gebhart/patrepeval huggingface dataset:
Expression of B7.1 in a MUC1‐expressing mouse mammary epithelial tumour cell line inhibits tumorigenicity but does not induce autoimmunity in MUC1 transgenic mice (1999)

The MUC1 epithelial mucin, which is overexpressed and aberrantly glycosylated in breast and other carcinomas, is also expressed on the apical surface of most normal glandular epithelial cells. Since clinical trials evaluating the efficacy of MUC1-based vaccines have been initiated in breast cancer patients, it is important to address the question of whether an effective immune response to the cancer associated mucin can be generated without inducing autoimmunity. Since non-classic cytotoxic T lymphocyte (CTL) responses to MUC1 have been reported, it is also relevant to examine the role of costimulatory molecules in the effective presentation of MUC1 based antigens. We have therefore looked at the effect of expressing B7.1 on the tumorigenicity of a MUC1 expressing mammary epithelial cell line (410.4) in a transgenic mouse expressing MUC1 on its normal glandular epithelial tissues. Coexpression of B7.1 with MUC1 in 410. 4 cells resulted in a dramatic inhibition of tumour growth which depended on the activity of CD4+ and CD8+ T cells. The epithelial tissues in the transgenic mice able to reject the B7.1, MUC1-expressing tumours showed no evidence of degeneration and the mice survived their normal life span. The results demonstrate that an immune response to the MUC1 antigen can be induced in MUC1 transgenic mice and that presentation of the antigen, whether directly or by cross-priming, is markedly enhanced by coexpression of B7.1.
A receptor-induced binding site in fibrinogen elicited by its interaction with platelet membrane glycoprotein IIb-IIIa (1991)

The interaction of fibrinogen with membrane glycoprotein GPIIb-IIIa regulates platelet aggregation. This ligand:integrin receptor interaction elicits conformational changes in GPIIb-IIIa as evidenced by the induction of ligand-induced binding sites which are recognized by antibodies that react selectively with the occupied receptor. The dynamic nature of these conformational changes is now demonstrated by the identification and characterization of a receptor-induced binding site (RIBS) elicited in fibrinogen bound to GPIIb-IIIa. A monoclonal antibody to fibrinogen, anti-Fg-RIBS-I, failed to bind to nonstimulated platelets in the presence or absence of fibrinogen. However, when platelets were stimulated with an agonist, the antibody reacted with platelet-bound fibrinogen even in the presence of a marked excess of unbound fibrinogen. A key element of the RIBS epitope has been precisely localized to residues 373-385 of the gamma chain of fibrinogen. Conformational elements also are important in defining the epitope. Fab fragments of the antibody inhibited platelet aggregation. As these fragments also inhibited fibrin polymerization, a commonality between these two diverse functions of fibrinogen in thrombus formation is indicated. In general, antibodies to RIBS and ligand-induced binding site provide unique probes for characterizing ligand:receptor interactions.
Investigation of the domestication of common bean (Phaseolus vulgaris) using multilocus sequence data (2011)

Multilocus sequence data collected from domesticated and related wild relatives provides a rich source of information on the effect of human selection on the diversity and adaptability of a species to complex environments. To evaluate the domestication history of common bean (Phaseolus vulgaris L.), multilocus sequence data from landraces representing the various races within the Middle American (MA) and Andean gene pools was evaluated. Across 13 loci, nucleotide diversity was similar between landraces and wild germplasm in both gene pools. The diversity data were evaluated using the approximate Bayesian computation approach to test multiple domestication models and estimate population demographic parameters. A model with a single domestication event coupled with bidirectional migration between wild and domesticated genotypes fitted the data better than models consisting of two or three domestication events in each genepool. The effective bottleneck population size was ~50% of the base population in each genepool. The bottleneck began ~8200 and ~8500 years before present and ended at ~6300 and ~7000 years before present in MA and Andean gene pools respectively. Linkage disequilibrium decayed to a greater extent in the MA genepool. Given the (1) geographical adaptation bottleneck in each wild gene pool, (2) a subsequent domestication bottleneck within each gene pool, (3) differentiation into gene-pool specific races and (4) variable extents of linkage disequilibrium, association mapping experiments for common bean would more appropriately be performed within each genepool.
Creutzfeldt-Jakob Disease (Spongiform Encephalopathy): Transmission to the Chimpanzee (1968)

Biopsy material taken from the brain of a patient with CreutzfeldtJakob disease with status spongiosus induced a similar fatal encephalopathy in a chimpanzee 13 months after inoculation.
Solid-State Supramolecular Organization, Established Directly from Powder Diffraction Data, and Photoluminescence Efficiency of Rigid-Core Oligothiophene-S,S-dioxides (2003)

The "rigid-core" material 3,5-dimethyl-2,3'-bis(3-methylthiophene)-dithieno[3,2-b:',3'-d]thiophene-4,4-dioxide (DTTOMe4) has the highest photoluminescence ever reported for thiophene-based molecules in the solid state. We report the structure of this material, determined directly from powder X-ray diffraction data using the Genetic Algorithm method for structure solution, followed by Rietveld refinement, and the structural properties are discussed in relation to the structures of the corresponding subsystems DTTO and DTTOMe. While the crystal structures of the latter compounds contain cofacial dimers, the crystal structure of DTTOMe4 comprises layers of molecules aligned in an antiparallel fashion. Intermediate neglect of differential overlap with single configuration interaction (INDO/SCI) calculations on the intermolecular interactions in the three crystal structures show that the different solid-state photoluminescence efficiencies of DTTOMe4, DTTOMe, and DTTO cannot be correlated with the different types of dipole-dipole alignment in the solid state. Instead, photoluminescence efficiencies correlate well with the rate of formation of nonradiatively decaying charge-transfer pairs upon photoexcitation. Because of larger intermolecular distances in DTTOMe4, the photoluminescence is less effectively quenched by charge-transfer processes than in DTTOMe and DTTO.
Receptor and antibody interactions of human interleukin-3 characterized by mutational analysis. (1991)

Human interleukin-3 (hIL-3) is a regulator of proliferation and differentiation of multipotent hemopoietic progenitor cells. Mutants of hIL-3 have been constructed by oligonucleotide-directed mutagenesis and expressed in Escherichia coli and Bacillus licheniformis. Purified muteins were assayed for induction of DNA synthesis in IL-3-dependent human cells and for binding to the IL-3 receptor. Residues at the NH2 and COOH termini together comprising one-quarter of the molecule could be removed without loss of biological function. Deletions of 6-15 residues within the central part of the molecule caused a large reduction (up to 5 logs) but no complete loss of activity. Substitution of evolutionary conserved residues resulted in a strong decrease of biological activity and demonstrated that the S-S bridge is an essential structural element in hIL-3. Interestingly, four muteins displayed a significantly higher potency of binding to the IL-3 receptor than in stimulating DNA synthesis. These results demonstrate that receptor binding may be (partly) disconnected from activation of DNA synthesis. Analysis of hIL-3 muteins demonstrated that the majority of monoclonal antibodies are directed against a small portion of the IL-3 molecule. The neutralizing potential of individual monoclonal antibodies could be increased by a combination of antibodies directed against nonoverlapping epitopes.
Transcriptomic Biomarkers for the Accurate Diagnosis of Myocarditis (2011)

Together, these findings demonstrate that transcriptomic biomarkers from a single endomyocardial biopsy can improve the clinical detection of patients with inflammatory diseases of the heart. This approach advances the clinical management and treatment of cardiac disorders with highly variable outcome.
Decreased calcium currents in motor nerve terminals of mice with Lambert‐Eaton myasthenic syndrome. (1995)

1. The effects of immunoglobulin G (IgG) from patients with Lambert-Eaton myasthenic syndrome on Ca2+ currents in mammalian motor nerve terminals are unknown. Therefore, we recorded these currents in phrenic nerves of mice injected with serum from either LEMS patients, myasthenia gravis patients, or healthy control individuals. 2. In control preparations, the endplate currents induced by repetitive stimulation at > or = 20 Hz were depressed as expected. However, in the LEMS animals quantal content decreased and either depression did not occur or synaptic facilitation occurred. 3. Ca2+ currents were smaller in LEMS animals. At 0.5 Hz stimulation frequency, normalized Ca2+ currents in LEMS animals were 57 +/- 14% of those in control. At higher frequencies, Ca2+ currents become smaller in control but not in LEMS animals. 4. Ca2+ currents in controls were unaffected by addition of nifedipine but were reduced by 37% upon addition of omega-conotoxin GVIA. In LEMS animals, however, the currents were depressed by 43% by nifedipine but were unaffected by omega-conotoxin GVIA. Thus, LEMS is associated with reduced Ca2+ currents and a shift to dihydropyridine sensitivity.
Apple polyphenol phloretin potentiates the anticancer actions of paclitaxel through induction of apoptosis in human hep G2 cells (2008)

Phloretin (Ph), which can be obtained from apples, apple juice, and cider, is a known inhibitor of the type II glucose transporter (GLUT2). In this study, real-time PCR analysis of laser-capture microdissected (LCM) human hepatoma cells showed elevated expression (>5-fold) of GLUT2 mRNA in comparison with nonmalignant hepatocytes. In vitro and in vivo studies were performed to assess Ph antitumor activity when combined with paclitaxel (PTX) for treatment of human liver cancer cells. Inhibition of GLUT2 by Ph potentiated the anticancer effects of PTX, resensitizing human liver cancer cells to drugs. These results demonstrate that 50-150 microM Ph significantly potentiates DNA laddering induced in Hep G2 cells by 10 nM PTX. Activity assays showed that caspases 3, 8, and 9 are involved in this apoptosis. The antitumor therapeutic efficacy of Ph (10 mg/kg body weight) was determined in cells of the SCID mouse model that were treated in parallel with PTX (1 mg/kg body weight). The Hep G2-xenografted tumor volume was reduced more than fivefold in the Ph + PTX-treated mice compared to the PTX-treated group. These results suggest that Ph may be useful for cancer chemotherapy and chemoprevention.
Design, simulation, and optimization of a miniaturized device for size‐fractioned DNA extraction (2007)

Fraction collection following electrophoresis has many applications in biology analysis. These assays typically need to identify specific fractions in the separated sample for further processing and require extraction of one or a group of fragments. Unfortunately, the conventional methods involve cumbersome procedures and are not amenable to integration, automation, and extraction of microscale samples. In this work, we present a scheme of chip-based electroelution for the extraction of DNA fragments, which allows the isolation and collection of target DNA fragments in a single device. Both theoretical analysis and experimental results have shown that there are some cross-contaminations from adjacent bands and a little loss of DNA recovery during target DNA extraction with the prototype miniaturized device. In order to improve the purity and yield of the extracted DNA fragment, an optimal channel configuration for DNA recovery miniaturized device was proposed. The simulations and the experimental results are in good agreement and confirm that with the optimized device design a high-efficiency DNA extraction is achieved.
argE-Encoded N-Acetyl-l-Ornithine Deacetylase from Escherichia coli Contains a Dinuclear Metalloactive Site (2005)

The catalytic and structural properties of the argE-encoded N-acetyl-L-ornithine deacetylase (ArgE) from Escherichia coli were investigated. On the basis of kinetic and ITC (isothermal titration calorimetry) data, Zn(II) binds to ArgE with Kd values that differ by approximately 20 times. Moreover, ArgE exhibits approximately 90% of its full catalytic activity upon addition of one metal ion. Therefore, ArgE behaves similarly to the aminopeptidase from Aeromonas proteolytica (AAP) in that one metal ion is the catalytic metal ion while the second likely plays a structural role. The N-acetyl-L-ornithine (NAO) deacetylase activity of ArgE showed a linear temperature dependence from 20 to 45 degrees C, indicating that the rate-limiting step does not change over this temperature range. The activation energy for NAO hydrolysis by ArgE was 25.6 kJ/mol when loaded with Zn(II) and 34.3 kJ/mol when loaded with Co(II). Electronic absorption and EPR (electron paramagnetic resonance) spectra of [Co x (ArgE)] and [CoCo(ArgE)] indicate that both divalent metal binding sites are five coordinate. In addition, EPR data show clear evidence of spin-spin coupling between the Co(II) ions in the active site but only after addition of a second equivalent of Co(II). Combination of these data provides the first physical evidence that the ArgE from E. coli contains a dinuclear Zn(II) active site, similar to AAP and the carboxypeptidase G2 from Pseudomonas sp. strain RS-16 (CPG2).
Influence of the pro-inflammatory cytokines on P-glycoprotein expression and functionality. (2004)

Cytokines may interfere with P-gp. Hence, in pathological conditions (inflammation, infection, ...), the expression and functionality of P-glycoprotein may be modulated with consequences for drug disposition and, consequently treatment efficacy.
The Group Administration Shell and the GASH Network Computing Environment (1994)

Managing large scale UNIX networks so that users can use resources on multiple systems is traditionally performed using NIS, NFS, and DNS. Proper use of these tools requires exacting maintenance of multiple databases under a single point of control. This is acceptable for a few dozen machines, but with hundreds of machines spread across several administrative groups, some mechanism is needed to share administrative control over the master administrative files. The Computer Science Division of the Applied Research Laboratories, The University of Texas at Austin (ARL:UT) has developed the Group Administration Shell (GASH) system, which gives different administrators permission to administer subsets of the laboratory NIS and DNS files. In addition to distributing administrative control in a secure fashion, GASH makes a large number of system administration tasks very simple, permitting technically untrained personnel to safely perform complex system administration tasks. The Network Computing Environment (NCE) built around GASH and standard UNIX tools such as NIS, DNS, and automounter provides a flexible and reliable way of completely abstracting the
Toll‐like receptor‐dependent activation of several human blood cell types by protamine‐condensed mRNA (2005)

We reported that RNA condensed on protamine is protected from RNase-mediated degradation and can be used for vaccination. Here, we show that such complexes are also danger signals that activate mouse cells through a MyD88-dependent pathway. Moreover, mRNA-protamine complexes stimulate human blood cells. They strongly activate DC and monocytes, leading to TNF-alpha and IFN-alpha secretion. In addition, protamine-RNA complexes directly activate B cells, NK cells and granulocytes. The detailed analysis of the activated cell types, the study of the cytokines released from PBMC cultured with protamine-RNA complexes and recently published results suggest that TLR-7 and TLR-8 may be involved in the recognition of protamine-stabilized RNA. Our data indicate that protamine-stabilized RNA, which may be similar to RNA condensed in the nucleocapsids of RNA viruses, is a strong danger signal. Thus, similarly to plasmid DNA, protamine-RNA combines antigen production and non-specific immunostimulation. The studies presented here explain the capacity of protamine-RNA to act as a vaccine, and pave the way towards the development of safe and efficient mRNA-based immunotherapies.
Degradation of Amyloid β-Protein by a Metalloprotease Secreted by Microglia and Other Neural and Non-neural Cells (1997)

Amyloid beta-protein (Abeta) is the major component of neuritic (amyloid) plaques in Alzheimer's disease, and its deposition is an early and constant event in the complex pathogenetic cascade of the disease. Although many studies have focused on the biosynthetic processing of the beta-amyloid precursor protein and on the production and polymerization of Abeta, understanding the degradation and clearance of Abeta has received very little attention. By incubating the conditioned medium of metabolically labeled Abeta-secreting cells with media of various cultured cell lines, we observed a time-dependent decrease in the amount of Abeta in the mixed media. The factor principally responsible for this decrease was a secreted metalloprotease released by both neural and non-neural cells. Among the cells examined, the microglial cell line, BV-2, produced the most Abeta-degrading activity. The protease was completely blocked by the metalloprotease inhibitor, 1,10-phenanthroline, and partially inhibited by EDTA, whereas inhibitors of other protease classes produced little or no inhibition. Substrate analysis suggests that the enzyme was a non-matrix metalloprotease. The protease cleaved both Abeta1-40 and Abeta1-42 peptides secreted by beta-amyloid precursor protein-transfected cells but failed to degrade low molecular weight oligomers of Abeta that form in the culture medium. Lipopolysaccharide, a stimulator of macrophages/microglia, activated BV-2 cells to increase their Abeta-degrading metalloprotease activity. We conclude that secreted Abeta1-40 and Abeta1-42 peptides are constitutively degraded by a metalloprotease released by microglia and other neural cells, providing a potential mechanism for the clearance of Abeta in brain tissue.
Facilitation of H2O2-induced A172 human glioblastoma cell death by insertion of oxidative stress-sensitive TRPM2 channels. (2008)

The melastatin-like transient receptor potential M2 (TRPM2) channel is a Ca2+ permeable channel that is activated by reactive oxygen species (ROS), and its activation induces necrotic cell death. The effect of insertion of TRPM2 into A172 human glioblastoma cells (A172 cells) was investigated. The insertion of TRPM2 channels enhanced cell death induced by H2O2 in the A172 cells. An H2O2-induced Ca2+ increase was observed in TRPM2-expressing cells, but not in wild-type cells. Proliferation, migration and invasion activities were not affected by the expression of TRPM2. TRPM2 seems to be a candidate for gene therapy in glioblastoma cells, since the insertion of TRPM2 into A172 cells can facilitate cell death through Ca2+ increase after H2O2 treatment without increasing malignancy.
Enhanced Immunological Tolerance by HLA-G1 from Neural Progenitor Cells (NPCs) Derived from Human Embryonic Stem Cells (hESCs) (2017)

Ectopic expression of HLA-G1, a non-classical major histocompatibility complex class I (MHC I) antigen that was originally discovered involving in engraftment tolerance during pregnancy, can enhance the immunological tolerance in differentiated neural progenitor cells (NPCs). Our study shows that stably overexpressing HLA-G1 in hESCs might be a feasible strategy for enhancing the engraftment of NPCs during transplantation.
Activatable Optical Probes for the Detection of Enzymes (2011)

The early detection of many human diseases is crucial if they are to be treated successfully. Therefore, the development of imaging techniques that can facilitate early detection of disease is of high importance. Changes in the levels of enzyme expression are known to occur in many diseases, making their accurate detection at low concentrations an area of considerable active research. Activatable fluorescent probes show immense promise in this area. If properly designed they should exhibit no signal until they interact with their target enzyme, reducing the level of background fluorescence and potentially endowing them with greater sensitivity. The mechanisms of fluorescence changes in activatable probes vary. This review aims to survey the field of activatable probes, focusing on their mechanisms of action as well as illustrating some of the <i>in vitro</i> and <i>in vivo</i> settings in which they have been employed.
Do Intraoperative Analgesics Influence Breast Cancer Recurrence After Mastectomy? A Retrospective Analysis (2010)

This retrospective analysis suggests that intraoperative administration of ketorolac decreases the risk of breast cancer relapse compared with other analgesícs.
Down-regulation of a calmodulin-related gene during transformation of human mammary epithelial cells. (1990)

A human cDNA library obtained from cultured normal mammary epithelial cells (HMECs) was searched by subtractive hybridization for genes whose decrease in expression might be relevant to epithelial transformation. One clone identified by this procedure corresponded to a 1.4-kilobase mRNA, designated NB-1, whose expression was decreased greater than 50-fold in HMECs tumorigenically transformed in vitro after exposure to benzo[a]pyrene and Kirsten sarcoma virus. Sequence analysis of NB-1 cDNA revealed an open reading frame with a high degree of homology to calmodulin. NB-1 expression could be demonstrated by polymerase chain reaction amplification in normal breast, prostate, cervix, and epidermal tissues. The presence of NB-1 transcripts was variable in primary breast carcinoma tissues and undetectable in tumor-derived cell lines of breast, prostate, or other origins. NB-1 mRNA expression could be down-regulated in cultured HMECs by exposure to reconstituted extracellular matrix material, while exposure to transforming growth factor type beta increased its relative abundance. The protein encoded by NB-1 may have Ca2+ binding properties and perform functions similar to those of authentic calmodulin. Its possible roles in differentiation and/or suppression of tumorigenicity in epithelial tissues remain to be examined.
Internet security professional reference (1996)

This complete reference shows how Internet and network security is implemented and details ways to keep it from being violated. Inadequacies in current security products and set-ups are pointed out and strategies to overcome them are detailed step by step.