gebhart/patrepeval huggingface dataset:
Structure and Function of Mucosal Antibodies (1970)

Justification for considering the secretory system as more or less distinct from that responsible for the formation of circulating antibody (systemic sys­ tem) stems from a number of lines of evidence. First, studies in the older medical and veterinary literature [for reviews see Tomasi & Bienenstock, (1); and Pierce (2) I suggest that the titers of specific antibodies present in external secretions vary independently from serum titers, indicating that secretory antibodies are not derived from serum, at least by simple transudation. Sec­ ond, in certain cases, titers of antibodies in external secretions are better cor­ related with resistance to and recovery from infection than are those of se­ rum. Third, more recent observations indicate that many external secretions contain antibodies primarily of the IgA type, whereas this immunoglobulin is a minor constituent of serum. The finding of a predominance of IgA-type plasma cells locally in secretory organs, and the observation that antibodies of the IgA type may be produced by local immunization, support the concept of local synthesis of secretory antibodies. Although most experimental work has thus far focused on IgA, which is present in highest concentrations in external fluids, other immunoglobulins including IgG and IgM are often detectable in significant amounts, particu­ larly when inflammation is present. Very little work has been done with these immunoglobulins. However, evidence is accumulating that both IgG and IgM and, more recently, IgE may be produced locally in small amounts. In this review, emphasis will be placed on secretory IgA which is the predomin­ ant species of antibody. It should be pointed out that the role of these other immunoglobulins, as well as immunoglobulin fragments, may be of consider­ able importance and deserves more attention in future studies.
Cloning and nucleotide sequence of the mono- and diacylglycerol lipase gene (mdlB) of Aspergillus oryzae (1996)

Aspergillus oryzae IF04202 produces at least two extracellular lipolytic enzymes Ll and L2 (cutinase, and mono-and diacylglycerol lipase, respectively). Southern hybridization of restriction enzyme-digested genomic DNA fragments with 23mer oligonucleotides synthesized according to the amino acid sequence of the L2 as probe suggested the presence of the L2 gene (tentatively designated as mdZB) and an additional weakly hybridizing region. A fragment containing the genomic mdZB gene was cloned in Escherichia c&i. Nucleotide sequencing of the fragment revealed an open reading frame, comprising 1021
Shear Stress and Cyclic Strain Modulation of Gene Expression in Vascular Endothelial Cells (1995)

Vascular endothelial cells are exposed to a complex humoral and hemodynamic environment. Investigations over the last two decades have demonstrated that hemodynamic forces cause alterations in endothelial cell function. More specifically, blood flow-induced wall shear stress and cyclic strain modulate gene expression of various bioactive molecules synthesized and secreted by endothelial cells. Although there currently is not a known unifying mechanism linking mechanical agonists to changes in gene expression, various second messengers, transcription factors, mechanically sensitive promoter elements, and cytoskeletal architecture have been proposed as mediators in the signal transduction pathway. Knowledge of the mechanisms by which hemodynamic forces modulate endothelial cell gene expression will lead to novel gene therapy applications and allow more effective management of cardiovascular diseases.
The bronchodilator response from inhaled terbutaline is influenced by the mass of small particles: a study on a dry powder inhaler (Turbuhaler) (1989)

This study was carried out to investigate if particles approximately less than 5 microns are optimal when delivered from a dry powder inhaler. It was performed as a cumulative dose response study of twelve asthmatic adults. Three different versions of a dry powder inhaler, Bricanyl Turbuhaler, were studied. Each inhaler delivered 0.5 mg of pure terbutaline sulphate with each dose. Out of this 0.5 mg, they delivered 90 micrograms, 40 micrograms and 5 micrograms, respectively, of particles approximately less than 5 microns with each dose at an inspiratory flow rate of 28 l.min-1. Terbutaline 0.5 mg, 0.5 mg, 1.0 mg and 2.0 mg was inhaled with a 30 min interval between the doses. Forced expiratory volume in one second (FEV1) and forced vital capacity (FVC) were measured 5 and 20 min after each dose. The bronchodilator response was greater with the inhaler delivering 90 micrograms of small particles with each dose than with the inhaler delivering 5 micrograms, thus confirming the importance of small (approximately less than 5 microns) particles.
Improvements in factor concentrates (2010)

Purpose of review The aim of this review is to highlight strategies being pursued to enhance current concentrate therapies for the hemophilias. During the past 5 years, significant progress has been made with a variety of protein-engineering initiatives, some of which are already in early-phase clinical trials. Recent findings The standard of care for hemophilia therapy involves the infusion of clotting factor concentrates either at the time of bleeding (on demand therapy) or in a prophylactic schedule to prevent bleeding episodes. This latter approach to therapy has been used in some parts of Europe for several decades and has recently been shown, in a prospective randomized study, to result in a significant reduction in musculoskeletal pathology. The aim of many of the novel concentrates under development is to prolong the half-life of the infused clotting factor and thus to reduce the frequency of infusions. Several different strategies are being evaluated for this purpose including conjugation with hydrophilic polymers and generation of fusion proteins that are recycled by the FcRn receptor. Summary The speed of progress with the development of several approaches to extend clotting factor half-lives has been encouraging. It is very likely that several of these concentrates will reach the clinic in the near future.
Experimental studies of nonlinearities in high density disk recording (1992)

Nonlinear amplitude reduction in high-density disk recording has been studied. Dibit responses were measured at two flying heights, and disks with varying coercivity, magnetic moment, and substantially different noise levels were used. It is shown that the nonlinear amplitude loss is reduced substantially at lower flying heights. Increasing coercivity or decreasing magnetic moment similarly reduces this loss. Measurements of disks with different noise levels indicate more reduction for the low-noise medium only at the lower flying height. By deconvolving isolated pulses, transition lengths for single transitions were determined at each flying height. It is also found that the nonlinear amplitude reduction curves scale with transition length at a fixed flying height, indicating a universal curve.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
On the role of surface diffusion in determining the shape or morphology of noble-metal nanocrystals (2013)

Controlling the shape or morphology of metal nanocrystals is central to the realization of their many applications in catalysis, plasmonics, and electronics. In one of the approaches, the metal nanocrystals are grown from seeds of certain crystallinity through the addition of atomic species. In this case, manipulating the rates at which the atomic species are added onto different crystallographic planes of a seed has been actively explored to control the growth pattern of a seed and thereby the shape or morphology taken by the final product. Upon deposition, however, the adsorbed atoms (adatoms) may not stay at the same sites where the depositions occur. Instead, they can migrate to other sites on the seed owing to the involvement of surface diffusion, and this could lead to unexpected deviations from a desired growth pathway. Herein, we demonstrated that the growth pathway of a seed is indeed determined by the ratio between the rates for atom deposition and surface diffusion. Our result suggests that surface diffusion needs to be taken into account when controlling the shape or morphology of metal nanocrystals.
Complementation of the Mitotic Activator, p80 cdc25 , by a Human Protein-tyrosine Phosphatase (1990)

The onset of M phase requires the activation of the pp34 protein kinase in all eukaryotes thus far examined. In Schizosaccharomyces pombe, pp34 is phosphorylated on Tyr15, and dephosphorylation of this residue regulates the initiation of mitosis. In this study, it is shown that dephosphorylation of Tyr15 triggered activation of the pp34-cyclin complex from fission yeast, that a human protein-tyrosine phosphatase can catalyze this event both in vitro and in vivo, and that activation of fission yeast pp34 does not require threonine dephosphorylation. The complementary DNA that encoded the tyrosine phosphatase replaced the mitotic activator p80cdc25, closely associating the cdc25(+)-activating pathway with tyrosine dephosphorylation of pp34.
In Vitro Kinetics of Prebiotic Inulin-Type Fructan Fermentation by Butyrate-Producing Colon Bacteria: Implementation of Online Gas Chromatography for Quantitative Analysis of Carbon Dioxide and Hydrogen Gas Production (2009)

Kinetic analyses of bacterial growth, carbohydrate consumption, and metabolite production of five butyrate-producing clostridial cluster XIVa colon bacteria grown on acetate plus fructose, oligofructose, inulin, or lactate were performed. A gas chromatography method was set up to assess H2 and CO2 production online and to ensure complete coverage of all metabolites produced. Method accuracy was confirmed through the calculation of electron and carbon recoveries. Fermentations with Anaerostipes caccae DSM 14662(T), Roseburia faecis DSM 16840(T), Roseburia hominis DSM 16839(T), and Roseburia intestinalis DSM 14610(T) revealed similar patterns of metabolite production with butyrate, CO2, and H2 as the main metabolites. R. faecis DSM 16840(T) and R. intestinalis DSM 14610(T) were able to degrade oligofructose, displaying a nonpreferential breakdown mechanism. Lactate consumption was only observed with A. caccae DSM 14662(T). Roseburia inulinivorans DSM 16841(T) was the only strain included in the present study that was able to grow on fructose, oligofructose, and inulin. The metabolites produced were lactate, butyrate, and CO2, without H2 production, indicating an energy metabolism distinct from that of other Roseburia species. Oligofructose degradation was nonpreferential. In a coculture of R. inulinivorans DSM 16841(T) with the highly competitive strain Bifidobacterium longum subsp. longum LMG 11047 on inulin, hardly any production of butyrate and CO2 was detected, indicating a lack of competitiveness of the butyrate producer. Complete recovery of metabolites during fermentations of clostridial cluster XIVa butyrate-producing colon bacteria allowed stoichiometric balancing of the metabolic pathway for butyrate production, including H2 formation.
Adhesive recognition sequences (1991)

Specific cellular adhesion and migration of cells are recurring themes in embryonic development, tumor cell metastasis, and wound healing. Recent advances in our understanding of the molecular basis of cell adhesive and migratory interactions with extracellular matrix molecules have converged on the concept that many cell interactions are dependent on specific adhesive recognition sequences. As will be described in detail below, certain short peptide sequences in adhesion proteins are thought to serve as sites for recognition and binding by specific plasma membrane receptors
Synthesis, Self-Assembly, and Drug-Loading Capacity of Well-Defined Cyclodextrin-Centered Drug-Conjugated Amphiphilic A14B7 Miktoarm Star Copolymers Based on Poly(ε-caprolactone) and Poly(ethylene glycol) (2010)

Novel drug-conjugated amphiphilic A(14)B(7) miktoarm star copolymers composed of 14 poly(epsilon-caprolactone) (PCL) arms and 7 poly(ethylene glycol) (PEG) arms with beta-cyclodextrin (beta-CD) as core moiety were synthesized by the combination of controlled ring-opening polymerization (CROP) and "click" chemistry. (1)H NMR, FT-IR, and SEC-MALLS analyses confirmed the well-defined A(14)B(7) miktoarm star architecture. These amphiphilic miktoarm star copolymers could self-assemble into multimorphological aggregates in aqueous solution, which were characterized by dynamic light scattering (DLS) and transmission electron microscopy (TEM). Moreover, the drug-loading efficiency and drug-encapsulation efficiency of the drug-conjugated miktoarm star copolymers were higher than those of the corresponding non-drug-conjugated miktoarm star copolymers.
Cloning and cleavage site mapping of DNA from bovine herpesvirus 1 (Cooper strain) (1983)

Sequences representative of most of the bovine herpesvirus 1 (Cooper strain) DNa were cloned in the plasmid vector pBR322 at the HindIII site. EcoRI, HpaI, and BamHI restriction endonuclease sites were mapped in each of the cloned fragments, and this information was used to construct a restriction endonuclease cleavage site map of the entire viral genome for the four enzymes.
Mechanisms of Thermal Decomposition of Organic Monolayers Grafted on (111) Silicon (2006)

The thermal stability of different organic layers on silicon has been investigated by in situ infrared spectroscopy, using a specially designed variable-temperature cell. The monolayers were covalently grafted onto atomically flat (111) hydrogenated silicon surfaces through the (photochemical or catalytic) hydrosilylation of 1-decene, heptadecafluoro-1-decene or undecylenic acid. In contrast to alkyl monolayers, which desorb as alkene chains around 300 degrees C by the breaking of the Si-C bond through a beta-hydride elimination mechanism, the alkyl layers functionalized with a carboxylic acid terminal group undergo successive chemical transformations. At 200-250 degrees C, the carboxyl end groups couple forming anhydrides, which subsequently decompose at 250-300 degrees C by loss of the functional group. In the case of fluorinated alkyl chains, the C-C bond located between CH2 and CF2 units is first broken at 250-300 degrees C. In either case, the remaining alkyl layer is stable up to 350 degrees C, which is accounted for by a kinetic model involving chain pairing on the surface.
Fibroblasts from Idiopathic Pulmonary Fibrosis and Normal Lungs Differ in Growth Rate, Apoptosis, and Tissue Inhibitor of Metalloproteinases Expression (2001)

Idiopathic pulmonary fibrosis (IPF) is a chronic lung disorder characterized by fibroblast proliferation and extracellular matrix accumulation. However, studies on fibroblast growth rate and collagen synthesis have given contradictory results. Here we analyzed fibroblast growth rate by a formazan-based chromogenic assay; fibroblast apoptosis by in situ end labeling (ISEL) and propidium iodide staining; percent of alpha-smooth muscle actin (alpha-SMA) positive cells by fluorescence-activated cell sorter; and alpha1-(I) collagen, transforming growth factor (TGF)-beta1, collagenase-1, gelatinases A and B, and tissue inhibitor of metalloproteinase (TIMP)-1, -2, -3, and -4 expression by reverse transcriptase/polymerase chain reaction in fibroblasts derived from IPF and control lungs. Growth rate was significantly lower in IPF fibroblasts compared with controls (13.3 +/- 38.5% versus 294.6 +/- 57%, P < 0.0001 at 13 d). Conversely, a significantly higher percentage of apoptotic cells was observed in IPF-derived fibroblasts (ISEL: 31.9 +/- 7.0% versus 15.5 +/- 7.6% from controls; P < 0.008). alpha-SMA analysis revealed a significantly higher percentage of myofibroblasts in IPF samples (62.8 +/- 25.2% versus 14.8 +/- 11.7% from controls; P < 0.01). IPF fibroblasts were characterized by an increase in pro-alpha1-(I) collagen, TGF-beta1, gelatinase B, and all TIMPs' gene expression, whereas collagenase-1 and gelatinase A expression showed no differences. These results suggest that fibroblasts from IPF exhibit a profibrotic secretory phenotype, with lower growth rate and increased spontaneous apoptosis.
Camptothecin, a specific inhibitor of type I DNA topoisomerase, induces DNA breakage at replication forks. (1988)

The structure of replicating simian virus 40 minichromosomes, extracted from camptothecin-treated infected cells, was investigated by biochemical and electron microscopic methods. We found that camptothecin frequently induced breaks at replication forks close to the replicative growth points. Replication branches were disrupted at about equal frequencies at the leading and the lagging strand sides of the fork. Since camptothecin is known to be a specific inhibitor of type I DNA topoisomerase, we suggest that this enzyme is acting very near the replication forks. This conclusion was supported by experiments with aphidicolin, a drug that blocks replicative fork movement, but did not prevent the camptothecin-induced breakage of replication forks. The drug teniposide, an inhibitor of type II DNA topoisomerase, had only minor effects on the structure of these replicative intermediates.
Effects of Oral S-Adenosyl-l-Methionine on Hepatic Glutathione in Patients with Liver Disease (1989)

S-Adenosyl-L-methionine (SAMe) is a physiologic precursor of thiols and sulfurated compounds, which are known to be decreased in patients with liver disease. The effect of its administration on the hepatic glutathione content of liver patients was investigated. Four groups of subjects were selected: a) 9 patients with alcoholic liver disease treated with SAMe (1.2 g/day orally for 6 months); b) 7 patients with non-alcoholic liver disease treated as above; c) 8 placebo-treated patients with alcoholic liver disease; and d) 15 normal subjects as a control group. Total and oxidized glutathione were assayed by high-performance liquid chromatography of liver biopsy specimens before and after the treatment period. In all patients pre-treatment hepatic glutathione was significantly decreased as compared with controls. SAMe therapy resulted in a significant increase of hepatic glutathione levels both in patients with alcoholic and in those with non-alcoholic liver diseases as compared with placebo-treated patients. SAMe may therefore exert an important role in reversing hepatic glutathione depletion in patients with liver disease.
Fluorescence Linked Enzyme Chemoproteomic Strategy for Discovery of a Potent and Selective DAPK1 and ZIPK Inhibitor (2013)

DAPK1 and ZIPK (also called DAPK3) are closely related serine/threonine protein kinases that regulate programmed cell death and phosphorylation of non-muscle and smooth muscle myosin. We have developed a fluorescence linked enzyme chemoproteomic strategy (FLECS) for the rapid identification of inhibitors for any element of the purinome and identified a selective pyrazolo[3,4-d]pyrimidinone (HS38) that inhibits DAPK1 and ZIPK in an ATP-competitive manner at nanomolar concentrations. In cellular studies, HS38 decreased RLC20 phosphorylation. In ex vivo studies, HS38 decreased contractile force generated in mouse aorta, rabbit ileum, and calyculin A stimulated arterial muscle by decreasing RLC20 and MYPT1 phosphorylation. The inhibitor also promoted relaxation in Ca(2+)-sensitized vessels. A close structural analogue (HS43) with 5-fold lower affinity for ZIPK produced no effect on cells or tissues. These findings are consistent with a mechanism of action wherein HS38 specifically targets ZIPK in smooth muscle. The discovery of HS38 provides a lead scaffold for the development of therapeutic agents for smooth muscle related disorders and a chemical means to probe the function of DAPK1 and ZIPK across species.
Heparin Induced Thrombocytopenia: a Prospective Study (1980)

Thrombocytopenia occurred in 11.6% of 43 patients prospectively randomized to receive either bovine lung or porcine mucosal heparin. Four patients received bovine heparin and developed mild to moderate thrombocytopenia after eight to twelve days which resolved when therapy was stopped in one to six days. One patient received porcine heparin and developed mild thrombocytopenia after four days. The thrombocytopenia resolved in one day in spite of continued heparin therapy. Serial blood samples from the five thrombocytopenic patients were studied for their in vitro effect upon normal platelets. These samples induced a high release of serotonin from normal platelets or caused normal platelets to aggregate in the presence of additional heparin. Release or aggregation coincided with or occurred shortly after nadir platelet counts were reached and returned toward normal following cessation of heparin. Our data constitute the first prospective study of heparin induced thrombocytopenia in which serial blood samples were studied before, during and following the onset of thrombocytopenia. They strongly support the presence of a heparin dependent co-factor, presumably an antibody, as the cause for thrombocytopenia.
Escherichia coli Aspartate Transcarbamylase: the Relation Between Structure and Function (1988)

The x-ray structures of the allosteric enzyme aspartate transcarbamylase from Escherichia coli have been solved and refined for both allosteric forms. The T form was determined in the presence of the heterotropic inhibitor cytidine triphosphate, CTP, while the R form was determined in the presence of the bisubstrate analog N-phosphonacetyl-L-aspartate. These two x-ray structures provide the starting point for an understanding of how allosteric enzymes are able to control the rates of metabolic pathways. Insights into the mechanisms of both catalysis and homotropic cooperativity have been obtained by using site-directed mutagenesis to probe residues thought to be critical to the function of the enzyme based on these x-ray structures.
Loadstar: A Load Shedding Scheme for Classifying Data Streams (2005)

We consider the problem of resource allocation in mining multiple data streams. Due to the large volume and the high speed of streaming data, mining algorithms must cope with the effects of system overload. How to realize maximum mining benefits under resource constraints becomes a challenging task. In this paper, we propose a load shedding scheme for classifying multiple data streams. We focus on the following problems: i) how to classify data that are dropped by the load shedding scheme? and ii) how to decide when to drop data from a stream? We introduce a quality of decision (QoD) metric to measure the level of uncertainty in classification when exact feature values of the data are not available because of load shedding. A Markov model is used to predict the distribution of feature values and we make classification decisions using the predicted values and the QoD metric. Thus, resources are allocated among multiple data streams to maximize the quality of classification decisions. Furthermore, our load shedding scheme is able to learn and adapt to changing data characteristics in the data streams. Experiments on both synthetic data and real-life data show that our load shedding scheme is effective in improving the overall accuracy of classification under resource constraints.