gebhart/patrepeval huggingface dataset:
Quantification of Ag-NOR proteins using Ag-NOR staining on western blots. (1994)

Ribosomal genes are associated with a set of silver-stained nucleolar proteins, the Ag-NOR proteins, whose amount is directly related to the duration of the cell cycle. Quantification of Ag-NOR proteins by image analysis is presently used to evaluate the rate of proliferation of cancer cells and nucleolar activity. Our objective was to establish a procedure to quantify independently each major Ag-NOR protein in cell extracts. Computerized densitometry established that the specific silver staining of Ag-NOR proteins (Ag-NOR staining) performed on Western blots makes it possible to quantify Ag-NOR proteins. Using purified Ag-NOR proteins, nucleolin, and protein B23, we observed that the intensity of Ag-NOR staining is proportional to the amount of protein. A linear relationship exists between the intensity of Ag-NOR staining and the amount of nucleolin, in the range of 0.2-1.6 micrograms. Using total nuclear extracts prepared from mammalian cells, the proportionality was maintained for total Ag-NOR-stained proteins or for a particular protein. We also determined the levels of nuclear proteins suitable for quantitative analysis. Individual Ag-NOR proteins can be quantified by computerized densitometry in nuclear extracts after Ag-NOR staining on Western blots. This procedure can be applied to establish the contribution of each Ag-NOR protein in general staining, estimate the variability of each Ag-NOR protein in normal and pathological conditions, and quantify each Ag-NOR protein contained per cell.
Lupus Anticoagulant is the Strongest Risk Factor for both Venous and Arterial Thrombosis in Patients with Systemic Lupus Erythematosus (1996)

Antiphospholipid antibodies (aPL) characterize patients at risk for both arterial and venous thrombotic complications. Recently it has been recognized that the presence of plasma proteins such as beta 2-glycoprotein I(beta 2 GPI) and prothrombin are essential for the binding of aPL to phospholipids and that these proteins are probably the real target of aPL. The discovery of these new antigens for aPL introduces the possibility of new assays to detect the presence of aPL. However, it is not known whether these assays improve the identification of patients at risk for thrombosis. In this retrospective study we compared the value of the classic assays LAC (lupus anticoagulant) and ACA (anticardiolipin antibodies) to detect aPL associated with thrombotic complications, with new assays which are based on the binding of aPL to the plasma proteins prothrombin and beta 2GPI. To do so, we have used these assays in a group of 175 SLE patients and correlated the positivity of the different assays with the presence of a history of venous and arterial thrombosis. Control groups were patients without SLE but with LAC and/or ACA and thrombosis (n = 23), patients with thrombosis without LAC and ACA (n = 40) and 42 healthy controls. In the univariate analysis, in which no distinction has been made between high and low antibody levels, we confirmed LAC and ACA to be related to both arterial and venous thrombosis. Anti-beta 2GPI- and anti-prothrombin-antibodies, both IgG and IgM correlate with venous thrombosis and anti-beta 2GPI-IgM with arterial thrombosis. Multivariate analysis showed that LAC is the strongest risk factor (OR 9.77; 95% CI 1.74-31.15) for arterial thrombosis. None of the other factors is a significant additional risk factor. For venous thrombosis LAC is the strongest risk factor (OR 6.55; 95% CI 2.36-18.17), but ACA-IgM above 20 MPL units also appeared to be a significant (p = 0.0159) risk factor (OR 3.90; 95% CI 1.29-11.80). Furthermore, the presence of anti-beta 2GPI- and/or anti-prothrombin-antibodies in LAC positive patients (n = 60) does not increase the risk for thrombosis. The results showed that (i) the LAC assay correlates best with a history of both arterial and venous thrombosis and (ii) neither the anti-beta 2GPI ELISA nor the anti-prothrombin ELISA gives additional information for a thrombotic risk in SLE patients.
Comparative Study of Photodynamic Properties of 13,15-N-cycloimide Derivatives of Chlorin p6¶ (2004)

Comparative study of 13,15-[N-(2-hydroxyethyl)]cycloimide chlorin p6 (2), 13,15-(N-acetoxy)cycloimide chlorin p6 (3), 13,15-(N-hydroxy)cycloimide chlorin p6 methyl ester (4) and 13,15-(N-methoxy)cycloimide chlorin p6 methyl ester (5) together with the previously investigated 13,15-[N-(3-hydroxypropyl)]cycloimide chlorin p6 (1) was performed. The dependence of the key photodynamic properties of 1-5 on the introduced substituents was analyzed. The photoinduced cell-killing activity of 4 is 100- and 280-fold higher than that of chlorin p6 and Photogem, respectively, as estimated on A549 human lung adenocarcinoma cells. The activity is reduced eight times in the order 4 > 5 > 1 > 2 > 3. The intracellular accumulation of 1-5 occurs in cytoplasm in a monomeric form bound to the lipids of cellular membranes. This form of 1, 2, 3, 4 and 5 is characterized by the high quantum yield of singlet oxygen generation, which depends on the introduced substituents, 0.66, 0.59, 0.35, 0.51 and 0.73, respectively. The photostability is two-fold less for 1 and four-fold less for 2, 3 and 5 than for 4. The rates of cellular uptake and efflux of 1-5 vary widely, thus providing the way to optimize the pharmacological properties of the photosensitizer (PS) using the respective substituents. Modifying the substituents, 1-5 were targeted to different cellular organelles. The enhanced accumulation in the Golgi apparatus and mitochondria complemented with diffuse staining of intracellular membranous structures is a property of 1-4. Compound 5 accumulates selectively in the lipid droplets and stains weakly perinuclear structures. Temperature-sensitive mechanisms of transport are responsible for the 1-4 uptake. Diffusion can play a role in the internalization of 5 but not of 1-4. Endocytosis via caveolae, clathrin-dependent and adenosine triphosphate-dependent pathways are not noticeably involved in the 1-5 internalization. Independently from their intracellular localization 1, 4 and 5 are highly efficient near-IR PS, which induce predominantly an apoptotic type of cell death under conditions providing ca 50% level of phototoxicity and necrosis at the 100% level of phototoxicity.
Review: Optimizing inducer and culture conditions for expression of foreign proteins under the control of thelac promoter (1996)

This review examines factors which influence the expression of foreign proteins in Escherichia coli under the transcriptional control of the lac and tac promoters, and discusses conditions for maximizing the production of a foreign protein using this system. Specifically, the influence of IPTG (isopropyl-beta-D-thiogalactoside) concentration, temperature, composition of the growth medium, the point in the growth curve at which cells are induced with either IPTG or lactose, and the duration of the induction phase are discussed.
Vector Fidelity of Ocean-Bottom Seismic Data (2002)

Abstract Vector fidelity is an important issue in applications of oceanbottom seismic (OBS) data that involves shear-wave splitting, azimuthal anisotropy and amplitude analysis. Here, we discuss characterization and compensation for vector infidelity. Two component (2C) vector infidelity, involving only the horizontal components of the OBS data, can be characterized and corrected for based on geometrical properties. Vector fidelity problems involving 3C and 4C data are more difficult to analyze because in general, the interaction of the wavefield with the ocean bottom, and the physical properties of the ocean bottom must be considered as well. Introduction Ocean-bottom seismic (OBS) data has proven to be a valuable tool for reservoir characterization and imaging. The fourcomponent (4C) OBS receiver stations include a 3C geophone, recording particle velocity, and a hydrophone recordingpressure. With 4C OBS acquisition, both compressional (P) and shear (S) waves can be measured directly. PS-converted waves provide an independent set of measurements that can be used in situations where P-wave imaging fails. Excellent examples from the North Sea include imaging through gas clouds at Tommeliten (Granli et al., 1999) and Valhall(Thomsen et al., 1997), and the OBS survey at the Alba field (Hanson et al., 1999) where the converted waves provide a clear image of the top of the reservoir sands. Another important application of OBS data is attenuation of multiplesby means of PZ-summation (Barr, 1997), which involves the vertical component of the geophone and the hydrophone. In simple 2D applications of OBS data, only the kinematical properties of the data are utilized for imaging pusposes. Often, the multicomponent data are processed as a set of independent scalar fields, assuming that the vertical component records only P-waves, and the horizontalcomponents record only S-waves. Because of ray bending and seismic velocities increasing with depth, this is sometimes an acceptable assumption. In more advanced application of OBS data, including S-wave splitting, azimuthal anisotropy andAVO analysis, the amplitude and vector properties of the OBS data become important. Consequently, the vector fidelity of OBS data is an issue of major interest to the oil and gas industry. Currently, two different types of OBS acquisition systems are in use:Cable-based OBS systems.Node-based OBS systems. Each type has its advantages and limitations. Cable-based systems allows for inexpensive and easy deployment of a large number of receiver stations. High fold is obtained in the inline direction. The geophone-ground coupling can be poor, in particular in the crossline direction. Node-based systems are more expensive and tedious to deploy. Vector fidelity is usually better than for cable-based system. Uniform azimuthal coverage can easily be obtained. Different from cable-based systems, there is no preferred direction introduced by the system design. One of the pioneering North-Sea OBS data sets was acquired with a node-based acquisition system (Berg et al., 1995).
The fundamentals of aging in HV polymer-film capacitors (1994)

This paper covers the basic phenomena involved in the aging of capacitors constructed using polymer films as the major dielectric material. A wide variety of aging phenomena can be identified, ranging from simple electrical, dielectric, thermal, radiation, chemical and physical aging, to aging originating from the specific construction of the capacitor. Some phenomena occur quickly, such as some morphological changes in the polymer, others occur progressively, and others occur later in the life of the capacitor. The polymers covered range from biaxially-oriented polypropylene, which is widely used in commercial utility and industrial capacitors, to polymers like polycarbonate, polysulfone, polyimide, and polyvinylidene fluoride, which are used in high-energy density, outer-space, high-temperature, or other special applications. The paper addresses two constructions of polymer film capacitor where the aging phenomena are significantly different due to the differences in construction: polymer/foil capacitors and metalized film capacitors. Metalized polymer film capacitors have the quality of clearing or self healing that is not present in film/foil capacitors. The discussion of aging in this paper is given from the perspective of these two designs.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Stability of Artificial Oil Bodies Constituted with Recombinant Caleosins (2009)

Caleosin is a unique calcium binding protein anchoring to the surface of seed oil bodies by its central hydrophobic domain composed of an amphiphatic alpha-helix and a proline-knot subdomain. Stable artificial oil bodies were successfully constituted with recombinant caleosin overexpressed in Escherichia coli. The stability of artificial oil bodies was slightly or severely reduced when the amphiphatic alpha-helix or proline-knot subdomain in the hydrophobic domain of caleosin was truncated. Deletion of the entire central hydrophobic domain substantially increased the solubility of the recombinant caleosin, leading to a complete loss of its capability to stabilize these oil bodies. A recombinant protein engineered with the hydrophobic domain of caleosin replaced by that of oleosin, the abundant structural protein of seed oil bodies, could stabilize the artificial oil bodies, in terms of thermo- and structural stability, as effectively as caleosin or oleosin.
Stochastic Gradient Descent as Approximate Bayesian Inference (2017)

Stochastic Gradient Descent with a constant learning rate (constant SGD) simulates a Markov chain with a stationary distribution. With this perspective, we derive several new results. (1) We show t...
Ultra-wideband hybrid amplifier comprising distributedRaman amplifierand erbium-doped fibre amplifier (1998)

An extremely large seamless flat-gain bandwidth of 90.5 nm (1556.0 – 1646.5 nm) and transparent-gain bandwidth of 108 nm (1540.0 – 1648.0 nm) for a 50 km transmission fibre are achieved using a novel hybrid amplifier. The amplifier comprises a low-noise distributed Raman amplifier pumped with dual wavelengths and an erbium-doped fluoride fibre amplifier.
Autoxidation of Intermediary Mesoionic 1,3-Oxazolium-5-olates Generated from Cyclic N-Acyl .ALPHA.-Amino Acids. (1997)

Mesoionic 1, 3-oxazolium-5-olates (munchnones) react fairly rapidly with oxygen to give the autoxidation products when the C-4 substituent is aromatic. The autoxidation occurred in the munchnones generated from N-acyl tetrahydroisoquinoline-1-carboxylic acids or tetrahydro-β-carboline-1-carboxylic acids. The mechanism was elucidated by 18O labeling experiments and involved a series of well-precedented autoxidative processes including oxygenation, cyclization of the resulting peroxy anion, and oxidative cleavage.
Results on aligned SiO2/SiO2 direct wafer-to-wafer low temperature bonding for 3D integration (2009)

To meet future 3D stacking requirements on wafer-to-wafer level, we successfully demonstrate oxide-oxide direct bonding on 200 mm with and without copper level utilizing face-to-face alignment and bonding within one process module as well as on the same chuck.
TILDE: A Temporally Invariant Learned DEtector (2015)

We introduce a learning-based approach to detect repeatable keypoints under drastic imaging changes of weather and lighting conditions to which state-of-the-art keypoint detectors are surprisingly sensitive. We first identify good keypoint candidates in multiple training images taken from the same viewpoint. We then train a regressor to predict a score map whose maxima are those points so that they can be found by simple non-maximum suppression. As there are no standard datasets to test the influence of these kinds of changes, we created our own, which we will make publicly available. We will show that our method significantly outperforms the state-of-the-art methods in such challenging conditions, while still achieving state-of-the-art performance on untrained standard datasets.
Ranking and new database architectures (2013)

Database platform support for efficient ranking can have positive performance implications for a number of rank-aware applications, including data exploration, social network analysis, and keyword search. This talk highlights two pieces of work where ranking appears in the research area of database architectures for new hardware. First, we highlight the Bw-tree, a new high-performance B+-tree supporting sorted key-sequential access. The Bw-tree is re-architected to run efficiently on new hardware: its in-memory operations are completely latch-free, removing blocking behavior while also improving multi-core cache behavior, while its storage layer implements a novel log-structured flash storage layer for that exploits fast sequential writes and mitigates adverse performance impact of random writes. Second, we highlight a new classification technique for identifying âĂIJcoldâĂİ (infrequently accessed) data in main-memory database systems. Using a log of sampled record accesses, our technique estimates record access frequencies using exponential smoothing. This classification approach is very efficient: it is able to accurately identify hot and cold records among 1M records in sub-second time from a log of 1B record accesses on a workstation class machine.
Secreted phosphoproteins associated with neoplastic transformation: close homology with plasma proteins cleaved during blood coagulation. (1988)

We have previously demonstrated that a wide variety of rodent and human tumor cells secrete markedly elevated levels of a transformation-related phosphoprotein with a molecular weight (depending on animal species) of 58,000 to 69,000. With antibody raised to the tumor-secreted phosphoprotein (rat), we have now identified an antigenically related protein in normal rat and human plasma. The rat plasma protein and the rat tumor-secreted phosphoproteins comigrated on polyacrylamide gels and were identically cleaved during blood coagulation as well as by purified thrombin. Mouse macrophages expressed a similar or identical phosphoprotein suggesting that monocytic cells may be a source of the normal plasma protein. Consistent with elevated secretion of this protein by tumor cells, plasma and sera from cancer patients contained elevated levels of this protein, raising the possibility that this circulating marker may prove useful for monitoring tumor burden. Amino acid sequence derived from the amino terminus of the rat tumor phosphoprotein indicates that it is distinct from previously sequenced proteins, but that it may be related to protein-tyrosine kinases encoded by viral and proto-onc genes.
A position-dependent silencer plays a major role in repressing alpha-fetoprotein expression in human hepatoma. (1991)

A large percentage of human hepatomas produce alpha-fetoprotein (AFP), but the levels of AFP expression vary greatly among hepatomas. To understand the molecular basis for this variation, we analyzed transcriptional regulatory activities associated with the 5'-flanking region of the AFP gene in two human hepatoma cell lines, HuH-7 and huH-1/cl-2, which produce a high and a low level of AFP, respectively. We found that the low level of AFP production in huH-1/cl-2 is due to the action of at least two silencer regions located between the enhancer and the promoter of the AFP gene. In contrast, no silencer activity is expressed in HuH-7. We identified 5'-CTTCATAACTAATACTT-3' to be a core sequence responsible for the negative regulatory activity. This sequence is repeated four times in a strong, distal silencer region, Sd, whereas one copy is present in a weak, proximal silencer region, Sp. The silencer reduces transcriptional initiation by blocking enhancer activation of the AFP promoter in a position-dependent manner. The silencer functions in the presence of positive transcription factors and may play a key role in developmental repression as well as variable expression of the AFP gene in hepatomas.
2-5A Ligands—A New Concept for the Treatment of Prostate Cancer (2007)

Several potent prostate specific membrane antigen (PSMA) inhibitors have been described recently. We generated a PSMA-specific 2-5A ligand called RBI 1033 by linking 2-5A to the N-acetylaspartylglutamate (NAAG)-based inhibitor ZJ-24. We measured the inhibitory activity of RBI 1033 to the folate hydrolase activity of PSMA. Amazingly, we found that compared to ZJ-24 (IC50 = 53.9 nM), RBI 1033 was more than 10 times more potent (IC50 = 4.78 nM) as a folate hydrolase inhibitor, while SMCC 2-5A lacking the ZJ-24 part, did not show much activity (IC50 = 1974 nM). Also, RBI 1033's affinity to PSMA was found to be 10 times higher than ZJ-24 itself.
Stimulation of hepatic regeneration after partial hepatectomy by infusion of a cytosol extract from regenerating dog liver. (1980)

A cytosol liver extract was prepared from adult dog livers and from liver remnants that had been regenerating for one, two and three days after 72 per cent partial hepatectomy. Given intraportally, the most active of these cytosols did not stimulate proliferation in the livers of normal dogs. However, infused during a six hour period into the portal vein of test group dogs, the cytosol from 48 and, especially, 72 hour regenerating livers augmented the regeneration response ordinarily produced by 44 per cent partial depatectomy. The effect was delayed. It became identifiable 48 hours after infusion and rached a peak at 72 hours. Neither augmentation nor significant inhibition of the normal regeneration response was produced by cytosol from normal liver and 24 hour regenerating liver or by six hour infusion of insulin. The amplification effect of active cytosol was equivocal when the infusions were given intraperitoneally and was not demonstrable at all by the intravenous route. In these investigations, it is confirmed that there are growth control factors in regenerating liver but the nature or physiologic significance of the factor or factors has not been clarified.
Cardioprotective Effects of a C1 Esterase Inhibitor in Myocardial Ischemia and Reperfusion (1995)

Blocking of the classic complement pathway by C1 INH appears to be an effective means of preserving ischemic myocardium from reperfusion injury. The mechanism of this cardioprotective effect appears to be inhibition of PMN-endothelium interaction; this inhibition leads to preservation of normal endothelial function, which results in reduced cardiac necrosis.