gebhart/patrepeval huggingface dataset:
Identification of helper T cell antigenic sites in mice from the haemagglutinin glycoprotein of measles virus (1993)

The aim of this study was to define the helper T cell epitopes on the haemagglutinin (H) of measles virus (MV) in BALB/c (H-2d) and TO (H-2s) mice. A panel of 55 synthetic peptides (15-mers, overlapping by five amino acids) representing 92.2% of the H protein were synthesized and tested for immunogenicity and ability to stimulate MV-primed lymphocytes in vitro. The results obtained show that mouse lymphocytes respond to defined regions of the H protein which differ according to mouse strain. Virus-primed lymphocytes from BALB/c mice responded in vitro to peptides 7, 38, 39 and 44 whereas lymphocytes from virus-primed TO mice responded only to peptide 39. When mice of both strains were immunized with the peptides, a number of peptides induced proliferative responses, showing that the T cell repertoire for epitopes on the H protein is broader than that following immunization with virus. In BALB/c mice, lymphocytes primed to peptides 37, 39, 40, 42 and 43 responded in vitro to MV and in TO mice, lymphocytes primed to peptides 14, 32, 39, 40 and 49 responded to the virus. Thus in both strains of mice peptide 39 behaved as a dominant T cell epitope following immunization with virus or peptides. When the results obtained experimentally were compared with sequences predicted to be T cell epitopes by a number of algorithms, the concordance was limited.
Effects of voltage-gated ion channel modulators on rat prostatic cancer cell proliferation: Comparison of strongly and weakly metastatic cell lines (2000)

We conclude that the mechanism(s) controlling the proliferation of the weakly metastatic AT-2 cells involves voltage-gated K(+) channels. In contrast, the proliferation of strongly metastatic MAT-LyLu cells is much less dependent upon voltage-gated K(+) channel activity.
Role of Reduced Exogenous Organic Compounds in the Physiology of the Blue-Green Bacteria (Algae): Photoheterotrophic Growth of a “Heterotrophic” Blue-Green Bacterium (1973)

The unicellular blue-green bacterium Agmenellum quadruplicatum strain BG-1 was found to be capable of rapid photoheterotrophic growth but unable to grow in the dark on a variety of reduced organic substrates. The generation time on glycerol was 12 h, and on CO(2), 3 h. Glycerol carbon was converted into cellular carbon with a very high efficiency. This high efficiency of carbon conversion, the action spectrum for growth on glycerol, cell pigmentation, gas exchange measurements, and immediate ability of photoheterotrophically grown cells to evolve O(2) (upon the addition of CO(2)) suggest the involvement of both photosystems I and II of photosynthesis during photoheterotrophic growth.
Similarity analysis for shape retrieval by example (1996)

This work proposes a query-by-example algorithm for shape retrieval from a color image database. The main contribution of this work is an unified approach for shape matching and similarity ranking using a modal representation. Prior work mostly performed point correspondence determination and similarity ranking of shapes in two distinct steps or performed one of them. We define a new shape-similarity metric and attempt to address the question "how similar two shapes in an image database are", which currently is an important problem in shape-based retrieval systems. Unlike most reported methods, the presented approach does not require extraction of connected boundaries or silhouettes. It is rotation-, and scale-invariant, and can handle mild deformations of objects. The results are promising for using the algorithm in the context of database query by image content.
Enhanced antitumor immunity by fusion of CTLA-4 to a self tumor antigen (2000)

The idiotypic determinant (Id) of the immunoglobulin expressed by a B-cell malignancy can serve as an effective tumor-specific antigen but is only weakly immunogenic. This study demonstrates that the immunogenicity of the tumor Id protein can be dramatically increased by directing it to antigen-presenting cells (APCs). Cytotoxic T-lymphocyte antigen 4 (CTLA-4) present on activated T cells has a strong binding affinity to both B7-1 and B7-2 molecules, which are primarily expressed on APCs. After construction of a fusion protein consisting of Id and CTLA-4 (Id-CTLA4), mice immunized with the fusion protein induced high titers of Id-specific antibody and T-cell proliferative responses without adjuvants and were protected from lethal tumor challenge. The Id-CTLA4 fusion protein was so potent that even low doses (down to 0.1 μg) of the immunogen were able to elicit strong antibody responses. By using an Id-CTLA4 mutant protein, the ability to bind B7 molecules on APCs was shown to be required for the enhanced immunogenicity of Id-CTLA4. These findings demonstrate that fusing CTLA-4 to a potential tumor antigen represents an effective approach to prime antitumor immunities in vivo and may be applicable to the design of vaccines for a variety of other diseases.
Progression from papilloma to carcinoma is accompanied by changes in antibody response to papillomavirus proteins (1993)

Cottontail rabbit papillomavirus induces benign tumors, papillomas, in rabbits which progress at a high frequency to malignant tumors, carcinomas. Cottontail rabbit papillomavirus therefore provides an experimental model for oncogenic human papillomaviruses. The nature of the antigens recognized by the host has not been identified at any stage of tumor development. Here, we characterized the humoral immune response to viral antigens in cottontail and domestic rabbits at the papilloma stage, in domestic rabbits at the carcinoma stage, and in animals in which papillomas had regressed. Antibodies to linear epitopes were identified by Western blotting (immunoblotting) with bacterial fusion proteins, and evidence for recognition of conformational epitopes was obtained by immunoprecipitation. An immune response to the early proteins E1, E2, E6, and E7 was detected only in a fraction of the animals, and all animals were negative for E4 and E5. The response to E6 and E7 peaked around 7 months and then decreased, while that to E1 and E2 remained level after an initial raise. The antibody response to structural proteins was low at the papilloma stage, and antibodies to L1 recognized predominantly conformational epitopes. As papillomas progressed to carcinomas, there was a drastic increase in the response to L1 and L2, suggesting a change in interaction between virus-infected host cells and the host's immune system.
Differing Src Signaling Levels Have Distinct Outcomes in Drosophila (2007)

High levels of Src activity are found in a broad spectrum of cancers. The roles of Src and its negative regulator Csk have been extensively studied, although results have often proved contradictory or the relevance to whole organisms is unclear. In Drosophila, overexpression of either Src orthologue resulted in apoptotic cell death, but paradoxically, reducing dCsk activity led to over-proliferation and tissue overgrowth. Here, we show that in Drosophila epithelia in situ, the levels of Src signaling determine the cellular outcome of Src activation. Apoptotic cell death was triggered specifically at high Src signaling levels; lower levels directed antiapoptotic signals while promoting proliferation. Furthermore, our data indicate that expression of kinase-dead Src isoforms do not necessarily act as dominant-negative factors, but can instead increase Src pathway activity, most likely by titrating Csk activity away from endogenous Src. The importance of Src activity levels was emphasized when we examined oncogenic cooperation between Src and Ras: malignant overgrowth was observed specifically when high Src signaling levels were achieved. We propose a model in which low levels of Src signaling promote survival and proliferation during early stages of tumorigenesis, whereas strong Src signaling, coupled with antiapoptotic signals, directs invasive migration and metastasis during advanced tumor stages.
Effects of sildenafil on long-term retention of an inhibitory avoidance response in mice (1999)

Sildenafil (1, 3, 10, and 30mg/kg, intraperitoneally (i.p.)), a cyclic guanosine monophosphate (cGMP)-specific phosphodiesterase type 5 (PDE5) inhibitor, facilitated retention performance of a one-trial step-through inhibitor avoidance task, when administered to male Swiss mice immediately after training, as indicated by performance on a retention test 48 h later. The dose-response curve was an inverted U in this dose range, although only the dose of 3 mg/kg of sildenafil produced significant effects. Sildenafil did not affect response latencies in mice not given the footshock on the training trial, indicating that the actions of sildenafil on retention were not due to non-specific proactive effects on retention performance. The effects of sildenafil (3 mg/kg, i.p.) were time-dependent, and the administration of sildenafil (3 mg/kg, i.p.) 30 min prior to the retention test did not affect retention in mice given post-training injections of vehicle or sildenafil (3 mg/kg, i.p.). However, the administration of sildenafil (3mg/kg, i.p.) 30 min before training also enhanced retention performace. Further, when mice were trained and received immediate post-training sildenafil (3 mg/kg) and were tested for retention either 1 week or 1 month later, at each retention interval the performance was comparable to that found with a 48-h retention interval. Finally, an enhancement of retention was also observed in female Swiss mice that received sildenafil (3 mg/kg, i.p.) immediately, but not 180min, after training. These findings could indicate that the actions of sildenafil on retention are not sex-dependent. The results suggest that sildenafil influences retention by modulating time-dependent mechanisms involved in memory storage and that the effects are long lasting. A possible participation of the nitric oxide (NO)-guanylyl cyclase-cGMP system also is suggested.
Tec protein-tyrosine kinase directly associates with Lyn protein-tyrosine kinase through its N-terminal unique domain. (1994)

Most of non-receptor-type protein-tyrosine kinases share common structures, such as N-terminal unique domains, Src homology region (SH)-2 domains, SH-3 domains and kinase domains. Although vast effort has brought some information about the in vivo roles of SH-2, -3 and kinase domains, little is still understood about the function of N-terminal unique domain. By utilizing the glutathione S-transferase (GST)-fusion system, we have investigated the role of N-terminal unique domain of the Tec protein-tyrosine kinase in a mouse IL-3-dependent myeloid cell line. We could reveal that the C-terminal half of the Tec N-terminal unique domain (NTec2 region) can bind to a set of tyrosine-phosphorylated cellular proteins in vitro in an IL-3-dependent manner. Surprisingly, p56/53Lyn constitutively binds to the NTec2 region. Among the NTec2-bound Lyn proteins, only the p56 form seems to be inducibly tyrosine-phosphorylated in response to IL-3. Binding domain of Lyn to the NTec2 region was localized to its SH-3 domain. Tec was also shown to make a stable complex with Lyn in vivo. This is the first report demonstrating the direct association between distinct cytoplasmic protein-tyrosine kinases, especially through N-terminal unique domain.
Cellular distribution of somatogenic receptors and insulin-like growth factor-I mRNA in the rat liver (1988)

Parenchymal and non-parenchymal cell fractions isolated from rat liver were analysed for the distribution of somatogenic receptors and for insulin-like growth factor-I (IGF-I) mRNA. The effect of hypophysectomy either alone or in combination with a single injection of human GH (hGH) on the levels of IGF-I mRNA was also studied in the two cell fractions. The contamination of parenchymal cells in the non-parenchymal cell fraction was in the range of 2-3%. Somatogenic receptors were found only in the parenchymal cell fraction. IGF-I mRNA was detected in both cell fractions, although the level of this mRNA was about fivefold higher in parenchymal cells. When RNA was studied by Northern gel analysis no major differences were observed in the size distribution of IGF-I transcripts in the two cell fractions. In hypophysectomized animals, the IGF-I mRNA level was decreased to 10 and 30% of control values in the parenchymal and non-parenchymal cell fractions respectively. Treatment of hypophysectomized animals with a single dose of hGH restored IGF-I mRNA in parenchymal and in non-parenchymal cells to the extent found in intact animals. In conclusion, our data indicate that somatogenic receptors are exclusively, and IGF-I mRNA predominantly, expressed in liver parenchymal cells compared with a total non-parenchymal cell fraction. The most marked effect of GH, correlating with the presence of somatogenic receptors, was seen in the parenchymal cells. The minor non-GH dependent expression of IGF-I mRNA suggests that this peptide may elicit effects in addition to the well-established GH-dependent activity.
Tissue factor: a link between C5a and neutrophil activation in antiphospholipid antibody–induced fetal injury (2007)

Fetal loss in patients with antiphospholipid (aPL) antibodies has been ascribed to thrombosis of placental vessels. However, we have shown that inflammation, specifically activation of complement with generation of the anaphylotoxin C5a, is an essential trigger of fetal injury. In this study, we analyzed the role of the procoagulant molecule tissue factor (TF) in a mouse model of aPL antibody-induced pregnancy loss. We found that either blockade of TF with a monoclonal antibody in wild-type mice or a genetic reduction of TF prevented aPL antibody-induced inflammation and pregnancy loss. In response to aPL antibody-generated C5a, neutrophils express TF potentiating inflammation in the deciduas and leading to miscarriages. Importantly, we showed that TF in myeloid cells but not fetal-derived cells (trophoblasts) was associated with fetal injury, suggesting that the site for pathologic TF expression is neutrophils. We found that TF expression in neutrophils contributes to respiratory burst and subsequent trophoblast injury and pregnancy loss induced by aPL antibodies. The identification of TF as an important mediator of C5a-induced oxidative burst in neutrophils in aPL-induced fetal injury provides a new target for therapy to prevent pregnancy loss in the antiphospholipid syndrome.
A comparative evaluation of digital imaging, retinal photography and optometrist examination in screening for diabetic retinopathy (2003)

Both manual grading methods produced similar results whether using a one- or two-field protocol. Technical failures rates, and hence need for recall, were lower with digital imaging. One-field grading of fundus photographs appeared to be as effective as two-field. The optometrists achieved the lowest sensitivities but reported no technical failures. Automated grading of retinal images can improve efficiency of resource utilization in diabetic retinopathy screening.
Passive and Active Immunotherapy for Experimental Pneumococcal Pneumonia by Polyvalent Human Immunoglobulin or F(ab')2 Fragments Administered Intranasally (1996)

Experimental pneumococcal pneumonia in leukopenic BALB/c mice enabled evaluation of passive immunotherapy with human polyvalent intravenous immune globulin (IVIG) given intravenously or intranasally and with F(ab')2 fragments administered intranasally. For intravenous and intranasal IVIG, the respective effective doses were < 5 but > 0.5 mg/kg and < 250 but > 2.5 micrograms/kg. For F(ab')2 fragments, the effective dose was < 500 but > 2.5 micrograms/kg. Assessment of the acquired immune responses of passively protected mice and convalescing controls 3 weeks after primary infection showed that antibody responses to whole bacteria were serotype-specific in all mice. Mice protected with IVIG and F(ab')2 fragments had more antibodies to pneumolysin than did controls. In addition, treated mice acquired greater resistance to reinfection than untreated survivors. Thus, local passive immunotherapy may be an effective means of treating pneumococcal pneumonia and may promote acquired resistance to reinfection.
Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands. (1996)

Precise mapping of DNA methylation patterns in CpG islands has become essential for understanding diverse biological processes such as the regulation of imprinted genes, X chromosome inactivation, and tumor suppressor gene silencing in human cancer. We describe a new method, MSP (methylation-specific PCR), which can rapidly assess the methylation status of virtually any group of CpG sites within a CpG island, independent of the use of methylation-sensitive restriction enzymes. This assay entails initial modification of DNA by sodium bisulfite, converting all unmethylated, but not methylated, cytosines to uracil, and subsequent amplification with primers specific for methylated versus unmethylated DNA. MSP requires only small quantities of DNA, is sensitive to 0.1% methylated alleles of a given CpG island locus, and can be performed on DNA extracted from paraffin-embedded samples. MSP eliminates the false positive results inherent to previous PCR-based approaches which relied on differential restriction enzyme cleavage to distinguish methylated from unmethylated DNA. In this study, we demonstrate the use of MSP to identify promoter region hypermethylation changes associated with transcriptional inactivation in four important tumor suppressor genes (p16, p15, E-cadherin, and von Hippel-Lindau) in human cancer.
An Artificial Lithium Protective Layer that Enables the Use of Acetonitrile‐Based Electrolytes in Lithium Metal Batteries (2018)

The resurgence of the lithium metal battery requires innovations in technology, including the use of non-conventional liquid electrolytes. The inherent electrochemical potential of lithium metal (-3.04 V vs. SHE) inevitably limits its use in many solvents, such as acetonitrile, which could provide electrolytes with increased conductivity. The aim of this work is to produce an artificial passivation layer at the lithium metal/electrolyte interface that is electrochemically stable in acetonitrile-based electrolytes. To produce such a stable interface, the lithium metal was immersed in fluoroethylene carbonate (FEC) to generate a passivation layer via the spontaneous decomposition of the solvent. With this passivation layer, the chemical stability of lithium metal is shown for the first time in 1 m LiPF<sub>6</sub> in acetonitrile.
Primary Structure of v- raf : Relatedness to the src Family of Oncogenes (1984)

A replication-defective, acute transforming retrovirus (murine sarcoma virus 3611) was isolated from mouse and molecularly cloned. The nucleotide sequence of 1.5 kilobases encompassing the transforming gene (v-raf) was determined. This sequence, which predicts the amino acid sequence of a gag-raf fusion protein, terminates 180 nucleotides from the 3' end of the acquired cellular sequence. Comparison of the predicted amino acid sequence of v-raf with the predicted amino acid sequences of other oncogenes reveals significant homologies to the src family of oncogenes. There is a lack of homology within the sequence of the tyrosine acceptor domain described for the phosphotyrosine kinase members of the src family of transforming proteins. Phylogenetic arrangement of this family of oncogenes suggests that tyrosine-specific phosphorylation may be a recently acquired activity.
Silicone rubber/graphite nanosheet electrically conducting nanocomposite with a low percolation threshold (2007)

Abstract A novel electrically conductive nanocomposite was successfully fabricated by dispersing homogeneously conductive graphite nanosheets (GN) in an insulating silicone rubber (SR) matrix. GN were prepared by powdering expanded graphite with sonication in aqueous alcoholic solution. The particular geometry of GN 30–80 nm in thickness with high aspect ratio contributes to the advantage of forming the conducting network, so that the percolation threshold of SR/GN nanocomposite is about 0.009, much lower than that of composites with conventional graphite. The SR/GN nanocomposite presents a remarkable piezoresistive behavior under much low pressure, related to the low elastic modulus of the composite. The elastic modulus of the nanocomposite with various GN content and at the different speed of compression was discussed. POLYM. COMPOS., 28:493–498, 2007. © 2007 Society of Plastics Engineers
Effects of Modifiers of Glycosaminoglycan Biosynthesis on Outflow Facility in Perfusion Culture (2008)

Disrupting GAG chain biosynthesis increased outflow facility in perfusion culture and induced atypical ECM molecule interactions in cell culture. This study provides direct evidence of the critical role of GAG chains in regulating outflow resistance in human TM.
Thermal conversion of biomass and biomass components to biofuels and bio-chemicals (2012)

This thesis examined the conversions of biomass and biomass components to petrochemicals and total aliphatic gasoline like products. There are three major projects of the thesis. Since biomass is very complicated, to understand the thermal decomposition pathways of biomass, the pyrolytic behaviors of various biomass components including lignin and cellulose under different reaction were investigated in the first phase. Due to complexity and limited volatility, the thermal decomposition products from biomass bring insurmountable obstacles to the traditional analysis methods such as GC-MS, UV and FT-IR. Therefore, precise characterization of the whole portion of thermal decomposition products has significant impacts on providing insight into the pyrolysis pathways and evaluating the upgrading processes. Various NMR methods to characterize different functional groups presented in liquid and solid pyrolysis products by 1H, 13C, 31P, 2D-HSQC and solid state 13C-NMR were introduced in the second phase. Nevertheless, the major drawback towards commercialization of pyrolysis oils are their challenging properties including poor volatility, high oxygen content, molecular weight, acidity and viscosity, corrosiveness and cold flow problems. In situ upgrading the properties of pyrolysis oils during thermal conversion process by employing zeolites has been discussed in the third phase. The further hydrogenation of pyrolysis oils to total aliphatic gasoline like products by heterogeneous catalysis in “green medium” – water has also been examined in the third project.