gebhart/patrepeval huggingface dataset:
Toxic shock syndrome toxin-1-induced death is prevented by CTLA4Ig (1996)

Lethal toxic shock syndrome (TSS) results from the MHC class II presentation of bacterial superantigens, most commonly toxic shock syndrome-1 (TSST-1), to specific TCR Vbeta-bearing T cells. This superantigen-induced stimulation of whole T cell subsets leads to the exuberant cytokine production that in turn causes the shock syndrome. Since T cell activation and cytokine production are known to be dependent upon costimulatory signals, we reasoned that interfering with costimulation could effect TSS outcome. To test that hypothesis, we evaluated the effect of CTLA4Ig, a fusion protein known to block costimulatory signaling, on TSST-1-induced responses. CTLA4Ig not only blocked TSST-1-stimulated T cell proliferation by 90% in vitro, it also strikingly ameliorated TSST-1 induced TSS in vivo. While all mice co-administered TSST-1 and control Ig died, 75% of the CTLA4Ig plus TSST-1-treated mice survived. This salutary CTLA4Ig effect correlated with markedly diminished TSST-1 induced serum levels of TNF-alpha and IFN-gamma, but TSST-1-triggered IL-2 release was not affected. Surprisingly, while CTLA4Ig treatment group survivors remained sensitive to TSS induced by an unrelated superantigen (staphylococcal enterotoxin B), they were completely resistant to a second TSST-1 challenge. Furthermore, this TSST-1 resistance could be transferred to naive C57BL/6 mice using CD8+ T cells from CTLA4Ig plus TSST-1-primed mice. These data suggest several novel interpretations: 1) that the release of TNF-alpha and IL-2 have a different costimulatory signal dependence in vivo, 2) that the TSS resistance conferred by CTLA4Ig was superantigen specific, and 3) that the delayed and transferable resistance to TSST-1 was due, at least in part, to CD8+ T cells with suppressor function.
A reconfigurable compute engine for real-time vision automata prototyping (2002)

Describes a reconfigurable computer engine called the Data-Flow Functional Computer (DFFC), which is dedicated to rapid prototyping of real-time vision automata. The computer consists of a regular 3D array of very coarse grain application-specific FPGAs, called the 'field-programmable operator array' (FPOA). Each FPOA includes two configurable data paths and ten input/output ports. Specific development tools allow easy and efficient use of the computer. A high-level description (in a functional language) is compiled into a DFFC configuration using an operator library. Several significant applications (connected component labelling, nonlinear filtering, coloured object tracking) have been implemented using our tools. An environment for automatic derivation of vision automata from a DFFC configuration is currently under development.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Of Mice and Not Men: Differences between Mouse and Human Immunology (2004)

Mice are the experimental tool of choice for the majority of immunologists and the study of their immune responses has yielded tremendous insight into the workings of the human immune system. However, as 65 million years of evolution might suggest, there are significant differences. Here we outline known discrepancies in both innate and adaptive immunity, including: balance of leukocyte subsets, defensins, Toll receptors, inducible NO synthase, the NK inhibitory receptor families Ly49 and KIR, FcR, Ig subsets, the B cell (BLNK, Btk, and lambda5) and T cell (ZAP70 and common gamma-chain) signaling pathway components, Thy-1, gammadelta T cells, cytokines and cytokine receptors, Th1/Th2 differentiation, costimulatory molecule expression and function, Ag-presenting function of endothelial cells, and chemokine and chemokine receptor expression. We also provide examples, such as multiple sclerosis and delayed-type hypersensitivity, where complex multicomponent processes differ. Such differences should be taken into account when using mice as preclinical models of human disease.
Chemoselective Oxidation of Carbon-Carbon Double or Triple Bonds to 1,2-Diketones with DMSO-Based Reagents (1995)

HBr/DMSO selectively oxidizes the double bond in (E)-1-(2-phenylethylen)-4-(phenylethynyl)benzene (1) to 1,2-diketone 2. However, I2/DMSO and PdCl2/DMSO oxidize only the triple bond in 1 to 1,2-diketone 3. A similar trend of chemoselectivity is shown for the oxidation of (E)-1,4-diphenyl-1-buten-3-yne (6) with the DMSO-based reagents.
Multiplexed Protein Arrays Enabled by Polymer Pen Lithography: Addressing the Inking Challenge (2009)

High-end printer: A novel way of using a polymer pen lithography (PPL) array mould to localize different inks on the pens of a PPL array has been developed. This technique allows for rapid pen inking and subsequent generation of multiplexed patterns of up to 150 000 nano- and microscale protein features per second (see picture). It is a general approach, which in principle can be extended to any substance that can be transported by PPL.
Gene Therapy with BMN 270 Results in Therapeutic Levels of FVIII in Mice and Primates and Normalization of Bleeding in Hemophilic Mice (2017)

Hemophilia A is an X-linked bleeding disorder caused by mutations in the gene encoding the factor VIII (FVIII) coagulation protein. Bleeding episodes in patients are reduced by prophylactic therapy or treated acutely using recombinant or plasma-derived FVIII. We have made an adeno-associated virus 5 vector containing a B domain-deleted (BDD) FVIII gene (BMN 270) with a liver-specific promoter. BMN 270 injected into hemophilic mice resulted in a dose-dependent expression of BDD FVIII protein and a corresponding correction of bleeding time and blood loss. At the highest dose tested, complete correction was achieved. Similar corrections in bleeding were observed at approximately the same plasma levels of FVIII protein produced either endogenously by BMN 270 or following exogenous administration of recombinant BDD FVIII. No evidence of liver dysfunction or hepatocyte endoplasmic reticulum stress was observed. Comparable doses in primates produced similar levels of circulating FVIII. These preclinical data support evaluation of BMN 270 in hemophilia A patients.
Influence of Moisture on CO2 Separation from Gas Mixture by a Nanoporous Adsorbent Based on Polyethylenimine-Modified Molecular Sieve MCM-41 (2005)

Adsorption separation of CO2 from simulated flue gas containing CO2, O2, and N2 with and without moisture was investigated using a novel nanoporous adsorbent based on polyethylenimine (PEI)-modified mesoporous molecular sieve MCM-41 in a flow system. The CO2 adsorption capacity and CO2 separation selectivity of MCM-41 were greatly improved by loading PEI into its nanosized pore channels, which made the resulting adsorbent operating like a “molecular basket” for CO2. CO2 adsorption capacity of the MCM-41-PEI adsorbent for the simulated moist flue gas was higher than that for the simulated dry flue gas. CO2 separation selectivity of the MCM-41-PEI adsorbent was also improved in the presence of moisture when compared with those in the dry gas condition. The influence of moisture concentrations in the simulated flue gas on the CO2 adsorption separation performance was also examined. The results of adsorption/desorption separation cycles showed that the MCM-41-PEI adsorbent was stable over 10 cycles of adsorption/desorption operations. The hydrothermal stability of the “molecular basket” adsorbent was better than that of the MCM-41 support alone.
Reliability of thin oxides grown on deuterium implanted silicon substrate (2001)

We have investigated the reliability of gate oxide with deuterium incorporated at the Si/SiO/sub 2/ interface through low energy ion implantation into the silicon substrate before thin gate oxide growth. Deuterium implantation at a dose of 1/spl times/10/sup 14//cm/sup 2/ at 25 keV showed improved breakdown characteristics. Charge-to-breakdown seems to correlate well with the interface state density measured by the conductance method.
Evaluation of a novel point-of-care system, the i-STAT portable clinical analyzer (1993)

We evaluated a novel system designed for rapid, point-of-care measurement of sodium, potassium, chloride, urea nitrogen, glucose, and hematocrit. The i-STAT Portable Clinical Analyzer (PCA) system is composed of a hand-held analyzer and disposable cartridges. Sample analysis takes place in the cartridge, which contains a series of thin-film electrodes microfabricated on silicon chips. The PCA was evaluated for precision, accuracy, and utility in emergency department and stat laboratory settings. Precision did not differ significantly between these two locations, the CVs being as follows: sodium, 0.46-0.89%; potassium, 1.06-1.45%; chloride, 0.69-2.76%; urea nitrogen, 2.54-6.12%; and glucose, 4.39-5.19%. The assessment of accuracy was based on comparison of patients' sample values analyzed by the PCA and the Kodak Ektachem 700 (or the Coulter ST for hematocrit). Regression statistics were acceptable for all analytes except chloride, for which the regression data were influenced by the limited range of results. A difference plot of the chloride comparison showed that the bias rarely exceeded 5 mmol/L. Mean hematocrit values significantly differed between the PCA and the Coulter ST, apparently because of different calibration procedures.
Identification of the Heme Compound Copurified with Deoxyribonucleic Acid (DNA) from Bloodstains, a Major Inhibitor of Polymerase Chain Reaction (PCR) Amplification (1994)

Abstract The heme compound found in deoxyribonucleic acid (DNA) extracted from bloodstains, which is regarded as a major inhibitor of polymerase chain reaction (PCR), was characterized in comparison with alkaline and acid hematin, histidine and ammonia hemochromogens, and globin and serum albumin hemochromogens digested by proteinase K. Alkaline and acid hematin were almost completely removed by phenol/chloroform treatment and ethanol precipitation, so as not to be copurified with DNA from the specimens. Spectrophotometric results indicated that the contaminant was likely to be the product of proteinase K digestion of some heme-blood protein complex, which was not completely extracted by organic solvents and remained in the ethanol precipitates of DNA. The results of polyacrylamide gradient gel electrophoresis and intensity of the inhibition of PCR suggested that the ligand of the contaminant was a somewhat large molecule, resistant to the proteolysis by proteinase K. The addition of bovine serum albumin to the reaction mixture prevented the inhibition of PCR by the heme compounds, probably by binding to the heme. This showed that the inhibition was not due to the irreversible inactivation of the enzyme.
Formation of Thermoresponsive Poly(N‐isopropylacrylamide)/Dextran Particles by Atom Transfer Radical Polymerization (2003)

Abstract Thermoresponsive poly( N ‐isopropylacrylamide)/dextran hybrid particles were formed by surface‐initiated, aqueous atom transfer radical polymerization via the attachment of a polymerization initiator onto dextran microspheres and polymerization of N ‐isopropylacrylamide. The resulting hybrid particles were about 250 μm in diameter, and showed thermoresponsiveness: the average diameter changed from 273 μm to 214 μm when the temperature was increased from 25 °C to 40 °C (22% decrease). Schematic description of the procedure. magnified image Schematic description of the procedure.
Stimulatory effects of the protein tyrosine phosphatase inhibitor, pervanadate, on T-cell activation events. (1993)

Ligation of the multimeric T-cell antigen receptor complex (TCR) triggers a pleiotropic cellular activation response that includes lymphokine secretion, cell-cycle progression, and ultimately, T-cell proliferation. The earliest detectable biochemical event triggered by TCR cross-linkage is the tyrosine phosphorylation of specific intracellular proteins, which, in turn, propagate receptor-mediated signals into the cytoplasm and nucleus. In this study, we have examined the effects of pervanadate, a powerful inhibitor of protein tyrosine phosphatases (PTP), on the activation state of the human leukemic T-cell line, Jurkat. Treatment of Jurkat cells with pervanadate rapidly induced a series of proximal T-cell activation events that closely resembled those induced by TCR-dependent stimuli. Moreover, pervanadate treatment, like TCR cross-linkage, stimulated interleukin-2 production in wild-type Jurkat cells, indicating that the biochemical events initiated by this TCR-independent stimulus were sufficient to induce lymphokine gene expression. Exposure of intact cells to pervanadate also stimulated the in vitro catalytic activities of both p59fyn and p56lck, src family kinases strongly implicated in TCR-mediated signaling. The stimulatory effects of pervanadate on protein tyrosine kinase-mediated signaling events were accompanied by a marked inhibition of CD45-associated PTP activity. However, the ability of pervanadate to stimulate tyrosine phosphorylation in CD45-negative Jurkat cells suggests that PTPs other than CD45 are important intracellular targets for pervanadate. These studies demonstrate that inhibition of PTP activities in Jurkat cells leads to a T-cell activation response that is remarkably similar to that induced by TCR crosslinkage.
P2Z-Independent and P2Z Receptor-Mediated Macrophage Killing byPseudomonas aeruginosaIsolated from Cystic Fibrosis Patients (1999)

We demonstrate that a mucoid, alginate-producing strain of Pseudomonas aeruginosa isolated from the lungs of a cystic fibrosis (CF) patient secretes multiple enzymes with nucleoside diphosphate kinase (Ndk), ATPase, adenylate kinase, 5'-nucleotidase, and ATP-modifying enzymatic activities. The secretion is triggered at high cell density and in complex media but is greatly reduced when the mucoid cells are grown in mineral salts media or in presence of 5.0 mM Ca2+ or Mg2+. Interestingly, the secretion is triggered primarily in the mucoid CF isolate of strain 8821M (or in strain FRD1) but not in a nonmucoid laboratory strain, PAO1. The purified secreted Ndk shows 100% match in its N-terminal amino acid sequence with that of purified intracellular Ndk and demonstrates similar enzymatic properties. The N-terminal sequence of the purified ATPase isolated from an ndk knockout mutant shows its identity with that of the heat shock chaperonin Hsp60. During fractionation, the flowthrough fraction from a Mono Q column demonstrates the presence of 5'-nucleotidase, adenylate kinase, and a putative ATP reductase activity. These fractions demonstrate high cytotoxic activities for murine peritoneal primary macrophages which can be further stimulated in the presence of ATP or inhibited by pretreatment of macrophages with oxidized ATP (oATP). The cytotoxicity associated with ATP-induced stimulation is believed to be due to activation of macrophage surface-associated P2Z (P2X7) receptors, which are one of the purinergic receptors responsible for pore formation on macrophage membrane. Blocking of these receptors by pretreatment with oATP blocks ATP-induced macrophage cell death. Thus mucoid P. aeruginosa cells elaborate enzymes that modulate the external ATP levels of macrophages, thereby modulating macrophage cell death through P2Z receptor activation. Evidence for the presence of secreted cytotoxic agents that act independently of P2Z receptor activation is also presented.
Mixing Multiple Translation Models in Statistical Machine Translation (2012)

Statistical machine translation is often faced with the problem of combining training data from many diverse sources into a single translation model which then has to translate sentences in a new domain. We propose a novel approach, ensemble decoding, which combines a number of translation systems dynamically at the decoding step. In this paper, we evaluate performance on a domain adaptation setting where we translate sentences from the medical domain. Our experimental results show that ensemble decoding outperforms various strong baselines including mixture models, the current state-of-the-art for domain adaptation in machine translation. 1
Structure of M1 RNA as determined by psoralen cross-linking (1988)

The RNA moiety of ribonuclease P from Escherichia coli (M1 RNA) has been photoreacted with 4'-(hydroxymethyl)-4,5',8-trimethylpsoralen (HMT) and long-wave UV light (320-380 nm) in a buffer containing 60 mM Mg2+, where the RNA moiety acts as a true catalyst of tRNA processing. Limited specific digestion and two-dimensional gel electrophoresis yield fragments cross-linked by HMT. By photoreversal of the isolated cross-linked fragments and enzymatic sequencing of the fragments, the positions of the cross-links have been elucidated. This method allows us to locate the cross-link to +/- 15 nucleotides. Further assignments of the exact locations of the cross-links have been made on the basis of the known photoreactivity of the psoralen with different bases. Nine unique cross-links have been isolated in the M1 RNA including four long-range interactions. The short-range interactions are discussed here in detail.
PTEN Inhibition to Facilitate Intrinsic Regenerative Outgrowth of Adult Peripheral Axons (2010)

In vivo regeneration of peripheral neurons is constrained and rarely complete, and unfortunately patients with major nerve trunk transections experience only limited recovery. Intracellular inhibition of neuronal growth signals may be among these constraints. In this work, we investigated the role of PTEN (phosphatase and tensin homolog deleted on chromosome 10) during regeneration of peripheral neurons in adult Sprague Dawley rats. PTEN inhibits phosphoinositide 3-kinase (PI3-K)/Akt signaling, a common and central outgrowth and survival pathway downstream of neuronal growth factors. While PI3-K and Akt outgrowth signals were expressed and activated within adult peripheral neurons during regeneration, PTEN was similarly expressed and poised to inhibit their support. PTEN was expressed in neuron perikaryal cytoplasm, nuclei, regenerating axons, and Schwann cells. Adult sensory neurons in vitro responded to both graded pharmacological inhibition of PTEN and its mRNA knockdown using siRNA. Both approaches were associated with robust rises in the plasticity of neurite outgrowth that were independent of the mTOR (mammalian target of rapamycin) pathway. Importantly, this accelerated outgrowth was in addition to the increased outgrowth generated in neurons that had undergone a preconditioning lesion. Moreover, following severe nerve transection injuries, local pharmacological inhibition of PTEN or siRNA knockdown of PTEN at the injury site accelerated axon outgrowth in vivo. The findings indicated a remarkable impact on peripheral neuron plasticity through PTEN inhibition, even within a complex regenerative milieu. Overall, these findings identify a novel route to propagate intrinsic regeneration pathways within axons to benefit nerve repair.
Optimized T7 Amplification System for Microarray Analysis (2001)

Glass cDNA microarray technologies offer a highly parallel approach for profiling expressed gene sequences in disease-relevant tissues. However, standard hybridization and detection protocols are insufficient for milligram quantities of tissue, such as those derived from needle biopsies. Amplification systems utilizing T7 RNA polymerase can provide multiple cRNA copies from mRNA transcripts, permitting microarray studies with reduced sample inputs. Here, we describe an optimized T7-based amplification system for microarray analysis that yields between 200- and 700-fold amplification. This system was evaluated with both mRNA and total RNA samples and provided microarray sensitivity and precision that are comparable to our standard production process without amplification. The size distributions of amplified cRNA ranged from 200 bp to 4 kb and were similar to original mRNA profiles. These amplified cRNA samples were fluorescently labeled by reverse transcription and hybridized to microarrays comprising approximately 10,000 cDNA targets using a dual-channel format. Replicate hybridization experiments were conducted with the same and different tissues in each channel to assess the sensitivity and precision of differential expression ratios. Statistical analysis of differential expression ratios showed the lower limit of detection to be about 2-fold within and between amplified data sets, and about 3-fold when comparing amplified data to unamplified data (99.5% confidence).
A Communication Technique for Multipath Channels (1958)

Application of principles of statistical communication theory has led to a new communication system, called Rake, designed expressly to work against the combination of random multipath and additive noise disturbances. By coding the Mark-Space sequence of symbols to be transmitted into a wide-band signal, it becomes possible at the receiver to isolate those portions of the transmitted signal arriving with different delays, using correlation detection techniques. Before being recombined by addition, these separated signals are continuously and automatically processed so as to 1) apply to each an optimum weighting coefficient, derived from a measurement of the ionosphere response, and 2) introduce in each an appropriate delay such that they are all brought back into time coincidence. After a brief introduction, a functional description of the system is presented. There follows a review of the communication theory studies, which indicate that such systems have certain optimal properties. Details of design of an experimental prototype Rake system are followed by the results of limited field tests of this prototype. Conclusions and recommendations for future work are given.
Retinal damage after 3 to 4 months of elevated intraocular pressure in a rat glaucoma model. (2000)

The three-vein episcleral/limbal vein occlusion model for inducing glaucomatous pathology in the rat eye gives a consistent long-term elevation of IOP. After 3 to 4 months of approximately 100% increased IOP, the ERG responses begin to decline, there is a variable focal loss of RGCs, and some of the remaining RGCs show characteristics of stress and apoptosis. These changes seem consistent with retinal damage in human glaucoma (focal field defects), and this rat model appears to mimic some features of primary open-angle glaucoma.
New substrate passivation method dedicated to HR SOI wafer fabrication with increased substrate resistivity (2005)

We propose in this letter a new passivation method to get rid of parasitic surface conduction in oxidized high resistivity (HR) silicon and HR silicon-on-insulator (SOI) wafers. The method consists in passivating the HR substrate with a rapid thermal anneal (RTA)-crystallized layer of silicon. The electrical efficiency of this new passivation technique is analyzed and shown to be superior over previously published methods. The surface roughness as well as the stability over temperature of this layer are also investigated. It is shown that this new passivation method is the only one simultaneously combining a low surface roughness and a high stability over long thermal anneals. In the context of SOI technology, it therefore appears as the most suitable technique for the substrate passivation of HR SOI wafers, for which a bonding between an oxidized silicon wafer and a passivated HR substrate is required.
Pathogenic strategies of the oral anaerobe, Porphyromonas gingivalis (1995)

Adult periodontitis is a chronic inflammatory disease that affects over 49 million people in the USA alone. Porphyromonas (formerly Bacteroides) gingivalis, a Gram-negative anaerobe, has a diverse repertoire of virulence factors that may be involved in the induction or progression of periodontitis.