gebhart/patrepeval huggingface dataset:
Detection and characterization of apoptotic peripheral blood lymphocytes in human immunodeficiency virus infection and cancer chemotherapy by a novel flow immunocytometric method (1994)

We have developed a quantitative and sensitive flow cytometric method for the detection of human apoptotic lymphocytes that, unlike previously described assays, allows their identification in mixed populations of peripheral blood leukocytes as well as their immunophenotyping. Apoptotic lymphocytes are identified on the basis of peculiar light scatter changes, reflecting their smaller size and their modified nucleus/cytoplasm organization, and of the decreased expression of surface CD45 molecules. Based on these criteria, apoptotic lymphocytes generated by exposure to ionizing radiation can be easily distinguished from viable cells and from necrotic lymphocytes generated by treatment with antibody and complement. Using this assay, we reappraised the phenomenon of the in vitro apoptosis of lymphocytes from patients with human immunodeficiency virus (HIV) infection. Lymphocytes from HIV patients, unlike those from normal HIV-negative subjects, undergo apoptosis upon simple in vitro culture. We found that the percentages of lymphocytes undergoing apoptosis were significantly higher in patients with low CD4 cell counts (< 400/microL) than in patients at earlier stages (> 400 CD4 cells/microL). However, phenotypic analysis disclosed that apoptotic lymphocytes generated in these cultures were mostly CD8+ T cells and CD19+ B cells. Thus, in contrast to what has been previously suggested, the phenomenon of in vitro lymphocyte apoptosis might not be pathogenetically related to the depletion of CD4+ T cells in acquired immunodeficiency syndrome. Nevertheless, it might represent an useful marker of disease progression. Our assay allows the analysis of unfractionated peripheral blood leukocytes and thus the identification of apoptotic lymphocytes circulating in vivo. Apoptotic lymphocytes could indeed be detected in the circulation of a patient with cancer shortly after high-dose cytotoxic chemotherapy. By contrast, no apoptotic lymphocytes could be detected in vivo in patients with early or advanced HIV infection.
Modulation of HLA class I antigen and ICAM‐2 on endothelial cells after in vitro infection with human cytomegalovirus (1998)

The aim of the present work is to investigate the expression of HLA class I antigen and intercellular adhesion molecule-2 (ICAM-2) on the surface of human umbilical cord endothelial cells (HUVEC) after infection with human cytomegalovirus (HCMV). The expression of HLA class I antigen and ICAM-2 were determined (using antibodies against HLA class I antigen and ICAM-2) by attachment inhibition assay and flow cytometric analysis. Attachment inhibition assay demonstrated that HCMV increased the expression of HLA class I antigen. This was confirmed by flow cytometric analysis, which showed an increase in HLA class I antigen expression on HCMV-infected HUVEC. The results of the expression of ICAM-2 using attachment inhibition assay revealed that ICAM-2 is involved significantly in the increased adhesion of T lymphocytes to HCMV-infected HUVEC. However, flow cytometric analysis revealed that there were no changes in the expression of ICAM-2 on HCMV-infected HUVEC. One possible explanation for this is that HCMV induces the activation of ICAM-2 on the surface of HCMV-infected endothelial cells without affecting its expression.
The Promise and Perils of Wnt Signaling Through β-Catenin (2002)

Wnt pathways are involved in the control of gene expression, cell behavior, cell adhesion, and cell polarity. In addition, they often operate in combination with other signaling pathways. The Wnt/beta-catenin pathway is the best studied of the Wnt pathways and is highly conserved through evolution. In this pathway, Wnt signaling inhibits the degradation of beta-catenin, which can regulate transcription of a number of genes. Some of the genes regulated are those associated with cancer and other diseases (for example, colorectal cancer and melanomas). As a result, components of the Wnt/beta-catenin pathway are promising targets in the search for therapeutic agents. Information about Wnt pathways is available both in canonical terms and at the species level. In addition to the canonical Wnt/beta-catenin pathway, information is now available for Drosophila, Caenorhabditis elegans, and Xenopus. The STKE Connections Maps for these pathways provide an important tool in accessing this large body of complex information.
Portable Queries Using the Brick Schema for Building Applications (2016)

Sensorized commercial buildings are a rich target for building a new class of applications that improve operational and energy efficiency of building operations that take into account human activities. Such applications, however, rarely experience widespread adoption due to the lack of a common descriptive schema that would enable porting these applications and systems to different buildings. Our demo presents Brick [4], a uniform schema for representing metadata in buildings. Our schema defines a concrete ontology for sensors, subsystems and relationships among them, which enables portable applications. Using a web application, we will demonstrate real buildings that have been mapped to the Brick schema, and show application queries that extracts relevant metadata from these buildings. The attendees would be able to create example buildings and write their own queries.
“Autoimmune rejection” of neonatal heart transplants in experimental Chagas disease is a parasite-specific response to infected host tissue (1997)

Infection with the protozoan parasite Trypanosoma cruzi often results in chronic heart- and gut-associated disease known as Chagas disease. In this study we show that contrary to previous reports, neonatal hearts transplanted into mice chronically infected with T. cruzi do not exhibit signs of autoimmune-type rejection or any significant inflammatory response. In addition to an absence of inflammation, these syngeneic heart transplants survive for more than 1 year and are absolutely free of parasites as determined by in situ PCR analysis. However, if well-established transplanted hearts in chronically infected mice are directly injected with live parasites, a rapid and dramatic inflammatory response ensues that results in cessation of heart function. Likewise, transplanted hearts established in mice prior to systemic infection with T. cruzi or hearts transplanted into mice during the acute stage of T. cruzi infection become parasitized and develop inflammatory foci. In these cases where the transplanted hearts become parasitized, the ensuing inflammatory response is nearly identical to that observed in the native hearts of T. cruzi-infected mice in terms of cell types present and adhesion molecules and cytokines expressed. Importantly, this response is strikingly different from that observed in the allogeneic heart rejection. These results clearly document that parasitization of heart tissue is both necessary and sufficient for the induction of tissue damage in Chagas disease and strongly argue against a principal autoimmune etiology for this disease.
Phenyl-T-Butyl-Nitrone is Active Against Traumatic Shock in Rats (1986)

Oxygen free-radicals appear to be involved in the pathogenesis of shock; therefore trapping of these radicals would modify the evolution of experimental shock. Experiments were performed on rats submitted to 100% lethal whole body trauma (rotating drum) and their survival, pathology, acid-base status and hematocrit level observed. The spin trapping agent phenyl-t-butyl-nitrone (PBN) was administered before trauma (50, 100, 150 mg/kg i.p.) or at various intervals (30, 60 minutes) after establishment of a severe traumatic shock. It appeared that PBN administration was highly effective both in prevention and in reversion of traumatic shock in rats.
Biotinylation of histones in human cells (2001)

An enzymatic mechanism has been proposed by which biotinidase may catalyze biotinylation of histones. Here, human cells were found to covalently bind biotin to histones H1, H2A, H2B, H3, and H4. Cells respond to proliferation with increased biotinylation of histones; biotinylation increases early in the cell cycle and remains increased during the cycle. Notwithstanding the catalytic role of biotinidase in biotinylation of histones, mRNA encoding biotinidase and biotinidase activity did not parallel the increased biotinylation of histones in proliferating cells. Biotinylation of histones might be regulated by enzymes other than biotinidase or by the rate of histone debiotinylation.
Theoretical hole mobility in a narrow Si/SiGe quantum well (1993)

Calculations of the hole mobility in a strained SiGe quantum well on (001) Si are carried out for the case of a narrow well in which the subband splittings are large due to quantum-size effects. An envelope-function model for the valence-band structure and hole wave functions in an infinite square well and calculations of scattering rates in a single parabolic band with an isotropic effective mass are used to delineate limitations on mobility imposed by lattice scattering, background impurities, alloy scattering, and interface roughness. Additional scattering mechanisms associated with compositional fluctuations in the SiGe layer are also discussed. Narrow wells (60 \AA{}) with high Ge content (40%) have large subband splittings and exhibit a light mass for hole densities well beyond ${10}^{12}$ ${\mathrm{cm}}^{\mathrm{\ensuremath{-}}2}$. Scattering rates in such structures are greatly reduced as a result of the light mass and large subband splittings. Numerical results indicate that hole mobilities in the mid ${10}^{3}$ ${\mathrm{cm}}^{2}$/V s at room temperature and in the mid ${10}^{4}$ ${\mathrm{cm}}^{2}$/V s at low temperature could be possible in narrow SiGe wells as a result of the favorable modifications in band structure and scattering.
Specificity of Minor-Groove and Major-Groove Interactions in a Homeodomain-DNA Complex (1995)

To assess the importance of minor-groove and major-groove interactions in homeodomain-DNA recognition, the binding properties of variants of the altered-specificity engrailed homeodomain, containing Lys50, and its DNA site TAATCC were determined. This homeodomain contacts bases in the minor groove of the DNA using Arg3 and Arg5 from its N-terminal arm and contacts bases in the major groove of the DNA using Ile47, Lys50, and Asn51 from its third alpha-helix. Mutation of Arg3 or Ile47 to alanine reduces binding affinity 10-20-fold while mutation of Arg5, Asn51, or Lys50 to alanine reduces binding affinity > 100-fold, indicating that both minor-groove and major-groove interactions contribute to the overall binding energy. Binding site selections and affinity measurements show that the homeodomain can also discriminate among different base pairs in the minor groove and the major groove. However, the interactions between Lys50 of the recognition helix and the major-groove edges of base pairs 5 and 6 are more specific than interactions mediated by Arg3 and Arg5 in the N-terminal arm and the minor-groove edges of base pairs 1 and 2.
A pilot study of paclitaxel and carboplatin for recurrent ovarian cancer (2001)

Combination chemotherapy with paclitaxel and platinum is the most effective regimen for advanced ovarian cancer. Second-line chemotherapy with paclitaxel (135 mg/m2, 24 h) and carboplatin (AUC 5-6) is also effective for patients who relapse on the same regimen after 6 months or more. However, it has been shown that the same efficacy and less myelosuppression can be achieved with a 3-h infusion of paclitaxel (135 mg/m2), and that dose intensification of carboplatin to an AUC values larger than 4-6 is meaningless. Therefore, we decided to conduct a pilot study of paclitaxel (135 mg/m2, 3 h) and carboplatin (AUC 4-5) for ovarian cancer patients who had relapsed or were resistant to a platinum-containing regimen without paclitaxel. Eligibility criteria included patients with relapsed or resistant ovarian cancer (no specified duration from prior therapy), age 16-75 years, with performance status 0-2, and adequate bone marrow, renal, and hepatic function. Paclitaxel was administered at a fixed dose of 135 mg/m2 followed by one of two carboplatin doses (AUC 4 or 5). Specific doses were alternated between individual patients by the order in which they entered the study. Treatment was repeated every 3 weeks, and more than 4 cycles were administered. A total of 11 patients were enrolled. Carboplatin was administered to 6 patients at an AUC of 4 and to 5 patients at an AUC of 5. The age of patients ranged from 18 to 65 years (median: 54). Other patient data (number of patients): serous (8), non serous (3), patients with measurable disease (9), assessable/CA 125 (3), study drug administration less than 6 months after prior therapy (5), study drug administration 6 months or more after prior therapy (6). Response was defined by CT and CA 125 level. CR was observed in 25% (2/8), PR in 38% (3/8), NC in 25% (2/8), and PD in 13% (1/8) of the patients. The response rate with assessable patients was 100% (3/3), and the overall response rate was 73% (8/11). Two patients with grade 1 tachycardia and grade 4 thrombocytopenia, respectively, refused further treatment after 2 cycles. No other patients experienced grade 4 hematologic toxicity or grade 3 non-hematologic toxicity. The median survival duration after paclitaxel and carboplatin therapy was 21+ months (6-26+ months). This regimen is easy to manage in heavily pretreated patients and seems to have good efficacy. To further assess the efficacy, a phase II study is needed.
Membrane biogenesis: cotranslational integration of the bacteriophage f1 coat protein into an Escherichia coli membrane fraction. (1979)

The coat protein (CP) of bacteriophage f1 is integrated into an Escherichia coli plasma membrane fraction consisting of inverted vesicles when it is synthesized in a cell-free, coupled transcription--translation system supplemented with the inverted vesicles. By using proteolytic enzymes as probes, we found by subsequent peptide mapping and determination of the sequence of the proteolytic products that CP was inserted into the inverted vesicles in an orientation indistinguishable from that in inverted vesicles prepared from infected E. coli: only a COOH-terminal portion of approximately 10 residues was accessible to proteolysis, whereas the remainder of CP (CP') was entirely protected. Protection of CP' was dependent on the integrity of the vesicle membrane, because it was abolished when proteolysis was done in the presence of nonionic detergents. Insertion was observed when the inverted vesicles were present during translation in the cell-free system, not when they were added after translation. Thus, the asymmetric insertion of this type of integral membrane protein is strictly coupled to translation. These findings are discussed with respect to prokaryotic membrane biogenesis and are related to bacteriophage f1 assembly and infection.
Lysine methyltransferase G9a methylates the transcription factor MyoD and regulates skeletal muscle differentiation (2012)

Skeletal muscle cells have served as a paradigm for understanding mechanisms leading to cellular differentiation. The proliferation and differentiation of muscle precursor cells require the concerted activity of myogenic regulatory factors including MyoD. In addition, chromatin modifiers mediate dynamic modifications of histone tails that are vital to reprogramming cells toward terminal differentiation. Here, we provide evidence for a unique dimension to epigenetic regulation of skeletal myogenesis. We demonstrate that the lysine methyltransferase G9a is dynamically expressed in myoblasts and impedes differentiation in a methyltransferase activity-dependent manner. In addition to mediating histone H3 lysine-9 di-methylation (H3K9me2) on MyoD target promoters, endogenous G9a interacts with MyoD in precursor cells and directly methylates it at lysine 104 (K104) to constrain its transcriptional activity. Mutation of K104 renders MyoD refractory to inhibition by G9a and enhances its myogenic activity. Interestingly, MyoD methylation is critical for G9a-mediated inhibition of myogenesis. These findings provide evidence of an unanticipated role for methyltransferases in cellular differentiation states by direct posttranslational modification of a transcription factor.
Long-Term Ascorbic Acid Administration Reverses Endothelial Vasomotor Dysfunction in Patients With Coronary Artery Disease (1999)

In patients with CAD, long-term ascorbic acid treatment has a sustained beneficial effect on EDNO action. Because endothelial dysfunction may contribute to the pathogenesis of cardiovascular events, this study indicates that ascorbic acid treatment may benefit patients with CAD.
Anionic N‐Heterocyclic Carbenes with N,N′‐Bis(fluoroaryl) and N,N′‐Bis(perfluoroaryl) Substituents (2010)

A series of rhodium complexes, [Rh(cod)(NHC-F(x))(OH(2))] (cod = 1,5-cyclooctadiene; NHC = N-heterocyclic carbene), incorporating anionic N-heterocyclic carbenes with 2-tert-butylmalonyl backbones and 2,6-dimethylphenyl (x = 0), 2,6-difluorophenyl (x = 4), 2,4,6-trifluorophenyl (x = 6), and pentafluorophenyl (x = 10) N,N'-substituents, respectively, has been prepared by deprotonation of the corresponding zwitterionic precursors with potassium hexamethyldisilazide, followed by immediate reaction of the resulting potassium salts with [{RhCl(cod)}(2)]. These complexes could be converted to the related carbonyl derivatives [Rh(CO)(2)(NHC-F(x))(OH(2))] by displacement of the COD ligand with CO. IR and NMR spectroscopy demonstrated that the degree of fluorination of the N-aryl substituents has a considerable influence on the σ-donating and π-accepting properties of the carbene ligands and could be effectively used to tune the electronic properties of the metal center. The carbonyl groups on the carbene ligand backbone provided a particularly sensitive probe for the assessment of the metal-to-ligand π donation. The ortho-fluorine substituents on the N-aryl groups in the carbene ligands interacted with the other ligands on rhodium, determining the conformation of the complexes and creating a pocket suitable for the coordination of water to the metal center. Computational studies were used to explain the influence of the fluorinated N-substituents on the electronic properties of the ligand and evaluate the relative contribution of the σ- and π-interactions to the ligand-metal interaction.
Integrin cytoplasmic domain-binding proteins (2000)

Integrins are a large family of cell surface receptors that mediate cell adhesion and influence migration, signal transduction, and gene expression. The cytoplasmic domains of integrins play a pivotal role in these integrin-mediated cellular functions. Through interaction with the cytoskeleton, signaling molecules, and other cellular proteins, integrin cytoplasmic domains transduce signals from both the outside and inside of the cell and regulate integrin-mediated biological functions. Identification and functional analyses of integrin cytoplasmic domain-binding proteins have been pursued intensively. In recent years, more cellular proteins have been reported to directly interact with integrin cytoplasmic domains and some of these interactions may play important roles in integrin-mediated biological responses. Integrin (&bgr;) chains, for example, interact with actin-binding proteins (e.g. talin and filamin), which form mechanical links to the cytoskeleton. These and other proteins (e.g. FAK, ILK and novel proteins such as TAP20) might also link integrins to signaling mechanisms and, in some cases (e.g. JAB1) mediate integrin-dependent gene regulation.
Temporal Modulation of TGF-β1 and β-Actin Gene Expression in Pig Skin and Muscular Fibrosis after Ionizing Radiation (1993)

, Jean-Louis Lefaix, Philippe Pinton, , , Temporal Modulation of TGF-β1 and β-Actin Gene Expression in Pig Skin and Muscular Fibrosis after Ionizing Radiation, Radiation Research, Vol. 134, No. 1 (Apr., 1993), pp. 63-70
Aggregation Behavior of Amphiphiles Functionalized with Dipeptide Segments and Enantioselective Ester Hydrolysis in Their Bilayer Membranes (1985)

Abstract Four amphiphiles having dipeptide segments, which consist of one histidyl residue and another amino acid residue, and the dihexadecyl moiety for the double-chain segment (N+C5AlaHis2C16, N+C5LeuHis2C16, N+C5PheHis2C16, and N+C5HisAla2C16) were synthesized, and the aggregate morphology of them was characterized by electron microscopy and differential scanning calorimetry. The amphiphiles, which have the histidyl residue bound to the dihexadecylamine component (N+C5AlaHis2C16, N+C5LeuHis2C16, N+C5PheHis2C16) formed both multi- and single-walled aggregates in the aqueous dispersion state, while their sonicated solutions involved only single-walled vesicles. On the other hand, the amphiphile, which has the alanyl residue bound to the dihexadecylamine component (N+C5HisAla2C16) afforded tubular aggregates in the aqueous dispersion. The hydrolysis of enantiomeric esters of various hydrophobic nature, which was carried out in the single-walled vesicles, showed relatively small enantioselectivity. The reasons for such catalytic performance of the vesicles were discussed from the kinetic and mechanistic viewpoints; the kinetic analysis being carried out on the basis of the organic pseudo-phase concept.
Role of surface roughness in hysteresis during adhesive elastic contact (2010)

In experiments that involve contact with adhesion between two surfaces, as found in atomic force microscopy or nanoindentation, two distinct contact force (P) vs. indentation-depth (h) curves are often measured depending on whether the indenter moves towards or away from the sample. The origin of this hysteresis is not well understood and is often attributed to moisture, plasticity or viscoelasticity. Here we report experiments that show that hysteresis can exist in the absence of these effects, and that its magnitude depends on surface roughness. We develop a theoretical model in which the hysteresis appears as the result of a series of surface instabilities, in which the contact area grows or recedes by a finite amount. The model can be used to estimate material properties from contact experiments even when the measured P-h curves are not unique.
Fabrication of high-performance LDDFET's with Oxide sidewall-spacer technology (1982)

A fabrication process for the Lightly Doped Drain/Source Field-Effect Transistor, LDDFET, that utilizes RIE produced SiO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> sidewall spacers is described. The process is compatible with most conventional polysilicon-gated FET processes and needs no additional photomasking steps. Excellent control and reproducibility of the n <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-</sup> region of the LDD device are obtained. Measurements from dynamic clock generators have shown that LDDFET's have as much as 1.9X performance advantage over conventional devices.