gebhart/patrepeval huggingface dataset:
The RNase H-like superfamily: new members, comparative structural analysis and evolutionary classification (2014)

Ribonuclease H-like (RNHL) superfamily, also called the retroviral integrase superfamily, groups together numerous enzymes involved in nucleic acid metabolism and implicated in many biological processes, including replication, homologous recombination, DNA repair, transposition and RNA interference. The RNHL superfamily proteins show extensive divergence of sequences and structures. We conducted database searches to identify members of the RNHL superfamily (including those previously unknown), yielding >60 000 unique domain sequences. Our analysis led to the identification of new RNHL superfamily members, such as RRXRR (PF14239), DUF460 (PF04312, COG2433), DUF3010 (PF11215), DUF429 (PF04250 and COG2410, COG4328, COG4923), DUF1092 (PF06485), COG5558, OrfB_IS605 (PF01385, COG0675) and Peptidase_A17 (PF05380). Based on the clustering analysis we grouped all identified RNHL domain sequences into 152 families. Phylogenetic studies revealed relationships between these families, and suggested a possible history of the evolution of RNHL fold and its active site. Our results revealed clear division of the RNHL superfamily into exonucleases and endonucleases. Structural analyses of features characteristic for particular groups revealed a correlation between the orientation of the C-terminal helix with the exonuclease/endonuclease function and the architecture of the active site. Our analysis provides a comprehensive picture of sequence-structure-function relationships in the RNHL superfamily that may guide functional studies of the previously uncharacterized protein families.
Expression of the Fc receptor for IgG (Fc gamma RII/CDw32) by human circulating T and B lymphocytes (1993)

Tissue-specific isoforms of the human FcR for IgG Fc gamma RII (CDw32) have previously been described by using mAb. These mAb were shown to exhibit different patterns of reactivity with lymphocytes. Among human PBL, Fc gamma RII has been detected on B cells but not T cells when assessed by flow cytometry and microscopy with the use of mAb KB61 and 41H16. Although KB61 and 41H16 were found to react with B cells, the mAb IV.3, CIKM5, and 2E1 did not react with any PBL subset. In this study, we show that KB61 and 41H16 react strongly with the majority (93-96%) of B cells (CD20+), and weakly with a proportion (18-42%) of T cells (CD3+), including 10 to 14% of CD4+ and 27 to 69% of CD8+ cells. In addition, mRNA for Fc gamma RII was detected in purified CD3+CD8high+ lymphocytes by polymerase chain reaction. KB61 and 41H16 also reacted with a majority of CD3-CD16/CD56+ cells, and CD3-CD20- cells. These findings indicate that a subset of T cells and non-T/non-B cells express Fc gamma RII, and are of interest in the light of previous studies which postulate that human Fc gamma R+ cells and Fc gamma RII+ murine T cells suppress the B cell immune response.
Response time and display rate in human performance with computers (1984)

The pace of human-computer interaction is an important issue to computer scientists and computer users alike. Experimental results have begun to shed some light on this complex, controversml, and vital subject. This paper revmws the theory and reports on experimental results concerning display rates, response time expectations and attitudes, user productivity, and variability. The decomposition of concerns and tasks helps to clarify the issues, but substanhal effort remains before a predictive model can emerge.
Prognostic Value of Thoracic FDG PET Imaging After Treatment for Non-Small Cell Lung Cancer (2000)

FDG PET has prognostic value and strongly correlates with survival rates of patients with treated lung cancer. Patients with positive FDG PET results have a significantly worse prognosis than patients with negative results. Additionally, FDG PET may be helpful in guiding therapeutic treatments.
Bovine Spongiform Encephalopathy (BSE): Causes and Consequences of a Common Source Epidemic (1997)

Bovine spongiform encephalopathy (BSE) is a transmissible spongiform encephalopathy (TSE) or prion disease of cattle first recognized in 1986 in the United Kingdom, where it produced a common source epidemic that peaked in January 1993 and has subsided markedly since that time. The epidemic began simultaneously at many geographic locations and was traced to contamination of meat and bone meal (MBM), a dietary supplement prepared from rendering of slaughterhouse offal. It appears that the epidemic was initiated by the presence of the agent of scrapie (a long-standing TSE of sheep) that was first transmitted to cattle, beginning in the early 1980s, when most rendering plants abandoned the use of organic solvents in the preparation of MBM. The epidemic was probably accelerated by the recycling of infected bovine tissues prior to the recognition of BSE. To terminate the epidemic, a prohibition on the feeding of ruminant-derived protein to ruminants was introduced in the United Kingdom in July 1988. The ruminant feed ban accounts for the decline of the epidemic after an interval of about 5 years, approximately equivalent to the average incubation period of BSE. Relatively few cases of BSE have occurred in cattle born after 1993, and it is predicted that the epidemic will terminate about the year 2000 based on an extrapolation of the present declining curve. A comparison of data from the United Kingdom with data from relatively low incidence countries, such as Switzerland, indicates that this epidemic has been mainly confined to the United Kingdom because of a unique concatenation of risk factors, including: 1) a high ratio of sheep to cattle; 2) a relatively high rate of endemic scrapie; 3) the heavy feeding of MBM to dairy cattle; and 4) changes in the rendering process used to prepare MBM. Recently, cases of a variant form of Creutzfeldt-Jakob disease (a TSE of humans) have been reported in the United Kingdom. These cases, at least 10 of which had onset in 1994-1995, are distinguished by their occurrence in subjects under age 40 years, by their clinical presentation, and by their neurohistopathologic picture. The appearance of this novel disease and its concentration in the United Kingdom have raised the question that it might represent the transmission of BSE to humans. However, the cases gave no history indicating an unusual exposure to live cattle, to the preparation of beef products, or of dietary exposure to bovine tissues, and it remains to be determined whether they are associated with BSE.
Photoradiation in the Treatment of Recurrent Breast Carcinoma<xref ref-type="fn" rid="fn2">2</xref> (1979)

Theodore Roosevelt compliments Josephine P. Peabody on her poem Harvest Moon but also takes the opportunity to criticize President Wilson for not entering World War. He refers to another of her poems about sheep equating it to the League to Enforce Peace and make the point that pacifism will not work in this situation.
Not nonsense but antisense--applications of antisense oligonucleotides in different fields of medicine. (1997)

This brief overview will give the reader an idea what antisense oligonucleotides are, how they act, what one can do with them, and what future perspectives might emerge. The idea behind this new therapeutic strategy is the selective blockage of a specific gene in vivo, which is responsible for a certain disease. Anti-sense oligonucleotides are short, traditionally 15 to 25 bases long, single stranded DNA fragments, which are targeted against a specific mRNA. This is the classical antisense mechanism. These DNA fragments can also be targeted against a specific genomic DNA sequence which is known as antigene therapy. The oligonucleotides have to be modified in order to increase their stability in vivo. Three mechanisms of action have been reported for the oligonucleotides: 1. Oligonucleotides are designed in a complementary (antisense) orientation to their target (sense) mRNA to which they hybridize in a strictly base pair specific manner (Watson-Crick base pairing) and thus block translation. 2. They can bind to the genomic DNA in the nucleus and thus block transcription (Hoogsten-type base triplets). A third, unspecific mechanism of action is the binding of the oligonucleotide to a target protein in what has been referred to as aptamer-binding. In addition, other nonspecific effects of cytokine and neutrophil activation were observed. The antisense strategy is a useful research tool for the identification of specific gene-protein functions. The first in vivo animal studies and clinical experiences have been carried out in the fields of cardiovascular medicine, oncology and virology yielding promising results. Currently, the first clinical trials using antisense oligonucleotides for the inhibition of gene expression are being performed; the results will be available in the next years.
Efficiency of collisionally-activated dissociation and 193-nm photodissociation of peptide ions in fourier transform mass spectrometry (1990)

For tandem mass spectrometry, the Fourier transform instrument exhibits advantages for the use of collisionally-activated dissociation (CAD). The CAD energy deposited in larger ions can be greatly increased by extending the collision time to as much as 120 s, and the efficiency of trapping and measuring CAD product ions is many times greater than that found for triple-quadrupole or magnetic sector instruments, although the increased pressure from the collision gas is an offsetting disadvantage. A novel system that uses the same laser for photodesorption of ions and their subsequent photodissociation can produce complete dissociation of larger oligopeptide ions and unusually abundant fragment ions. In comparison to CAD, much more internal energy can be deposited in the primary ions using 193-nm photons, sufficient to dissociate peptide ions of m/z > 2000. Mass spectra closely resembling ion photodissociation spectra can also be obtained by' neutral photodissociation (193-nm laser irradiation of the sample) followed by ion photodesorption.
Glycopyrrolate: pharmacology and clinical use (1983)

This is a review of glycopyrrolate whose function in clinical practice is compared with that of atropine.
NF‐κB regulation: lessons from structures (2012)

The signaling module that specifies nuclear factor-κΒ (NF-κB) activation is a three-component system: NF-κB, inhibitor of NF-κΒ (IκΒ), and IκΒ kinase complex (IKK). IKK receives upstream signals from the surface or inside the cell and converts itself into a catalytically active form, leading to the destruction of IκB in the inhibited IκB:NF-κB complex, leaving active NF-κB free to regulate target genes. Hidden within this simple module are family members that all can undergo various modifications resulting in expansion of functional spectrum. Three-dimensional structures representing all three components are now available. These structures have allowed us to interpret cellular observations in molecular terms and at the same time helped us to bring forward new concepts focused towards understanding the specificity in the NF-κB activation pathway.
Evaluation of lump ores for use in modern blast furnaces as part of mixed burden practice (2008)

AbstractAbstractIt was felt that because the metallurgical properties of natural lump ores were not comprehensive and insufficiently understood, the technology development of using lump ore in modern blast furnaces (BFs) has been restricted. Analysis and investigation of each metallurgical property of natural lump ores has indicated that the lump ores could meet the requirements of modern BFs, except for the softening and melting properties, however, interaction between sinter and the lump ores was found in the high temperature zone of BF, which could significantly improve softening and melting properties of lump ores. The ferrous burden structure also could be optimised by the interaction of the mixed burden. Thus the findings contribute to eliminating the long term worry about the use of lump ores in modern BFs, and indicate the technical direction for using lump ores.Keywords: LUMP ORESINTERINTERACTIONSOFTENING PROPERTIESBLAST FURNACEBLAST BURDEN
Chinese hamster ovary (CHO) host cell engineering to increase sialylation of recombinant therapeutic proteins by modulating sialyltransferase expression (2015)

N-Glycans of human proteins possess both α2,6- and α2,3-linked terminal sialic acid (SA). Recombinant glycoproteins produced in Chinese hamster overy (CHO) only have α2,3-linkage due to the absence of α2,6-sialyltransferase (St6gal1) expression. The Chinese hamster ST6GAL1 was successfully overexpressed using a plasmid expression vector in three recombinant immunoglobulin G (IgG)-producing CHO cell lines. The stably transfected cell lines were enriched for ST6GAL1 overexpression using FITC-Sambucus nigra (SNA) lectin that preferentially binds α2,6-linked SA. The presence of α2,6-linked SA was confirmed using a novel LTQ Linear Ion Trap Mass Spectrometry (LTQ MS) method including MSn fragmentation in the enriched ST6GAL1 Clone 27. Furthermore, the total SA (mol/mol) in IgG produced by the enriched ST6GAL1 Clone 27 increased by 2-fold compared to the control. For host cell engineering, the CHOZN(®) GS host cell line was transfected and enriched for ST6GAL1 overexpression. Single-cell clones were derived from the enriched population and selected based on FITC-SNA staining and St6gal1 expression. Two clones ("ST6GAL1 OE Clone 31 and 32") were confirmed for the presence of α2,6-linked SA in total host cell protein extracts. ST6GAL1 OE Clone 32 was subsequently used to express SAFC human IgG1. The recombinant IgG expressed in this host cell line was confirmed to have α2,6-linked SA and increased total SA content. In conclusion, overexpression of St6gal1 is sufficient to produce recombinant proteins with increased sialylation and more human-like glycoprofiles without combinatorial engineering of other sialylation pathway genes. This work represents our ongoing effort of glycoengineering in CHO host cell lines for the development of "bio-better" protein therapeutics and cell culture vaccine production.
Transcriptional diversity at the duplicated human CD8β loci (1993)

In order to understand the structural organization of the human CD8 beta locus, genomic clones containing CD8 beta sequences were isolated and analyzed. Physical linkage of these clones with the CD8 alpha locus using pulsed-field electrophoresis revealed a duplication of the CD8 beta locus. CD8B-1 lies 35 kb upstream from the CD8 alpha locus and contains eight exons, including four alternatively spliced cytoplasmic exons. The CD8B-2 gene contains six exons and is at present unlinked to CD8B-1. Analysis of sequences upstream to the leader exon of the CD8B-1 and CD8B-2 genes revealed a GC-rich promoter which lacks canonical "CCAAT" and "TATA" motifs, but which has sites for multiple transcriptional activators and three additional elements which are conserved in the murine CD8 beta promoter. Seven unique CD8 beta cDNA isoforms were isolated and characterized, which derive from alternative splicing of the transmembrane and/or cytoplasmic exons. Three cDNA are membrane spanning, while the remaining four isoforms lack a transmembrane region and are potentially secreted. These transcripts are differentially expressed in the thymus and in the periphery. Transfection experiments in murine fibroblasts confirmed that the membrane CD8 beta isoforms could be expressed as heterodimers with the CD8 alpha chain. The regulated expression of multiple CD8 beta cytoplasmic isoforms and their potential role in T lymphocyte signal transduction is discussed.
Epitaxial growth of BaTiO3 thin films by organometallic chemical vapor deposition (1992)

Epitaxial BaTiO3 thin films were grown in situ on (100) LaAlO3 by low-pressure organometallic chemical vapor deposition using the precursors Ba (hexafluoroacetylacetonate)2 (tetraglyme) and titanium tetraisopropoxide. The phase composition and epitaxial quality were sensitive to the reactant partial pressures and growth temperature. Deposition at 800 °C yielded [100]-oriented BaTiO3 films. In-plane epitaxy was confirmed for the BaTiO3 films by x-ray diffraction.
Intracellular Interaction of Simian Immunodeficiency Virus Gag and Env Proteins (1999)

In polarized epithelial cells, the assembly and release of human immunodeficiency virus type 1 (HIV-1) occur at the basolateral side of the plasma membrane, and the site of assembly is determined by the site of expression of the Env protein. In order to investigate whether the expression of the Env proteins exclusively in the endoplasmic reticulum (ER) can alter the site of virus assembly, we coexpressed the simian immunodeficiency virus (SIV) Gag protein and mutant SIV Env proteins having an ER retrieval signal (KKXX motif). In cells expressing the wild-type (wt) Env protein or coexpressing Env and Gag proteins, the Env protein was processed into the surface (SU) and transmembrane (TM) proteins. In contrast, in cells expressing the mutant Env proteins alone or in combination with Gag, the Env proteins were retrieved to the ER and were not proteolytically processed. Coexpression of the Gag and ER-retained mutant Env proteins resulted in a transient decrease in the release of the Gag protein into the medium, suggesting an interaction between the Gag and ER-retrieved Env proteins. Using saponin-permeabilized cells coexpressing Gag and Env proteins, we obtained further evidence for Env-Gag interaction. A monoclonal antibody specific to the SIV Gag protein was found to coimmunoprecipitate both the Gag and Env proteins. The interaction was specific, as coexpressed SIV Env proteins without the cytoplasmic tail or a chimeric HIV-1 Env proteins with the CD4 cytoplasmic tail were not coimmunoprecipitated by the Gag-specific antibody. Electron microscopic analyses indicated that assembly of virus particles occurred only at the surfaces of cells in which the Gag protein was coexpressed with either the wt or ER-retrieved mutant Env protein. These data indicate that although the Env and Gag proteins interact intracellularly, the site of assembly of SIV is not redirected to an intracellular organelle by the retrieval of the Env protein to the ER.
A Novel Biologically Active Selenoorganic Compound. VIII. Biotransformation of Ebselen (1988)

1. The metabolism of ebselen, a Se-containing heterocyclic compound, in rats, pigs and human volunteers has been investigated. 2. Unchanged ebselen is not present in urine, plasma or bile. All metabolites of ebselen have in common that the isoselenazolone ring is opened. 3. Both in pigs and human, the dominant metabolite in plasma and urine is a Se-glucuronide. This is the major metabolite in rats as well but, additionally, some selenomethyl-derivatives of ebselen can be detected.
Distance Relay Response to Transformer Energization: Problems and Solutions (2007)

Modern distance relays use various filtering algorithms to extract the fundamental frequency component of power system voltage and current waveforms. The relays then use the filtered voltages and currents in such numerous algorithms as distance, overcurrent, under/overvoltage, and frequency. Use of filtered voltages and currents generally provides a protective relay immunity to power system harmonics such as those resulting from transformer energization. This paper focuses on the application of distance relays on or near power transformers. It reviews digital filtering algorithms and shows both digital filter and distance element algorithm responses to power transformer inrush. Without careful setting of digital relays in such applications, power transformer inrush can cause distance relay measurement errors and unwanted operations. This paper provides guidelines for setting distance relays applied directly on a power transformer and for applications of relays to a line on which transformers are connected. The paper demonstrates these guidelines through the use of actual power system events and events modeled on a real-time digital simulator
Overexpression of the Wilms' tumor gene WT1 in colorectal adenocarcinoma (2003)

Expression of the Wilms' tumor gene WT1 was examined in 59 cases of colorectal adenocarcinoma to examine the involvement of WT1 in tumorigenesis. Quantitative real-time reverse transcription-polymerase chain reaction (RT-PCR) showed that WT1 mRNA was expressed in the range from 7.2 x 10(-5) to 4.9 x 10(-1) levels (WT1 expression level in K562 leukemic cells was defined as 1.0) in all (100%) of the 28 cases of colorectal adenocarcinoma examined, and that the WT1 mRNA expression levels were higher in 20 (71%) of the 28 cases compared to those of normal-appearing mucosal tissues examined. Immunohistochemical analysis using an anti-WT1 antibody was performed on 46 cases of colorectal adenocarcinoma (15 of the 28 cases with WT1 mRNA expression and 31 newly collected cases), and the expression of WT1 protein was detected in 41 (89%) of the 46 cases. The direct sequencing analysis of the WT1 genomic DNA showed no mutations in any of the 10 exons of the WT1 gene in any of 5 different colorectal adenocarcinomas. These results may indicate an important role of the wild-type WT1 gene in tumorigenesis of colorectal adenocarcinoma.
Secretory Sphingomyelinase, a Product of the Acid Sphingomyelinase Gene, Can Hydrolyze Atherogenic Lipoproteins at Neutral pH (1998)

The subendothelial aggregation and retention of low density lipoprotein (LDL) are key events in atherogenesis, but the mechanisms in vivo are not known. Previous studies have shown that treatment of LDL with bacterial sphingomyelinase (SMase) in vitro leads to the formation of lesion-like LDL aggregates that become retained on extracellular matrix and stimulate macrophage foam cell formation. In addition, aggregated human lesional LDL, but not unaggregated lesional LDL or plasma LDL, shows evidence of hydrolysis by an arterial wall SMase in vivo, and several arterial wall cell types secrete a SMase (S-SMase). S-SMase, however, has a sharp acid pH optimum using a standard in vitro SM-micelle assay. Thus, a critical issue regarding the potential role of S-SMase in atherogenesis is whether the enzyme can hydrolyze lipoprotein-SM, particularly at neutral pH. We now show that S-SMase can hydrolyze and aggregate native plasma LDL at pH 5.5 but not at pH 7.4. Remarkably, LDL modified by oxidation, treatment with phospholipase A2, or enrichment with apolipoprotein CIII, which are modifications associated with increased atherogenesis, is hydrolyzed readily by S-SMase at pH 7.4. In addition, lipoproteins from the plasma of apolipoprotein E knock-out mice, which develop extensive atherosclerosis, are highly susceptible to hydrolysis and aggregation by S-SMase at pH 7.4; a high SM:PC ratio in these lipoproteins appears to be an important factor in their susceptibility to S-SMase. Most importantly, LDL extracted from human atherosclerotic lesions, which is enriched in sphingomyelin compared with plasma LDL, is hydrolyzed by S-SMase at pH 7.4 10-fold more than same donor plasma LDL, suggesting that LDL is modified in the arterial wall to increase its susceptibility to S-SMase. In summary, atherogenic lipoproteins are excellent substrates for S-SMase, even at neutral pH, making this enzyme a leading candidate for the arterial wall SMase that hydrolyzes LDL-SM and causes subendothelial LDL aggregation.