gebhart/patrepeval huggingface dataset:
Achieving alloengraftment without graft-versus-host disease: approaches using mixed allogeneic bone marrow transplantation. (1988)

Two opposing immunologically-mediated phenomena currently limit the success of bone marrow transplantation (BMT) in HLA-identical situations and impede the application of this therapeutic modality across MHC barriers. These phenomena are: (1) the response of T cells within the donor marrow allograft to recipient alloantigen, resulting in graft-versus-host disease (GVHD) with its attendant morbidity and mortality; and (2) the response of recipient cells which have survived the ablative conditioning regimen against alloantigen borne by the donor marrow allograft, leading to failure of alloengraftment. While T cell depletion of donor marrow has successfully reduced the incidence of severe GVHD, this reduction has been associated with an increased incidence of failure of alloengraftment. In this communication we review several recent approaches being studied in animal models in our laboratory to avoid such undesirable effects of host-anti-donor and donor-anti-host alloaggression. The first approach is based on the observation that administration of T cell-depleted (TCD) syngeneic bone marrow (BM) appears to limit GVHD while still permitting engraftment by co-administered non-TCD allogeneic BM. This anti-GVH effect of TCD syngeneic marrow can be enhanced by delaying the administration of allogeneic BM by 8 days following whole body irradiation and syngeneic BMT. Evidence that natural suppressor cells derived from syngeneic marrow may be responsible for this phenomenon is reviewed. We also present evidence for the existence of a non-stem cell bone marrow subpopulation, distinct from those T cells which cause GVHD, which is capable of increasing levels of allogeneic chimerism.(ABSTRACT TRUNCATED AT 250 WORDS)
Total Synthesis of (−)-4,8,10-Tridesmethyl Telithromycin (2011)

Novel sources of antibiotics are required to address the serious problem of antibiotic resistance. Telithromycin (2) is a third-generation macrolide antibiotic prepared from erythromycin (1) and used clinically since 2004. Herein we report the details of our efforts that ultimately led to the total synthesis of (-)-4,8,10-tridesmethyl telithromycin (3) wherein methyl groups have been replaced with hydrogens. The synthesis of desmethyl macrolides has emerged as a novel strategy for preparing bioactive antibiotics.
Plasma-related characteristics of a steady-state glow discharge at atmospheric pressure (1993)

Summary form only given. A large-volume (up to 2.8 liters), low-power (less than 200 W), steady-state glow discharge plasma has been generated which allows many surface modification and other plasma processing operations to be carried out at one atmosphere, rather than in expensive vacuum systems which enforce batch processing. The plasma-related characteristics and surface-treatment applications of this atmospheric pressure, steady-state glow discharge have been examined in the present work. The plasma floating potential is measured as a function of RF frequency, RF voltage, and type of working gas. Helium, a mixture of helium and air, and argon are used as working gases. Surface treatment of organic materials has been carried out. This plasma can modify the physical, chemical, and electrical surface properties of the materials.
Catalytic activities of polymer‐supported metal complexes in oxidation of phenol and epoxidation of cyclohexene (2007)

Abstract The metal complexes of N , N ′‐bis ( o ‐hydroxy acetophenone) propylene diamine (HPPn) Schiff base were supported on cross‐linked polystyrene beads. The complexation of iron(III), copper(II), and zinc(II) ions on polymer‐anchored HPPn Schiff base was 83.4, 85.7, and 84.5 wt%, respectively, whereas the complexation of these metal ions on unsupported HPPn Schiff base was 82.3, 84.5, and 83.9 wt%. The iron(III) complexes of HPPn Schiff base were octahedral in geometry, whereas copper(II) and zinc(II) ions complexes were square planar and tetrahedral. Complexation of metal ions increased the thermal stability of HPPn Schiff base. Catalytic activity of metal complexes was tested by studying the oxidation of phenol and epoxidation of cyclohexene in the presence of hydrogen peroxide. The polymer‐supported HPPn Schiff base complexes of iron(III) ions showed 73.0 wt% conversion of phenol and 90.6 wt% conversion of cyclohexene at a molar ratio of 1:1:1 of substrate to catalyst and hydrogen peroxide, but unsupported complexes of iron(III) ions showed 63.8 wt% conversion for phenol and 83.2 wt% conversion for cyclohexene. The product selectivity for catechol (CTL) and epoxy cyclohexane (ECH) was 93.1 and 98.3 wt%, respectively with supported HPPn Schiff base complexes of iron(III) ions but was lower with HPPn Schiff base complexes of copper(II) and zinc(II) ions. Activation energy for the epoxidation of cyclohexene and phenol conversion with unsupported HPPn Schiff base complexes of iron(III) ions was 16.6 kJ mol −1 and 21.2 kJ mol −1 , respectively, but was lower with supported complexes of iron(III) ions. Copyright © 2007 John Wiley &amp; Sons, Ltd.
Neutrophil attractant/activation protein-1 and monocyte chemoattractant protein-1 in rabbit. cDNA cloning and their expression in spleen cells (1991)

Rabbit neutrophil attractant/activation protein-1 (NAP-1) and monocyte chemoattractant protein-1 (MCP-1) were investigated. Rabbit spleen cells stimulated with 5 micrograms/ml of Con A produced both neutrophil and monocyte chemotactic activity. Physicochemical characteristics of those activities obtained by HPLC gel filtration and HPLC chromatofocusing were very similar to those of human NAP-1 and MCP-1, suggesting that rabbit spleen cells produce NAP-1 and MCP-1 after Con A stimulation. A cDNA library was constructed from mRNA purified from Con A-stimulated rabbit spleen cells and screened with oligonucleotide probes. By two rounds of screening, NAP-1 and MCP-1 cDNA were cloned. NAP-1 cDNA comprises 1500 bp with an open reading frame that encodes for a 101-amino acid protein highly similar to human NAP-1. MCP-1 cDNA comprises 607 bp with an open reading frame that encodes for a 124-amino acid protein highly similar to human MCP-1. Expression of NAP-1 and MCP-1 mRNA by rabbit spleen cells was studied. Both Con A- and LPS-stimulated spleen cells expressed NAP-1 and MCP-1 mRNA, but the kinetics of expression were different. Con A rapidly induced high NAP-1 and MCP-1 mRNA expression. LPS also rapidly induced NAP-1 mRNA expression, but high MCP-1 mRNA expression was not observed until 15 h after stimulation. Immunoprecipitation of metabolically labeled NAP-1 and MCP-1 with anti-human NAP-1 or MCP-1 polyclonal antibodies was attempted. Immunoprecipitated rabbit NAP-1 with a molecular mass of about 7 kDa was detected by SDS-PAGE and radioautography, but MCP-1 was not. Cloned rabbit NAP-1 and MCP-1 will give us opportunities to study the role of NAP-1 and MCP-1 in vivo.
A parallel graph decomposition algorithm for DNA sequencing with nanopores (2004)

We have developed an algorithm that addresses these issues. It can be considered an extreme variation of the well-known Eulerian path approach. It searches over a space of de Bruijn graphs until it finds one in which (a) the impact of errors is eliminated and (b) both possible orientations of the two ssDNA sequences can be identified separately and unambiguously. Our algorithm is able to correctly reconstruct real DNA sequences of the order of 10(6) bases (e.g. the bacterium Mycoplasma pneumoniae) from simulated erroneous reads on a modest workstation in about 1 h. We describe, and give measured timings of, a parallel implementation of this algorithm on the Cray Multithreaded Architecture (MTA-2) supercomputer, whose architecture is ideally suited to this 'unstructured' problem. Our parallel implementation is crucial to the problem of rapidly sequencing long DNA sequences and also to the situation where multiple nanopores are used to obtain a high-bandwidth stream of reads.
The TIMP2 Membrane Type 1 Metalloproteinase “Receptor” Regulates the Concentration and Efficient Activation of Progelatinase A (1998)

We have used C-terminal domain mutants to further define the role of interactions of progelatinase A and membrane type 1 matrix metalloproteinase (MT1 MMP) in the binding of TIMP2 and in the cell-associated activation of progelatinase A. Soluble constructs of MT1 MMP were used to demonstrate that binding with TIMP2 occurs primarily through N-terminal domain interactions, leaving the C-terminal domain free for interactions with progelatinase A. The rate of autolytic activation of progelatinase A initiated by MT1 MMP cleavage could be potentiated by concentration of the proenzyme by binding to heparin. Residues 568-631 of the progelatinase A C-terminal domain are important in formation of the heparin binding site, since replacement of this region with the corresponding stromelysin-1 sequence abolished binding to heparin and the potentiation of activation. The same region of gelatinase A was required for binding of latent and active enzyme to TIMP2, but residues 418-474 were not important. A similar pattern was seen using cell membrane-associated MT1 MMP; residues 568-631 were required for binding and activation of progelatinase A, whereas residues 418-474 were not. Neither region was required for activation in solution. The addition of TIMP2 to HT1080 membrane preparations expressing MT1 MMP, but depleted of endogenous TIMP2, resulted in potentiation of progelatinase A activation. This effect was dependent upon TIMP2 binding to MT1 MMP rather than at an independent membrane site. Together, the data suggest that TIMP2 forms a receptor with MT1 MMP that regulates the concentration and efficient generation of functionally active gelatinase A.
Migration of monocytes across endothelium and passage through extracellular matrix involve separate molecular domains of PECAM-1. (1995)

During the inflammatory response, the adhesion molecule PECAM plays a crucial role in transendothelial migration, the passage of leukocytes across endothelium. We report here an additional role for PECAM in the subsequent migration of monocytes through the subendothelial extracellular matrix. PECAM has six immunoglobulin (Ig) superfamily domains. Monoclonal antibodies whose epitopes map to domains 1 and/or 2 selectively block monocyte migration through the endothelial junction, whereas those that map to domain 6 block only the migration through the extracellular matrix, trapping the monocyte between the endothelium and its basal lamina. Therefore, transendothelial migration (diapedesis) and passage through extracellular matrix (interstitial migration) are distinct and separable phases of monocyte emigration. Furthermore, distinct and separate Ig domains of PECAM are involved in mediating these two steps.
Fungal biodiversity – as found in nasal mucus (2003)

The biodiversity of fungi isolated from the nasal mucus of patients suffering from chronic rhinosinusitis and from healthy persons was monitored over 28 months. Mucus samples were obtained by flushing the noses of patients with saline or by endoscopic sinus surgery. Fungi from mucus were cultivated on agar plates. Identification was performed microscopically and by polymerase chain reaction with subsequent sequencing of the ribosomal internal transcribed spacer region. Altogether, 619 strains of fungi were cultivated from 233 subjects. Eighty-one species were identified, with a maximum of nine different species per person. The most prevalent isolates belonged to the genera Penicillium, Aspergillus, Cladosporium, Alternaria and Aureobasidium. Whereas Aspergillus and Penicillium spp. occurred in more or less the same numbers throughout the year, Cladosporium spp., Alternaria spp. and Aureobasidium pullulans showed a significantly higher occurrence during late summer and early autumn.
In vivo gene silencing of CD81 by lentiviral expression of small interference RNAs suppresses cocaine‐induced behaviour (2005)

The tetraspanin CD81 is induced in the mesolimbic dopaminergic pathway after cocaine administration. To further investigate its role, a regulatable lentivirus (Lenti-CD81) bearing the CD81 gene under the control of a tetracycline-inducible promoter and lentiviruses expressing short hairpin RNA (shRNA) targeted against CD81 (Lenti-CD81-shRNAs) have been prepared. Infection of HEK293T cells in vitro with Lenti-CD81-shRNAs resulted in 96.5% gene silencing (from quantitative real-time PCR(qRT-PCR) and immunocytochemistry). In vivo delivery of Lenti-CD81-shRNA into the nucleus accumbens or ventral tegmental area resulted in 91.3 and 94% silencing of endogenous CD81, respectively. Stereotaxic injection of Lenti-CD81 into these regions, resulting in CD81 overexpression, induced a four- to fivefold increase in locomotor activity after chronic cocaine administration, which returned to basal levels when Lenti-CD81-shRNA had been coinjected or when CD81 expression was blocked by doxycycline. Furthermore, silencing endogenous CD81 in vivo resulted in a significant decrease in locomotor activity over controls, again suppressing cocaine-induced behaviour.
Isolation and Characterization of Monoclonal Antibodies Against Structural Proteins of Infectious Laryngotracheitis Virus (2003)

Thirteen infectious laryngotracheitis virus (ILTV)-specific monoclonal antibodies (MAbs) were isolated after immunization of mice with purified infectious laryngotracheitis virions. On the basis of their reactions in western blot analyses of ILTV-infected cells, the MAbs were assigned to five different virus proteins or protein groups. Two of the viral target proteins could be identified after transient expression of cloned ILTV genes in eucaryotic cells. The MAbs of group II detected a 60-kD protein that was shown to be the ILTV homologue of herpes simplex virus type 1 (HSV-1) glycoprotein (g)C. The MAbs of group I reacted with the positional homologue of HSV-1 gJ, which is encoded by the open reading frame (ORF) 5 gene within the unique short genome region of ILTV. The ORF 5 gene product of ILTV was previously described as a 60-kD glycoprotein (gp60), whereas multiple protein bands with apparent molecular masses of 85, 115, 160, and 200 kD were identified in the present study. Immunoelectron microscopy revealed that both gC and gJ of ILTV are localized in the envelope of virus particles, whereas the 15-kD protein detected by the MAbs of group III presumably represents a tegument component. Immunofluorescence analyses of infected cells demonstrated that the epitopes of the gC- and gJ-specific MAbs are conserved in all tested ILTV isolates originating from different parts of the world and that these MAbs are also suitable for in situ antigen detection in tissues of ILTV-infected chickens. The remaining ILTV-specific MAbs recognized viral proteins of 22 kD (group IV) and 38 kD (group V) that were not further characterized up to now.
Involvement of nucleic acid synthesis in cell killing mechanisms of topoisomerase poisons. (1990)

The primary cytotoxic mechanism of camptothecin has been proposed to involve an interaction between the replication machinery and the camptothecin-mediated topoisomerase I-DNA cleavable complex (Y. H. Hsiang, M.G. Lihou, and L.F. Liu, Cancer Res., 49:5077-5082, 1989). In the present study, we show that killing of V79 cells by the topoisomerase II poisons 4'-(9-acridinylamino)methanesulfon-m-anisidide (m-AMSA) and etoposide may involve ongoing RNA synthesis in addition to ongoing DNA synthesis. V79 cells synchronized by mitotic shake-off were treated with topoisomerase poisons in the presence of inhibitors of nucleic acid synthesis. S-Phase V79 cells were more sensitive to the topoisomerase I poison camptothecin and the topoisomerase II poison m-AMSA than G1-phase cells. The greater sensitivity of S-phase cells to killing by m-AMSA and camptothecin was abolished during cotreatment, but not posttreatment, with aphidicolin, suggesting that ongoing DNA synthesis in involved in cell killing by both topoisomerase I and II poisons. Cotreatment with transcription inhibitors, such as 5,6-dichloro-1-beta-D-ribofuranosyl benzimidazole or cordycepin, partially protected cells from the cytotoxic effects of m-AMSA but had no effect on camptothecin-mediated cytotoxicity. These results suggest that ongoing RNA transcription may be involved in cell killing by topoisomerase II poisons but not topoisomerase I poisons. Cotreatment with camptothecin reduced m-AMSA-mediated cytotoxicity in G1-phase V79 cells, suggesting a possible antagonism between topoisomerase I and II poisons. This antagonistic effect between topoisomerase I and II poisons could be explained by the strong inhibitory effect of camptothecin on RNA transcription.
Pancreaticoduodenectomy for Cancer of the Head of the Pancreas 201 Patients (1995)

The survival of patients with pancreatic adenocarcinoma treated by pancreaticoduodenectomy is improving. Aspects of tumor biology, such as DNA content, tumor diameter, nodal status and margin status, are the strongest predictors of outcome.
Functional Characterization of the X-Linked Inhibitor of Apoptosis (XIAP) Internal Ribosome Entry Site Element: Role of La Autoantigen in XIAP Translation (2000)

X-linked inhibitor of apoptosis protein (XIAP) is a key regulator of programmed cell death triggered by various apoptotic triggers. Translation of XIAP is controlled by a 162-nucleotide (nt) internal ribosome entry site (IRES) element located in the 5' untranslated region of XIAP mRNA. XIAP IRES mediates efficient translation of XIAP under physiological stress and enhances cell protection against serum deprivation and radiation-induced apoptosis. In the present report we describe the assembly of a sequence-specific RNA-protein complex consisting of at least four cytosolic proteins on the XIAP IRES element. We determine that the core binding sequence is approximately 28 nt long and is located 34 nt upstream of the initiation site. Moreover, we identify the La autoantigen as a protein that specifically binds XIAP IRES in vivo and in vitro. The biological relevance of this interaction is further demonstrated by the inhibition of XIAP IRES-mediated translation in the absence of functional La protein. The results suggest an important role for the La protein in the regulation of XIAP expression, possibly by facilitating ribosome recruitment to the XIAP IRES.
Aberrant somatic hypermutation in transformation of follicular lymphoma and chronic lymphocytic leukemia to diffuse large B-cell lymphoma. (2006)

The molecular mechanisms involved in histologic transformation of follicular lymphoma (FL) and B-chronic lymphocytic leukemia (B-CLL) to diffuse large B-cell lymphoma (DLBCL) are heterogeneous and largely unknown. Here we explored whether aberrant somatic hypermutation, leading to the acquisition of new mutations in PIM-1, PAX-5, RhoH/TTF and c-MYC genes, is involved in transformation from FL or B-CLL to DLBCL. Eighteen sequential pairs of FL/DLBCL (n=9) and B-CLL/DLBCL (n=9) were investigated. Our findings demonstrate that acquisition of novel mutations due to aberrant somatic hypermutation was associated with DLBCL transformation in 5/9 (55.5%) cases of FL and 2/9 (22.2%) cases of B-CLL.
Pesticide exposures and other agricultural risk factors for leukemia among men in Iowa and Minnesota. (1990)

Mortality surveys and death certificate studies have suggested an association between leukemia and farming. To investigate whether exposure to carcinogens in an agricultural setting is related to risk of leukemia, the authors conducted a population-based case-control interview study of 578 white men with leukemia and 1245 controls living in Iowa and Minnesota. Consistent with recent mortality studies, there were slight, but significant, elevations in risk for all leukemia [odds ratio (OR) 1.2] and chronic lymphocytic leukemia (OR 1.4) for farmers compared to nonfarmers. There were no significant associations with leukemia for exposure to specific fungicides, herbicides (including 2,4-D and 2,4,5-T), or crop insecticides. However, significantly elevated risks for leukemia of greater than or equal to 2.0 were seen for exposure to specific animal insecticides including the organophosphates crotoxyphos (OR 11.1), dichlorvos (OR 2.0), and famphur (OR 2.2) and the natural product pyrethrins (OR 3.7) and the chlorinated hydrocarbon methoxychlor (OR 2.2). There were also smaller, but significant, risks associated with exposure to nicotine (OR 1.6) and DDT (OR 1.3). This finding of elevated risks for insecticides used on animals deserves further evaluation.
Evaluation of Histone 3 Lysine 27 Trimethylation (H3K27me3) and Enhancer of Zest 2 (EZH2) in Pediatric Glial and Glioneuronal Tumors Shows Decreased H3K27me3 in H3F3A K27M Mutant Glioblastomas (2013)

H3F3A mutations are seen in ∼30% of pediatric glioblastoma (GBMs) and involve either the lysine residue at position 27 (K27M) or glycine at position 34 (G34R/V). Sixteen genes encode histone H3, each variant differing in only a few amino acids. Therefore, how mutations in a single H3 gene contribute to carcinogenesis is unknown. H3F3A K27M mutations are predicted to alter methylation of H3K27. H3K27me3 is a repressive mark critical to stem cell maintenance and is mediated by EZH2, a member of the polycomb-group (PcG) family. We evaluated H3K27me3 and EZH2 expression using immunohistochemistry in 76 pediatric brain tumors. H3K27me3 was lowered/absent in tumor cells but preserved in endothelial cells and infiltrating lymphocytes in six out of 20 GBMs. H3K27me3 showed strong immunoreactivity in all other tumor subtypes. Sequencing of GBMs showed H3F3A K27M mutations in all six cases with lowered/absent H3K27me3. EZH2 expression was high in GBMs, but absent/focal in other tumors. However, no significant differences in EZH2 expression were observed between H3F3A K27M mutant and wild type GBMs, suggesting that EZH2 mediated trimethylation of H3K27 is inhibited in GBM harboring K27M mutations. Our results indicate that H3F3A K27M mutant GBMs show decreased H3K27me3 that may be of both diagnostic and biological relevance.
Phase I Trial of ISIS 5132, an antisense oligonucleotide inhibitor of c-raf-1, administered by 24-hour weekly infusion to patients with advanced cancer. (2001)

Raf-1 is a serine/threonine kinase that functions as a critical effector of Ras-mediated signal transduction via the mitogen-activated protein kinase pathway. Constitutive activation of this pathway directly contributes to malignant transformation in many human tumors. A 20-base phosphorothioate oligonucleotide complementary to c-raf-1 mRNA (ISIS 5132; CGP 69846A) has been shown to specifically suppress Raf-1 expression both in vitro and in vivo. This Phase I trial, involving 22 patients with advanced cancer, was designed to evaluate the safety, feasibility, and maximum tolerated dose of ISIS 5132 administration as a weekly 24-h i.v. infusion. Pharmacokinetic analysis was performed, and c-raf-1 mRNA levels in peripheral blood mononuclear cells were assessed using quantitative reverse transcription-PCR. This trial defined a maximum tolerated dose of 24 mg/kg/week on this schedule. Two of four patients treated at 30 mg/kg/week had serious adverse events after the first dose of ISIS 5132, including acute hemolytic anemia and acute renal failure and anasarca. There were no major responses documented. Dose-dependent complement activation was demonstrated on this schedule, but not on previously evaluated schedules, of ISIS 5132 administration. In contrast to other trials of ISIS 5132, there appeared to be no consistent suppression of peripheral blood mononuclear cell c-raf-1 mRNA level on this schedule at any of the dose levels analyzed. These data suggest that the efficacy and toxicity profiles of antisense oligonucleotides may be highly dependent on the schedule of administration and support the analysis of the putative molecular target in the evaluation of novel therapeutics.