with large amounts of GTP-bound Ras, and it was Raf independent. Interestingly, only one of the Ras isoforms, K-RasB, was able to bind to calmodulin. Furthermore, calmodulin inhibition preferentially activated K-Ras. Interaction between calmodulin and K-RasB is direct and is inhibited by the calmodulin kinase II calmodulin-binding domain. Thus, GTP-bound K-RasB is a calmodulin-binding protein, and we suggest that this binding may be a key element in the modulation of Ras signaling.
Velocity analysis for tilted transversely isotropic media: A physical modeling example (2001)

Abstract Transverse isotropy with a tilted symmetry axis (TTI media) has been recognized as a common feature of shale formations in overthrust areas, such as the Canadian Foothills. Since TTI layers cause serious problems in conventional imaging, it is important to be able to reconstruct the velocity model suitable for anisotropic depth migration. Here, we discuss the results of anisotropic parameter estimation on a physical-modeling data set. The model represents a simplified version of a typical overthrust section from the Alberta Foothills, with a horizontal reflector overlaid by a bending transversely isotropic layer. Assuming that the TTI layer is homogeneous and the symmetry axis stays perpendicular to its boundaries, we invert P-wave normal-moveout (NMO) velocities and zero-offset traveltimes for the symmetry-direction velocity V0 and the anisotropic parameters ∊ and δ. The coefficient ∊ is obtained using the traveltimes of a wave that crosses a dipping TTI block and reflects from the bottom of the model. The inversion for ∊ is based on analytic expressions for NMO velocity in media with intermediate dipping interfaces. Our estimates of both anisotropic coefficients are close to their actual values. The errors in the inversion, which are associated primarily with the uncertainties in picking the NMO velocities and traveltimes, can be reduced by a straighforward modification of the acquisition geometry. It should be emphasized that the moveout inversion also gives an accurate estimate of the thickness of the TTI layer, thus reconstructing the correct depth scale of the section. Although the physical model used here was relatively simple, our results demonstrate the principal feasibility of anisotropic velocity analysis and imaging in overthrust areas. The main problems in anisotropic processing for TTI models are likely to be caused by the lateral variation of the velocity field and overall structural complexity.
Sublingual Vaccine with GroEL Attenuates Atherosclerosis (2014)

Autoimmune responses to heat-shock protein 60 (HSP60) contribute to the progression of atherosclerosis, whereas immunization with HSP60 may induce atheroprotective responses. We assessed the capacity of an atheroprotective vaccine that targeted a recombinant HSP60 from Porphyromonas gingivalis (rGroEL) to induce a protective mucosal immune response. Female apolipoprotein E-deficient spontaneously hyperlipidemic (Apoe shl ) mice received sublingual delivery of rGroEL prior to P. gingivalis 381 injection. The animals were euthanized 16 weeks later. Sublingual immunization with rGroEL induced significant rGroEL-specific serum IgG responses. Antigen-specific cells isolated from spleen produced significantly high levels of IL-10 and IFN-γ after antigen re-stimulation in vitro. Flow cytometric analysis indicated that the frequencies of both IL-10 + and IFN-γ + CD4 + Foxp3 + cells increased significantly in submandibular glands (SMG). Furthermore, sublingual immunization with rGroEL significantly reduced atherosclerosis lesion formation in the aortic sinus and decreased serum CRP, MCP-1, and ox-LDL levels. These findings suggest that sublingual immunization with rGroEL is associated with the increase of IFNγ + or IL-10 + Foxp3 + cells in SMG and a systemic humoral response, which could be an effective strategy for the prevention of naturally occurring or P. gingivalis-accelerated atherosclerosis.
Permeabilising effects of sub-inhibitory concentrations of microcystin on the growth of<i>Escherichia coli</i> (2003)

Microcystin, a cyanotoxin produced by Microcystis aeruginosa, lacks potent antibacterial activity. When tested in combination, in vitro, inhibitory values for a range of hydrophobic antibiotics were significantly reduced in the presence of at least 1/20 x the minimum inhibitory concentration of microcystin. The degree of inhibition was equivalent to that of a well-characterised permeabilizing agent, polymyxin B nonapeptide. The permeabilizing ability of sub-inhibitory concentrations of microcystin to affect the envelope of Escherichia coli was demonstrated by a rapid and sustained reduction in absorbance values of lysozyme-treated cells and by enhanced uptake of crystal violet in microcystin-treated cultures. Direct effects of appropriate concentrations of microcystin on the integrity of bacterial outer and inner membranes were measured by release of specific enzyme markers. Although the exact mechanism for permeabilizing E. coli with microcystin has not been elucidated, the effects were consistent with permeability changes to the enterobacterial outer membrane caused by polymyxin B nonapeptide.
Synthesis of 2‐deoxy sugars (1988)

Abstract The reduction of acetylated or benzoylated glycosyl halides or selenides with low concentrations of tributylstannane leads to 2‐deoxy sugars. An important step in this radical‐chain reaction is the cis ‐selective migration of an ester group. The broad applicability of this method is demonstrated by the synthesis of mono‐ and dideoxy sugars, of α‐ and β‐deoxy sugars, of deoxypyranoses and deoxyfuranoses, of deoxypentosyl‐ and ‐hexosyl carbohydrates.
BDNF/TrkB signaling as an anti-tumor target (2011)

Several examples of molecularly targeted anticancer therapies successfully translated from the laboratory bench to the clinical setting, including imatinib, gefitinib, trastuzumab, erlotinib and ce...
Treatment of hirsutism with spironolactone (1982)

Clinical and endocrine evaluations of 39 patients with hirsutism were performed to determine the effectiveness and site(s) of action of an antiandrogenic compound, spironolactone. Treatment with spironolactone at a dose of 200 mg/day resulted in a clear beneficial effect on the quantity and quality of facial hair growth in 19 of 20 patients with moderate to severe hirsutism. Regression of hirsutism in terms of diameter, density, and the rate of facial hair growth was noticeable within two months. The maximal effect was observed at six months and was maintained at 12 months of treatment. Spironolactone was equally effective in reducing hirsutism in women with polycystic ovary syndrome and idiopathic hirsutism. These clinical observations were associated with a prompt and sustained reduction in levels of androgen of ovarian origin without affecting levels of adrenal androgen and cortisol. Apart from diuresis, which was limited to the first few days of treatment, there were no discernible side effects during the one year of this study. Our results indicate that spironolactone is a highly effective and safe agent for the treatment of hirsutism through its inhibitory action on both ovarian androgen secretion and peripheral androgen action. (<i>JAMA</i>1982;247:1295-1298)
Functional Bregman Divergence and Bayesian Estimation of Distributions (2008)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> A class of distortions termed functional Bregman divergences is defined, which includes squared error and relative entropy. A functional Bregman divergence acts on functions or distributions, and generalizes the standard Bregman divergence for vectors and a previous pointwise Bregman divergence that was defined for functions. A recent result showed that the mean minimizes the expected Bregman divergence. The new functional definition enables the extension of this result to the continuous case to show that the mean minimizes the expected functional Bregman divergence over a set of functions or distributions. It is shown how this theorem applies to the Bayesian estimation of distributions. Estimation of the uniform distribution from independent and identically drawn samples is presented as a case study. </para>
Lightning current and flashover path measurement on high voltage transmission lines (2006)

A method of measurement the current and the path of a lighting flashover is put forward. When a lighting break an insulator string on high voltage power transmission lines, an impulse current will flow through the string, and an impulse voltage will appear at the tower end of the string. A voltage sensor can measure the voltage pulse. An inductance coil current sensor can measure the current pulse. Contrasting the polar of the sensor signals, we can distinguish the shielding failure and back flashover, and obtain the polarity of the lighting. To establish this method, the authors designed a voltage sensor, a current sensor and an optical fiber transmission system. An impulse current generator was used to generate lighting current about 10 kA, which flow through a 2.5Omega resistance to simulate the lighting flashover. The voltage sensor and the current sensor were place above the resistance to measure the signals. The outputs of the sensors were converted to light signal and transmitted by optical fiber to measurement system. The experiment result shown this method has excellent feasibility.
Krumbiegel, I.: Die Straußenvögel. Die Neue Brehm-Bücherei, Heft 362. — Wittenberg (A. Ziemsen) 1966; 128 S., 84 Abb. 2 Farbtafeln; MDN 9,20 (1967)

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Molecular genetics and molecular biology advances in brain tumors (1996)

As the genes that regulate cell growth and proliferation are being identified and their encoded proteins characterized, our understanding of the molecular basis of tumor development is expanding rapidly. This review focuses on recent studies examining alterations of growth-regulatory genes in brain tumors, including those involving the inactivation of gene products that normally suppress cell growth (tumor-suppressor genes) or those involving the activation of gene products that promote cell growth (oncogenes) and presents information concerning the molecular biology associated with these changes.
Adaptor Protein Shc Is an Isoform-specific Direct Activator of the Tyrosine Kinase c-Src (2002)

The activity of c-Src protein-tyrosine kinase is up-regulated under a number of receptor signaling pathways. However, the activation mechanism of c-Src under physiological conditions has remained unclear. We show here that the Shc adaptor protein is a novel direct activator of c-Src in epidermal growth factor receptor signaling in A431 human epidermoid carcinoma cells. Among the three Shc isoforms, P66 and P52, but not P46, were found to interact with and activate c-Src in vitro and in vivo. Activation of c-Src accompanied autophosphorylation of c-Src in the activation segment, but the carboxyl-terminal dephosphorylation was not observed. We have identified the interaction sites between Shc and c-Src and constructed a point mutant of Shc that abolishes the c-Src activation. Using this mutant, we have confirmed that the Shc-mediated c-Src activation triggers Stat-p21/WAF1/Cip1 pathway that has been implicated in the cell cycle arrest and apoptosis of epidermal growth factor-stimulated A431 cells.