gebhart/patrepeval huggingface dataset:
Insulinotropic Hormone Glucagon-Like Peptide-1 Differentiation of Human Pancreatic Islet-Derived Progenitor Cells into Insulin-Producing Cells (2002)

Glucagon-like peptide-1 (GLP-1) is an intestinal incretin hormone, derived from the processing of proglucagon, that exerts insulinotropic actions on insulin-producing pancreatic islet beta-cells. Recently GLP-1 was shown to stimulate the growth and differentiation (neogenesis) of beta-cells and appears to do so by inducing the expression of the homeodomain protein IDX-1 (islet duodenum homeobox-1; also known as PDX-1, pancreatic and duodenal homeobox gene; and as IPF-1, insulin promoter factor), which is required for pancreas development and the expression of beta-cell-specific genes. Earlier we identified multipotential progenitor cells in the islet and ducts of the pancreas, termed nestin-positive islet-derived progenitor cells (NIPs). Here we report the expression of functional GLP-1 receptors on NIPs and that GLP-1 stimulates the differentiation of NIPs into insulin-producing cells. Furthermore, confluent NIP cultures express the proglucagon gene and secrete GLP-1. These findings suggest a model of islet development in which pancreatic progenitor cells express both GLP-1 receptors and proglucagon with the formation of GLP-1. Locally produced GLP-1 may act as an autocrine/paracrine developmental morphogen on receptors on NIPs, resulting in the activation of IDX-1 and the expression of the proinsulin gene conferring a beta-cell phenotype. GLP-1 may be an important morphogen both for the embryonic development of the pancreas and for the neogenesis of beta-cells in the islets of the adult pancreas.
Aging and innate immune cells (2004)

The innate immune system serves an important role in preventing microbial invasion. However, it experiences significant changes with advancing age. Among the age-associated changes are: Aged macrophages and neutrophils have impaired respiratory burst and reactive nitrogen intermediates as a result of altered intracellular signaling, rendering them less able to destroy bacteria. Aged neutrophils are also less able to respond to rescue from apoptosis. Aged dendritic cells (DC) are less able to stimulate T and B cells. The altered T cell stimulation is a result of changes in human leukocyte antigen expression and cytokine production, and lower B cell stimulation is a result of changes in DC immune complex binding. Natural killer (NK) cells from the elderly are less capable of destroying tumor cells. NK T cells increase in number and have greater interleukin-4 production with age. Levels of various complement components are also altered with advancing age.
Sulfuryl Transfer: The Catalytic Mechanism of Human Estrogen Sulfotransferase (1998)

Estrogen sulfotransferase (EST) catalyzes the transfer of the sulfuryl group from 3'-phosphoadenosine 5'-phosphosulfate (PAPS) to 17beta-estradiol (E2). The sulfation of E2 prevents it from binding to, and thereby activating, the estrogen receptor. The regulation of EST appears to be causally linked to tumorigenesis in the breast and endometrium. In this study, recombinant human EST is characterized, and the catalytic mechanism of the transfer reaction is investigated in ligand binding and initial rate experiments. The native enzyme is a dimer of 35-kDa subunits. The apparent equilibrium constant for transfer to E2 is (4.5 +/- 0.2) x 10(3) at pH 6.3 and T = 25 +/- 2 degrees C. Initial rate studies provide the kinetic constants for the reaction and suggest a sequential mechanism. E2 is a partial substrate inhibitor (Ki = 80 +/- 5 nM). The binding of two E2 per EST subunit suggests that the partial inhibition occurs through binding at an allosteric site. In addition to providing the dissociation constants for the ligand-enzyme complexes, binding studies demonstrate that each substrate binds independently to the enzyme and that both the E.PAP.E2S and E.PAP.E2 dead-end complexes form. These results strongly suggest a Random Bi Bi mechanism with two dead-end complexes.
Synthesis and Structure Identification of Thiol Conjugates of (−)-Epigallocatechin Gallate and Their Urinary Levels in Mice (2005)

(-)-Epigallocatechin gallate (EGCG), the most abundant and most biologically active compound in tea, has been proposed to have many beneficial health effects. The metabolic fate of EGCG, however, is not well understood. In the present study, we found that EGCG can be oxidized by peroxidase and hydrogen peroxide and then reacted with cysteine or glutathione to form conjugates. The structures of the cysteine and glutathione conjugates of EGCG were identified using 2D NMR and MS. Two thiol conjugates of EGCG (2'-cysteinyl EGCG and 2' '-cysteinyl EGCG) were identified by ESI-LC-MS/MS analysis from the urine samples of mice administered 200 or 400 mg/kg EGCG, i.p. These conjugates were not found in urine samples of mice after receiving EGCG at 50 mg/kg i.p., or 2000 mg/kg i.g., or in human urine following consumption of 3 g of decaffeinated green tea solids (containing 333 mg EGCG). At high doses, EGCG is believed to be oxidized to form EGCG quinone, which can react with glutathione to form the thiol conjugates. These results suggest that detectable amounts of thiol conjugates of EGCG are formed only after rather high doses of EGCG are given to the mice.
To prune, or not to prune: exploring the efficacy of pruning for model compression (2017)

Model pruning seeks to induce sparsity in a deep neural network's various connection matrices, thereby reducing the number of nonzero-valued parameters in the model. Recent reports (Han et al., 2015; Narang et al., 2017) prune deep networks at the cost of only a marginal loss in accuracy and achieve a sizable reduction in model size. This hints at the possibility that the baseline models in these experiments are perhaps severely over-parameterized at the outset and a viable alternative for model compression might be to simply reduce the number of hidden units while maintaining the model's dense connection structure, exposing a similar trade-off in model size and accuracy. We investigate these two distinct paths for model compression within the context of energy-efficient inference in resource-constrained environments and propose a new gradual pruning technique that is simple and straightforward to apply across a variety of models/datasets with minimal tuning and can be seamlessly incorporated within the training process. We compare the accuracy of large, but pruned models (large-sparse) and their smaller, but dense (small-dense) counterparts with identical memory footprint. Across a broad range of neural network architectures (deep CNNs, stacked LSTM, and seq2seq LSTM models), we find large-sparse models to consistently outperform small-dense models and achieve up to 10x reduction in number of non-zero parameters with minimal loss in accuracy.
Role of carbohydrates in glycoprotein hormone signal transduction (1989)

The structure of the polypeptide chains and oligosaccharide moieties of the alpha and beta subunits of pituitary and placental glycoprotein hormones are known. The dimeric polypeptide structure (but not the carbohydrate) is important for binding of the hormone to specific receptors. The N-linked but not O-linked carbohydrates, on the other hand, are required in some manner to activate the effector system. Hormones with depleted carbohydrate content (deglycosylated hormones) interact with receptor but are unable to activate intracellular events. Because of such discordant properties, these forms act as competitive inhibitors of hormone action. Through a combination of chemical deglycosylation procedures and site-directed mutagenesis, the first site of N-glycosylation from the NH2 terminus of the common alpha subunit has been identified to be more critical for glycoprotein hormone signal transduction. Control of glycosylation by the endocrine milieu could contribute to regulation of hormone function by secreting variable forms of agonist/antagonist.
In vivo activity of nuclease-resistant siRNAs (2004)

Chemical modifications have been incorporated into short interfering RNAs (siRNAs) without reducing their ability to inhibit gene expression in mammalian cells grown in vitro. In this study, we begin to assess the potential utility of 2′-modified siRNAs in mammals. We demonstrate that siRNA modified with 2′-flouro (2′-F) pyrimidines are functional in cell culture and have a greatly increased stability and a prolonged half-life in human plasma as compared to 2′-OH containing siRNAs. Moreover, we show that the 2′-F containing siRNAs are functional in mice and can inhibit the expression of a target gene in vivo. However, even though the modified siRNAs have greatly increased resistance to nuclease degradation in plasma, this increase in stability did not translate into enhanced or prolonged inhibitory activity of target gene reduction in mice following tail vein injection. Thus, this study shows that 2′-F modified siRNAs are functional in vivo, but that they are not necessarily more potent than unmodified siRNAs in animals.
An Easier, Reproducible, and Mass‐Production Method to Study the Blood–Brain Barrier In Vitro (1990)

To provide an "in vitro" system for studying brain capillary function, we have developed a process of coculture that closely mimics the "in vivo" situation by culturing brain capillary endothelial cells on one side of a filter and astrocytes on the other. Under these conditions, endothelial cells retain all the endothelial cell markers and the characteristics of the blood-brain barrier, including tight junctions and gamma-glutamyl transpeptidase activity. The average electric resistance for the monolayers was 661 omega cm2. The system is impermeable to inulin and sucrose but allows the transport of leucine. Arabinose treatment increases transcellular transport flux by 70%. The relative ease with which such monolayers can be produced in large quantities would facilitate the "in vitro" study of brain capillary functions.
Current and Investigational Therapies for Patients with CLL (2006)

Clinical and laboratory investigations are driving the rapid change in treatments for patients with chronic lymphocytic leukemia (CLL). Randomized trials have demonstrated superior activity for fludarabine combined with cyclophosphamide versus single-agent fludarabine or chlorambucil as initial treatment. Chemoimmunotherapy holds promise for further improvement and is being tested in randomized trials. New combinations and agents are being identified and tested. Eliminating minimal residual disease is a therapeutic endpoint that may prove to prolong survival and is also under investigation in prospective clinical trials. Work continues toward improving survival and potentially curing patients of this disease.
Global Epiproteomic Signatures Distinguish Embryonic Stem Cells from Differentiated Cells (2007)

Complex organisms contain a variety of distinct cell types but only a single genome. Therefore, cellular identity must be specified by the developmentally regulated expression of a subset of genes from an otherwise static genome. In mammals, genomic DNA is modified by cytosine methylation, resulting in a pattern that is distinctive for each cell type (the epigenome). Because nucleosomal histones are subject to a wide variety of post-translational modifications (PTMs), we reasoned that an analogous "epiproteome" might exist that could also be correlated with cellular identity. Here, we show that the quantitative evaluation of nucleosome PTMs yields epiproteomic signatures that are useful for the investigation of stem cell differentiation, chromatin function, cellular identity, and epigenetic responses to pharmacologic agents. We have developed a novel enzyme-linked immunosorbent assay-based method for the quantitative evaluation of the steady-state levels of PTMs and histone variants in preparations of native intact nucleosomes. We show that epiproteomic responses to the histone deacetylase inhibitor trichostatin A trigger changes in histone methylation as well as acetylation, and that the epiproteomic responses differ between mouse embryonic stem cells and mouse embryonic fibroblasts (MEFs). ESCs subjected to retinoic acid-induced differentiation contain reconfigured nucleosomes that include increased content of the histone variant macroH2A and other changes. Furthermore, ESCs can be distinguished from embryonal carcinoma cells and MEFs based purely on their epiproteomic signatures. These results indicate that epiproteomic nucleosomal signatures are useful for the investigation of stem cell identity and differentiation, nuclear reprogramming, epigenetic regulation, chromatin dynamics, and assays for compounds with epigenetic activities. Disclosure of potential conflicts of interest is found at the end of this article.
Accutin, a New Disintegrin, Inhibits Angiogenesis In Vitro and In Vivo by Acting as Integrin vβ3 Antagonist and Inducing Apoptosis (1998)

Endothelial integrins play an essential role in angiogenesis and cell survival. Accutin, a new member of disintegrin family derived from venom of Agkistrodon acutus, potently inhibited human platelet aggregation caused by various agonists (eg, thrombin, collagen, and, adenosine diphosphate [ADP]) through the blockade of fibrinogen binding to platelet glycoprotein IIb/IIIa (ie, integrin IIbβ3). In this report, we describe that accutin specifically inhibited the binding of monoclonal antibody (MoAb) 7E3, which recognizes integrin vβ3, to human umbilical vein endothelial cells (HUVECs), but not those of other anti-integrin MoAbs such as 2β1, 3β1, and 5β1. Moreover, accutin, but not the control peptide GRGES, dose-dependently inhibited the 7E3 interaction with HUVECs. Both 7E3 and GRGDS, but not GRGES or Integrelin, significantly blocked fluorescein isothiocyanate-conjugated accutin binding to HUVEC. In functional studies, accutin exhibited inhibitory effects on HUVEC adhesion to immobilized fibrinogen, fibronectin and vitronectin, and the capillary-like tube formation on Matrigel in a dose- and RGD-dependent manner. In addition, it exhibited an effective antiangiogenic effect in vivo when assayed by using the 10-day-old embryo chick CAM model. Furthermore, it potently induced HUVEC apoptotic DNA fragmentation as examined by electrophoretic and flow cytometric assays. In conclusion, accutin inhibits angiogenesis in vivo and in vitro by blocking integrin vβ3 of endothelial cells and by inducing apoptosis. The antiangiogenic activity of disintegrins might be explored as the target of developing the potential antimetastatic agents. © 1998 by The American Society of Hematology.
Concentration, compartmentation and metabolic function of intracellular free Mg2+. (2006)

Intracellular total Mg2+ and free Mg2+ are compartmentalized between cell organelles and within the cytosol. Different values of [Mg2+]i in the cytosol of the same cell type were measured by various investigators. A main reason for the differences is the uncertainty of the dissociation constants used for the Mg furaptra complex in the fluorescence method and for MgATP when 31P NMR was employed. The more realistic KD values of Mg furaptra and MgATP measured under in situ conditions are higher than the KDs used by most investigators. The [Mg2+]is obtained and the KDs used by various authors were presented. The role of intracellular Mg2, in metabolic functions and the action of various effectors on [Mg2+]i and [Ca2+] was reviewed. Intracellular Mg2+ may have a permissive role supporting the effector-induced mechanisms that are mediated by Ca2+ as a second messenger.
Anaerobic Degradation of Cyanuric Acid, Cysteine, and Atrazine by a Facultative Anaerobic Bacterium (1983)

A facultative anaerobic bacterium that rapidly degrades cyanuric acid (CA) was isolated from the sediment of a stream that received industrial wastewater effluent. CA decomposition was measured throughout the growth cycle by using a high-performance liquid chromatography assay, and the concomitant production of ammonia was also measured. The bacterium used CA or cysteine as a major, if not the sole, carbon and energy source under anaerobic, but not aerobic, conditions in a defined medium. The cell yield was greatly enhanced by the simultaneous presence of cysteine and CA in the medium. Cysteine was preferentially used rather than CA early in the growth cycle, but all of the CA was used without an apparent lag after the cysteine was metabolized. Atrazine was also degraded by this bacterium under anaerobic conditions in a defined medium.
Complex immunomodulatory effects of interferon‐β in multiple sclerosis include the upregulation of T helper 1‐associated marker genes (2001)

Multiple sclerosis (MS) is considered an autoimmune disease that is mediated by proinflammatory T helper-1 lymphocytes. The putative mechanism of interferon-beta (IFN-beta), an approved treatment for MS, includes the inhibition of T-cell proliferation, blocking of blood-brain-barrier opening and T-cell transmigration into the brain via interference with cell adhesion, and the upregulation of anti-inflammatory cytokines. In the present study, a gene expression analysis of IFN-beta-treated peripheral blood mononuclear cells by cDNA microarray documents the broad effects of IFN-beta that are not purely anti-inflammatory. Specifically, we addressed the effect of IFN-beta on T helper-1 differentiation- or lineage markers such as the IL-12 receptor beta2 chain and the chemokine receptor CCR5 that have been implicated in the pathogenesis of MS. Both markers were significantly upregulated in vitro and in vivo under IFN-beta therapy, supporting that this cytokine exerts complex effects on the immune system. The combination of cDNA microarray and quantitative PCR will expand our knowledge of the immunological effects of such pleiotropic agents as IFN-beta, may provide a key to why certain patients fail to respond, and eventually may influence our view of the disease pathogenesis.
Geometric Disassembly of Dendrimers:  Dendritic Amplification (2003)

Geometric disassembly of dendritic structures was realized by a cascade cleavage reaction triggered by an initially stimulated group at the dendrimer core. Release of an exponential number of dendrimer fragments was a result of the branching nature of the cleavage pathway. Evidence for the completion of the disassembly process was provided by the absorbance peak of the p-nitrophenoxide ion that was covalently installed at the periphery of the dendrons for this purpose. The release by dendrimer disassembly of an exponential number of dendrimer fragments that serve to alter the properties of a system is termed dendritic amplification.
A SOI-RF-CMOS technology on high resistivity SIMOX substrates for microwave applications to 5 GHz (1997)

A silicon-on-insulator (SOI) RF complementary metal-oxide-semiconductor (CMOS) technology for microwave applications up to 5 GHz has been developed. The technology is based on ultra large scale integration (ULSI) CMOS processing using a high resistivity separation through implanted oxygen (SIMOX) substrate of typically 10 k/spl Omega/cm. Dedicated RF n-channel and RF p-channel MOSFET's with an effective channel length of 0.20 and 0.40 /spl mu/m have been fabricated using a multiple gate finger design. Maximum frequencies of operation f/sub max/ of 46 GHz (NMOS) and 16 GHz (PMOS) have been measured. Metal-Insulator-Metal (MIM) capacitances with up to 63 pF with 70 nF/cm/sup 2/, planar inductances with up to 25 nH and a quality factor up to 12 and coplanar waveguides with a loss <2.8 dB/cm at 5 GHz are monolithically integrated in the technology without additional processes and materials. Using this SOI-CMOS technology we have fabricated integrated silicon RF circuits, e.g., amplifiers, oscillators, and mixers, operating in the 2 GHz range.
A Fluorinated Dendrimer-Based Nanotechnology Platform (2010)

A novel fluorinated dendrimer-based nanotechnology platform in (19)F MRI and a new bifunctional DOTA chelate were prepared and characterized. We introduce 2 methods for reducing the (19)F longitudinal relaxation time: (a) Increasing the generation; (b) covalent and noncovalent introduction of Gd(III)-chelates. A new bifunctional Gd(III)-chelate is presented. The investigations of imaging on rats suggest potential importance of the dendrimers in (19)F MRI application.
Identification of the Bacillus subtilis pur operon repressor. (1995)

Transcription of the Bacillus subtilis pur operon is repressed in response to a signal of excess adenine. We have purified the repressor protein and have identified, cloned, and overexpressed the purR regulatory gene that controls transcription initiation of the operon. B. subtilis purR encodes a 62-kDa homodimer that binds to the pur operon control region. The PurR binding site which overlaps the promoter encompasses approximately 110 bp. The protein-DNA interaction is inhibited by 5-phosphoribosyl 1-pyrophosphate. A mutation that deletes the repressor binding site or one that disrupts purR abolishes binding activity in vitro and repression of transcription in vivo in response to the excess adenine signal. These results lead to a model in which an excess-adenine signal is transmitted to PurR via the 5-phosphoribosyl 1-pyrophosphate pool. In addition, purR is autoregulated. There is no structural or mechanistic similarity between the B. subtilis and Escherichia coli purine repressors.
Localization of cervical and cervicomedullary stimulation leads for pain treatment using median nerve somatosensory evoked potential collision testing (2010)

Somatosensory evoked potentials can be used safely and successfully for predicting the lateralization of cervical spinal cord stimulator placement. Moreover, they can also intraoperatively alert the surgical team to inadvertent displacement of a lead during anchoring. Further studies are needed to determine whether apart from assisting with proper lateralization, SSEP collision testing may help to optimize electrode positioning and improve pain control outcomes.
An adaptive input shaping control scheme for vibration suppression in slewing flexible structures (1993)

The application of an input precompensation scheme for vibration suppression in slewing flexible structures, with particular application to flexible-link robotic manipulator systems, is considered. The control from such input shaping schemes corresponds to a feedforward term that convolves in real time the desired reference input with a sequence of impulses and produces a vibration-free output. The robustness of such an algorithm with respect to modal frequency variations is not satisfactory but can be improved by convolving the input with a longer sequence of impulses, the tradeoff being a decrease in the transient response speed. An adaptive precompensation scheme that can be implemented by combining a frequency domain identification scheme, used to estimate the modal frequencies online, with a subsequent scheme for adjusting the spacing between the impulses is proposed. The combined adaptive input shaping scheme provides the most rapid slew that results in a vibration-free output. Experimental results for a single flexible link are presented to verify the technique.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Preparation of substituted N-phenyl-4-aryl-2-pyrimidinamines as mediator release inhibitors (1993)

The role of immunologically released mediators, such as histamine, leukotrienes, and platelet-activating factor, is well-established for asthma and other allergic disorders. Developing therapeutic agents which would block mediator release from mast cells and other relevant cell types would provide a rational approach to asthma therapy. Using human basophil as a screen, a series of 4-aryl-2-(phenylamino)pyrimidines was found which inhibited mediator release. These compounds were prepared by condensing acetyl heterocycles with dimethylformamide dimethyl acetal to form enaminones which are cyclized with aryl guanidines to give pyrimidines. After examining a large number of analogs, N-[3-(1H-imidazol-1-yl)phenyl]-4-(2-pyridinyl)-2- pyrimidinamine (1-27) was chosen for toxicological evaluation.