gebhart/patrepeval huggingface dataset:
Anaphylactoid shock – a common cause of death in heroin addicts? (1997)

We measured mast-cell tryptase in postmortem blood from 22 heroin addicts dying suddenly after injection. In 32%, the concentration of tryptase was elevated (> or = 10 micrograms/l), and the mean value of tryptase was significantly different from a control group dying from known, nonimmunologic causes (P < 0.05). The increased tryptase concentrations indicate that death was preceded by systemic mast-cell degranulation. All victims of drug deaths had morphine in blood, most below 0.2 microgram/ml. In 71% of the victims of drug-related deaths with tryptase values > or = 10 micrograms/l, the intermediate degradation product, 6-monoacetyl-morphine, was not found in blood, whereas this was the case in only two victims with values below that cutoff point. This indicates that those with high tryptase concentrations survived longer than those with lower values. No correlation was found between the IgE levels and tryptase in either group, supporting the hypothesis that tryptase release was not mediated by an allergic reaction. The well-known property of opiates to stimulate unspecifically the liberation of histamine and other constituents of mast-cell granules offers one explanation of our observations. The results suggest that many heroin fatalities are caused by an anaphylactoid reaction.
The Supramolecular Structure of Self-Assembly Formed by Capsanthin Derivatives (2002)

Carotenoids form structured self-assembly upon aqueous dilution of their organic solutions. In order to test the proposal predicting carotenoid aggregates to be organized in closely packed H-type (card-pack) manner by intermolecular hydrogen bonds, the trihydroxy derivative of capsanthin (1), (6'R)-capsanthol (2) ((all-E,3R,3'S,5'R,6'R)-beta,kappa-carotene-3,3',6'-triol) was acetylated to obtain all varieties of mono-, di- and triacetates and the corresponding supramolecules were studied by UV/Vis- and CD spectroscopy. It was verified that derivatives lacking hydroxyl functions at either of the end-groups form the loosely organized J-type (head-to-tail) aggregates. A model for the structure of the J-type self-assembly is proposed. Evidence was also obtained suggesting that close contacts of carotenoid molecules are not confined to hydrogen bonding.
Frequency response of 1.3µm InGaAsP high speed semiconductor lasers (1987)

The frequency response of a group of 1.3 μm InGaAsP vapor-phase-regrown buried heterostructure lasers of various cavity lengths is analyzed by fitting the measured response curves. The dependence of resonant frequency f <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</inf> and damping rate <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">\Gamma</tex> on bias power is determined. The differential gain coefficient for InGaAsP is determined as <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3.5 \times 10^{-16}</tex> cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . The damping rate is found to be proportional to the square of the resonant frequency with a proportionality factor which is independent of device geometry and facet reflectivity. The existence of such a universal relationship between <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">\Gamma</tex> and f <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</inf> and the observed magnitude of the damping rate is explained by the interband relaxation model of nonlinear gain.
p28, an Anionic Cell-Penetrating Peptide, Increases the Activity of Wild Type and Mutated p53 without Altering Its Conformation (2013)

p28, a cell penetrating peptide, binds to the DNA binding domain (DBD) of p53, inducing a post-translational increase in intracellular levels of wild type and mutant p53 activating pathways that inhibit cancer cell proliferation at G2/M. Cancer cells respond to p28 with an increase in p53 activity, except when mutations either alter DNA contact or completely unfold the DBD. The increase in p53 activity is accompanied by a significant reduction in the level of the E3 ligase COP1, with no alteration in p53 conformation. This suggests p28 can activate p53 over a wide range of conformational mutations by inhibiting the binding of COP1 to p53.
Autoimmune disease and chronic lymphocytic leukemia: autoimmune hemolytic anemia, pure red cell aplasia, and autoimmune thrombocytopenia. (1998)

Immune dysregulation, a hallmark of chronic lymphocytic leukemia (CLL), manifests itself in three autoimmune diseases: warm autoimmune hemolytic anemia (AIHA); idiopathic thrombocytopenia (ITP); and, pure red cell aplasia (PRCA). AIHA occurs in 11% of advanced stage CLL patients. Prednisone is the first treatment of choice, with 90% responses and 65% complete responses. More than 60% of patients relapse when treatment is stopped. Intravenous immunoglobulin, the next line of treatment, causes responses in 40% of patients. While the data are very limited, cyclosporine A is a reasonable choice for third-line therapy. Alkylating agents, danazol, plasma exchange, immunoabsorption, vincristine-loaded platelets, splenectomy, and splenic irradiation are also reported to cause responses. The data on mechanisms of AIHA are most consistent with immune dysregulation leading to loss of tolerance to a self antigen which in turn leads to the immune-based hemolytic anemia. PRCA is underrecognized in CLL with 6% of CLL patients having PRCA when tested for it. Unlike AIHA, PRCA often occurs in early stage disease. Anemia, reticulocytopenia, and a marrow virtually devoid of red blood cell precursors are hallmarks of PRCA. Corticosteroid therapy is the first line of treatment. If a response is not obtained in 4 weeks, cyclosporine A should be added. Although the data on pathophysiology are very limited, PRCA appears to be the result of an abnormal T cell that both fails in its normal function to support growth and inhibits the growth of erythroid progenitor cells. ITP occurs in 2-3% of CLL patients, occurs in early stage disease and may be a presenting manifestation. Initial therapy for ITP mirrors the guidelines for primary ITP. Initial therapy should consist of prednisone. Seventy percent of patients respond. Splenectomy is a reasonable second-line treatment. Autoimmune phenomena, largely related to blood cells, are based in the immune dysregulation of CLL. Longer survivals in CLL patients, more treatment regimens per patient, and more immunosuppression with modern treatments, allow us to predict an increasing incidence of autoimmune blood cell diseases in CLL.
Contextual Visual Similarity (2016)

Measuring visual similarity is critical for image understanding. But what makes two images similar? Most existing work on visual similarity assumes that images are similar because they contain the same object instance or category. However, the reason why images are similar is much more complex. For example, from the perspective of category, a black dog image is similar to a white dog image. However, in terms of color, a black dog image is more similar to a black horse image than the white dog image. This example serves to illustrate that visual similarity is ambiguous but can be made precise when given an explicit contextual perspective. Based on this observation, we propose the concept of contextual visual similarity. To be concrete, we examine the concept of contextual visual similarity in the application domain of image search. Instead of providing only a single image for image similarity search (\eg, Google image search), we require three images. Given a query image, a second positive image and a third negative image, dissimilar to the first two images, we define a contextualized similarity search criteria. In particular, we learn feature weights over all the feature dimensions of each image such that the distance between the query image and the positive image is small and their distances to the negative image are large after reweighting their features. The learned feature weights encode the contextualized visual similarity specified by the user and can be used for attribute specific image search. We also show the usefulness of our contextualized similarity weighting scheme for different tasks, such as answering visual analogy questions and unsupervised attribute discovery.
Alzheimer's Disease Amyloid-β Binds Copper and Zinc to Generate an Allosterically Ordered Membrane-penetrating Structure Containing Superoxide Dismutase-like Subunits (2001)

Amyloid beta peptide (Abeta) is the major constituent of extracellular plaques and perivascular amyloid deposits, the pathognomonic neuropathological lesions of Alzheimer's disease. Cu(2+) and Zn(2+) bind Abeta, inducing aggregation and giving rise to reactive oxygen species. These reactions may play a deleterious role in the disease state, because high concentrations of iron, copper, and zinc have been located in amyloid in diseased brains. Here we show that coordination of metal ions to Abeta is the same in both aqueous solution and lipid environments, with His(6), His(13), and His(14) all involved. At Cu(2+)/peptide molar ratios >0.3, Abeta coordinated a second Cu(2+) atom in a highly cooperative manner. This effect was abolished if the histidine residues were methylated at N(epsilon)2, indicating the presence of bridging histidine residues, as found in the active site of superoxide dismutase. Addition of Cu(2+) or Zn(2+) to Abeta in a negatively charged lipid environment caused a conformational change from beta-sheet to alpha-helix, accompanied by peptide oligomerization and membrane penetration. These results suggest that metal binding to Abeta generated an allosterically ordered membrane-penetrating oligomer linked by superoxide dismutase-like bridging histidine residues.
Phase specificity of 5-azacytidine against mammalian cells in tissue culture. (1970)

Summary 5-Azacytidine (1 to 5 μg/ml) significantly inhibited mitosis of L1210 cells in culture only after 2 hr of incubation. The inhibition of mitosis was correlated to the inhibition of DNA synthesis. With asynchronous DON and L1210 cells, the cell-kill (inhibition of proliferative capacity) reached a saturation value at high doses of the drug. Any further increase in drug concentration did not result in a corresponding increase in percentage of cell-kill. This indicated that 5-azacytidine kills cells in certain phases of the cell cycle. With synchronous DON cells, it was shown that the drug was lethal predominantly in the S phase. 5-Azacytidine caused considerable chromosome damage when L1210 cells in culture were exposed to the drug at 5 μg/ml for 2 hr at 37°.
A neutrophil elastase inhibitor prevents bleomycin-induced pulmonary fibrosis in mice (2012)

Neutrophil elastase plays pivotal roles in the pathogenesis of pulmonary fibrosis. The neutrophil elastase inhibitor, sivelestat, could alleviate pulmonary fibrosis; however, the antifibrotic mechanisms have not yet been clarified. We examined the antifibrotic mechanisms, mainly focusing on a key fibrotic cytokine, transforming growth factor (TGF)-β1, in this study. To elucidate the antifibrotic mechanisms of sivelestat, we examined a murine model of bleomycin-induced early-stage pulmonary fibrosis. After intratracheal instillation of bleomycin, sivelestat was administered intraperitoneally once a day for 7 or 14 days. Bronchoalveolar lavage fluid and lung samples were examined on day 7 or day 14 after bleomycin instillation. In the bleomycin-induced early-stage pulmonary fibrosis model, the neutrophil elastase level was increased in the lungs. Sivelestat significantly inhibited the increase in lung collagen content, fibrotic changes, the numbers of total cells (including macrophages, neutrophils and lymphocytes), the levels of the active form of TGF-β1 and phospho-Smad2 in bleomycin-induced early-stage pulmonary fibrosis. The total TGF-β1 levels and relative changes of TGF-β1 mRNA expression, however, were not decreased significantly by sivelestat. These results suggest that sivelestat alleviated bleomycin-induced pulmonary fibrosis via inhibition of both TGF-β activation and inflammatory cell recruitment in the lung.
Characterization of HIV-Specific Proliferative T Cell Responses in HIV-Infected Persons (2001)

Virus-specific helper T cell responses are thought to be an important host defense in HIV infection. The proliferative responses to HIV p24, p55, and gp120 were tested in a cohort of 27 HIV-infected subjects. Vigorous proliferative responses directed at the Gag protein with stimulation indices in excess of 6 were detected in 10 of the individuals tested but an Env-specific response was present in only 1 subject. Viral load and proliferative activity to Gag were inversely correlated in untreated individuals. Proliferation was also observed in some individuals treated in the chronic phase of infection, and responses were maintained over time in the absence of detectable viremia. Positive proliferative responses could also occasionally be detected in treated persons with CD4(+) cell counts below 200/microl. Thus, vigorous Gag-specific proliferative responses are present in a minority of HIV-infected individuals and can be detected in individuals receiving highly active antiretroviral therapy at advanced disease stages. Proliferative responses are maintained for an extended time period in the presence of antiviral therapy.
Differential titration of plasmin and plasminogen in milk using sandwich ELISA with monoclonal antibodies (1997)

Two sandwich enzyme-linked immunosorbent assays (ELISA) have been developed for quantitation of bovine milk plasminogen and plasmin. The assays used two monoclonal antibodies, one specific for plasminogen and the other specific for plasminogen plus plasmin. Plasmin concentration was obtained by subtracting the first concentration from the second. The assays were sensitive (linear range, 5-75 ng/ml), repeatable (CV, 8 and 5% for plasmin and plasminogen titration respectively), specific (no cross reactivity with the major milk proteins) and directly applicable to skimmed milk with no particular pretreatment of the sample. However, ELISA did not permit complete titration of milk plasminogen and plasmin (only 60-90% could be quantified). This lack of accuracy was due to casein interfering with the plasmin-plasminogen titration by ELISA. Results obtained with ELISA or an enzymic technique on 20 milk samples collected from individual cows milked throughout pregnancy showed that the ELISA was particularly suitable for analysis of late lactation or mastitic milk where proteinase inhibitors interfered with enzymic quantitation.
Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea (2010)

Marine dissolved organic matter (DOM) contains as much carbon as the Earth's atmosphere, and represents a critical component of the global carbon cycle. To better define microbial processes and activities associated with marine DOM cycling, we analyzed genomic and transcriptional responses of microbial communities to high-molecular-weight DOM (HMWDOM) addition. The cell density in the unamended control remained constant, with very few transcript categories exhibiting significant differences over time. In contrast, the DOM-amended microcosm doubled in cell numbers over 27 h, and a variety of HMWDOM-stimulated transcripts from different taxa were observed at all time points measured relative to the control. Transcripts significantly enriched in the HMWDOM treatment included those associated with two-component sensor systems, phosphate and nitrogen assimilation, chemotaxis, and motility. Transcripts from Idiomarina and Alteromonas spp., the most highly represented taxa at the early time points, included those encoding TonB-associated transporters, nitrogen assimilation genes, fatty acid catabolism genes, and TCA cycle enzymes. At the final time point, Methylophaga rRNA and non-rRNA transcripts dominated the HMWDOM-amended microcosm, and included gene transcripts associated with both assimilatory and dissimilatory single-carbon compound utilization. The data indicated specific resource partitioning of DOM by different bacterial species, which results in a temporal succession of taxa, metabolic pathways, and chemical transformations associated with HMWDOM turnover. These findings suggest that coordinated, cooperative activities of a variety of bacterial "specialists" may be critical in the cycling of marine DOM, emphasizing the importance of microbial community dynamics in the global carbon cycle.
Recombinant factor VIIa reverses the anticoagulant effect of the long‐acting pentasaccharide idraparinux in healthy volunteers (2004)

We investigated whether the anticoagulant effect of idraparinux, a selective long-acting factor Xa inhibitor, could be neutralized by recombinant factor VIIa (rFVIIa) in healthy male volunteers. We performed a randomized, placebo-controlled trial, comparing idraparinux [7.5 mg subcutaneous (s.c.)] followed at 3 h by rFVIIa [90 microg/kg intravenous (i.v.)] (n = 6), or idraparinux (7.5 mg s.c) followed after 1 week by rFVIIa (90 microg/kg i.v.)(n = 6). rFVIIa, given 3 h after idraparinux, significantly reversed the increased thrombin generation time (TGT), the increased activated partial thromboplastin time (aPTT) and prothrombin time (PT), and the reduced prothrombin fragment 1+2 (F1+2) levels caused by idraparinux, although no clear effect of rFVIIa on the endogenous thrombin potential (ETP) was observed. One week after idraparinux, injection of rFVIIa resulted in a similar relative reduction of the remaining increased aPTT, PT and TGT, with correction to pre-idraparinux values. A clear increase of F1+2 was observed, together with a small increase in ETP. We conclude that rFVIIa has significant effects on the idraparinux-inhibited thrombin generation and clotting parameters. These results suggest that rFVIIa may be useful in serious bleeding complications in idraparinux treated patients.
2,6-Dibenzhydryl-N-(2-phenyliminoacenaphthylenylidene)-4-methylbenzenamine Nickel Dibromides: Synthesis, Characterization, and Ethylene Polymerization (2011)

A series of 2,6-dibenzhydryl-N-(2-phenyliminoacenaphthylenylidene)-4-methylbenzenamines (L1−L5) and the nickel(II) dibromide complexes thereof (C1−C5) were synthesized and fully characterized. The molecular structures of representative complexes were determined by single-crystal X-ray diffraction and revealed a distorted-pyramidal geometry at nickel. All nickel(II) procatalysts exhibited very high activity for the polymerization of ethylene, with activities as high as the range of 107 g of PE (mol of Ni)−1 h−1.
Breast Cancers: MR Imaging of Folate-Receptor Expression with the Folate-Specific Nanoparticle P1133 (2010)

The FR-targeted USPIO P1133 demonstrates a specific retention in FR-positive breast cancers. Because FR expression correlates with tumor aggressiveness and prognosis, persistent P1133 tumor enhancement may be used as a noninvasive indicator for tumors with poor outcome.
Profiling of cancer cells using protein microarrays: discovery of novel radiation-regulated proteins. (2001)

The advent of DNA microarray technology will likely have a major impact on the molecular classification and understanding of human cancer. Obtaining a global perspective of proteins expressed in cancer cells is considerably more challenging. Here we describe a microarray-based platform that can be used to measure protein levels and activities in a complex biological milieu such as a cellular lysate. Using a protein microarray made up of 1920 elements (146 distinct antibodies) we were able to monitor alterations of protein levels in LoVo colon carcinoma cells treated with ionizing radiation. The protein microarray approach revealed radiation-induced up-regulation of apoptotic regulators including p53, DNA fragmentation factor 40/caspase activated DNase, DNA fragmentation factor 45/inhibitor of caspase activated DNase, tumor necrosis factor-related apoptosis-inducing ligand, death receptor 5, decoy receptor 2, FLICE-like inhibitory protein, signal transducers and activators of transcription 1alpha, and uncoupling protein 2, among others. Consistent with this observation, an increased percentage of apoptosis was observed in irradiated LoVo cells. Interestingly, we also observed radiation-induced down-regulation of carcinoembryonic antigen, a prototypic cancer biomarker. Selected proteins assessed by microarray were validated by traditional immunoblotting. Taken together, our work suggests that protein/antibody microarrays will facilitate high-throughput proteomic studies of human cancer and carcinogenesis.
Apabetalone Mediated Epigenetic Modulation is Associated with Favorable Kidney Function and Alkaline Phosphatase Profile in Patients with Chronic Kidney Disease (2018)

A post-hoc analysis of CKD subjects from the SUSTAIN and ASSURE randomized controlled trials demonstrated favorable effects of apabetalone on ALP and eGFR, and generated the hypothesis that epigenetic modulation by BET inhibition may potentially offer a novel therapeutic strategy to treat CVD and progressive kidney function loss in CKD patients. This is being examined in the phase III trial BETonMACE.
Highly Isotactic Poly(vinyl alcohol). 2. Preparation and Characterization of Isotactic Poly(vinyl alcohol) (1999)

The preparation and characterization of highly isotactic poly(vinyl alcohol)s (PVOHs) derived from poly(tert-butyl vinyl ether) (PtBVE) polymerized with BF3·OEt2 were investigated. The mm sequence fraction increased with decreasing BF3·OEt2 concentration, and it reached as high as 78−79%, which seems to be the highest value of all so-called isotactic PVOHs reported so far, but only if the catalyst concentration was reduced to below 0.5 × 10-3 mol/L. An increase in mm sequence fraction may be caused by highly isospecific propagation of a new kind of species, which is thought to be generated from ligand exchange of the BF3 complex from ether to water. We also studied the polymerization of tBVE with various BF3 complexes, such as BF3·2CH3COOH, BF3·2CH3OH, or BF3·2CH3OH. The mm sequence fraction increased in the following order: BF3·2CH3COOH < BF3·OEt2 < BF3·2MeOH < BF3·2H2O. It increased with a reduction in the catalyst concentration for each type of catalyst.