gebhart/patrepeval huggingface dataset:
Control of tumor progression by maintenance of apoptosis (1996)

The ability to induce multiple apoptotic regressions of an androgen-dependent tumor cell population by repeated cycles of androgen withdrawal and replacement may be advantageous in therapeutic strategies aimed at delaying or preventing tumor progression. With greater insight into factors that either initiate or limit apoptosis, more efficient application of intermittent therapy might be achieved, especially if methods could be devised to increase the length or number of treatment cycles. Both calreticulin and clusterin represent proteins with a potential role in the regulation of apoptosis. Calreticulin may inhibit target gene transcription by interacting with steroid hormone receptors, thereby masking their DNA-binding sites and triggering the onset of the apoptotic process. Clusterin, on the other hand, is a membrane-stabilizing protein that appears to be involved in limiting the autophagic lysis of epithelial cells during apoptosis. Also, the increasing tendency for nuclear localization of clusterin after androgen withdrawal may preserve the nuclear environment, limiting the lethal effect of treatment. Thus, tumor progression, characterized by the loss of apoptotic potential, appears to be linked in part to the inappropriate activation of TRPM-2 gene, which accounts for the constitutive expression of clusterin.
Epstein-Barr virus-dependent lymphoproliferative disease: critical role of IL-6 (2000)

Epstein-Barr virus (EBV)-induced lymphoproliferative disease (lpd) is a B cell neoplasm that affects patients who are immunosuppressed in the context of organ transplantation or HIV infection. A model for the aggressive form of this entity was generated by xenotransplantation of SCID mice with human peripheral blood leukocytes from individuals with prior contact with EBV. This model, where large B cell lymphoma occurs, was used to test the hypothesis that IL-6 has a major role in EBV-induced B cell tumorigenesis. IL-6 is known to differentiate B cells into immunoglobulin-secreting plasma cells and induce EBV replication, and xenochimeric animals have detectable serum levels of human IL-6. Human IL-6 inhibition with a neutralizing monoclonal antibody decreased tumor incidence from 62 % to 27 %. In addition, anti-IL-6 treatment significantly improved xenotransplanted animal survival, with median survival at > 245 days when compared to that of controls at 132 days. In conclusion, IL-6 plays a critical role in the pathogenesis of EBV-induced human lpd, and IL-6 inhibition may represent a new and promising preventive or therapeutic approach against this malignancy.
FYVE-finger proteins – effectors of an inositol lipid (1999)

The binding of cytosolic proteins to specific intracellular membranes containing phosphorylated derivatives of phosphatidylinositol (PtdIns) is a common theme in vital cellular processes, such as cytoskeletal function, receptor signalling and membrane trafficking. Recently, several potential effectors of the phosphoinositide 3-kinase product PtdIns 3-phosphate (PtdIns(3)P) have emerged through the observation that a conserved zinc-finger-like domain, the FYVE-finger, binds specifically to this lipid. Here we review current knowledge about the structural basis for the FYVE-PtdIns(3)P interaction, its role in membrane recruitment of proteins and the functions of FYVE-finger proteins in membrane trafficking and other cellular processes.
Fast Image Deconvolution using Hyper-Laplacian Priors (2009)

This document is supplementary material to our NIPS 2009 paper [1] of the same name. While we choose to solve the w sub-problem (Eqn. 5) in [1] using a LUT or analytically (for some specific values of α), a number of numerical alternatives exist. The simplest and fastest approach is to use Newton-Raphson (NR) to find the roots of the polynomials in Eqn. 10 and Eqn 11 of [1]. As shown in Table 1, 4 iterations of NR take a similar time to our analytic solution. However, the numerical algorithm has poor stability, particularly when the polynomials skim the x-axis. In practice, we found it gave spurious solutions around 1-2 % of the time, an unacceptable rate given the iterative nature of our overall algorithm. Applying NR directly to Eqn. 5 of [1] is similarly unreliable. Although techniques with greater stability than NR exist, they are computationally more expensive. For example, we also compare to Matlab’s roots command, based on solving an eigenvalue problem, but this was several orders of magnitude slower than our analytic approach. Another benefit of our algorithms is that they are easily parallelizable. In addition to using Matlab’s. * and. ˆ operators, Algorithms 2 and 3 in [1] can be multi-threaded using the Intel Math Kernel Library (MKL) to give a ∼2 times speedup on a quad-core CPU (see Table 1). Lastly, the LUT approach can be used for values of α not restricted to 1/2 or 2/3. Figure 1 shows the advantage of using a LUT (or analytic method) over using a Newton-Raphson
Optical Biosensors for Monitoring Dynamic Mass Redistribution in Living Cells Mediated by Epidermal Growth Factor Receptor Activation (2005)

This paper reported the identification and mechanism of dynamic mass redistribution in living cells mediated by epidermal growth factor receptor (EGFR) activation using resonant waveguide grating (RWG) biosensors. In response to epidermal growth factor (EGF) stimulation, human epidermoid carcinoma A431 cells gave rise to a dynamic response due to dynamic mass redistribution (DMR) in the cells. The DMR response was strongly dependent on cell culture conditions and EGF concentrations. The DMR response of quiescent A431 cells was found to be saturable to the concentration of EGF, and was able to be fully suppressed by a specific and potent EGFR tyrosine kinase inhibitor, AG1478. The effect of various known inhibitors/drugs on the DMR response of quiescent A431 cells clearly showed that the EGF-induced DMR involves the Ras/mitogen-activated protein (MAP) kinase pathway, and mainly proceeds through MEK. The DMR signatures obtained here offer integrated quantitative and dynamic representation of EGFR activation and can be used to screen modulators that can regulate critical targets in both the upstream and the downstream EGFR signaling pathways.
Length Scales at which Classical Elasticity Breaks Down for Various Materials (2007)

At what characteristic length scale does classical continuum elasticity cease to accurately describe small deformation mechanical behavior? The two dominant physical mechanisms that lead to size dependency of elastic behavior at the nanoscale are surface energy effects and nonlocal interactions. The latter arises due to the discrete structure of matter and the fluctuations in the interatomic forces that are smeared out within the phenomenological elastic modulus at coarser sizes. While surface energy effects have been well characterized in the literature, little is known about the length scales at which nonlocal effects manifest for different materials. Using a combination of empirical molecular dynamics and lattice dynamics (empirical and ab initio), we provide estimates of nonlocal elasticity length scales for various classes of materials: semiconductors, metals, amorphous solids, and polymers.
Endotoxic properties of synthetic pentaacyl lipid A precursor Ib and a structural isomer (1987)

A pentaacyl precursor of lipid A biosynthesis, termed precursor Ib, and a structural isomer have been chemically synthesized. These compounds were, in comparison to synthetic Escherichia-coli type lipid A or lipopolysaccharide, analyzed for their activity in typical endotoxin test systems. It was found that both precursor Ib and the isomer exhibited similar or only slightly lower pyrogenic, lethal and Shwartzman-phenomenon-inducing activity than lipid A. All preparations were comparable in their B-lymphocyte mitogenicity, macrophage-activating capacity and immunoreactivity towards lipid A antisera. The proton nuclear magnetic resonance spectra of the 1-dephospho derivative of synthetic and bacterial precursor Ib were indistinguishable proving that the previously proposed structure for precursor Ib is correct.
Stearoyl-acyl carrier protein delta 9 desaturase from Ricinus communis is a diiron-oxo protein. (1993)

A gene encoding stearoyl-acyl carrier protein delta 9 desaturase (EC 1.14.99.6) from castor was expressed in Escherichia coli. The purified catalytically active enzyme contained four atoms of iron per homodimer. The desaturase was studied in two oxidation states with Mössbauer spectroscopy in applied fields up to 6.0 T. These studies show conclusively that the oxidized enzyme contains two (identical) clusters consisting of a pair of antiferromagnetically coupled (J > 60 cm-1, H = JS1.S2) Fe3+ sites. The diferric cluster exhibited absorption bands from 300 to 355 nm; addition of azide elicited a charge transfer band at 450 nm. In the presence of dithionite, the clusters were reduced to the diferrous state. Addition of stearoyl-CoA and O2 returned the clusters to the diferric state. These properties are consistent with assigning the desaturase to the class of O2-activating proteins containing diiron-oxo clusters, most notably ribonucleotide reductase and methane monooxygenase hydroxylase. Comparison of the primary structures for these three catalytically diverse proteins revealed a conserved pair of the amino acid sequence -(Asp/Glu)-Glu-Xaa-Arg-His- separated by approximately 100 amino acids. Since each of these proteins can catalyze O2-dependent cleavage of unactivated C--H bonds, we propose that these amino acid sequences represent a biological motif used for the creation of reactive catalytic intermediates. Thus, eukaryotic fatty acid desaturation may proceed via enzymatic generation of a high-valent iron-oxo species derived from the diiron cluster.
Resistance to antiretroviral drugs. (1998)

There are many questions regarding testing for viral resistance to antiretroviral drugs and interpretation of test results. The most appropriate time for testing and the compartment from which to derive virus are still uncertain. Both phenotypic and genotypic tests are used to measure drug susceptibility; however, interpretation of results of these assessments is not clear-cut. Furthermore, correlation of these test results with clinical outcome or pharmacological data is limited by lack of studies and other confounding factors.
Evolutionarily Conserved Herpesviral Protein Interaction Networks (2009)

Herpesviruses constitute a family of large DNA viruses widely spread in vertebrates and causing a variety of different diseases. They possess dsDNA genomes ranging from 120 to 240 kbp encoding between 70 to 170 open reading frames. We previously reported the protein interaction networks of two herpesviruses, varicella-zoster virus (VZV) and Kaposi's sarcoma-associated herpesvirus (KSHV). In this study, we systematically tested three additional herpesvirus species, herpes simplex virus 1 (HSV-1), murine cytomegalovirus and Epstein-Barr virus, for protein interactions in order to be able to perform a comparative analysis of all three herpesvirus subfamilies. We identified 735 interactions by genome-wide yeast-two-hybrid screens (Y2H), and, together with the interactomes of VZV and KSHV, included a total of 1,007 intraviral protein interactions in the analysis. Whereas a large number of interactions have not been reported previously, we were able to identify a core set of highly conserved protein interactions, like the interaction between HSV-1 UL33 with the nuclear egress proteins UL31/UL34. Interactions were conserved between orthologous proteins despite generally low sequence similarity, suggesting that function may be more conserved than sequence. By combining interactomes of different species we were able to systematically address the low coverage of the Y2H system and to extract biologically relevant interactions which were not evident from single species.
Transformational and altered signal transduction by a naturally occurring mutant EGF receptor. (1996)

An amino-truncated variant form of the epidermal growth factor receptor (EGFRvIII) has been identified in human brain, breast, lung and ovarian tumors. We have found that overexpression of this mutant EGF receptor in NIH3T3 cells results in transformation as a result of the activation of the receptor kinase via ligand-independent dimerization. Transformation was correlated with tyrosine phosphorylation of only a subset of the proteins observed in cells overexpressing the normal EGF receptor. This suggested that further studies on cells expressing the EGFRvIII might provide insights into the pathways most relevant to transformation. In clones expressing high levels of mutant EGF receptor, the levels of both Grb2 and SHC were decreased. Despite this decrease, much of the endogenous Grb2 immunoprecipitated with EGFRvIII. Interestingly, no increase in ras-GTP loading was found in clones expressing the EGFRvIII and MAP kinase assays indicated only a small increase in activity. These results indicate that high-level expression of the EGFRvIII induces down-regulation of the ras-MAP kinase pathway and that other components involved in EGF receptor signal transduction may play a greater role in neoplastic transformation by the EGFRvIII.
Recent progress in the immunological monitoring of carcinomas using monoclonal antibodies (1985)

In efforts to improve the specificity and sensitivity of tests to monitor patients with carcinoma, monoclonal antibody technology has been widely embraced by the scientific community. Results clearly indicate that novel antigen determinants have been identified and that significant improvements have been realized for the study of "classical" tumor antigens previously detected with polyclonal reagents. The concept of tumor specificity has also been amenable to an increased level of objectivity as based upon the probelike characteristic of monoclonal antibodies. It is apparent from this work that an antigen does not have to be tumor specific to be useful as a marker.
Variability of the Glycoprotein G Gene in Clinical Isolates of Herpes Simplex Virus Type 1 (1999)

Glycoprotein G (gG) of herpes simplex virus type 1 (HSV-1) has been used as a prototype antigen for HSV-1 type-specific serodiagnosis, but data on the sequence variability of the gene coding for this protein in wild-type strains are lacking. In this study, direct DNA sequencing of the gG-1 genes from PCR products was performed with clinical HSV-1 isolates from 11 subjects as well as with strains Syn 17(+), F, and KOS 321. The reference strains Syn 17(+) and F showed a high degree of conservation, while KOS 321 carried 13 missense mutations and, in addition, 12 silent mutations. Three clinical isolates showed mutations leading to amino acid alterations: one had a mutation of K(122) to N, which is a gG-1-to-gG-2 alteration; another contained all mutations which were observed in KOS 321 except two silent mutations; and the third isolate carried five missense mutations. Two clinical isolates as well as strain KOS 321 showed a mutation (F(111)-->V) within the epitope of a gG-1-reactive monoclonal antibody (MAb). When all viruses were tested for reactivity with the anti-gG-1 MAb, the three strains with the F(111)-->V mutation were found to be unreactive. Furthermore, gG-1 antibodies purified from sera from the two patients carrying strains mutated in this epitope were less reactive when they were tested by an HSV-1-infected-cell assay. Therefore, our finding that the sequence variability of the gG-1 gene also affects B-cell epitope regions of this protein in clinical isolates may have consequences for the use of this protein as a type-specific antigen for serodiagnosis.
Origami fabrication of nanostructured, three-dimensional devices: Electrochemical capacitors with carbon electrodes (2006)

The Nanostructured Origami™ process consists of patterning a two-dimensional (2-D) membrane with desired micro- and nanoscale features and then folding it into a three-dimensional (3-D) configuration. Electrochemical capacitors, or supercapacitors, are ideal for origami fabrication because their performance can be enhanced through the use of 3-D geometry and nanostructured materials. A supercapacitor with an electrode area of 350×350μm was created using the origami process and characterized using electrochemical analysis methods. The experimentally measured capacitance values of approximately 1μF are consistent with theoretical predictions.
3D simulation of the aqueous flow in the human eye (2012)

Glaucoma results in an increase in the resistance of the aqueous humor outflow, which in turn leads to an increase of the intraocular pressure (IOP). Several treatments are proposed to reduce and stabilize the IOP that include medications, filtering surgery and glaucoma drainage devices (GDD). So far computational fluid dynamics (CFD) modeling of the eye drainage system has not yet been well studied. Therefore our goal was to provide a 3D CFD model of the eye based on the anatomy of a real human eye. Such a tool would serve for future evaluation of new glaucoma surgical techniques involving, for example, GDD. The model was based on stacks of microphotographs from human eye slides from which digital processing of the images of the eye structure and 3D reconstruction of the model were performed. Simulations of the distribution of pressure and flow velocity in the model of a healthy eye gave results comparable to physiology references. Mimicking glaucoma conditions led to an increase of the IOP from normal range, which went down to lower values after a filtering procedure. Further refinements in the boundary conditions for the filtering procedure shall improve the accuracy of this innovative tool for modeling glaucoma surgery.
Clonal proliferation of murine lymphohemopoietic progenitors in culture. (1992)

We have used a two-step clonal culture system to unequivocally demonstrate that individual primitive lymphohemopoietic progenitor cells have the capacity for differentiation along either the myeloid or the B-lymphoid lineage. Highly enriched murine marrow cells were plated individually in culture by micromanipulation in the presence of pokeweed mitogen-stimulated spleen cell conditioned medium, erythropoietin, steel factor (SF), and interleukin (IL) 7. Forty-five percent of the single cells formed primary colonies expressing multiple hemopoietic lineages. When aliquots from individual colonies were replated in secondary methyl cellulose culture containing SF and IL-7, 41% of the primary colonies gave rise to lymphocyte colonies. Cells of the lymphocyte colonies were blast-like and B220+, sIg-, Mac-1-, Gr-1-, Ly-1-, L3T4-, Ly-2-, and CD3-. Thirty to 70% of the cells were Thy-1+. mu-chain mRNA was detected in most of the cells by in situ hybridization with an antisense RNA probe. When lymphocyte colonies derived from a single cell were pooled and individually injected into scid mice, donor-type IgM was measurable in the serum of mice and spleens contained donor-type B cells. We then carried out initial screening of growth factors to identify growth factors that might replace pokeweed mitogen-stimulated spleen cell conditioned medium in the primary culture. Combinations of two factors that included SF plus IL-6, IL-11, or granulocyte colony-stimulating factor were all effective in the primary culture in the maintenance of the B-lymphoid potential. Interestingly, IL-3 could neither replace nor act synergistically with SF to support the lymphoid potential of the primary cultures. Our observations demonstrate that many primitive progenitors previously believed to be myeloid-committed also possess B-lymphoid potential. This culture system should prove valuable for elucidation of the mechanisms regulating early stages of lymphohemopoiesis.
Biomarkers of Tissue Injury (2008)

Biomarkers of tissue injury have evolved empirically over the last 50-100 years. With the advent of immunoassays and discovery tools such as RNA expression and proteomics, more systematic approaches to the discovery of biomarkers can be expected in the future. This review discusses the evolution of biomarkers of muscle, liver, heart and brain injury and illustrates that a modern discovery tool, such as mRNA profiling, would have predicted the biomarkers for cardiac injury (heart attacks) that actually evolved over 50 years by empiric approaches. We also discuss how novel biomarkers for brain injury were identified using RNA expression approaches. It is our prediction that there will be a growth in the number of valuable biomarkers for identifying cell and organ injury in the next 5-10 years.
Combining frequency and spatial domain information for fast interactive image noise removal (1996)

Article Free Access Share on Combining frequency and spatial domain information for fast interactive image noise removal Authors: Anil N. Hirani Sony Corporation, Research Center, Sony Corporation, 6-7-35 Kitashinagawa Shinagawa-ku, Tokyo 141, Japan Sony Corporation, Research Center, Sony Corporation, 6-7-35 Kitashinagawa Shinagawa-ku, Tokyo 141, JapanView Profile , Takashi Totsuka Sony Corporation, Research Center, Sony Corporation, 6-7-35 Kitashinagawa Shinagawa-ku, Tokyo 141, Japan Sony Corporation, Research Center, Sony Corporation, 6-7-35 Kitashinagawa Shinagawa-ku, Tokyo 141, JapanView Profile Authors Info & Claims SIGGRAPH '96: Proceedings of the 23rd annual conference on Computer graphics and interactive techniquesAugust 1996 Pages 269–276https://doi.org/10.1145/237170.237264Online:01 August 1996Publication History 55citation1,306DownloadsMetricsTotal Citations55Total Downloads1,306Last 12 Months31Last 6 weeks11 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Game theory, on-line prediction and boosting (1996)

We study the close connections between game theory, on-line prediction and boosting. After a brief review of game theory, we describe an algorithm for learning to play repeated games based on the on-line prediction methods of Littlestone and Warmuth. The analysis of this algorithm yields a simple proof of von Neumann's famous minmax theorem, as well as a provable method of approximately solving a game. We then show that the on-line prediction model is obtained by applying this gameplaying algorithm to an appropriate choice of game and that boosting is obtained by applying the same algorithm to the "dual" of this game.