gebhart/patrepeval huggingface dataset:
<title>Convenient cell fusion assay for rapid screening for HIV entry inhibitors</title> (2000)

Human immunodeficiency viruses (HIV)-induced cell fusion is a critical pathway of HIV spread from infected cells to uninfected cells. A rapid and simple assay was established to measure HIV-induce cell fusion. This study is particularly useful to rapid screen for HIV inhibitors that block HIV cell-to-cell transmission. Present study demonstrated that coculture of HIV-infected cells with uninfected cells at 37 degree(s)C for 2 hours resulted in the highest cell fusion rate. Using this cell fusion assay, we have identified several potent HIV inhibitors targeted to the HIV gp41 core. These antiviral agents can be potentially developed as antiviral drugs for chemotherapy and prophylaxis of HIV infection and AIDS.
Tyrosine Sulfation Influences the Chemokine Binding Selectivity of Peptides Derived from Chemokine Receptor CCR3 (2011)

The interactions of chemokines with their G protein-coupled receptors play critical roles in the control of leukocyte trafficking in normal homeostasis and in inflammatory responses. Tyrosine sulfation is a common post-translational modification in the amino-terminal regions of chemokine receptors. However, tyrosine sulfation of chemokine receptors is commonly incomplete or heterogeneous. To investigate the possibility that differential sulfation of two adjacent tyrosine residues could bias the responses of chemokine receptor CCR3 to different chemokines, we have studied the binding of three chemokines (eotaxin-1/CCL11, eotaxin-2/CCL24, and eotaxin-3/CCL26) to an N-terminal CCR3-derived peptide in each of its four possible sulfation states. Whereas the nonsulfated peptide binds to the three chemokines with approximately equal affinity, sulfation of Tyr-16 gives rise to 9-16-fold selectivity for eotaxin-1 over the other two chemokines. Subsequent sulfation of Tyr-17 contributes additively to the affinity for eotaxin-1 and eotaxin-2 but cooperatively to the affinity for eotaxin-3. The doubly sulfated peptide selectively binds to both eotaxin-1 and eotaxin-3 approximately 10-fold more tightly than to eotaxin-2. Nuclear magnetic resonance chemical shift mapping indicates that these variations in affinity probably result from only subtle differences in the chemokine surfaces interacting with these receptor peptides. These data support the proposal that variations in sulfation states or levels may regulate the responsiveness of chemokine receptors to their cognate chemokines.
Human Glucagon Receptor Monoclonal Antibodies: Antagonism of Glucagon Action and Use in Receptor Characterization (1996)

This paper describes the development and characterization of the first monoclonal antibody specific for the recently cloned human glucagon receptor (hGR), and its use in probing receptor structure and function. We demonstrate specificity of one of the antibodies, CIV395.7A, by immunofluorescence staining and immunoprecipitation analysis. In addition, CIV395.7A specifically competes with glucagon for the hormone binding site on the receptor, indicating that the antibody's specific recognition epitope overlaps with the receptor's hormone binding domain. As a consequence, the mAB antagonizes glucagon-stimulated signal transduction as assayed by in vitro cAMP accumulation. Binding inhibition studies further reveal that the antibody specifically recognizes the human and rat GR, but not mouse. Using hGR/glucagon-like peptide I receptor chimeras, we have localized the recognition epitope of the antibody to the membrane-proximal half of the amino-terminal extension of the receptor, thus defining a domain on the receptor which is involved in glucagon binding.
Biosynthesis of the unusual 5,5-gem-dimethyl-deoxysugar noviose: investigation of the C-methyltransferase gene cloU (2006)

The aminocoumarin antibiotic clorobiocin contains an unusual branched deoxysugar with a 5,5-gem-dimethyl structure. Inactivation of the putative C-methyltransferase gene cloU was carried out, which led to the loss of the axial methyl group at C-5 of this deoxysugar moiety. This result establishes the function of cloU, and at the same time it proves that the biosynthesis of the deoxysugar moiety of clorobiocin proceeds via a 3,5-epimerization of the dTDP-4-keto-6-deoxyglucose intermediate. The inactivation was carried out on a cosmid which contained the entire clorobiocin biosynthetic gene cluster. Expression of the modified cluster in a heterologous host led to the formation of desmethyl-clorobiocin and a structural isomer thereof. Both compounds were isolated on a preparative scale, their structures were elucidated by 1H-NMR and mass spectroscopy and their antibacterial activity was assayed.
Gene amplification causes overproduction of the first three enzymes of UMP synthesis in N-(phosphonacetyl)-L-aspartate-resistant hamster cells. (1979)

Mutant Syrian hamster cells resistant to N-(phosphonacetyl)-L-aspartate (PALA), a transition state analog inhibitor of aspartate transcarbamylase, overproduce CAD, a multifunctional protein which catalyzes the first three reactions of de novo UMP biosynthesis. Increased levels of a single mRNA cause the overproduction of CAD in all PALA-resistant mutants examined thus far. A recombinant plasmid containing a 2,3-kilobase insert complementary to the 3'-proximal region of this 7.9-kilobase mRNA has been prepared and used to show that the CAD gene is amplified in each of the 10 PALA-resistant mutants examined. Rates of association of CAD sequences in DNA isolated from PALA-sensitive and PALA-resistant cells with labeled plasmid DNA indicated that the degree of amplification is approximately equal to the degree of overproduction of protein and mRNA in each mutant. The patterns of digestion of these DNAs with restriction enzymes confirmed this result and showed that the lower limit for the size of the amplified unit is 19 kilobases, much larger than the mRNA. A comparison of restriction endonuclease digests of the cloned cDNA with digests of genomic DNA indicated that part of this difference is attributable to intervening sequences in the CAD gene. A 10.2-kilobase RNA which contains CAD sequences is found in cytoplasmic fractions from some PALA-resistant mutants but not in wild type cells. Restriction patterns were analyzed by a new method in which fragments of DNA are transferred from agarose gels to diazo paper with a high efficiency which is independent of size.
Prodrugs for antibody- and gene-directed enzyme prodrug therapies (ADEPT and GDEPT). (1999)

Antibody- and gene-directed enzyme prodrug therapy are two-step targeting strategies designed to improve the selectivity of antitumour agents. The approaches are based on the activation of specially designed prodrugs by antibody-enzyme conjugates targeted to tumour-associated antigens (ADEPT) or by enzymes expressed by exogenous genes in tumour cells (GDEPT). Herein the design, synthesis, physico-chemical and biological properties, kinetics and clinical trials of the prodrugs and the enzymes carboxypeptidase G2 and nitroreductase are reviewed for ADEPT and GDEPT.
Evolution of the apomixis transmitting chromosome in Pennisetum (2011)

Given that phylogenetic analysis merged Cenchrus and newly investigated Pennisetum species into a single clade containing a terminal cluster of Cenchrus apomicts, the presumed monophyletic origin of Cenchrus is supported. The Apospory-Specific Genomic Region likely preceded speciation in Cenchrus and its lateral transfer through hybridization and subsequent chromosome repatterning may have contributed to further speciation in the two genera.
SurroundSense (2009)

A growing number of mobile computing applications are centered around the user's location. The notion of location is broad, ranging from physical coordinates (latitude/longitude) to logical labels (like Starbucks, McDonalds). While extensive research has been performed in physical localization, there have been few attempts in recognizing logical locations. This paper argues that the increasing number of sensors on mobile phones presents new opportunities for logical localization. We postulate that ambient sound, light, and color in a place convey a photo-acoustic signature that can be sensed by the phone's camera and microphone. In-built accelerometers in some phones may also be useful in inferring broad classes of user-motion, often dictated by the nature of the place. By combining these optical, acoustic, and motion attributes, it may be feasible to construct an identifiable fingerprint for logical localization. Hence, users in adjacent stores can be separated logically, even when their physical positions are extremely close. We propose SurroundSense, a mobile phone based system that explores logical localization via ambience fingerprinting. Evaluation results from 51 different stores show that SurroundSense can achieve an average accuracy of 87% when all sensing modalities are employed. We believe this is an encouraging result, opening new possibilities in indoor localization.
A family of human receptors structurally related to Drosophila  Toll (1998)

The discovery of sequence homology between the cytoplasmic domains of Drosophila Toll and human interleukin 1 receptors has sown the conviction that both molecules trigger related signaling pathways tied to the nuclear translocation of Rel-type transcription factors. This conserved signaling scheme governs an evolutionarily ancient immune response in both insects and vertebrates. We report the molecular cloning of a class of putative human receptors with a protein architecture that is similar to Drosophila Toll in both intra- and extracellular segments. Five human Toll-like receptors--named TLRs 1-5--are probably the direct homologs of the fly molecule and, as such, could constitute an important and unrecognized component of innate immunity in humans. Intriguingly, the evolutionary retention of TLRs in vertebrates may indicate another role--akin to Toll in the dorsoventralization of the Drosophila embryo--as regulators of early morphogenetic patterning. Multiple tissue mRNA blots indicate markedly different patterns of expression for the human TLRs. By using fluorescence in situ hybridization and sequence-tagged site database analyses, we also show that the cognate Tlr genes reside on chromosomes 4 (TLRs 1, 2, and 3), 9 (TLR4), and 1 (TLR5). Structure prediction of the aligned Toll-homology domains from varied insect and human TLRs, vertebrate interleukin 1 receptors and MyD88 factors, and plant disease-resistance proteins recognizes a parallel beta/alpha fold with an acidic active site; a similar structure notably recurs in a class of response regulators broadly involved in transducing sensory information in bacteria.
Advanced MS-DOS programming: The Microsoft guide for Assembly language and C programmers (1986)

This guide addresses key programming topics, including character devices, mass storage, memory management and process management. The reference section details each MS-DOS function call and interrupt and the BIOS interrupts. New and expanded material in this edition includes, system functions for all current versions of MS-DOS, ROM BIOS information for fixed disk, EGA, VGA, PC/AT and PS/2, version 4.0 of the Lotus/Intel/Microsoft expanded memory specification, writing well-behaved versus hardware-dependent applications, and compatibility considerations for OS/2.
Factors associated with opioid dispensation for patients with COPD and lung cancer in the last year of life: A retrospective analysis (2010)

These opioids are dispensed only for a small proportion of patients with COPD at the end of their lives. Future researchers could explore the efficacy and safety of opioid use for patients with advanced COPD, and whether their limited use is justified.
Regulation of monocyte integrin expression by beta-family chemokines. (1994)

In the present study we investigated the ability of three monocyte chemokines (MCP-1, MIP-1 alpha, and RANTES) to modulate monocyte adhesion molecules in an attempt to evaluate their potential to induce tissue infiltration of macrophages in vivo. All three chemokines tested induced increased expression of the alpha-chains of two members of beta 2 family of integrins, CD11b and CD11c, and their common beta-chain (CD18). They had no effect on CD11a expression. Enhancement of CD11b and CD11c was dose dependent and followed a distinct time course with peak levels at 4 h. Levels declined to reach basal levels by 24 h. In contrast, IL-1 induced enhancement remained high after 24 h of stimulation. However, the increases caused by chemokines were not mediated by IL-1 as indicated by lack of inhibition by the IL-1R antagonist. Studies on the mechanism of integrin up-regulation showed that mobilization of cytosolic free calcium is an important signaling event in this response and that up-regulation is associated with mobilization from intracellular pools mediated by microtubules. Enhanced CD11b and CD11c expression by chemokines was also found to result in enhancement of monocyte binding to endothelial cells. Further studies indicated that monocyte binding to endothelial cells follows similar dose-response kinetics as the up-regulation of integrins and can be partially blocked by Abs to CD11b and CD11c. These results suggest that modulation of the integrin expression by chemokines may facilitate the tissue trafficking of monocytes during inflammation.
Conditionally lethal amber mutations in the leader peptidase gene of Escherichia coli (1989)

The lep gene of Escherichia coli encodes the leader peptidase which cleaves amino-terminal leader sequences of secreted proteins. To facilitate the study of structure-function relationships of the leader peptidase, 22 amber mutations in lep were isolated by localized mutagenesis. These amber mutants grew at 32 degrees C but not at 42 degrees C in the presence of a temperature-sensitive amber suppressor. Most of them were lethal under sup0 conditions. However, one amber mutant, the lep-9 mutant, exhibited temperature-sensitive growth in the sup0 strain, indicating that the amber fragment is active at 32 degrees C but not at 42 degrees C. Protein precursors of the maltose-binding protein and OmpA accumulate strikingly in the lep-9 mutant.
Bedside determination of fluid accumulation after cardiac surgery using segmental bioelectrical impedance (1998)

Cardiac surgery produced a significant decrease in segmental trunk BIA, reflecting fluid accumulation at the trunk level.
Cloning and Characterization of the Gene Encoding Lipoamide Dehydrogenase in Saccharomyces Cerevisiae (1987)

The LPD1 gene of S. cerevisiae, which encodes lipoamide dehydrogenase (EC 1.8.1.4), has been cloned and characterized. The LPD1 gene is present as a single copy in the yeast genome and is transcribed to give a polyadenylated mRNA species of approximately 2.0 kb. The synthesis of lipoamide dehydrogenase in yeast is subject to carbon catabolite repression since both the level of the LPD1 transcript and the accumulation of the lipoamide dehydrogenase subunit polypeptide were greatly reduced in wild-type cells grown on glucose compared to those grown on a variety of non-fermentable carbon sources. Strains defective in LPD1 but transformed with the LPD1 gene on a high copy number vector exhibited elevated levels of the LPD1 transcript as well as increased lipoamide dehydrogenase activity when grown on glycerol. Immunoblotting experiments confirmed that such transformants over-expressed lipoamide dehydrogenase protein. Transcription from the LPD1 sequence on plasmid pGP1 still appeared to be subject to some catabolite repression despite the presence of multiple copies of the plasmid in the cell.
Fibroindex, a practical index for predicting significant fibrosis in patients with chronic hepatitis C (2007)

The FibroIndex is a simple and reliable index for predicting significant fibrosis in chronic hepatitis C and could also be used as a surrogate marker during antifibrotic treatment for chronic hepatitis C.
[Volume rendering technique in 3D vascular imaging]. (1997)

We used volume rendering technique (VRT) for generating three-dimensional (3D) images of the vasculature from spiral computed tomography (CT) data sets. This paper describes the methods used for volume rendering and focuses on the specific aspects of volume rendering as applied to vascular imaging.
Genome-wide screen of promoter methylation identifies novel markers in melanoma (2009)

DNA methylation is an important component of epigenetic modifications, which influences the transcriptional machinery aberrant in many human diseases. In this study we present the first genome-wide integrative analysis of promoter methylation and gene expression for the identification of methylation markers in melanoma. Genome-wide promoter methylation and gene expression of eight early-passage human melanoma cell strains were compared with newborn and adult melanocytes. We used linear mixed effect models (LME) in combination with a series of filters based on the localization of promoter methylation relative to the transcription start site, overall promoter CpG content, and differential gene expression to discover DNA methylation markers. This approach identified 76 markers, of which 68 were hyper- and eight hypomethylated (LME, P < 0.05). Promoter methylation and differential gene expression of five markers (COL1A2, NPM2, HSPB6, DDIT4L, MT1G) were validated by sequencing of bisulfite-modified DNA and real-time reverse transcriptase PCR, respectively. Importantly, the incidence of promoter methylation of the validated markers increased moderately in early and significantly in advanced-stage melanomas, using early-passage cell strains and snap-frozen tissues (n = 18 and n = 24, respectively) compared with normal melanocytes and nevi (n = 11 and n = 9, respectively). Our approach allows robust identification of methylation markers that can be applied to other studies involving genome-wide promoter methylation. In conclusion, this study represents the first unbiased systematic effort to determine methylation markers in melanoma and revealed several novel genes regulated by promoter methylation that were not described in cancer cells before.
Oxytocin Augmentation in Arrest Disorders in the Presence of Thick Meconium: Influence on Neonatal Outcome (1994)

The objective of this report was to study the effect of oxytocin augmentation in arrest disorders in the presence of thick meconium on meconium aspiration and fetal acidosis. We evaluated 3,321 singleton, term deliveries with cephalic presentation at our institution. Eight percent (253/3,321) had thick meconium in labor, and these patients comprised the study sample. Of the 253 women with thick meconium, 84 had an arrest disorder in the active phase of labor with normal fetal heart rate tracing at the time of diagnosis. Seventy-four percent (62/84) of the women with arrest were treated with oxytocin (group 1) and 26% (22/84) delivered by cesarean section without augmentation (group 2). There was a significant (p < 0.05) increase in the incidence of meconium aspiration (14.5 vs. 4.5%) and low (< 7.20) cord arterial pH (27.8 vs. 4.5%) in patients who received oxytocin compared to those who did not. Of the women who received oxytocin, 36 delivered vaginally, and 2 neonates had meconium aspiration. The remaining 26 women had cesarean sections following oxytocin augmentation and had a significantly higher (p < 0.05) frequency of meconium aspiration (26.9 vs. 4.5%) and low cord arterial pH (38.5 vs. 4.5%) compared to women who had cesarean sections without oxytocin augmentation. The findings suggest that oxytocin augmentation in arrest disorders in the presence of thick meconium may be associated with a higher risk of meconium aspiration and low umbilical cord arterial pH.
Expression Patterns of Aurora Kinase B, Heat Shock Protein 47, and Periostin in Esophageal Squamous Cell Carcinoma (2009)

To elucidate the proteins related to the development and progress of esophageal squamous cell carcinoma (ESCC), we performed gene expression profile analysis of 14 ESCC tissues. We identified 182 genes that were commonly upregulated (p < 10(-5)) and 54 genes that were downregulated in ESCC tissues (p < 10(-6)). In order to validate the gene expression profiles, we did semiquantitative RT-PCR analysis and found 11 genes upregulated in greater than 70% of 19 tissue samples. We further examined the protein expression level and the distribution patterns of four genes: aurora kinase B (AURKB), periostin (POSTN), heat shock protein 47 (HSP47), and matrix metalloprotease 1 (MMP1). Ultimately, three genes (AURKB, HSP47, POSTN) were verified to be increased at both the mRNA and protein levels. Among them, AURKB and HSP47 were found to increase in the early development stage of ESCC and POSTN might be considered to function in the cell-cell interactions between cancer cell and adjacent stromal cells. Accordingly, these studies may provide valuable information for the identification of the genes that are necessary to study further their functions. Moreover, these genes might be used as potential diagnostic or therapeutic target molecules for ESCC patients.
Mapping the Epitopes of Antibodies (2007)

(2007). Mapping the Epitopes of Antibodies. Biotechnology and Genetic Engineering Reviews: Vol. 24, No. 1, pp. 1-30.
Effects of Tea (Camellia sinensis) Chemical Compounds on Ethanol Metabolism in ICR Mice (1996)

The effects of a green tea (Camellia sinensis) extract on ethanol metabolism in ICR male mice were studied. A crude green tea extract (GTE) and the tea components as (-)-epigallocatechin gallate (EGCg), (-)-epigallocatechin (EGC), and caffeine were administered before the tests. One hour later, the mice were orally given 2g/kg body weight (b.w.) of ethanol (20% ethanol w/v). The results show that the levels in the blood and liver of ethanol and acetaldehyde were lower, and that the levels of acetate and acetone were higher than in the controls orally given 500 mg/kg b.w. of GTE. After the administration of 75 mg/kg b.w. and 225 mg/kg b.w. of EGCg, the acetate and acetone concentrations in the blood and liver were lower than in the controls. The mice given caffeine at the same dose as that in GTE showed almost the same effects as the group treated with GTE. This suggests that EGCg and caffeine, the principal components of GTE, both had an effect on ethanol metabolism.
Lipofectamine and Related Cationic Lipids Strongly Improve Adenoviral Infection Efficiency of Primitive Human Hematopoietic Cells (1998)

Adenoviral vectors have the potential to infect a large number of cell types including quiescent cells. Their use in hematopoietic cells is limited by the episomal form of their DNA, leading to transgene loss in the progeny cells. However, the use of this vector may be interesting for short-term in vitro modifications of primitive human hematopoietic cells. Therefore, we have investigated the ability of adenovirus to transduce cord blood CD34+ cells. Several promoters were tested using the lacZ reporter gene. The PGK and CMV promoters induced transgene expression in 18-25% of the cells, whereas the HTLV-I and especially the RSV promoter were almost inactive. To improve infection efficiency, adenovirus was complexed with cationic lipids. Lipofectamine, Cellfectin, and RPR120535b, but not Lipofectin, Lipofectace, or DOTAP, markedly improved transgene expression in CD34+ cells (from 19 to 35%). Lipofectamine strongly enhanced infection efficiency of the poorly infectable primitive CD34+ CD38low cells (from 11 to 28%) whereas the more mature CD34+ CD38+ cells were only slightly affected (from 24 to 31%). Lipofectamine tripled the infection of CFU-GMs and LTCICs derived from the CD34+ CD38low cell fraction (from 4 to 12% and from 5 to 16%, respectively) and doubled that of BFU-Es (from 13 to 26%). We conclude that cationic lipids can markedly increase the efficiency of adenovirus-mediated gene transfer into primitive hematopoietic cells.