gebhart/patrepeval huggingface dataset:
Solution structure of an arabinonucleic acid (ANA)/RNA duplex in a chimeric hairpin: comparison with 2'-fluoro-ANA/RNA and DNA/RNA hybrids (2001)

Hybrids of RNA and arabinonucleic acid (ANA) as well as the 2'-fluoro-ANA analog (2'F-ANA) were recently shown to be substrates of the enzyme RNase H. Although RNase H binds to double-stranded RNA, no cleavage occurs with such duplexes. Therefore, knowledge of the structure of ANA/RNA hybrids may prove helpful in the design of future antisense oligonucleotide analogs. In this study, we have determined the NMR solution structures of ANA/RNA and DNA/RNA hairpin duplexes and compared them to the recently published structure of a 2'F-ANA/RNA hairpin duplex. We demonstrate here that the sugars of RNA nucleotides of the ANA/RNA hairpin stem adopt the C3'-endo (north, A-form) conformation, whereas those of the ANA strand adopt a 'rigid' O4'-endo (east) sugar pucker. The DNA strand of the DNA/RNA hairpin stem is flexible, but the average DNA/RNA hairpin structural parameters are close to the ANA/RNA and 2'F-ANA/RNA hairpin parameters. The minor groove width of ANA/RNA, 2'F-ANA/RNA and DNA/RNA helices is 9.0 +/- 0.5 A, a value that is intermediate between that of A- and B-form duplexes. These results rationalize the ability of ANA/RNA and 2'F-ANA/RNA hybrids to elicit RNase H activity.
Liquid crystal polarization independent beam steering switches for operation at 1.5 microns (2002)

The rapidly evolving demands of telecommunications systems have created a new market for high capacity all-optical photonic switches. Holographic optical switching may offer a scalable and reliable approach to realizing such systems. The advantages and technical challenges associated with this technology will be discussed, with reference to two prototype demonstrators recently produced under the auspices of the ROSES project. The first is a single beam deflector operating as a 1/spl times/8 switch and the second is a 3/spl times/3 optical switch which demonstrates the principle of crossbar operation.
Separation of musical sources and structure from single-channel polyphonic recordings (2006)

The thesis deals principally with the separation of pitched sources from singlechannel polyphonic musical recordings. The aim is to extract from a mixture a set of pitched instruments or sources, where each source contains a set of similarly sounding events or notes, and each note is seen as comprising partial, transient and noise content. The work also has implications for separating nonpitched or percussive sounds from recordings, and in general, for unsupervised clustering of a list of detected audio events in a recording into a meaningful set of source classes. The alignment of a symbolic score/MIDI representation with the recording constitutes a pre-processing stage. The three main areas of contribution are: firstly, the design of harmonic tracking algorithms and spectralfiltering techniques for removing harmonics from the mixture, where particular attention has been paid to the case of harmonics which are overlapping in frequency. Secondly, some studies will be presented for separating transient attacks from recordings, both when they are distinguishable from and when they are overlapping in time with other transients. This section also includes a method which proposes that the behaviours of the harmonic and noise components of a note are partially correlated. This is used to share the noise component of a mixture of pitched notes between the interfering sources. Thirdly, unsupervised clustering has been applied to the task of grouping a set of separated notes from the recording into sources, where notes belonging to the same source ideally have similar features or attributes. Issues relating to feature computation, feature selection, dimensionality and dependence on a symbolic music representation are explored. Applications of this work exist in audio spatialisation, audio restoration, music content description, effects processing and elsewhere.
Enhanced Exposure of the CD4-Binding Site to Neutralizing Antibodies by Structural Design of a Membrane-Anchored Human Immunodeficiency Virus Type 1 gp120 Domain (2009)

The broadly neutralizing antibody immunoglobulin G1 (IgG1) b12 binds to a conformationally conserved surface on the outer domain of the human immunodeficiency virus type 1 (HIV-1) gp120 envelope (Env) glycoprotein. To develop outer domain proteins (ODs) that could be recognized selectively by CD4-binding-site (CD4-BS) antibodies, membrane-anchored ODs were generated from an HIV-1 clade B virus, TA1 R3A, which was highly sensitive to neutralization by the IgG1 b12 antibody. A 231-residue fragment of gp120 (residues 252 to 482) linked to transmembrane regions from CD4 showed b12 binding comparable to that of the native Env spike as measured by flow cytometry. Truncation of the beta 20-beta 21 hairpin (residues 422 to 436 to Gly-Gly) improved overall protein expression. Replacement of the immunodominant central 20 amino acids of the V3 loop (residues 302 to 323) with a basic hexapeptide (NTRGRR) increased b12 reactivity further. Surface calculations indicated that the ratio of b12 epitope to exposed immunogenic surface in the optimized OD increased to over 30%. This OD variant [OD(GSL)(Deltabeta 20-21)(hCD4-TM)] was recognized by b12 and another CD4-BS-reactive antibody, b13, but not by eight other CD4-BS antibodies with limited neutralization potency. Furthermore, optimized membrane-anchored OD selectively absorbed neutralizing activity from complex antisera and b12. Structurally designed membrane-anchored ODs represent candidate immunogens to elicit or to allow the detection of broadly neutralizing antibodies to the conserved site of CD4 binding on HIV-1 gp120.
Modulation of Nitric Oxide Production in Human Macrophages by Apolipoprotein-E and Amyloid-Beta Peptide (1997)

Induction of oxidative stress has been implicated as a causative factor in chronic neurodegenerative diseases such as Alzheimer's disease. Apolipoprotein-E (apoE) and amyloid-beta peptide (A beta) have been reported to alter the redox state of the brain. Using human monocyte-derived macrophages as a model of brain microglia, physiological levels of apolipoprotein-E were found to stimulate nitric oxide (NO) production in polyinosinic:polycytidylic acid (poly I:C) primed cells. ApoE treatment released 68% more NO than cells treated with poly I:C alone and almost threefold more NO than unprimed cells. In contrast to mouse microglia, human cells failed to generate NO in response to A beta peptides, with or without poly I:C treatments. Furthermore, the combination of A beta plus apoE inhibited the increase in NO production induced by apoE. Since Alzheimer's is strongly associated with the presence of an APOE4 allele, our study predicts a mechanism where apoE and A beta regulate nitric oxide production in human brain.
Design of a Martian Autonomous Rotary-Wing Vehicle (2003)

The design of a Martian autonomous rotary wing vehicle (MARV) is described. MARV is a 50-kg gross takeoff mass, coaxial helicopter designed for Mars exploration. Powered by a fuel cell system, it carries a payload of 10.8 kg over a range of 25 km with an endurance of 39 min including hover capability for 1 min. MARV is designed in response to the Request For Proposal from NASA/Sikorsky for the Year 2000 American Helicopter Society student design competition. The design covers aerodynamic and structural design of rotor blades, vehicle power plant, fuselage and landing gear, control system, transmission, and vehicle lander communications. A detailed mechanism for autonomous deployment of the vehicle from the lander is also described. This preliminary design study indicates that controlled vertical flight on Mars is feasible with existing technology
The ornithine decarboxylase gene is a transcriptional target of c-Myc. (1993)

Constitutive c-myc expression suppresses cell cycle arrest, promotes entry into S phase, and results in the growth factor-independent expression of ornithine decarboxylase (ODC; EC 4.1.1.17). The ODC gene contains a conserved repeat of the Myc binding site, CACGTG, in intron 1. In this report, we demonstrate that c-Myc is a potent transactivator of ODC promoter-reporter gene constructs in fibroblasts that requires the CACGTG repeat. These sites conferred Myc responsiveness on heterologous promoter constructs, suggesting that ODC is regulated by Myc at the level of transcription initiation. Analysis of deletion and point mutants of c-myc revealed that domains required for transactivation of the ODC promoter did not include the leucine zipper of the Myc protein. This suggests that Myc may interact with transcription factors other than Max to transactivate the ODC gene.
Pyruvate kinase type M2 is phosphorylated at tyrosine residues in cells transformed by Rous sarcoma virus (1988)

Chicken embryo cells (CECs) contain pyruvate kinase (PK) type M2 (M2-PK). Transformation of CECs by Rous sarcoma virus (RSV) leads to a reduction in the affinity of PK for the substrate phosphoenolpyruvate. In vitro, M2-PK can be phosphorylated at tyrosine residues by pp60v-src, the transforming protein of RSV. To study tyrosine phosphorylation of M2-PK in intact RSV-transformed cells, the protein was immunoprecipitated from 32P-labeled normal and RSV-SR-A-transformed CECs. Phosphoamino acid analysis of immunoprecipitated M2-PK revealed that M2-PK of both normal and transformed CECs contained phosphoserine and small amounts of phosphothreonine. Only M2-PK of transformed CECs contained phosphotyrosine in addition. For enzyme kinetic studies M2-PK was partially purified by chromatography upon DEAE-Sephacel and hydroxyapatite. A decreased affinity for phosphoenolpyruvate was observed 3 h after the onset of transformation using the temperature-sensitive mutant of RSV, ts-NY 68. The kinetic changes were correlated with tyrosine phosphorylation of M2-PK, but there is no direct evidence that they are caused by post-translational modification of the enzyme.
Tumorigenic conversion of a non‐tumorigenic rat urothelial cell line by overexpression of H2O2‐generating peroxisomal fatty acyl‐CoA oxidase (1997)

Hydrogen peroxide (H2O2) and some cytokines that are released during the inflammatory process are important factors for the development of unirary bladder carcinoma and for its growth. Sustained induction of H2O2-generating peroxisomal fatty acyl-CoA oxidase (ACOX) in the liver of rats and mice by non-genotoxic peroxisome proliferators leads to the development of liver tumors. To examine the role of intracelluar H2O2 generated by ACOX during urinary bladder carcinogenesis, we overexpressed rat ACOX in a non-tumorigenic rat urothelial cell line, MYP3, under the control of the cytomegalovirus promoter. The clones overexpressing rat ACOX, when exposed to a fatty-acid substrate (150 μM linoleic acid), demonstrated strikingly higher levels of intracellular H2O2 (p > 0.001) and formed colonies in soft agar in proportion to the duration of exposure to linoleic acid. Furthermore, all the transformants, which were selected at random from soft agar, demonstrated an accelerated growth potential on a plastic surface, as well as tumorigenicity in athymic nude mice. In addition, the growth of these transformants was stimulated by cytokines, interleukin-6 and tumor necrosis factor-α, better than the growth of ACOX-overex pressing, but non-transformed cells or that of the parental cells. Our results clearly demonstrate that H2O2 induced by ACOX acts as a carcinogen on urothelial cells, and that transformed cells have acquired an advantage for growth over nonneoplastic cells because of their selective response to the stimulatory action of several cytokines. Int. J. Cander 70:716–721, 1997. © Wiley-Liss, Inc.
Efficient Bayesian inference methods via convex optimization and optimal transport (2013)

In this paper, we consider many problems in Bayesian inference - from drawing samples to posteriors, to calculating confidence intervals, to implementing posterior matching algorithms, by finding maps that push one distribution to another. We show that for a large class of problems (with log-concave likelihoods and log-concave priors), these problems can be efficiently solved using convex optimization. We provide example applications within the context of dynamic statistical signal processing.
Decreased Plakophilin-1 Expression Promotes Increased Motility in Head and Neck Squamous Cell Carcinoma Cells (2007)

Desmosomes are prominent cell-cell adhesive junctions found in a variety of epithelial tissues, including the oral epithelium. The transmembrane core of the desmosome is composed of the desmosomal cadherins that interact extracellularly to mediate cell-cell adhesion. The cytoplasmic domain of desmosomal cadherins interact with plaque proteins that in turn interact with the keratin intermediate filament cytoskeleton. Plakophilin 1 is a major desmosomal plaque component that functions to recruit intermediate filaments to sites of cell-cell contact via interactions with desmoplakin. Decreased assembly of desmosomes has been reported in several epithelial cancers. We examined plakophilin-1 expression in an esophageal squamous cell carcinoma tissue microarray and found that plakophilin-1 expression inversely correlates with tumor grade. In addition, we sought to investigate the effect of plakophilin-1 expression on desmosome assembly and cell motility in oral squamous cell carcinoma cell lines. Cell lines expressing altered levels of plakophilin-1 were generated and the ability of these cells to recruit desmoplakin to sites of cell-cell contact was examined. Our results show that decreased expression of plakophilin-1 results in decreased desmosome assembly and increased cell motility and invasion. These data lead us to propose that loss of plakophilin-1 expression during head and neck squamous cell carcinoma (HNSCC) progression may contribute to an invasive phenotype.
Suppression of parasitic bipolar action in ultra-thin-film fully-depleted CMOS/SIMOX devices by Ar-ion implantation into source/drain regions (1998)

This paper proposes a new technique that can effectively suppress the parasitic bipolar action (PBA) in ultrathin-film fully-depleted (FD)nMOSFET's/SIMOX with a floating body. In this technique, recombination centers are created in the source and drain (S/D) regions by deep Ar-ion implantation. They act to reduce the number of holes that accumulate in the body region by increasing the hole current flowing from the body region into the source region. Consequently, the rise of the body potential is lowered, and the parasitic bipolar action can be suppressed. A 0.25-/spl mu/m gate nMOSFET/SIMOX fabricated with an Ar dose of 2/spl times/10/sup 14/ cm/sup -2/ exhibited excellent improvements in electrical characteristics: a reduction in the off-leakage current of over two orders of magnitude and an increase in the drain-to-source breakdown voltage beyond 0.6 V.
Polynucleotide phosphorylase functions both as a 3′ → 5′ exonuclease and a poly(A) polymerase in Escherichia coli (2000)

In vitro, polynucleotide phosphorylase of Escherichia coli can both synthesize RNA by using nucleotide diphosphates as precursors and exonucleolytically degrade RNA in the presence of inorganic phosphate. However, because of the high in vivo concentration of inorganic phosphate in exponentially growing cells, it has been assumed that the enzyme works exclusively as an exonuclease. Here we demonstrate that, contrary to this prediction, polynucleotide phosphorylase not only synthesizes long, highly heteropolymeric tails in vivo, but also accounts for all of the observed residual polyadenylylation in poly(A) polymerase I deficient strains. In addition, the enzyme is responsible for adding the C and U residues that are found in poly(A) tails in exponentially growing cultures of wild type E. coli.
Motion recovery for video content classification (1995)

Like other types of digital information, video sequences must be classified based on the semantics of their contents. A more-precise and completer extraction of semantic information will result in a more-effective classification. The most-discernible difference between still images and moving pictures stems from movements and variations. Thus, to go from the realm of still-image repositories to video databases, we must be able to deal with motion. Particularly, we need the ability to classify objects appearing in a video sequence based on their characteristics and features such as shape or color, as well as their movements. By describing the movements that we derive from the process of motion analysis, we introduce a dual hierarchy consisting of spatial and temporal parts for video sequence representation. This gives us the flexibility to examine arbitrary sequences of frames at various levels of abstraction and to retrieve the associated temporal information (say, object trajectories) in addition to the spatial representation. Our algorithm for motion detection uses the motion compensation component of the MPEG video-encoding scheme and then computes trajectories for objects of interest. The specification of a language for retrieval of video based on the spatial as well as motion characteristics is presented.
Native HIV-1 Tat Protein Targets Monocyte-Derived Dendritic Cells and Enhances Their Maturation, Function, and Antigen-Specific T Cell Responses (2002)

Vaccination of cynomolgus monkeys with the biologically active HIV-1 Tat protein induces specific Th1 responses, including CTLs. Similar responses are also induced by vaccination with tat DNA, but not by vaccination with inactivated Tat or Tat peptides. This suggested that the native Tat protein may act differently on APC as compared with inactivated Tat or peptide Ag. In this study, we show that biologically active Tat is very efficiently taken up by monocyte-derived dendritic cells (MDDC) in a time (within minutes)- and dose-dependent (starting from 0.1 ng/ml) fashion, whereas uptake is very poor or absent with other APC, including T cell blasts and B lymphoblastoid cell lines. Although maturation of MDDC reduces their pino/phagocytic activity, mature MDDC take up Tat much more efficiently than immature cells. In addition, Tat uptake is abolished or greatly hampered by oxidation/inactivation of the protein or by performing the experiments at 4 degrees C, suggesting that MDDC take up native Tat by a receptor-mediated endocytosis. After uptake, active Tat protein induces up-regulation of MHC and costimulatory molecules and production of IL-12, TNF-alpha, and beta chemokines, which drive Th1-type immune response. In contrast, these effects are lost by oxidation and inactivation of the protein. Finally, native Tat enhances Ag presentation by MDDC, increasing Ag-specific T cell responses. These data indicate that native Tat selectively targets MDDC, is taken up by these cells via specialized pathways, and promotes their maturation and Ag-presenting functions, driving Th1-type immune responses. Thus, Tat can act as both Ag and adjuvant, capable of driving T cell-mediated immune responses.
Adrenergic neurohumoral influences on FFA release from bone marrow adipose tissue. (1985)

It is well known that both the sympathetic nervous system and several hormones control adipose tissue lipolysis. However, the relative importance of these different lipolytic agents may vary according to the animal species and according to the adipose territories in a same species. The action of noradrenaline administration on tibial intraosseous lipolysis was compared with the effects of splanchnic nerve and lumbar sympathetic chain stimulation in chloralose-anaesthetized dogs. The osseous nutrient artery was infused through the homolateral femoral artery in order to check constant blood flow. The levels of free fatty acids (FFA) were compared in femoral artery blood and in the osseous nutrient vein. Noradrenaline was injected in the infusion line. Lumbar sympathetic chain and splanchnic nerve were stimulated at frequencies of 3-10 Hz and 5-10 Hz respectively. Noradrenaline (at 411 p mol/min i.e. a dose three times higher than that required for adrenaline) induced FFA mobilization from tibial adipose bone marrow. Splanchnic nerve stimulation elicited an increase in the FFA levels in the nutrient vein whereas lumbar sympathetic chain stimulation had no remained without any effect. It is concluded that circulating adrenaline seems more important than noradrenaline released by sympathetic nerve endings in the control of activity of tibial bone marrow adipocytes.
Search for Hsp90 Inhibitors with Potential Anticancer Activity:  Isolation and SAR Studies of Radicicol and Monocillin I from Two Plant-Associated Fungi of the Sonoran Desert (2006)

In an effort to discover small molecule inhibitors of Hsp90, we have screened over 500 EtOAc extracts of Sonoran desert plant-associated fungi using a two-stage strategy consisting of a primary cell-based heat shock induction assay (HSIA) followed by a secondary biochemical luciferase refolding assay (LRA). Bioassay-guided fractionation of extracts active in these assays derived from Chaetomium chiversii and Paraphaeosphaeria quadriseptata furnished the Hsp90 inhibitors radicicol (1) and monocillin I (2), respectively. In SAR studies, 1, 2, and their analogues, 3-16, were evaluated in these assays, and the antiproliferative activity of compounds active in both assays was determined using the breast cancer cell line MCF-7. Radicicol and monocillin I were also evaluated in a solid-phase competition assay for their ability to bind Hsp90 and to deplete cellular levels of two known Hsp90 client proteins with relevance to breast cancer, estrogen receptor (ER), and the type 1 insulin-like growth factor receptor (IGF-1R). Some inferences on SAR were made considering the crystal structure of the N-terminus of yeast Hsp90 bound to 1 and the observed biological activities of 1-16. Isolation of radicicol and monocillin I in this study provides evidence that we have developed an effective strategy for discovering natural product-based Hsp90 inhibitors with potential anticancer activity.
Renegotiation in Finitely Repeated Games (1993)

Perfect equilibria of finitely repeated games may be vulnerable to the possibility of renegotiation among players. We study the limiting properties of the set of payoffs from equilibria that are immune to renegotiation. Our main result is that the limit of the set of payoffs from renegotiation proof equilibria is either a singleton or a connected subset of the Pareto efficient frontier. A simple sufficient condition for the latter to occur is also provided.
<title>Secure communications using quantum cryptography</title> (1997)

The secure distribution of the secret random bit sequences known as `key' material, is an essential precursor to their use for the encryption and decryption of confidential communications. Quantum cryptography is an emerging technology for secure key distribution with single-photon transmissions: Heisenburg's uncertainty principle ensures that an adversary can neither successfully tap the key transmissions, nor evade detection (eavesdropping raises the key error rate above a threshold value). We have developed experimental quantum cryptography systems based on the transmission of non-orthogonal single-photon states to generate shared key material over multi-kilometer optical fiber paths and over line-of-sight links. In both cases, key material is built up using the transmission of a single- photon per bit of an initial secret random sequence. A quantum-mechanically random subset of this sequence is identified, becoming the key material after a data reconciliation stage with the sender. In our optical fiber experiment we have performed quantum key distribution over 24-km of underground optical fiber using single-photon interference states, demonstrating that secure, real-time key generation over `open' multi-km node-to-node optical fiber communications links is possible.