gebhart/patrepeval huggingface dataset:
Characterization of mAb AP422, a novel phosphorylation‐dependent monoclonal antibody against tau protein (1996)

A monoclonal antibody (AP422) specific for phosphoserine 422 in microtubule-associated protein tau has been produced. It strongly labels paired helical filament (PHF) tau from Alzheimer's disease brain in a phosphorylation-dependent manner. By contrast, AP422 only labels a small fraction of fetal tau and a very small fraction of tau from adult brain. The amount of tau phosphorylated at Ser-422 in normal brain is minor relative to that phosphorylated at sites recognized by other phosphorylation-dependent anti-tau antibodies of known epitope. It follows that AP422 is the most specific anti-tau antibody available for detecting the neurofibrillary lesions of Alzheimer's disease. We also show that Ser-422 in tau is a good in vitro substrate for mitogen-activated protein kinase, but not for glycogen synthase kinase-3 or neuronal cdc2-like kinase.
Fiber Optic Bragg Grating Sensors (1990)

This paper describes a new method that we have developed to generate Bragg grating filters in germania-doped communication fibers and discusses their applications as sensors. The gratings are formed by exposing a short section of the core, through the side of the fiber, to an interference pattern of intersecting coherent beams of UV light. A permanent periodic index modulation is produced by the interference fringes. It forms a phase grating which acts as a band rejection filter, passing wavelengths that are not in resonance with the grating and strongly reflecting wavelengths which satisfy the Bragg condition. The grating wavelength is sensitive to changes temperature and strain. Measurements of the shift in Bragg wavelength with these quantities are reported and compared with computed estimates of the sensitivity. A large number of independent gratings can be easily written along a length of fiber to make a distributed sensor system. We have also demonstrated that Bragg gratings can wavelength tune laser diodes, which could be used for detecting the wavelength shift of the Bragg sensors.
GM-CSF Gene-Transduced Tumor Vaccines (2005)

GVAX is a GM-CSF gene-transduced tumor vaccine. Expression of the GM-CSF gene within either autologous or allogeneic tumor cell populations has demonstrated evidence of immune stimulation in patients and evidence of antitumor activity particularly in prostate cancer and non-small-cell lung cancer. Results of preclinical studies justify clinical investigation. A summary of clinical results is presented.
Comparative genomics of Lactobacillus crispatus suggests novel mechanisms for the competitive exclusion of Gardnerella vaginalis (2014)

Our pan-genome analysis provides insights into the intraspecific genome variability and the collective molecular mechanisms of the species L. crispatus. Using this approach, we described the differences and similarities between the genomes and identified features likely to be important for urogenital health. Notably, the conserved genetic backbone of L. crispatus accounted for close to 60% of the ortholog groups of an average L. crispatus strain and included factors for the competitive exclusion of G. vaginalis, providing an explanation on how this urogenital species could improve vaginal health.
Prostaglandin D2Protects Neonatal Mouse Brain from Hypoxic Ischemic Injury (2007)

Prostaglandin D2 (PGD) is synthesized by hematopoietic PGD synthase (HPGDS) or lipocalin-type PGDS (L-PGDS), depending on the organ in which it is produced, and binds specifically to either DP1 or DP2 receptors. We investigated the role of PGD2 in the pathogenesis of hypoxic-ischemic encephalopathy (HIE) in neonatal mice at postnatal day 7. In wild-type mice, hypoxia-ischemia increased PGD2 production in the brain up to 90-fold compared with the level in sham-operated brains at 10 min after cessation of hypoxia. Whereas the size of the infarct was not changed in L-PGDS or DP2 knock-out mouse brains compared with that in the wild-type HIE brains, it was significantly increased in HPGDS-L-PGDS double knock-out or DP1 knock-out mice. The PGD2 level in L-PGDS, HPGDS, and HPGDS-L-PGDS knock-out mice at 10 min of reoxygenation was 46, 7, and 1%, respectively, of that in the wild-type ones, indicating the infarct size to be in inverse relation to the amount of PGD2 production. DP1 receptors were exclusively expressed in endothelial cells after 1 h of reoxygenation, and cerebral blood flow decreased more rapidly after the onset of hypoxia and did not return to the baseline level after reoxygenation in HPGDS-L-PGDS knock-out mice. Endothelial cells were severely damaged in HPGDS-L-PGDS and DP1 knock-out mice after 1 h of reoxygenation. In the human neonatal HIE brain, HPGDS-positive microglia were increased in number. In conclusion, it is probable that PGD2 protected the neonatal brain from hypoxic-ischemic injury mainly via DP1 receptors by preventing endothelial cell degeneration.
Proteasome inhibitors disrupt the unfolded protein response in myeloma cells (2003)

Novel agents that target the proteasome, a proteolytic complex responsible for the degradation of ubiquitinated proteins, have demonstrated remarkable therapeutic efficacy in multiple myeloma, a plasma cell malignancy. However, the mechanism by which these compounds act remains unknown. A signaling pathway called the unfolded protein response (UPR) allows cells to handle the proper folding of proteins. The transcription factor XBP-1, a regulator of the UPR, is also required for plasma cell differentiation, suggesting a link between the UPR and plasma cell differentiation. Here we show that proteasome inhibitors target XBP-1 and the UPR in myeloma cells. Proteasome inhibitors suppress the activity of the translumenal endoplasmic reticulum endoribonuclease/kinase, IRE1 alpha, to impair the generation of the active, spliced XBP-1 species and simultaneously stabilize the unspliced species that acts as a dominant negative. Myeloma cells rendered functionally deficient in XBP-1 undergo increased apoptosis in response to endoplasmic reticulum stress. Identification of compounds that target the activity of IRE1 alpha/XBP-1 may yield novel therapies for the treatment of multiple myeloma and other malignancies that rely on an intact UPR.
A novel host factor for integration of mycobacteriophage L5 (1996)

Bacterial integration host factors (IHFs) play central roles in the cellular processes of recombination, DNA replication, transcription, and bacterial pathogenesis. We describe here a novel mycobacterial IHF (mIHF) of Mycobacterium smegmatis and Mycobacterium tuberculosis that stimulates integration of mycobacteriophage L5. mIHF is the product of a single gene and is unrelated at the sequence level to other integration host factors. By itself, mIHF does not bind preferentially to attP DNA, although it significantly alters the pattern of integrase (Int) binding, promoting the formation of specific integrase-mIHF-attP intasome complexes.
A program for the design of linear phase finite impulse response digital filters (1972)

This paper presents an algorithm that can be used to design finite impulse response (FIR) digital filters with linear phase. The presentation is in the form of a block diagram together with the Fortran IV listing of the program.
Palladium‐Catalyzed Carbonylation Reactions of Aryl Halides and Related Compounds (2009)

Palladium-catalyzed carbonylation reactions of aromatic halides in the presence of various nucleophiles have undergone rapid development since the pioneering work of Heck and co-workers in 1974, such that nowadays a plethora of palladium catalysts are available for different carbonylative transformations. The carboxylic acid derivatives, aldehydes, and ketones prepared in this way are important intermediates in the manufacture of dyes, pharmaceuticals, agrochemicals, and other industrial products. In this Review, the recent academic developments in this area and the first industrial processes are summarized.
Process Fault Tolerance: Semantics, Design and Applications for High Performance Computing (2005)

With increasing numbers of processors on current machines, the probability for node or link failures is also increasing. Therefore, application-level fault tolerance is becoming more of an important issue for both end-users and the institutions running the machines. In this paper we present the semantics of a fault-tolerant version of the message passing interface (MPI), the de-facto standard for communication in scientific applications, which gives applications the possibility to recover from a node or link error and continue execution in a well-defined way. We present the architecture of fault-tolerant MPI, an implementation of MPI using the semantics presented above as well as benchmark results with various applications. An example of a fault-tolerant parallel equation solver, performance results as well as the time for recovering from a process failure are furthermore detailed.
Critical role for OX40 ligand in the development of pathogenic Th2 cells in a murine model of asthma (2003)

Bronchial asthma is characterized by massive infiltration of eosinophils and airway hyperreactivity (AHR), which are caused by overproduction of Th2 cytokines (IL-4, IL-5, and IL-13) by allergen-specific T cells. We recently demonstrated a critical contribution of OX40 ligand (OX40L) to the development of Th2-mediated experimental leishmaniasis. In this study, we have examined the role of OX40L in the development of Th2-mediated pulmonary inflammation by utilizing OX40L-deficient mice and a neutralizing anti-OX40L mAb in a murine model of asthma. Sensitization and airway challenge with ovalbumin in wild-type BALB/c mice induced a typical allergic asthma characterized by AHR, accumulation of eosinophils, increased mucus production, and high levels of Th2 cytokines in the lung. All these asthmatic responses were not induced in OX40L-deficient BALB/c mice. Administration of neutralizing anti-OX40L mAb in wild-type BALB/c mice during the sensitization period also abolished the induction of asthmatic responses. In contrast, administration of anti-OX40L mAb during the challenge period did not inhibit the asthmatic responses. These results indicate a critical role for OX40L in the induction phase, which leads to the development of pathogenic Th2 cells, but not in the effector phase, which includes migration and activation of pathogenic Th2 cells in the lung.
A High-Yielding Supramolecular Reaction (2002)

The X-ray crystal structure determinations of twelve cocrystals involving iso-nicotinamide and a variety of carboxylic acids have revealed a very consistent pattern of hydrogen-bond preferences. The combination of a monocarboxylic acid, an amide, and a pyridine moiety leads, in every case, to discrete "supermolecules" (consisting of two molecules of iso-nicotinamide and two molecules of the relevant carboxylic acid) with well-defined and robust connectivity. The two dominant (regularly occurring) supramolecular synthons in these crystal structures are (1) the heteromeric carboxylic acid.pyridine hydrogen bond and (2) a self-complementary amide.amide hydrogen-bond interaction, both of which prevail in the presence of widely differing chemical functionalities. In four of these cocrystals, a dicarboxylic acid is employed, which alters the structural outcome from discrete entities to infinite assemblies (or to a hexameric complex in a "U-shaped" dicarboxylic acid), which is fully expected since the two primary supramolecular synthons remain intact. This structural study shows that iso-nicotinamide is a supramolecular reagent that can produce well-defined supermolecules (containing carboxylic acids) in very high yields.
Characterization of Human Recombinant Annexin II Tetramer Purified from Bacteria:  Role of N-Terminal Acetylation (1997)

Annexin II tetramer (AIIt) is a Ca2+-dependent, phosphatidylserine-binding, and F-actin-bundling phosphoprotein which is localized to both the extracellular and cytoplasmic surfaces of the plasma membrane. The tetramer is composed of two p36 heavy chains and two p11 light chains. We have produced prokaryotic cDNA expression constructs for both p36 and p11. Both proteins were expressed in large amounts in Escherichia coli upon induction with IPTG. Electrospray ionization mass spectrometry and amino acid sequence analysis of purified recombinant p36 (rp36) and recombinant p11 (rp11) suggested that the recombinant proteins were identical to their native counterparts except for the lack of N-terminal acetylation of rp36. Furthermore, the non-acetylated rp36 bound rp11 and formed AIIt. The circular dichroism spectra and urea denaturation profiles of acetylated AIIt and non-acetylated rAIIt were identical. In addition, both the acetylated AIIt and non-acetylated rAIIt were similar in their Ca2+ dependence and concentration dependence of phospholipid liposome aggregation, chromaffin granule aggregation, and F-actin bundling. These results suggest that N-terminal acetylation of p36 is not in fact necessary for binding of the protein to p11 and that N-terminal acetylation does not affect the conformational stability of AIIt or the in vitro activities of AIIt. The availability of large amounts of rAIIt will facilitate further characterization of the structure-function relationships of the protein.
A Dose‐Ranging Study of Azathioprine Pharmacokinetics After Single‐Dose Administration of a Delayed‐Release Oral Formulation (1997)

6-Mercaptopurine and its prodrug azathioprine are an effective treatment for inflammatory bowel disease, but widespread use has been limited by concern about toxicity. Ileocolonic delivery of azathioprine as a 50-mg delayed-release oral capsule has been shown to decrease bioavailability, thus potentially decreasing toxicity. This study aimed to determine the bioavailability and pharmacokinetic parameters of delayed-release oral azathioprine capsules at doses of 200 mg, 400 mg, and 600 mg relative to 100 mg of standard oral azathioprine tablets. Thirty healthy human volunteers each received delayed-release oral azathioprine at one of the three doses (n = 10 for each group). All participants also received a 100-mg tablet of standard oral azathioprine. Plasma concentrations of 6-mercaptopurine were determined by high-pressure liquid chromatography. The relative bioavailabilities of 6-mercaptopurine after ileocolonic azathioprine administration via delayed-release oral capsules at doses of 200 mg, 400 mg, and 600 mg (means of 15%, 15%, and 12%, respectively) were all significantly less than 100% compared with standard oral azathioprine at a 100-mg dose. Ileocolonic delivery of azathioprine by a delayed-release oral capsule formulation at doses up to 600 mg considerably reduces 6-mercaptopurine bioavailability, relative to standard oral azathioprine tablets. The therapeutic potential of this ileocolonic delivery formulation, which can limit toxicity by local delivery of azathioprine, should be investigated in patients with inflammatory bowel disease.
Searching for Activation Functions (2017)

The choice of activation functions in deep networks has a significant effect on the training dynamics and task performance. Currently, the most successful and widely-used activation function is the Rectified Linear Unit (ReLU). Although various hand-designed alternatives to ReLU have been proposed, none have managed to replace it due to inconsistent gains. In this work, we propose to leverage automatic search techniques to discover new activation functions. Using a combination of exhaustive and reinforcement learning-based search, we discover multiple novel activation functions. We verify the effectiveness of the searches by conducting an empirical evaluation with the best discovered activation function. Our experiments show that the best discovered activation function, $f(x) = x \cdot \text{sigmoid}(βx)$, which we name Swish, tends to work better than ReLU on deeper models across a number of challenging datasets. For example, simply replacing ReLUs with Swish units improves top-1 classification accuracy on ImageNet by 0.9\% for Mobile NASNet-A and 0.6\% for Inception-ResNet-v2. The simplicity of Swish and its similarity to ReLU make it easy for practitioners to replace ReLUs with Swish units in any neural network.
Theoretical and experimental studies on the chemical vapor deposition of boron carbide (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTheoretical and experimental studies on the chemical vapor deposition of boron carbideLionel G. VandenbulckeCite this: Ind. Eng. Chem. Prod. Res. Dev. 1985, 24, 4, 568–575Publication Date (Print):December 1, 1985Publication History Published online1 May 2002Published inissue 1 December 1985https://pubs.acs.org/doi/10.1021/i300020a015https://doi.org/10.1021/i300020a015research-articleACS PublicationsRequest reuse permissionsArticle Views213Altmetric-Citations33LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts
Semiconductor wafer bonding. A flexible approach to materials combinations in microelectronics; micromechanics and optoelectronics (2002)

The wafer bonding approach, originally developed mostly for the fabrication of silicon-on-insulator (SOI) substrates, has matured to a flexible technology giving access to materials combinations with applications far beyond the original area of SOI substrates. The paper will first review our present understanding of silicon-silicon wafer bonding and then proceed to bonding of dissimilar wafers and various thinning approaches including that associated with hydrogen implantation. Finally, low temperature wafer bonding approaches such as room temperature wafer bonding under ultra high vacuum conditions will be discussed.
3D TFT-SONOS memory cell for ultra-high density file storage applications (2004)

For the first time, a scalable, low power, deep-submicron TFT-SONOS (Thin-Film Transistor Silicon-Oxide-Nitride-Oxide-Silicon) memory cell is described with characteristics rivaling those of single crystal devices (>10/sup 6/ cycles, /spl sim/1.6 V window after 10 years on cycled cell at 85 C) showing the promise of 3D integration and ultra-small cell footprints. The ability to vertically stack device layers enables the current memory density record of /spl sim/200 Mbyte/cm/sup 2/, set by 90 nm NAND, to be surpassed.
Conditions controlling the proliferation of haemopoietic stem cells in vitro (1977)

A liquid culture system is described whereby proliferation of haemopoietic stem cells (CFU-S), production of granulocyte precursor cells (CFU-C), and extensive granulopoiesis can be maintained in vetro for several months. Such cultures consist of adherent and non-adherent populations of cells. The adherent population contains phagocytic mononuclear cells, "epithelial" cells, and "giant fat" cells. The latter appear to be particularly important for stem cell maintenance and furthermore there is a strong tendency for maturing granulocytes to selectively cluster in and around areas of "giant fat" cell aggregations. By "feeding" the cultures at weekly intervals, between 10 to 15 "population doublings" of functionally normal CFU-S regularly occurs. Increased "population doublings" may be obtained by feeding twice weekly. The cultures show initially extensive granulopoiesis followed, in a majority of cases, by an accumulation of blast cells. Eventually both blast cells and granulocytes decline and the cultures contain predominantly phagocytic mononuclear cells. Culturing at 33 degrees C leads to the development of a more profuse growth of adherent cells and these cultures show better maintenance of stem cells and increased cell density. When tested for colony stimulating activity (CSA) the cultures were uniformly negative. Addition of exogenous CSA caused a rapid decline in stem cells, reduced granulopoiesis and an accumulation of phagocytic mononuclear cells.
Potential role of monocyte chemoattractant protein 1/JE in monocyte/macrophage-dependent IgA immune complex alveolitis in the rat (1992)

We have examined the role of monocyte chemoattractant protein 1 (MCP 1) in the pathogenesis of monocyte/macrophage-dependent IgA immune complex alveolitis in the rat. Rat MCP 1 was cloned and expressed in order to facilitate analysis of its function in rat models of human disease. A cDNA library was constructed from rat pulmonary artery endothelial cells stimulated with TNF-alpha. The cDNA library was screened with synthetic oligonucleotide probes based on the recently published rat MCP 1 cDNA sequence. Among numerous MCP 1-positive clones, four full length (approximately 480 bp) cDNA were rescued, amplified by polymerase chain reaction, and ligated into a pJVETLZ baculovirus transfer vector. Spodoptera frugiperda insect cells (Sf-21) infected with baculovirus recombinants (Auto-grapha california nuclear polyhedrosis virus) bearing properly oriented MCP 1 cDNA (AcMCP 1) directed the expression of unique peptides of 18, 21, and 23 kDa. Treatment of AcMCP 1-infected Sf-21 cells with tunicamycin resulted in reduced production of the 21- and 23-kDa proteins and an increase in 16- to 18-kDa products, the predicted size range of uncleaved and nonglycosylated rat MCP 1. Denatured and refolded 23-kDa and 21-kDa rat MCP 1 species exhibited dose-dependent monocyte-specific chemotactic activity at concentrations as low as 10(-10) M whereas the 18-kDa species exhibited negligible activity. Antibodies that react with the immunoblot, block rat rMCP 1-directed monocyte chemotaxis, and neutralize monocyte-specific chemotactic activity secreted by TNF-stimulated rat endothelial cells were raised in rabbits immunized with the 23-kDa MCP 1 species. Intravenous administration of anti-MCP 1 antibodies upon initiation of IgA immune complex lung injury resulted in a marked reduction in lung injury as measured by pulmonary vascular permeability, alveolar hemorrhage, and pulmonary monocyte/macrophage recruitment and pulmonary monocyte/macrophage recruitment. These data suggest that MCP 1 may play an important role in the pathogenesis of monocyte/macrophage-dependent IgA immune complex alveolitis in the rat.