gebhart/patrepeval huggingface dataset:
Use of a hybrid vaccinia virus-T7 RNA polymerase system for expression of target genes. (1987)

A novel expression system based on coinfection of cells with two recombinant vaccinia viruses has been developed. One recombinant vaccinia virus contained the bacteriophage T7 RNA polymerase gene under control of a vaccinia virus promoter. The second recombinant vaccinia virus contained a target gene of choice flanked by bacteriophage T7 promoter and termination sequences. Maximum expression of the target gene occurred when cells were infected with 10 PFU of each recombinant virus. Although T7 RNA polymerase synthesis began shortly after infection, the target gene was not expressed until late times and was largely inhibited when DNA replication was blocked. Target gene transcripts were analyzed by agarose gel electrophoresis and had the predicted size. With this system, Escherichia coli beta-galactosidase, hepatitis B virus surface antigen, and human immunodeficiency virus envelope proteins were made. In each case, the level of synthesis was greater than had previously been obtained with the more conventional recombinant vaccinia virus expression system.
Beyond the endoplasmic reticulum: atypical GRP78 in cell viability, signalling and therapeutic targeting (2011)

GRP78 (glucose-regulated protein of 78 kDa) is traditionally regarded as a major ER (endoplasmic reticulum) chaperone facilitating protein folding and assembly, protein quality control, Ca(2+) binding and regulating ER stress signalling. It is a potent anti-apoptotic protein and plays a critical role in tumour cell survival, tumour progression and angiogenesis, metastasis and resistance to therapy. Recent evidence shows that GRP78 can also exist outside the ER. The finding that GRP78 is present on the surface of cancer but not normal cells in vivo represents a paradigm shift on how GRP78 controls cell homoeostasis and provides an opportunity for cancer-specific targeting. Cell-surface GRP78 has emerged as an important regulator of tumour cell signalling and viability as it forms complexes with a rapidly expanding repertoire of cell-surface protein partners, regulating proliferation, PI3K (phosphoinositide 3-kinase)/Akt signalling and cell viability. Evidence is also emerging that GRP78 serves as a receptor for viral entry into host cells. Additionally, a novel cytosolic form of GRP78 has been discovered prominently in leukaemia cells. These, coupled with reports of nucleus- and mitochondria-localized forms of GRP78, point to the previously unanticipated role of GRP78 beyond the ER that may be critical for cell viability and therapeutic targeting.
Monodisperse Au Nanoparticles for Selective Electrocatalytic Reduction of CO2 to CO (2013)

We report selective electrocatalytic reduction of carbon dioxide to carbon monoxide on gold nanoparticles (NPs) in 0.5 M KHCO3 at 25 °C. Among monodisperse 4, 6, 8, and 10 nm NPs tested, the 8 nm Au NPs show the maximum Faradaic efficiency (FE) (up to 90% at -0.67 V vs reversible hydrogen electrode, RHE). Density functional theory calculations suggest that more edge sites (active for CO evolution) than corner sites (active for the competitive H2 evolution reaction) on the Au NP surface facilitates the stabilization of the reduction intermediates, such as COOH*, and the formation of CO. This mechanism is further supported by the fact that Au NPs embedded in a matrix of butyl-3-methylimidazolium hexafluorophosphate for more efficient COOH* stabilization exhibit even higher reaction activity (3 A/g mass activity) and selectivity (97% FE) at -0.52 V (vs RHE). The work demonstrates the great potentials of using monodisperse Au NPs to optimize the available reaction intermediate binding sites for efficient and selective electrocatalytic reduction of CO2 to CO.
A complex of platelet glycoproteins Ic and IIa identified by a rat monoclonal antibody. (1987)

A rat monoclonal antibody, GoH3, recognizes cell surface antigens on epithelial cells in a variety of tissues in both man and mouse. Furthermore, the antibody showed reactivity with endothelial cells and blood platelets. The molecule recognized by GoH3 on platelets was determined by immunoprecipitation, followed by analysis on one- and two-dimensional sodium dodecyl sulfate-polyacrylamide gels. GoH3 precipitated glycoproteins Ic and IIa from both human and mouse platelets. Glycoprotein Ic consists of disulfide-linked heavy and light chains which both appeared to be glycosylated. As determined by enzymatic digestion followed by gel analyses, both "complex" and "high mannose" type of N-linked oligosaccharides are present on the heavy and light chain of human glycoprotein Ic and on the heavy chain of mouse glycoprotein Ic. The light chain of mouse glycoprotein Ic only carries high mannose type of N-linked oligosaccharides. The N-linked glycans on human and mouse glycoprotein IIa are all of the complex type. The glycoproteins Ic and IIa co-sedimented in sucrose gradients and formed complexes upon treatment of intact platelets with the chemical cross-linking reagent dithiobis(succinimidyl propionate). Dissociation of the complex by chaotropic agents followed by immunoprecipitation establishes that the epitope recognized by GoH3 is located on the Ic molecule. These results provide evidence that the two glycoproteins, Ic and IIa, exist as a heterodimer complex in the platelet membrane.
A model for the representation and focussed retrieval of structured documents based on fuzzy aggregation (2005)

Effective retrieval of structured documents should exploit the content and structural knowledge associated with the documents. This knowledge can be used to focus retrieval to the best entry points: document components that contain relevant information, and from which users can browse to retrieve further relevant components. To enable this, suitable representation methods must be developed. This paper presents a model for representing structured documents to allow for their focussed retrieval. The model is founded on fuzzy aggregation, an approach based on the fuzzy representation of linguistic quantifiers and ordered weighted averaging operators. By defining the representation of a document component as the fuzzy aggregation of its related components, we arrive at a document representation that supports the selection of best entry points.
Inhaled nitric oxide for hypoxemic respiratory failure: passing bad gas? (2000)

Technology: Inhaled nitric oxide for the treatment of hypoxemic respiratory failure

Use: Nitric oxide (NO) has been rapidly embraced by critical care physicians to treat hypoxemic lung diseases such as acute respiratory distress syndrome[1][1] and, perhaps more rationally, persistent pulmonary
The therapeutic potential of modulating the ceramide/sphingomyelin pathway (2002)

ified by various enzymes in the Golgi apparatus to form complex glycosphingolipids.
A novel cis-acting element controlling the rat CYP2D5 gene and requiring cooperativity between C/EBP beta and an Sp1 factor. (1994)

The rat CYP2D5 gene encodes a cytochrome P450 and is expressed in liver cells. Its expression commences a few days after birth, and maximal mRNA levels are achieved when animals reach puberty. Transfection and DNA binding studies were performed to investigate the mechanism controlling developmentally programmed, liver-specific expression of CYP2D5. Transfection studies using a series of CYP2D5 upstream DNA chloramphenicol acetyltransferase gene fusion constructs identified a segment of DNA between nucleotides -55 and -156 that conferred transcriptional activity in HepG2 cells. Activity was markedly increased by cotransfection with a vector expressing C/EBP beta but was unaffected by vectors producing other liver-enriched transcription factors (C/EBP alpha, HNF-1 alpha, and DBP). DNase I footprinting revealed a region protected by both HepG2 and liver cell nuclear extracts between nucleotides -83 and -112. This region displayed some sequence similarity to the Sp1 consensus sequence and was able to bind the Sp1 protein, as assessed by a gel mobility shift assay. The role of Sp1 in CYP2D5 transcription was confirmed by trans activation of the 2D5-CAT construct in Drosophila melanogaster cells by using an Sp1 expression vector. C/EBP beta alone was unable to directly bind the -83 to -112 region of the promoter but was able to produce a ternary complex when combined with HepG2 nuclear extracts or recombinant human Sp1. C/EBP alpha was unable to substitute for C/EBP beta in forming this ternary complex. A poor C/EBP binding site is present adjacent to the Sp1 site, and mutagenesis of this site abolished formation of the ternary complex with the CYP2D5 regulatory region. These result establish that two transcription factors can work in conjunction, possibly by protein-protein interaction, to activate the CYP2D5 gene.
Synthesis and Herbicidal Activity of N-Oxide Derivatives (2000)

As part of an ongoing program on the chemistry and biological activity of N-oxide-containing molecules, a number of novel 1,2, 5-oxadiazole N-oxide, benzo[1,2-c]1,2,5-oxadiazole N-oxide, and quinoxaline N,N'-dioxide derivatives were synthesized and evaluated for their herbicidal activity. Many of these compounds exhibited moderate to good herbicidal pre-emergence activity against Triticum aestivum. Dose-response studies were done on the more representative compounds (12, 20, and 26). The most active compound, butylcarbamoylbenzo[1,2-c]1,2,5-oxadiazole N-oxide, 26, displayed herbicidal activity at concentrations as low as 24 g/ha.
The deleted in colon cancer (DCC) gene is consistently expressed in colorectal cancers and metastases. (1996)

The DCC (deleted in colorectal cancer) gene was originally identified as a candidate tumour suppressor gene in colon carcinogenesis on the basis of allelic losses in chromosome 18q.21 in 70% of colon cancers. Reverse transcriptase polymerase chain reaction (RT-PCR) of DCC mRNA suggests that DCC expression may also be reduced in colon cancers. We have used monoclonal antibodies generated against the DCC immunoglobulin-like domain to investigate DCC isoforms and DCC protein expression during colon cancer progression. Normal mucosa and colonic tumour specimens representative of the range of colonic tumour progression from benign adenomatous polyps to metastases were compared by Western blot analyses. We show that while M(r) 194 000 DCC is present in normal colonic mucosa and adenomatous polyps, it is also similarly expressed in colorectal carcinomas and colonic metastases in the liver. The presence of DCC protein is consistent with the presence of DCC mRNA transcripts in the same tissue specimens. Notably DCC was not completely lost in any colonic tumour specimens examined, even those that had progressed to metastatic cancers. Quantitation of DCC protein expression in tissue specimens by densitometry demonstrated that both normal and malignant specimens exhibit a wide range of DCC protein levels and there was no significant correlation between diminished DCC protein expression and colon cancer progression. These results demonstrate the pattern of expression of the DCC gene product in colonic tumour progression and show that absence of DCC expression is not associated with colonic tumour progression.
Purification and Characterization of a 2-Oxoglutarate-linked ATP-independent Deacetoxycephalosporin C Synthase of Streptomyces lactamdurans (1987)

The deacetoxycephalosporin C (DAOC) synthase (expandase) of Streptomyces lactamdurans was highly purified, as shown by SDS-PAGE and isoelectric focusing. The enzyme catalysed the oxidative ring expansion that converts penicillin N into DAOC. The enzyme was very unstable but could be partially stabilized in 25 mM-Tris/HCl, pH 9.0, in the presence of DTT (0.1 mM). The enzyme required 2-oxoglutarate, oxygen and Fe2+, but did not need ATP, ascorbic acid, Mg2+ or K+. The optimum temperature was between 25 and 30 degrees C. The DAOC synthase showed a high specificity for the penicillin substrate. Only penicillin N but not isopenicillin N, penicillin G or 6-aminopenicillanic acid served as substrates. 2-Oxoglutarate analogues were not used as substrates although 2-oxobutyrate and 3-oxoadipate inhibited the enzyme by 100% and 56% respectively. The enzyme was strongly inhibited by Cu2+, Co2+ and Zn2+. The apparent Km values for penicillin N, 2-oxoglutarate and Fe2+ were 52 microM, 3 microM and 71 microM respectively. The enzyme was a monomer with a molecular mass of 27,000 Da +/- 1,000.
Organometallic 99mTc-aquaion labels peptide to an unprecedented high specific activity. (1999)

The novel labeling method using the organometallic 99mTc-aquaion combines the advantage of highest specific activities with minimal functionalization of proteins and peptides under retention of biologic affinity.
α1-Antitrypsin Portland Inhibits Processing of Precursors Mediated by Proprotein Convertases Primarily within the Constitutive Secretory Pathway (1997)

We studied the extent of cellular inhibitory activity of alpha1-antitrypsin Portland (alpha1-PDX), a potent inhibitor of proprotein convertases of the subtilisin/kexin type. We compared the inhibitory effects of alpha1-PDX on the intracellular processing of two model precursors (pro-7B2 and POMC) mediated by six of the seven known mammalian convertases, namely furin, PC1, PC2, PACE4, PC5-A, PC5-B, and PC7. The substrates selected were pro7B2, a precursor cleaved within the trans-Golgi network (TGN), and pro-opiomelanocortin, which is processed in the TGN and secretory granules. Biosynthetic analyses were performed using either vaccinia virus expression in BSC40, GH4C1, and AtT20 cells, or stable transfectants of alpha1-PDX in AtT20 cells. Results revealed that alpha1-PDX inhibits processing of these precursors primarily within the constitutive secretory pathway and that alpha1-PDX is cleaved into a shorter form by some convertases. Evidence is presented demonstrating that in contrast to the full-length alpha1-PDX (64 kDa), the cleaved (56 kDa) secreted product does not significantly inhibit furin activity in vitro. Cellular expression of alpha1-PDX results in modified contents of mature secretory granules with increased levels of partially processed products. Biosynthetic and immunocytochemical analyses of AtT20/alpha1-PDX cells demonstrated that alpha1-PDX is primarily localized within the TGN, and that a small proportion enters secretory granules where it is mostly stored as the cleaved product.
Diverse Bacteria Inhabit Living Hyphae of Phylogenetically Diverse Fungal Endophytes (2010)

Both the establishment and outcomes of plant-fungus symbioses can be influenced by abiotic factors, the interplay of fungal and plant genotypes, and additional microbes associated with fungal mycelia. Recently bacterial endosymbionts were documented in soilborne Glomeromycota and Mucoromycotina and in at least one species each of mycorrhizal Basidiomycota and Ascomycota. Here we show for the first time that phylogenetically diverse endohyphal bacteria occur in living hyphae of diverse foliar endophytes, including representatives of four classes of Ascomycota. We examined 414 isolates of endophytic fungi, isolated from photosynthetic tissues of six species of cupressaceous trees in five biogeographic provinces, for endohyphal bacteria using microscopy and molecular techniques. Viable bacteria were observed within living hyphae of endophytic Pezizomycetes, Dothideomycetes, Eurotiomycetes, and Sordariomycetes from all tree species and biotic regions surveyed. A focus on 29 fungus/bacterium associations revealed that bacterial and fungal phylogenies were incongruent with each other and with taxonomic relationships of host plants. Overall, eight families and 15 distinct genotypes of endohyphal bacteria were recovered; most were members of the Proteobacteria, but a small number of Bacillaceae also were found, including one that appears to occur as an endophyte of plants. Frequent loss of bacteria following subculturing suggests a facultative association. Our study recovered distinct lineages of endohyphal bacteria relative to previous studies, is the first to document their occurrence in foliar endophytes representing four of the most species-rich classes of fungi, and highlights for the first time their diversity and phylogenetic relationships with regard both to the endophytes they inhabit and the plants in which these endophyte-bacterium symbiota occur.
Catadioptric lens development for DUV and VUV projection optics (2003)

According to the International Technology Roadmap for Semiconductors (ITRS), the 65nm technology node is forecast to appear in 2007. In this paper, we propose two specifications for the projection optics at 65nm nodes. The one is over 1.0 numerical aperture (NA) at 193nm lithography by liquid immersion. The other is 0.85 NA at 157nm lithography. Since it almost impossible for traditional dioptric optics to realize these specifications, catadioptric is supposedly the leading optics for an extreme optical lithography, like 65nm node. Described in the paper are feasibility study for catadioptric optics, and our assembly strategy. Emphasis is placed on our selection methodology among a variety of catadioptric configurations.
Tunable Atomic Magnetometer for Detection of Radio-Frequency Magnetic Fields (2005)

We describe an alkali-metal magnetometer for detection of weak magnetic fields in the radio-frequency (rf) range. High sensitivity is achieved by tuning the Zeeman resonance of alkali atoms to the rf frequency and partially suppressing spin-exchange collisions in the alkali-metal vapor. We demonstrate magnetic field sensitivity of 2 fT/Hz(1/2) at a frequency of 99 kHz with a resonance width of 400 Hz. We also derive a simple analytic expression for the fundamental limit on the sensitivity of the rf magnetometer and show that a sensitivity of about 0.01 fT/Hz(1/2) can be achieved in a practical system with a measurement volume of 200 cm3.
Inflammatory cell profiles and T‐lymphocyte subsets in chronic obstructive pulmonary disease and severe persistent asthma (2004)

In spite of treatment with inhaled steroids, SPA and COPD exhibit distinct sputum inflammatory cell patterns, although SPA with fixed airflow limitation and COPD patients have similar numbers of neutrophils.
Peripheral neuropathy and antiretroviral drugs (2001)

Patients treated with nucleoside analogue reverse transcriptase inhibitors (NRTIs) develop a varying degree of myopathy or neuropathy after long-term therapy. Zidovudine (AZT) causes myopathy; zalcitabine (ddC), didanosine (ddl) and lamuvidine (3TC) cause neuropathy; stavudine (d4T) and fialuridine (FIAU) cause neuropathy or myopathy and lactic acidosis. The tissue distribution of phosphorylases responsible for phosphorylation of NRTIs relates to their selective tissue toxicity. The myopathy is characterized by muscle wasting, myalgia, fatigue, weakness and elevation of CK. The neuropathy is painful, sensory and axonal. In vitro, NRTIs inhibit the gamma-DNA polymerase, responsible for replication of mtDNA, and cause mtDNA dysfunction. In vivo, patients treated with AZT, the best studied NRTI, develop a mitochondrial myopathy with mtDNA depletion, deficiency of COX (complex IV), intracellular fat accumulation, high lactate production and marked phosphocreatine depletion, as determined with in vivo MRS spectroscopy, due to impaired oxidative phosphorylation. Animals or cultured cells treated with NRTIs develop neuropathy, myopathy, or cell destruction with similar changes in the mitochondria. There is evidence that the NRTI-related neuropathy is also due to mitochondrial toxicity. The NRTIs (AZT, ddC, ddl, d4T, 3TC) contain azido groups that compete with natural thymidine triphosphate as substrates of DNA pol-gamma and terminate mtDNA synthesis. In contrast, FIAU that contains 3'-OH groups serves as an alternate substrate for thymidine triphosphate with DNA pol-gamma and is incorporated into the DNA causing permanent mtDNA dysfunction. The NRTI-induced mitochondrial dysfunction has an influence on the clinical application of these agents, especially at high doses and when combined. They have produced in humans a new category of acquired mitochondrial toxins that cause clinical manifestations resembling the genetic mitochondrial disorders.
Ticagrelor versus Clopidogrel in Patients with Acute Coronary Syndromes (2009)

In patients who have an acute coronary syndrome with or without ST-segment elevation, treatment with ticagrelor as compared with clopidogrel significantly reduced the rate of death from vascular causes, myocardial infarction, or stroke without an increase in the rate of overall major bleeding but with an increase in the rate of non-procedure-related bleeding. (ClinicalTrials.gov number, NCT00391872.)
Architectural Characterization of TCP/IP Packet Processing on the Pentium&#174; M Microprocessor (2005)

A majority of the current and next generation server applications (Web services, e-commerce, storage, etc.) employ TCP/IP as the communication protocol of choice. As a result, the performance of these applications is heavily dependent on the efficient TCP/IP packet processing within the termination nodes. This dependency becomes even greater as the bandwidth needs of these applications grow from 100 Mbps to 1 Gbps to 10 Gbps in the near future. Motivated by this, we focus on the following: (a) to understand the performance behavior of the various modes of TCP/IP processing, (b) to analyze the underlying architectural characteristics of TCP/IP packet processing and (c) to quantify the computational requirements of the TCP/IP packet processing component within realistic workloads. We achieve these goals by performing an in-depth analysis of packet processing performance on Intel's state-of-the-art low power Pentium/spl reg/ M microprocessor running the Microsoft Windows* Server 2003 operating system. Some of our key observations are - (i) that the mode of TCP/IP operation can significantly affect the performance requirements, (ii) that transmit-side processing is largely compute-intensive as compared to receive-side processing which is more memory-bound and (iii) that the computational requirements for sending/receiving packets can form a substantial component (28% to 40%) of commercial server workloads. From our analysis, we also discuss architectural as well as stack-related improvements that can help achieve higher server network throughput and result in improved application performance.
Blood Group Precursor T-Antigen Expression in Human Urinary Bladder Carcinoma (1982)

Tumor deletion of the ABH blood group antigens (BGAg) heralds an unfavorable prognosis in human bladder cancer. The T antigen (Thomsen-Friedenreich antigen: TAg), a precursor of other BGAg, has previously been found in malignant but not most normal cells, in which the TAg is cryptic but can be unmasked with neuraminidase (NMD). We investigated the prognostic significance of TAg expression in bladder cancer by staining paraffin sections with a T-specific lectin (peanut agglutinin [PNA]) immunoperoxidase technic. Seventy-two cases of low grade, low stage bladder cancer, 21 cases of high grade bladder cancer, and 68 controls were studied. All normals expressed the TAg only after NMD treatment (Cryptic TAg+). The Grade III cancers, all invasive, either expressed the TAg (TAg+)(67%) or lacked T even after NMD (Cryptic TAg-) (29%), indicating that the T structure was lost rather than masked as in normal tissue. Thirty-nine per cent of 23 Grade I and II cancers which were TAg+ or Cryptic TAg- subsequently became invasive (Stage B), compared with 10% of 49 Cryptic TAg+ cancers. For 32 Grade I and II, ABH BGAg negative cancers, 64% of TAg+ or Cryptic TAg- cancers became invasive, compared with 17% of cancers which had Cryptic TAg+. Thus, the TAg may be a prognostically useful immunohistochemical tumor marker in bladder cancer, especially for tumors negative for ABH BGAg.