gebhart/patrepeval huggingface dataset:
Autoantibody Profiles Reveal Ubiquilin 1 as a Humoral Immune Response Target in Lung Adenocarcinoma (2007)

There is considerable evidence that the presence of cancer can elicit a humoral immune response to specific proteins in the host, and these resulting autoantibodies may have potential as noninvasive biomarkers. To characterize the autoantibody repertoire present in the sera of patients with lung adenocarcinoma, we developed a high-density peptide microarray derived from biopanning a lung cancer phage display library. Using a 2,304-element microarray, we interrogated a total of 250 sera from Michigan lung cancer patients and noncancer controls to develop an "autoantibody profile" of lung adenocarcinoma. A set of 22 discriminating peptides derived from a training set of 125 serum samples from lung adenocarcinoma patients and control subjects was found to predict cancer status with 85% sensitivity and 86% specificity in an independent test set of 125 sera. Sequencing of the immunoreactive phage-peptide clones identified candidate humoral immune response targets in lung adenocarcinoma, including ubiquilin 1, a protein that regulates the degradation of several ubiquitin-dependent proteasome substrates. An independent validation set of 122 serum samples from Pittsburgh was examined using two overlapping clones of ubiquilin 1 that showed 0.79 and 0.74 of the area under the receiver operating characteristics curve, respectively. Significantly increased levels of both ubiquilin 1 mRNA and protein, as well as reduced levels of the phosphorylated form of this protein, were detected in lung tumors. Immunofluorescence using anti-ubiquilin 1 antibodies confirmed intracellular expression within tumors cells. These studies indicate that autoantibody profiles, as well as individual candidates, may be useful for the noninvasive detection of lung adenocarcinoma.
The Safety, Plasma Pharmacokinetics, and Antiviral Activity of Subcutaneous Enfuvirtide (T-20), a Peptide Inhibitor of gp41-Mediated Virus Fusion, in HIV-Infected Adults (2002)

Enfuvirtide (T-20) is a novel antiretroviral agent that blocks HIV-1 cell fusion. A 28-day randomized dose-comparison study was conducted to determine the safety, pharmacokinetics, and antiviral activity of enfuvirtide in 78 HIV-infected adults, most with extensive treatment experience. Patients received enfuvirtide, added to a failing regimen, either by continuous subcutaneous infusion (CSI: 12.5, 25, 50 or 100 mg/day) or by subcutaneous (SC) injection (50 or 100 mg twice daily). Dose-related decreases in viral load were observed, with a maximum mean reduction from baseline of 1.6 log(10) copies/ml (p< 0.001) seen in the 100 mg bid SC group. Most responses diminished by 28 days. Plasma pharmacokinetics and antiviral responses were more consistent for SC injection than for CSI because of technical difficulties experienced with CSI. Injection site reactions were common but generally mild. These results indicate that enfuvirtide is a promising new therapeutic agent for HIV-infected patients, including those with prior antiretroviral treatment.
Anti-Inflammatory Effects of Adult Stem Cells in Sustained Lung Injury: A Comparative Study (2013)

Lung diseases are a major cause of global morbidity and mortality that are treated with limited efficacy. Recently stem cell therapies have been shown to effectively treat animal models of lung disease. However, there are limitations to the translation of these cell therapies to clinical disease. Studies have shown that delayed treatment of animal models does not improve outcomes and that the models do not reflect the repeated injury that is present in most lung diseases. We tested the efficacy of amnion mesenchymal stem cells (AM-MSC), bone marrow MSC (BM-MSC) and human amniotic epithelial cells (hAEC) in C57BL/6 mice using a repeat dose bleomycin-induced model of lung injury that better reflects the repeat injury seen in lung diseases. The dual bleomycin dose led to significantly higher levels of inflammation and fibrosis in the mouse lung compared to a single bleomycin dose. Intravenously infused stem cells were present in the lung in similar numbers at days 7 and 21 post cell injection. In addition, stem cell injection resulted in a significant decrease in inflammatory cell infiltrate and a reduction in IL-1 (AM-MSC), IL-6 (AM-MSC, BM-MSC, hAEC) and TNF-α (AM-MSC). The only trophic factor tested that increased following stem cell injection was IL-1RA (AM-MSC). IL-1RA levels may be modulated by GM-CSF produced by AM-MSC. Furthermore, only AM-MSC reduced collagen deposition and increased MMP-9 activity in the lung although there was a reduction of the pro-fibrogenic cytokine TGF-β following BM-MSC, AM-MSC and hAEC treatment. Therefore, AM-MSC may be more effective in reducing injury following delayed injection in the setting of repeated lung injury.
Investigation of Kinetics of Methotrexate for Therapeutic Treatment of Intraocular Lymphoma (2010)

By making use of the results of this study, one could select a dosing interval for serial injections of methotrexate or establish a treatment schedule using a controlled release methotrexate implant for the treatment of PIOL.
Human Immunodeficiency Virus Type 1 Neutralization Measured by Flow Cytometric Quantitation of Single-Round Infection of Primary Human T Cells (2002)

There is currently intensive research on the design of novel human immunodeficiency virus type 1 (HIV-1) vaccine immunogens that can elicit potent neutralizing antibodies. A prerequisite for comparing and optimizing these strategies is the ability to precisely measure neutralizing antibody responses. To this end, we sought to develop an assay that directly quantifies single-round HIV-1 infection of peripheral blood mononuclear cells (PBMC). Initial experiments demonstrated that essentially all productively infected PBMC could be identified by flow cytometric detection of intracellular p24 antigen (p24-Ag). After infection of PBMC with HIV-1, p24(+) lymphocytes could be distinguished beginning 1 day postinfection, and the majority of CD8(-) T cells were p24-Ag positive by 3 to 4 days postinfection. To directly quantify first-round infection, we included a protease inhibitor in PBMC cultures. The resulting 2-day assay was highly sensitive and specific for the detection of HIV-1-infected PBMC. Serial dilutions of virus stocks demonstrated that the number of target cells infected was directly related to the amount of infectious virus input into the assay. In neutralization assays, the flow cytometric enumeration of first-round infection of PBMC provided quantitative data on the number of target cells infected and on the inactivation of infectious virus due to reaction with antibody. We also used this single-round assay to compare the percentage of cells expressing p24-Ag to the number of copies of HIV-1 gag per 100 PBMC. The precision and reproducibility of this assay will facilitate the measurement of HIV-1 neutralization, particularly incrementally improved neutralizing antibody responses generated by new candidate vaccines.
Continuous wave laser ablation of tissue: analysis of thermal and mechanical events (1993)

Thermal and mechanical events during continuous wave (CW) laser ablation of biological and phantom media were investigated. Porcine aortae, collagen fibers, and polyacrylamide control samples were subjected to argon laser irradiation while infrared and high-speed (240 images/s) video cameras were used to monitor their surfaces. Subsequent analysis of simultaneous changes in surface temperature and physical features correlated thermal and mechanical events. Video images recorded prior to ablation onset of tissue slabs clearly revealed two distinct phases: 1) progressive growth of a surface dehydration zone, and 2) surface deformation, implying subsurface bubble formation. Surface temperature recordings and video imaging revealed that the onset of CW ablation of soft biological media often initiated with a violent explosion, surface tearing, and tissue ejection. Histological inspection revealed intense coagulation in superficial layers near the irradiation site, whereas chiefly mechanical disruption was noted at the base of the crater. Ablation characteristics were consistent with theoretical calculations which indicate subsurface temperature peaks that increase in magnitude and surface proximity as energy deposition rates are increased. Results also suggested that mechanical properties of target media strongly influenced the extent of pressure built up, the nature of ablation onset, and the characteristics of the overall ablation pathway.
Analysis of a monopole mounted near or at the edge of a half-plane (1981)

The problem of a monopole antenna mounted near or at the edge of a half-plane is solved using a hybrid moment method solution with an integral expression for the exact half-plane Green's function. Results are presented for input impedance of a <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">\lambda/4</tex> monopole versus distance from the half-plane edge and versus angle for an edge-mounted antenna, Simple expressions for the surface current density induced on the half-plane are derived, and an attachment mode is constructed for use with the author's previously developed surface patch moment method solution when a wire is attached at or near an edge of a finite plate. Results obtained from the MM/GTD method are also presented for comparison.
Fetal Globin Gene Repressors as Drug Targets for Molecular Therapies To Treat the β-Globinopathies (2014)

The human β-globin locus is comprised of embryonic, fetal, and adult globin genes that are expressed in a developmental stage-specific manner. Mutations in the globin locus give rise to the β-globinopathies, β-thalassemia and sickle cell disease, which begin to manifest symptoms around the time of birth. Although the fetal globin genes are autonomously silenced in adult-stage erythroid cells, mutations lying both within and outside the locus lead to natural variations in the level of fetal globin gene expression, and some of these significantly ameliorate the clinical symptoms of the β-globinopathies. Multiple reports have now identified several transcription factors that are involved in fetal globin gene repression in definitive (adult)-stage erythroid cells (the TR2/TR4 heterodimer, MYB, KLFs, BCL11A, and SOX6). To carry out their repression functions, chromatin-modifying enzymes (such as DNA methyltransferase, histone deacetylases, and lysine-specific histone demethylase 1) are additionally involved as a consequence of forming large macromolecular complexes with the DNA-binding subunits of these cellular machines. This review focuses on the molecular mechanisms underlying fetal globin gene silencing and possible near-future molecularly targeted therapies for treating the β-globinopathies.
Inhibition of breast cancer cell growth in vitro by a tyrosine kinase inhibitor. (1992)

Human breast cancer cell proliferation is regulated by growth factors that bind to receptors with intrinsic tyrosine kinase (TK) activity, including the epidermal growth factor (EGF) receptor. To determine whether inhibition of receptor TK activity inhibits tumor growth, we studied the effects of a tyrosine kinase inhibitor, RG-13022, on cultured human breast cancer cells. RG-13022 represents a class of compounds which have been shown to inhibit preferentially the TK activity of the EGF receptor in a cell-free system and also to inhibit EGF-stimulated growth of cultured cells. RG-13022 significantly inhibited EGF-stimulated autophosphorylation of its receptor in two breast cancer cell lines that have abundant, although not amplified, EGF receptor content (MDA-231 and T47D). RG-13022 also inhibited EGF-stimulated DNA synthesis and proliferation of T47D and MCF-7 breast cancer cells in a reversible and dose-dependent manner. Inhibition was observed at 0.1 microM, and it was maximal at 10 microM. The effect was rapid (within 3 h), persisted for 18 h, and was partially reversed by 24 h at 1 microM. At 5 microM, inhibition persisted for more than 50 h. Inhibitory effects were also observed in a panel of estrogen receptor-positive and estrogen receptor-negative breast cancer cell lines. RG-13022 inhibited not only EGF-induced growth but also growth stimulated by insulin, insulin-like growth factor I, insulin-like growth factor II, or transforming growth factor alpha. RG-13022 also totally blocked estrogen-stimulated phosphorylation of the EGF receptor, as well as estrogen-induced cell proliferation, suggesting that functioning TK pathways are required for estrogen action. The TK inhibitor RG-13022 is a potent inhibitor of hormonally regulated growth of human breast cancer. Tyrosine kinase inhibitors have the potential of providing a new strategy for the "endocrine therapy" of breast cancer.
Two-Phase Flow in Microchannels (1997)

Abstract As the field of microfluidics continues to grow, it is becoming increasingly important to understand the mechanisms involved with heat transfer in two-phase flow through microgeometries. This importance is reiterated by the increasing number of applications which use phase change as the principal mechanism to conduct or remove heat. The purpose of this study was to investigate fluid mechanic and heat transfer characteristics of two-phase two-component flow in rectangular microchannels. Experiments were conducted using rectangular aluminum channels with hydraulic diameters ranging between 56 μm and 256 μm and aspect ratios which varied from 0.5 to 1.5. Both single- and two-phase tests yielded excellent correlations of the friction factor. Reynolds number and the combination of Reynolds number and Prandtl number were the dominant parameters in the prediction of pressure drop and heat transfer rate, respectively. The pressure drop predictions, based on available semi-empirical relations for two-phase flows, were shown to substantially over predict the measured pressure drop. Other findings showed that for single-phase flow, the transition from laminar to turbulent regimes of the friction factor was suppressed as the channel hydraulic diameter decreased. Two-phase friction factor data indicated a definite transition from laminar to turbulent regimes at a Reynolds number of 3,000 for all channel configurations tested. It is believed that the transition was due to the intense pressure fluctuations associated with two-phase flows. In both single- and two-phase experiments, Nusselt number data exhibited a trend similar to the macroscale turbulent regime correlations; however, the data were somewhat less than the macroscale predictions. In contrast to the friction factor data, both single- and two-phase Nusselt number data suggested no change in flow regimes occurred.
Anti-tumor Activity of Toll-Like Receptor 7 Agonists (2017)

Toll-like receptors (TLRs) are a class of pattern recognition receptors that play a bridging role in innate immunity and adaptive immunity. The activated TLRs not only induce inflammatory responses, but also elicit the development of antigen specific immunity. TLR7, a member of TLR family, is an intracellular receptor expressed on the membrane of endosomes. TLR7 can be triggered not only by ssRNA during viral infections, but also by immune modifiers that share a similar structure to nucleosides. Its powerful immune stimulatory action can be potentially used in the anti-tumor therapy. This article reviewed the anti-tumor activity and mechanism of TLR7 agonists that are frequently applied in preclinical and clinical investigations, and mainly focused on small synthetic molecules, including imiquimod, resiquimod, gardiquimod, and 852A, etc.
Binding of a peptide antigen to multiple HLA alleles allows definition of an A2-like supertype. (1995)

Direct MHC binding assays with radiolabeled peptides and HLA class I-expressing mammalian cells such as EBV-transformed B cell lines and PHA-activated blasts have been developed. Significant binding of the radiolabeled probe could be obtained if the target cells were preincubated overnight at 26 degrees C in the presence of beta 2-microglobulin. Under these conditions, up to a few percent of the HLA molecules expressed by either cell type could be bound by the labeled peptides. With these assays, the degree of cross-reactivity of the A*0201-restricted hepatitis B virus core 18-27 peptide with other A2 subtypes was examined. It was determined that this peptide epitope also binds the A*0202, A*0205, and A*0206 but not A*0207 subtypes. Inhibition experiments with panels of synthetic peptide analogues underlined the similar ligand specificities of the HLA-A*0201, A*0202, and A*0205 alleles. Analysis of the polymorphic residues that help form the B and F pockets of various HLA alleles allowed prediction of binding of the hepatitis B virus core 18-27 epitope to two other HLA alleles (HLA-A*6802 and A*6901). Thus, it appears that a family of at least six different HLA-A molecules may share overlapping ligand specificities (aliphatic residues in position 2 and at the C termini). These results suggest that broadly cross-reactive peptide epitopes can be identified and greatly enhance the prospective feasibility of peptide-based vaccination approaches.
Studies of activated GPIIb/IIIa receptors on the luminal surface of adherent platelets. Paradoxical loss of luminal receptors when platelets adhere to high density fibrinogen. (1993)

The accessibility of activated GPIIb/IIIa receptors on the luminal surface of platelets adherent to damaged blood vessels or atherosclerotic plaques is likely to play a crucial role in subsequent platelet recruitment. To define better the factors involved in this process, we developed a functional assay to assess the presence of activated, luminal GPIIb/IIIa receptors, based on their ability to bind erythrocytes containing a high density of covalently coupled RGD-containing peptides (thromboerythrocytes). Platelets readily adhered to wells coated with purified type I rat skin collagen and the adherent platelets bound a dense lawn of thromboerythrocytes. With fibrinogen-coated wells, platelet adhesion increased as the fibrinogen-coating concentration increased, reaching a plateau at about 11 micrograms/ml. Thromboerythrocyte binding to the platelets adherent to fibrinogen showed a paradoxical response, increasing at fibrinogen coating concentrations up to approximately 4-6 micrograms/ml and then dramatically decreasing at higher fibrinogen-coating concentrations. Scanning electron microscopy demonstrated that the morphology of platelets adherent to collagen was similar to that of platelets adherent to low density fibrinogen, with extensive filopodia formation and ruffling. In contrast, platelets adherent to high density fibrinogen showed a bland, flattened appearance. Immunogold staining of GPIIb/IIIa receptors demonstrated concentration of the receptors on the filopodia, and depletion of receptors on the flattened portion of the platelets. Thus, there is a paradoxical loss of accessible, activated GPIIb/IIIa receptors on the luminal surface of platelets adherent to high density fibrinogen. Two factors may contribute to this result: engagement of GPIIb/IIIa receptors with fibrinogen on the abluminal surface leading to the loss of luminal receptors, and loss of luminal filopodia that interact with thromboerythrocytes. These data provide insight into the differences in thrombogenicity between surfaces, and may provide a mechanism for purposefully passivating platelet-reactive artificial surfaces.
A Diagnostic Predictor Model for Indeterminate or Suspicious Thyroid FNA Samples (2008)

A predictor model was created using the variables age, nodule size, and FNA cytology to predict thyroid malignancy.
Semi-supervised learning for semantic video retrieval (2007)

The automatic understanding of audiovisual content for multimedia retrieval is a difficult task, since the meaning respectively the appearance of a certain event or concept is strongly determined by contextual information. For example, the appearance of a high-level concept, such as e.g. maps or news anchors, is determined by the used editing layout which usually is typical for a certain broadcasting station. In this paper, we show that it is possible to adaptively learn the appearance of certain objects or events for a particular test video utilizing unlabeled data in order to improve a subsequent retrieval process. First, an initial model is obtained via supervised learning using a set of appropriate training videos. Then, this initial model is used to rank shots for each test video v separately. This ranking is used to label the most relevant and most irrelevant shots in a video v for subsequent use as training data in a semi-supervised learning process. Based on these automatically labeled training data, relevant features are selected for the concept under consideration for video v. Then, two additional classifiers are trained on the automatically labeled data of this video. Adaboost and Support Vector Machines (SVM) are incorporated for feature selection and ensemble classification. Finally, the newly trained classifiers and the initial model form an ensemble. Experimental results on TRECVID 2005 video data demonstrate the feasibility of the proposed learning scheme for certain high-level concepts.
Data Backup and Recovery Based on Data De-Duplication (2010)

This paper via compares data de-duplication with other data storage methods, analyses characteristics of data de-duplication and applies the technology to data backup and recovery. Highlights special process of asynchronous backup and recovery based on data de-duplication. Data de-duplication can reduce backup volume, then save users data storage space, and cut the cost of storage, asynchronous backup makes it more reliable and controllable used in design process. Finally, it makes an analysis of the feature of backup recovery mode and its security problems, and gives improved advices.
Treatment of Neonatal Sepsis with Intravenous Immune Globulin (2011)

Therapy with intravenous immune globulin had no effect on the outcomes of suspected or proven neonatal sepsis.
Vertical Handover between Wireless Standards (2008)

The dynamics of handover between two coexisting wireless standards and the consequent exploitation of the offered diversity by the use of multi-standard terminals has been discussed. The potential capacity benefits of mobile-initiated vertical handovers are substantial. However, it is important to choose the correct VHO criteria in order to achieve optimum load balancing and equilibrium states (global and social). Two fast-handover schemes are presented, which exhibit fast convergence to the socially optimal states by allowing a subset of the necessary VHOs among the AIs. In all cases the scheme with replicator dynamics, had the best performance at the cost of an increased vertical handover rate.
Free Radicals in Disease (1998)

Partial reduction of molecular oxygen can generate reactive oxygen species (ROS), including the hydrogen peroxide, and the free radicals superoxide and hydroxyl. The formation of ROS is a feature of many degenerative diseases, such as atherosclerosis and neurodegeneration, Organisms contain a battery of defense mechanisms to prevent the formation of ROS, to scavenge them, and to repair the damage they cause. Free radicals are also involved in signal transduction pathways. For example, the free radical nitric oxide is involved in signal transduction in both the cardiovascular and central nervous systems. The interplay between nitric oxide and ROS has been a major focus of recent studies, as nitric oxide is an efficient radical scavenger. However, in some cases, such as in the formation of peroxynitrite from nitric oxide and superoxide, the product is potentially more deleterious that the parent radicals. This review describes the major chemical species involved in oxidative stress and free radical biochemistry, and gives a brief overview of their role in pathological conditions.