gebhart/patrepeval huggingface dataset:
The T cell repertoire for recognition of a phylogenetically distant protein antigen. Peptide specificity and MHC restriction of staphylococcal nuclease-specific T cell clones. (1986)

Previous studies (1) have indicated that the repertoire of murine T cells specific for a potentially complex protein antigen is in fact specific for a limited number of antigenic epitopes on that antigen in association with a given Ia molecule. Since those studies generally analyzed responses to antigens that differ in only a few amino acids from homologous murine molecules, it was possible that tolerance to self proteins was responsible for the limited T cell repertoire seen in responses to closely related proteins. It was therefore of interest to determine whether T cell recognition of a structurally and phylogenetically more distant protein molecule would also show specificity for a limited number of immunodominant peptides on that molecule. A series of experiments was designed to study the antigen fine specificity and MHC restriction of T cell clones specific for the bacterially derived antigen staphylococcal nuclease (Nase). T cell clones generated in (H-2b X H-2a)F1 (B6AF1) T cells were shown to be specific for Nase and to be restricted by either Ab alpha Ab beta or Ek alpha Ek beta. The fine specificity of these clones was then analyzed using cyanogen bromide and tryptic fragments and a series of overlapping 20-amino-acid synthetic peptides corresponding to and spanning the entire sequence of the Nase molecule. Two Ab alpha Ab beta-restricted clones were highly responsive to peptide 91-110, and not to other synthetic Nase peptides. In contrast, seven Ek alpha Ek beta-restricted clones were consistently responsive to peptide 81-100 and not to 91-110 or to other Nase peptides. Certain of these Ek alpha Ek beta-restricted T cells expressed an interesting crossreactivity, in that they responded to peptide 51-70 as well as to 81-100, although the response to 51-70 was characterized by a markedly shifted dose-response curve, indicating a reduced efficiency of activation by this peptide. Analysis of the amino acid sequences of these regions indicates that this unexpected crossreaction may have a structural basis. A single Nase-specific T cell line generated from BALB/c T cells was, in contrast to any of the B6AF1 clones studied, responsive only to peptide 61-80 and not to other peptides, including 81-100 or 91-110. Collectively, these findings show that Nase-specific T cells are responsive to discrete Nase peptides. Moreover, the present findings suggest that in T cell recognition of a complex and highly foreign protein antigen, a limited number of peptide epitopes are preferentially recognized by T cells in association with a given Ia molecule.
Anti-Herpes Virus Activity of 5-Methoxymethyl-2′-Deoxycytidine in Combination with Deaminase Inhibitors (1990)

5-Methoxymethyl-2′-deoxycytidine (MMdCyd) is an anti-metabolite with selective anti-herpes activity and low cytotoxicity. MMdCyd is dependent upon initial activation by the viral-induced deoxythymidine-deoxycytidine (dThd/dCyd) kinase for its activity against herpes simplex virus (HSV). Antiviral activity of MMdCyd is cell-dependent and is influenced by the deaminase content of the cell line used for assays. The antiviral potency against HSV-1 in this study was higher in RK-13 cells (ED 50 3–5 μm) than in Vero and HEP-2 cells (ED 50 14–26 μm). The potency of MMdCyd increased approximately 20-fold against HSV-1 and twofold against HSV-2 in the presence of tetrahydrodeoxyuridine (H 4 dUrd; which inhibits both dCyd deaminase and dCMP deaminase) in Vero cells. MdCyd in combination with H 4 dUrd was effective in preventing the cytopathogenic effect of HSV-1 and decreasing the production of infectious virus particles. The IC 99 (concentration required to reduce the yield of infectious virus obtained 72 h after infection by 99% relative to control cultures) was 1.6 μm. In combination with tetrahydrouridine (H 4 Urd; an inhibitor of Cyd/dCyd deaminase) the potency of MMdCyd was only slightly enhanced (ED 50 7–8 μm). Dihydrodeoxyuridine and deoxyuridine reversed the antiviral activity of MMdCyd. The minimum cytotoxic concentration for rapidly dividing cells (RK-13, HEP-2 and Vero) for MMdCyd was greater than 3 mm. H 4 Urd and H 4 dUrd were devoid of cytotoxicity and antiviral activity up to 2.12 mm (the highest concentration tested). Diacetyl-MMdCyd (pro-drug form) was approximatewly 20 times less potent than MMdCyd.
Putting out a HIT: crowdsourcing malware installs (2011)

Today, several actors within the Internet’s burgeoning underground economy specialize in providing services to like-minded criminals. At the same time, gray and white markets exist for services on the Internet providing reasonably similar products. In this paper we explore a hypothetical arbitrage between these two markets by purchasing “Human Intelligence ” on Amazon’s Mechanical Turk service, determining the vulnerability of and cost to compromise the computers being used by the humans to provide this service, and estimating the underground value of the computers which are vulnerable to exploitation. We show that it is economically feasible for an attacker to purchase access to high value hosts via Mechanical Turk, compromise the subset with unpatched, vulnerable browser plugins, and sell access to these hosts via Pay-Per-Install programs for a tidy profit. We also present supplementary statistics gathered regarding Mechanical Turk workers ’ browser security, antivirus usage, and willingness to run arbitrary programs in exchange for a small monetary reward. 1
Identification of a new class of biopolymer: bacterial synthesis of a sulfur-containing polymer with thioester linkages (2001)

This is the first report on the biosynthesis of a hitherto unknown, sulfur-containing polyester and also the first report on a bacterial polymer containing sulfur in the backbone. The Gram-negative polyhydroxyalkanoate (PHA)-accumulating bacterium Ralstonia eutropha synthesized a copolymer of 3-hydroxybutyrate and 3-mercaptopropionate, poly(3HB-co-3MP), when 3-mercaptopropionic acid or 3,3'-thiodipropionic acid was provided as carbon source in addition to fructose or gluconic acid under nitrogen-limited growth conditions. The peculiarity of this polymer was the occurrence of thioester linkages derived from the thiol groups of 3MP and the carboxyl groups of 3MP or 3HB, respectively, which occurred in addition to the common oxoester bonds of PHAs. Depending on the cultivation conditions and the feeding regime, poly(3HB-co-3MP) contributed up to 19% of the cellular dry weight, with a molar fraction of 3MP of up to 43%. The chemical structure of poly(3HB-co-3MP) was confirmed by GC/MS, IR spectroscopy, (1)H- and (13)C-NMR spectroscopy, and elemental sulfur analysis. The identification of this novel biopolymer reveals a new quality regarding the substrate range of PHA synthases and their capability for the synthesis of technically interesting polymers.
Definition of a continuous human cell line derived from neuroblastoma. (1970)

Summary A continuous hyperdiploid human cell line, IMR-32, was derived from neuroblastoma tissue. At least two morphologically distinct cell types comprise the population of IMR-32. These two cell types have the same characteristic chromosomal constitution and hyperdiploid stem line number, indicating a common clonal origin. One of the cell types, generally rarely observed because it occurs in minute numbers, appears to differentiate from the major or predominating cell. Marked ultrastructural differences were noted between the 2 cell types. The cell line proved a relatively poor host for virus replication, particularly for representative viruses of two of the human enterovirus groups. The electrophoretically more mobile lactic dehydrogenase isozymes of IMR-32 were retained after extended subcultivation.
Parallel optical memories (1992)

Reference EPFL-ARTICLE-158516View record in Web of Science Record created on 2010-11-25, modified on 2017-05-10
Correlation between Protein and mRNA Abundance in Yeast (1999)

We have determined the relationship between mRNA and protein expression levels for selected genes expressed in the yeast Saccharomyces cerevisiae growing at mid-log phase. The proteins contained in total yeast cell lysate were separated by high-resolution two-dimensional (2D) gel electrophoresis. Over 150 protein spots were excised and identified by capillary liquid chromatography-tandem mass spectrometry (LC-MS/MS). Protein spots were quantified by metabolic labeling and scintillation counting. Corresponding mRNA levels were calculated from serial analysis of gene expression (SAGE) frequency tables (V. E. Velculescu, L. Zhang, W. Zhou, J. Vogelstein, M. A. Basrai, D. E. Bassett, Jr., P. Hieter, B. Vogelstein, and K. W. Kinzler, Cell 88:243-251, 1997). We found that the correlation between mRNA and protein levels was insufficient to predict protein expression levels from quantitative mRNA data. Indeed, for some genes, while the mRNA levels were of the same value the protein levels varied by more than 20-fold. Conversely, invariant steady-state levels of certain proteins were observed with respective mRNA transcript levels that varied by as much as 30-fold. Another interesting observation is that codon bias is not a predictor of either protein or mRNA levels. Our results clearly delineate the technical boundaries of current approaches for quantitative analysis of protein expression and reveal that simple deduction from mRNA transcript analysis is insufficient.
Selection of monoclonal antibodies which induce internalization and phosphorylation of P185HER2 and growth inhibition of cells with HER2/neu gene amplification (1991)

In order to obtain further information on the biological role of the HER2/neu oncoprotein monoclonal antibodies (MAbs) were produced against the p185 extracellular domain. To immunize the mice and screen the hybridoma supernatants we selected a lung adenocarcinoma cell line (Calu-3), which demonstrated an over-expression of p185HER2 measured as the reactivity with polyclonal rabbit serum to the 14-amino-acid carboxy-terminal-HER2/neu. Two MAbs, designated MGR2 (IgG1) and MGR3 (IgG2), selected for reactivity on Calu-3 and negativity on A43I live cells, the reference target cell for EGF receptor expression, were found to immunoprecipitate a 185-kDa molecule. Immunodepletion experiments with the polyclonal antiserum and cross-competition experiments indicated that the 2 reagents recognized 2 different epitopes located on the p185HER2 molecule. One of the 2 MAbs, MGR3, was found to internalize, induce p185HER2 phosphorylation and inhibit tumor cell growth in vitro. These results indicate that MGR3 is directed against a determinant located in the p185HER2 ligand binding site and may compete with the p185HER2 ligand, but is incapable of inducing a complete mitotic signal.
Generation of Adeno-Associated Virus Vector Enabling Functional Expression of Oxytocin Receptor and Fluorescence Marker Genes Using the HumaneIF4GInternal Ribosome Entry Site Element (2009)

We developed the AAV-Oxtr-IRES-Venus vector to rescue the oxytocin receptor (Oxtr) gene functionally at restricted regions in the brains of Oxtr knockout mice. First we chose human eIF4G gene-derived IRES to co-express Venus, a fluorescent marker gene, with Oxtr. With selected human eIF4G IRES, we constructed the AAV-Oxtr-IRES-Venus vector, and it caused expression of the Venus gene in the brain when 1 microl of viral solution (9.4x10(7) vg) was injected into the medial amygdaloid nucleus. In primary neuronal cells transduced with this viral vector and followed by oxytocin administration, functional expression of OXTR was detected by Ca(2+) imaging assay.
Correlating Raman Spectral Signatures with Carrier Mobility in Epitaxial Graphene: A Guide to Achieving High Mobility on the Wafer Scale (2009)

We report a direct correlation between carrier mobility and Raman topography of epitaxial graphene (EG) grown on silicon carbide (SiC). We show the Hall mobility of material on SiC(0001) is highly dependent on thickness and monolayer strain uniformity. Additionally, we achieve high mobility epitaxial graphene (18100 cm(2)/(V s) at room temperature) on SiC(0001) and show that carrier mobility depends strongly on the graphene layer stacking.
Perceptions of Herceptin®: A Monoclonal Antibody for the Treatment of Breast Cancer (1999)

In September 1998 Trastuzumab (Herceptin) became the second monoclonal antibody approved for the treatment of a malignant condition, and the first antibody approved for the treatment of a solid tumor. It is a mouse-human chimeric antibody that produces anti-tumor effects by blocking the HER2-neu receptor, and can also interact with human immune cells to effect antibody dependent cell-mediated cytotoxicity. Pivotal trials in breast cancer showed that it has activity as a single agent in a subset of patients whose tumors greatly over-express HER2, but results were even more impressive when it was used in combination with chemotherapy. It should also prove to be useful in the treatment of subsets of patients with other adenocarcinomas whose tumors over-express HER2.
Conductive-bridge memory (CBRAM) with excellent high-temperature retention (2013)

High-temperature data retention is a critical hurdle for the commercialization of emerging nonvolatile memories. For Conductive-Bridge RAM (CBRAM) [1], we discuss high-temperature retention in terms of the physics of quantum point contacts, and we report on a family of CBRAM cells that achieve excellent retention at temperatures exceeding 200°C.
Comparative Genomics of Rice and Arabidopsis. Analysis of 727 Cytochrome P450 Genes and Pseudogenes from a Monocot and a Dicot (2004)

Data mining methods have been used to identify 356 Cyt P450 genes and 99 related pseudogenes in the rice (Oryza sativa) genome using sequence information available from both the indica and japonica strains. Because neither of these genomes is completely available, some genes have been identified in only one strain, and 28 genes remain incomplete. Comparison of these rice genes with the 246 P450 genes and 26 pseudogenes in the Arabidopsis genome has indicated that most of the known plant P450 families existed before the monocot-dicot divergence that occurred approximately 200 million years ago. Comparative analysis of P450s in the Pinus expressed sequence tag collections has identified P450 families that predated the separation of gymnosperms and flowering plants. Complete mapping of all available plant P450s onto the Deep Green consensus plant phylogeny highlights certain lineage-specific families maintained (CYP80 in Ranunculales) and lineage-specific families lost (CYP92 in Arabidopsis) in the course of evolution.
The natural history of vascular disease in homocystinuria and the effects of treatment (1997)

Among 40 patients with homocystinuria due to cystathionine beta-synthase deficiency diagnosed in the state of New South Wales, Australia (population 6 million) and followed long-term, there were 10 deaths at ages 2-30 years. Of these 8 were definite vascular deaths, one was a presumed vascular death, and the other was due to an accident and unrelated to homocystinuria. The vascular deaths were all early cases and only one patient, a pyridoxine-responsive 30-year-old woman, had been prescribed adequate treatment although it was uncertain that she was taking it. In 32 patients of mean age 30 years (range 9-66 years) there were 539 patient-years of treatment with pyridoxine, folic acid and hydroxocobalamin. There were 17 pyridoxine-responsive patients and all maintained plasma total free homocyst(e)ine levels < 20 mumol/L over an average treatment period of 16.6 years. The 15 nonresponsive patients received additionally 6-9 g of betaine daily. This resulted in a further 74% mean decline (+/-14% SD) in plasma total free homocyst(e)ine, persisting during an average (post-betaine) treatment period of 11 years; current mean +/- SD levels are 33 +/- 17 mumol/L (n = 15). There were two vascular events during treatment, one fatal pulmonary embolus (see above) and one myocardial infarction, whereas without treatment, 21 would have been expected, chi2 = 14.22, p = 0.0001, relative risk 0.09 (95% CI 0.02-0.38). There were no events during 258 patient-years of treatment in the 15 pyridoxine-nonresponsive patients (p < 0.005 versus expected untreated). Nineteen patients had a total of 19 major and 15 minor operations requiring anaesthetic, and three had successful pregnancies, one whilst receiving betaine. There were no thromboembolic complications. We conclude that treatment which effectively lowers circulating homocyst(e)ine, even to suboptimal levels, markedly reduces cardiovascular risk in patients with cystathionine beta-synthase deficiency, and that betaine therapy contributes importantly to this in pyridoxine-nonresponsive patients. Betaine as additional therapy is safe and effective for at least 16 years.
IP-10, a -C-X-C- chemokine, elicits a potent thymus-dependent antitumor response in vivo. (1993)

IP-10 is a member of the -C-X-C-chemokine superfamily of proinflammatory cytokines whose secretion is induced by interferon gamma (IFN-gamma) and lipopolysaccharide (LPS). To date no function has been described for IP-10. We have genetically engineered tumor cells to secrete high levels of murine IP-10 and demonstrate that while IP-10 has no effect on the growth of these tumor cells in culture, it elicits a powerful host-mediated antitumor effect in vivo. The IP-10 antitumor response is T lymphocyte dependent, non-cell autonomous, and appears to be mediated by the recruitment of an inflammatory infiltrate composed of lymphocytes, neutrophils, and monocytes. These results document an important biologic property of IP-10 and raise the possibility that some of the T cell-directed effects of IFN-gamma and LPS may be mediated by this chemokine.
Integrated Temperature, Humidity and Gas Sensors on Flexible Substrates for Low-Power Applications (2007)

Temperature, gas and humidity resistive/ capacitive sensors on flexible substrates from organic materials, suitable for RFID mobile applications, have been produced and investigated. The sensor implementation solutions are providing simple, versatile and low power temperature and gas detection. The device structure was developed together with the data evaluation strategies based on last generation SigmaDelta analog (resistance and capacitance) to digital converters. We demonstrate the possibility of developing gas sensors on humidity sensitive substrates, having temperature corrected responses. The proposed device concept is aimed to evolve towards "flexible & full plastic" implementations.
Optimal multi-dimensional fusion model for sensor allocation and accuracy assessment (2016)

I We describe a multi-dimensional model for fusion of activity based intelligence (ABI) hypothesis-driven evidence through optimal sensor management. We determine decision-making strategies based upon ability to perform data mining and pattern discovery utilizing open source, actionable information to prepare for specific events or situations from multiple information sources. Our solution is based on an analytical framework using game theory to support ingestion of data sources (evidence); integration of analytical algorithms for feature extraction, crowd source analysis, open source data mining, trends, and pattern analysis and linear game theory optimization to support multiple hypothesis analysis. This solution may also save money by offering a Pareto efficient, repeatable process for resource management. We combine operations research methods and remote sensing for decision-making with several possible actions, state of world, and a mixed pro bability metric. Our tool allows for calculating optimal strategies, provides greater knowledge about remote sensing access times and increases likelihood of a decision-maker making best decision. We fuse evidence using Dempster's Rule and Nash Equilibrium (NE) for allocation of demands by sensor modality. We discuss a method for calculating optimal detector to determine accuracy of resource allocation. By calculating all NE possibilities per period, optimization of sensor allocation is achieved for overall higher system efficiency. We model impact of decision-making on accuracy by adding more dimensions to decision-making process as sensitivity analysis. Future work is to implement the design on a distributed processing platform to support real-world-sized scenarios and simulations.
Contribution of virus and immune factors to herpes simplex virus type I-induced corneal pathology. (1990)

In vivo T-lymphocyte subpopulation depletion techniques were used to identify the roles of L3T4+ (CD4) and Lyt-2+ (CD8) T-lymphocytes in the pathogenesis of corneal stromal disease induced by two different strains of Herpes simplex virus type 1 (HSV-1). Histologic examination of infected corneas revealed significant differences in the composition of the inflammatory corneal infiltrates induced by the RE and KOS strains of HSV-1. The RE strain induced a predominantly polymorphonuclear leukocyte (PMN) infiltrate, which began approximately 1 week after infection and progressed through day 21. Depletion of CD4 cells before corneal infection with RE HSV-1 greatly reduced the incidence and severity of corneal disease; depletion of CD8 cells had no effect. The strain KOS HSV-1 induced an early PMN infiltrate that became predominantly mononuclear by day 21. Depletion of CD4 cells did not change the incidence or severity of KOS HSV-1-induced corneal stromal disease. The corneal lesions of these mice contained numerous CD8 cells. Depletion of CD8 cells before KOS HSV-1 infection of the cornea moderately reduced the incidence of stromal disease. However, in CD8-depleted mice with the disease, PMNs were the most prevalent infiltrating cells, and the disease appeared identical to that seen in RE HSV-1 infected corneas. Simultaneous depletion of CD4 and CD8 cells before KOS HSV-1 infection eliminated stromal disease. However, when T-cell depletion was discontinued in these mice, stromal disease developed in concert with the appearance of T-cells in the lymphoid organs and corneas. Thus, T-lymphocytes are a necessary component of HSV-1 corneal stromal disease. These results further suggest that RE HSV-1 preferentially activates CD4 cells in the cornea, and KOS HSV-1 preferentially activates CD8 cells in the cornea.
Oxidative stress affects cytoskeletal structure and cell-matrix interactions in cells from an ocular tissue: The trabecular meshwork (1999)

The trabecular meshwork (TM) is a specialized eye tissue that regulates the aqueous humor outflow and controls intraocular pressure. Cells in this tissue are essential for maintenance of the outflow system. Disturbance of the TM cell status by insults such as oxidative stress may lead to elevation of the intraocular pressure and development of glaucoma. In the present study, we investigated the effect of oxidative stress on the adhesion of human TM cells to extracellular matrix (ECM) proteins. Treatment with 1 mM of H2O2 for 10 or 30 min did not affect cell viability, whereas the adhesion of TM cells to fibronectin, laminin, and collagen types I and IV was significantly reduced. Phalloidin and immunostaining also revealed reorganization of actin and vimentin structures. The level of integrins alpha5beta1, alphavbeta3, and beta1 was not altered, although the distribution of paxillin and focal adhesion kinase in focal contacts was reduced. Concomitantly, the level of transcription factor NF-kappaB was enhanced by the H2O2 treatment. Nuclear extracts of the treated cells also contained a heightened NF-kappaB binding activity. These changes persisted for up to 6 h after the H2O2 treatment but were partially recovered by 24 h. We concluded that under sublethal oxidative stress conditions, the TM cell adhesion to the ECM was impaired. The short-term loss of cell-matrix adhesiveness may be related to the rearrangement of cytoskeletal structures. Extensive and repeated oxidative stress in vivo may result in reduced TM cell adhesion, leading to cell loss, compromised TM integrity, and pathologic consequences.