gebhart/patrepeval huggingface dataset:
Oncogenic H-Ras Up-Regulates Expression of ERCC1 to Protect Cells from Platinum-Based Anticancer Agents (2004)

Tumors frequently contain mutations in the ras genes, resulting in the constitutive activation of the Ras-activated signaling pathway. The activation of Ras is involved not only in tumor progression but also in the development of resistance of the tumor cells to platinum-based chemotherapeutic agents. To investigate the potential mechanisms underlying this resistance, we analyzed the effect of activated H-Ras on the expression of the nucleotide excision repair genes. Here we identified ERCC1, which is one of the key enzymes involved in nucleotide excision repair, as being markedly up-regulated by the activated H-Ras. From promoter analysis of ERCC1, an increase in the Ap1 transcriptional activity as a result of the expression of the oncogenic H-Ras was found to be crucial for this induction. In addition, ERCC1 small interfering RNA expression was shown to reduce the oncogenic H-Ras-mediated increase in the DNA repair activity as well as to suppress the oncogenic H-Ras-mediated resistance of the cells to platinum-containing chemotherapeutic agents. These results suggest that the oncogenic H-Ras-induced ERCC1, which activates the DNA repair capacity, may be involved in the protection of the cells against platinum-based anticancer agents.
Infectivity titration of a prototype strain of hepatitis E virus in cynomolgus monkeys (1994)

The infectivity titer of a standard stock of the SAR-55 strain of hepatitis E virus (HEV) was determined in cynomolgus macaques (Macaca fascicularis) and the effect of dose on the course of the infection was examined by weekly monitoring of alanine aminotransferase (ALT) and anti-HEV levels. Antibody to HEV (anti-HEV) was measured with ELISAs based on ORF-2 recombinant antigens consisting of either a 55 kDa region expressed in insect cells or shorter regions expressed as fusion proteins in bacteria. The ELISA based on the 55 kDa antigen was generally more sensitive. The infectivity titer of SAR-55 was 10(6) cynomolgus 50% infectious doses per gram of feces. The infectivity titer corresponded to the HEV genome titer of the inoculum as determined by reverse transcriptase-polymerase chain reaction (RT-PCR). Anti-HEV IgM was detected in only a portion of the animals that had an anti-HEV IgG response. Biochemical evidence of hepatitis was most prominent in animals that were inoculated with the higher concentrations of virus and the incubation period to seroconversion was prolonged in animals that received the lower doses.
Two-Dimensional Electronic Excitations in Self-Assembled Conjugated Polymer Nanocrystals (2000)

Several spectroscopic methods were applied to study the characteristic properties of the electronic excitations in thin films of regioregular and regiorandom polythiophene polymers. In the regioregular polymers, which form two-dimensional lamellar structures, increased interchain coupling strongly influences the traditional one-dimensional electronic properties of the polymer chains. The photogenerated charge excitations (polarons) show two-dimensional delocalization that results in a relatively small polaronic energy, multiple absorption bands in the gap where the lowest energy band becomes dominant, and associated infrared active vibrations with reverse absorption bands caused by electron-vibration interferences. The relatively weak absorption bands of the delocalized polaron in the visible and near-infrared spectral ranges may help to achieve laser action in nanocrystalline polymer devices using current injection.
Helicobacter pylori rocF Is Required for Arginase Activity and Acid Protection In Vitro but Is Not Essential for Colonization of Mice or for Urease Activity (1999)

Arginase of the Helicobacter pylori urea cycle hydrolyzes L-arginine to L-ornithine and urea. H. pylori urease hydrolyzes urea to carbon dioxide and ammonium, which neutralizes acid. Both enzymes are involved in H. pylori nitrogen metabolism. The roles of arginase in the physiology of H. pylori were investigated in vitro and in vivo, since arginase in H. pylori is metabolically upstream of urease and urease is known to be required for colonization of animal models by the bacterium. The H. pylori gene hp1399, which is orthologous to the Bacillus subtilis rocF gene encoding arginase, was cloned, and isogenic allelic exchange mutants of three H. pylori strains were made by using two different constructs: 236-2 and rocF::aphA3. In contrast to wild-type (WT) strains, all rocF mutants were devoid of arginase activity and had diminished serine dehydratase activity, an enzyme activity which generates ammonium. Compared with WT strain 26695 of H. pylori, the rocF::aphA3 mutant was approximately 1, 000-fold more sensitive to acid exposure. The acid sensitivity of the rocF::aphA3 mutant was not reversed by the addition of L-arginine, in contrast to the WT, and yielded a approximately 10, 000-fold difference in viability. Urease activity was similar in both strains and both survived acid exposure equally well when exogenous urea was added, indicating that rocF is not required for urease activity in vitro. Finally, H. pylori mouse-adapted strain SS1 and the 236-2 rocF isogenic mutant colonized mice equally well: 8 of 9 versus 9 of 11 mice, respectively. However, the rocF::aphA3 mutant of strain SS1 had moderately reduced colonization (4 of 10 mice). The geometric mean levels of H. pylori recovered from these mice (in log(10) CFU) were 6.1, 5.5, and 4.1, respectively. Thus, H. pylori rocF is required for arginase activity and is crucial for acid protection in vitro but is not essential for in vivo colonization of mice or for urease activity.
Trimeric assembly of the C-terminal region of Thrombospondin-1 or Thrombospondin-2 is necessary for cell spreading and fascin spike organisation (2002)

Thrombospondin-1 (TSP-1) and the highly related protein thrombospondin-2 (TSP-2) are trimeric extracellular molecules that have complex roles in wound healing, angiogenesis and matrix organisation. At the cellular level, TSP-1 supports cell adhesion and migration by the organisation of fascin spike cytoskeletal structures. To define the molecular requirements for assembly of fascin spikes by thrombospondins, we developed a panel of recombinant protein units of TSP-1 and TSP-2; these were designed according to the domain boundaries and included matched monomeric and trimeric units. These proteins were tested for their effects on cell attachment and fascin spike organisation using C2C12 skeletal myoblasts and vascular smooth muscle cells. In monomeric units, cell attachment activity was localised to the type 1 repeats or type 3 repeats/C-terminal globule, and both regions need to be present in the same molecule for maximal activity. On a molar basis, cell-attachment activities with monomeric units were low compared with intact TSP-1, and no monomeric unit induced cell spreading. Trimeric versions of the type 1 repeats were more adhesive but did not induce cell spreading. Strikingly, trimers that contained the type 3 repeats/C-terminal globule of either TSP-1 or TSP-2 supported cell spreading and fascin spike organisation, producing a similar activity to intact TSP-1. We conclude that trimeric assembly of the highly conserved TSP C-terminal region is necessary for organisation of the fascin-based cytoskeletal structures that are needed for thrombospondin-induced cell motility.
Transcriptional Differences between Normal and Glioma-Derived Glial Progenitor Cells Identify a Core Set of Dysregulated Genes (2013)

Glial progenitor cells (GPCs) are a potential source of malignant gliomas. We used A2B5-based sorting to extract tumorigenic GPCs from human gliomas spanning World Health Organization grades II-IV. Messenger RNA profiling identified a cohort of genes that distinguished A2B5+ glioma tumor progenitor cells (TPCs) from A2B5+ GPCs isolated from normal white matter. A core set of genes and pathways was substantially dysregulated in A2B5+ TPCs, which included the transcription factor SIX1 and its principal cofactors, EYA1 and DACH2. Small hairpin RNAi silencing of SIX1 inhibited the expansion of glioma TPCs in vitro and in vivo, suggesting a critical and unrecognized role of the SIX1-EYA1-DACH2 system in glioma genesis or progression. By comparing the expression patterns of glioma TPCs with those of normal GPCs, we have identified a discrete set of pathways by which glial tumorigenesis may be better understood and more specifically targeted.
Organ Injury Scaling (1989)

The Organ Injury Scaling (O.I.S.) Committee of the American Association for the Surgery of Trauma (A.A.S.T.) was appointed by President Trunkey at the 1987 Annual Meeting. The principal charge was to devise injury severity scores for individual organs to facilitate clinical research. The resultant classification scheme is fundamentally an anatomic description, scaled from 1 to 5, representing the least to the most severe injury. A number of similar scales have been developed in the past, but none has been uniformly adopted. In fact, this concept was introduced at the A.A.S.T. in 1979 as the Abdominal Trauma Index (A.T.I.) and has proved useful in several areas of clinical research. The enclosed O.I.S.'s for spleen, liver, and kidney represent an amalgamation of previous scales applied for these organs, and a consensus of the O.I.S. Committee as well as the A.A.S.T. Board of Managers. The O.I.S. differs from the Abbreviated Injury Score (A.I.S.), which is also based on an anatomic scale but designed to reflect the impact of a specific organ injury on ultimate patient outcome. The individual A.I.S.'s are, of course, the basic elements used to calculate the Injury Severity Score (I.S.S.) as well as T.R.I.S.S. methodology. To ensure that the O.I.S. interdiffuses with the A.I.S. and I.C.D.-9 codes, these are listed alongside the respective O.I.S. Both the currently used A.I.S. 85 and proposed A.I.S. 90 are provided because of the obligatory transition period. Indeed, A.I.S. 90 contains the identical descriptive text as the current O.I.S.'s. The Abdominal Trauma Index and other similar indices using organ injury scoring can be easily modified by replacing older scores with the O.I.S.'s.(ABSTRACT TRUNCATED AT 250 WORDS)
Mycobacterium bovisbacille Calmette–Guérin strains secreting listeriolysin ofListeria monocytogenes (1998)

Recombinant (r) Mycobacterium bovis strains were constructed that secrete biologically active listeriolysin (Hly) fusion protein of Listeria monocytogenes. The r-BCG strains pAT261:Hly or pMV306:Hly expressed plasmid multicopies or chromosomal single copies of the hly gene, respectively. Human and murine macrophage-like cell lines were infected with r-BCG pAT261:Hly and pMV306:Hly strains. Interestingly, intracellular persistence of both r-BCG strains was reduced in macrophages as compared with the parental BCG strain. By immunogold labeling Hly was detected in membrane structures and within the phagosomal space of macrophages. In addition, Hly was localized within cytoplasmic vacuoles outside the mycobacteria-containing phagosome of host cells infected with r-BCG pAT261:Hly or r-BCG pMV306:Hly. Hly fusions consistently colocalized with a lysosome-associated membrane glycoprotein, suggesting that membrane-attack conformation of Hly was not altered. Although r-BCG pAT261:Hly and r-BCG pMV306:Hly microorganims apparently did not egress into the cytoplasmic compartment of host cells, they both improved major histocompatibility complex class I presentation of cophagocytosed soluble protein as compared with wild-type BCG microbes. These data suggest that Hly secretion endows BCG with an improved capacity to stimulate CD8 T cells. Because CD8 T cells play a major role in protection against tuberculosis such Hly secreting r-BCG constructs are antituberculosis vaccine candidates.
Biomimetic Templating of Porous Lamellar Silicas by Vesicular Surfactant Assemblies (1996)

A biomimetic templating approach to the synthesis of lamellar silicas is demonstrated. The procedure is based on the hydrolysis and cross-linking of a neutral silicon alkoxide precursor in the interlayered regions of multilamellar vesicles formed from a neutral diamine bola-amphiphile. Unlike earlier surfactant-templating approaches, this method produces porous lamellar silicas (designated MSU-V) with vesicular particle morphology, exceptional thermal stability, a high degree of framework cross-linking, unusually high specific surface area and pore volume, and sorption properties that are typical of pillared lamellar materials. This approach circumvents the need for a separate pillaring step in building porosity into a lamellar host structure and offers new opportunities for the direct fabrication of adsorbents, catalysts, and nanoscale devices.
Tumor Amplified Protein Expression Therapy: Salmonella as a Tumor-Selective Protein Delivery Vector (2001)

Attenuated strains of Salmonella typhimurium, VNP20009 and YS7212, when injected systemically to tumor-bearing mice, accumulated preferentially in tumors at levels at least 200-fold and, more commonly, 1000-fold greater than in other normal tissues. This selectivity occurred in subcutaneously implanted murine tumors, including B16F10 melanoma, M27 lung carcinoma, and colon 38 carcinoma. The preferential accumulation was also manifested in animals bearing human tumor xenografts, including Lox, C8186, DLD1, SW620, HCT116, HTB177, DU145, MDA-MB-231, and Caki. Four to five days after a single IV injection of 1 x 10(6) colony-forming unit (cfu)/mouse, we routinely detected VNP20009 proliferation and accumulation at levels ranging from 1 x 10(8) to 2 x 10(9) cfu/g tumor. The amount of VNP20009 accumulated in the liver ranged from 3 x 10(4) to 2 x 10(6) cfu/g. The distribution of Salmonella in tumors was homogenous; YS7212 could be detected from the periphery to the interior portion of the tumors. Using mice with various immunodeficiencies, we also discovered the same preferential accumulation of Salmonella in tumors implanted in these mice. The use of Salmonella as a protein delivery vector was shown by IV administration of the bacteria expressing either green fluorescent protein (GFP) or cytosine deaminase (CD) into tumor-bearing mice. GFP and CD were detected in tumors, but not in livers, taken from mice inoculated with Salmonella carrying these genes. Bacteria accumulation and CD expression persisted in the tumors for up to 14 days after a single bolus IV administration of bacteria to tumor-bearing mice.
A T-strip loaded rectangular microstrip patch antenna for dual-frequency operation (2003)

Dual-frequency operation of a T-strip loaded microstrip patch antenna is introduced. The procedure for simultaneous input impedance matching at both resonant frequencies is also described. We performed both simulation and experiments, which show good consistency between each other. Finally, based on our simulation and experimental results, return losses and radiation patterns are also discussed.
Functional reintroduction of human telomeres into mammalian cells. (1991)

Telomeric sequences of eukaryotes consist of short tandem repeats organized in arrays of variable length in which the guanine-rich strand runs 5'----3' toward the chromosomal end. The terminal repeats in yeast are the only elements necessary for telomere function in this organism. To test whether mammalian terminal repeats can function after reintroduction into a mammalian cell, a repeat-containing terminal fragment from a human chromosome was electroporated into a hamster-human hybrid cell line. In 6 of 27 independent transformants analyzed, the introduced sequences were found at the ends of chromosomes, based on all available criteria. Terminal restriction-fragment heterogeneity and the survival of these chromosomes demonstrate that these telomeres are functional. Cytogenetic evidence from one of these cell lines suggests that chromosome breakage with healing at the integration site is the mechanism responsible for the terminal location.
Effect of ammoniation of rapeseed meal on the sinapine content of the meal (1982)

1. Two experiments were conducted to study the effects of ammoni‐ation of rapeseed meal on its sinapine content. 2. In the first experiment, five samples of a low‐glucosinolate meal (produced from Regent, Candle or Tower cultivars) and one sample of a high‐glucosinolate meal were eluted by one passage of ethanol ammoniated to concentrations of 0.2, 0.5 or 1.0 M NH3 at the ratio of 2 1 ammoniated ethanol/kg meal. Elution with 1.0M ammoniated ethanol decreased the sinapine content of the meals by as much as 80%. 3. In the second experiment, four low‐glucosinolate meals (from Candle cultivar) from a pilot processing plant were used. Two of the meals were obtained by sparging during desolventising with or without anhydrous ammonia (50 g anhydrous ammonia/kg meal) and two of the meals were produced by sparging during desolventising with or without hydrous ammonia (50 g anhydrous ammonia and 50 g steam/kg meal). Ammonia with steam caused the greatest decrease (65%) in sinapine content. 4. Total glucosinolate and 5‐vinyl‐2‐oxazolidinethione concentrations in the meals were also decreased (17 to 35%) by the ammoniation treatments in experiment 2.
An integrated transcriptome and expressed variant analysis of sepsis survival and death (2014)

ClinicalTrials.gov NCT00258869. Registered on 23 November 2005.
Fc epsilon R1-mediated tyrosine phosphorylation of multiple proteins, including phospholipase C gamma 1 and the receptor beta gamma 2 complex, in RBL-2H3 rat basophilic leukemia cells. (1992)

In basophils, mast cells, and the RBL-2H3 tumor mast cell line, cross-linking the high-affinity immunoglobulin E receptor (Fc epsilon R1) stimulates a series of responses, particularly the activation of phospholipase C (PLC), that lead to allergic and other immediate hypersensitivity reactions. The mechanism of activation of PLC, however, is not clear. Here, we show that cross-linking Fc epsilon R1 on RBL-2H3 cells causes the tyrosine phosphorylation of at least 12 cellular proteins, including PLC gamma 1 (PLC gamma 1) and the receptor beta and gamma subunits. 32P-labeled PLC gamma 1 can be detected by anti-phosphotyrosine antibody as early as 10 s after the addition of antigen. The tyrosine-phosphorylated 33-kDa beta subunit and 9- to 11-kDa gamma subunit of the Fc epsilon R1 are additionally phosphorylated on serine and theonine residues, respectively, and are found as complexes with other phosphotyrosine-containing proteins in antigen-stimulated cells. Our results indicate a means by which the Fc epsilon R1 may control PLC activity in RBL-2H3 cells and raise the possibility that other receptor-mediated signalling events in mast cells may also be controlled through protein tyrosine phosphorylation.
RXP 407, a phosphinic peptide, is a potent inhibitor of angiotensin I converting enzyme able to differentiate between its two active sites (1999)

The human somatic angiotensin converting enzyme (ACE) contains two homologous domains, each bearing a zinc-dependent active site. All of the synthetic inhibitors of this enzyme used in clinical applications interact with these two active sites to a similar extent. Recently, several lines of evidence have suggested that the N-terminal active site of ACE might be involved in specific hydrolysis of some important physiological substrates, like Acetyl-Seryl-Aspartyl-Lysyl-Proline, a negative regulator of hematopoietic stem cell differentiation and proliferation. These findings have stimulated studies aimed at identifying new ACE inhibitors able to block only one of the two active sites of this enzyme. By screening phosphinic peptide libraries, we discovered a phosphinic peptide Ac-Asp-(L)Phepsi(PO2-CH2)(L)Ala-Ala-NH2, called RXP 407, which is able to differentiate the two ACE active sites, with a dissociation constant three orders of magnitude lower for the N-domain of the enzyme. The usefulness of a combinatorial chemistry approach to develop new lead structures is underscored by the unusual chemical structure of RXP 407, as compared with classical ACE inhibitors. As a highly potent and selective inhibitor of the N-terminal active site of wild ACE (Ki = 12 nM), RXP 407, which is metabolically stable in vivo, may lead to a new generation of ACE inhibitors able to block in vivo only a subset of the different functions regulated by ACE.
Dendrimers, Arborols, and Cascade Molecules: Breakthrough into Generations of New Materials (1992)

Compounds with extremely branched molecular structures (for example 1) that are formed in iterative syntheses are penetrating many disciplines of chemistry. Compound 1 has 36 carboxyl groups on its periphery and can be considered a unimolecular micelle. Recently dendrimers have found their way into coordination chemistry through a compound which contains up to 22 metal centers per molecule (see also Balzani et al. Angew. Chem. Int. Ed. Engl. 1992, 31, 1493).
Selective depletion of CD8+ T lymphocytes for prevention of graft- versus-host disease after allogeneic bone marrow transplantation (1990)

Abstract The effects of selectively depleting CD8+ cells from donor bone marrow were assessed in 36 patients receiving transplantation from an HLA- identical sibling as treatment for leukemia. Donor bone marrow underwent ex vivo treatment using anti-Leu-2 monoclonal antibody and complement. Patients received cyclosporine post-transplant for 6 months. Thirty-three patients had initial engraftment. Three failed to have hematologic recovery, and one patient with initial engraftment had late graft failure. The actuarial incidence of grade greater than or equal to 2 acute graft-versus-host disease was 28% +/- 18% and was usually confined to the skin. Of 33 patients with engraftment, 32 were complete chimeras and one had mixed chimerism. The tempo of hematologic and immunologic recovery was comparable with that reported with transplantation of unmodified bone marrow, although CD4+ and CD8+ T cells recovered at comparable rates. The actuarial rate of leukemia relapse was 11% +/- 10%, occurring in three patients with acute leukemia but in none of 13 patients transplanted for chronic myelogenous leukemia. Actuarial survival was 57% +/- 17% at 2 years. These data indicate that after transplantation of marrow depleted of CD8+ cells, engraftment with prompt hematologic and immunologic recovery generally occurs, with a relatively low rate of acute graft- versus-host disease. Graft failure remains a problem despite retention of CD4+ cells within the donor marrow. The lack of leukemia relapse in patients with chronic myelogenous leukemia suggests retention of a graft-versus-leukemia effect, at least for this malignancy.
Critical role of interleukin-2 in the development of acute graft-versus-host disease (1993)

Prior work using the parent-into-F1 model of graft-versus-host disease (GVHD) has shown that production of IL-2 by donor CD4+ T cells is an early, initiating event in either acute or stimulatory forms of GVHD. The aim of the present study was to determine whether acute GVHD could be prevented by blocking the effects of IL-2 in vivo during the first 2 weeks of disease. Acute GVHD was induced in B6D2F1 mice by the injection of C57BL/6 spleen cells i.v. Mice were untreated or received either anti-IL-2 mAb (S4B6) or control mAb at the time of GVHD induction and 1 week later. At 2 weeks, untreated or control mAb treated GVHD mice exhibited findings typical of acute GVHD, i.e. (i) in vitro donor anti-host cytotoxic T lymphocyte (CTL) activity, (ii) significant reductions in both numbers and function of splenic lymphocytes, and (iii) in vitro suppressor cell activity which profoundly blocked IL-2 production by normal syngeneic spleen cells. All of these findings were reversed or significantly inhibited in acute GVHD mice receiving anti-IL-2 treatment. Additionally, anti-IL-2 treated GVHD mice exhibited features previously observed in stimulatory GVHD such as: (i) B cell hyperactivity, (ii) a mild defect in CD4+ T cell production of IL-2 in vitro, and (iii) the ability to induce in co-culture a similar CD4+ cell defect in normal, syngeneic F1 spleen cells.(ABSTRACT TRUNCATED AT 250 WORDS)