gebhart/patrepeval huggingface dataset:
Space-based detection of spoofing AIS signals using Doppler frequency (2014)

The Automatic Identification System (AIS) is a self-reporting system based on VHF radio to transmit a vessel’s identity, position, speed, heading and other parameters to improve maritime domain awareness. However, AIS information can be programmatically spoofed by terrorists or other criminals, who often choose to masquerade as innocent civilians and exploit the vulnerabilities of military and civilian infrastructures for their purposes. Therefore, detecting and localizing a spoofing AIS ship become a critical and challenging issue for maritime security. This paper presents an algorithm to detect and geolocalize a spoofing AIS emitter using space-based AIS signals with its Doppler frequency. With an AIS signal sensor on a fast orbiting satellite, the measured AIS Doppler frequency of an AIS emitter can be used to define a double-napped cone of which the satellite is at its vertex and satellite velocity coincides with its axis, such that the theoretical Doppler frequency derived from the radial velocity to the AIS emitter matches the measured Doppler frequency. All such matches can only lie on either cone extending out from the satellite, which cuts the Earth’s surface in two curves, so we know that the AIS emitter must lie somewhere on these curves. Two such AIS Doppler frequency measurements for the same stationary AIS emitter produce two valid curves which intersect at the position of the AIS emitter. Multiple Doppler frequency measurements can be used to better estimate the position fix of an AIS emitter, hence determine the spoofing AIS ship if the estimated position fix unreasonably differs from the position carried in its AIS message. A set of formulas are derived which relate an AIS emitter position to its Doppler frequency measurements.
Suppression of Stomatal Opening in Leaves Treated with Abscisic Acid (1970)

Small doses of abscisic acid (approximately 0.02 μg cm-2 of leaf) applied to the leaf surface as a 10-4 M solution caused marked stomatal closure in Xanthium pennsylvanicum, and the effect persisted for up to 9 days after application. Similar effects were found when 10-4 M abscisic acid was supplied to detached tobacco leaves via their petioles. CO2-free air did not cause a reversal of the closure, and it was therefore concluded that the effect was not due simply to an increase in the intercellular CO2concentration; a more direct effect on the stomatal apparatus is suggested. It is considered that abscisic acid could play an endogenous role in the control of stomatal aperture, and that this, and/or related substances, might be more useful as ‘anti-transpirants’ than the phytotoxic substances currently employed for this purpose.
Prostaglandin E<sub>2</sub>deficiency uncovers a dominant role for thromboxane A<sub>2</sub>in house dust mite-induced allergic pulmonary inflammation (2012)

Prostaglandin E(2) (PGE(2)) is an abundant lipid inflammatory mediator with potent but incompletely understood anti-inflammatory actions in the lung. Deficient PGE(2) generation in the lung predisposes to airway hyperresponsiveness and aspirin intolerance in asthmatic individuals. PGE(2)-deficient ptges(-/-) mice develop exaggerated pulmonary eosinophilia and pulmonary arteriolar smooth-muscle hyperplasia compared with PGE(2)-sufficient controls when challenged intranasally with a house dust mite extract. We now demonstrate that both pulmonary eosinophilia and vascular remodeling in the setting of PGE(2) deficiency depend on thromboxane A(2) and signaling through the T prostanoid (TP) receptor. Deletion of TP receptors from ptges(-/-) mice reduces inflammation, vascular remodeling, cytokine generation, and airway reactivity to wild-type levels, with contributions from TP receptors localized to both hematopoietic cells and tissue. TP receptor signaling ex vivo is controlled heterologously by E prostanoid (EP)(1) and EP(2) receptor-dependent signaling pathways coupling to protein kinases C and A, respectively. TP-dependent up-regulation of intracellular adhesion molecule-1 expression is essential for the effects of PGE(2) deficiency. Thus, PGE(2) controls the strength of TP receptor signaling as a major bronchoprotective mechanism, carrying implications for the pathobiology and therapy of asthma.
Representability of algebraic topology for biomolecules in machine learning based scoring and virtual screening (2018)

This work introduces a number of algebraic topology approaches, including multi-component persistent homology, multi-level persistent homology, and electrostatic persistence for the representation, characterization, and description of small molecules and biomolecular complexes. In contrast to the conventional persistent homology, multi-component persistent homology retains critical chemical and biological information during the topological simplification of biomolecular geometric complexity. Multi-level persistent homology enables a tailored topological description of inter- and/or intra-molecular interactions of interest. Electrostatic persistence incorporates partial charge information into topological invariants. These topological methods are paired with Wasserstein distance to characterize similarities between molecules and are further integrated with a variety of machine learning algorithms, including k-nearest neighbors, ensemble of trees, and deep convolutional neural networks, to manifest their descriptive and predictive powers for protein-ligand binding analysis and virtual screening of small molecules. Extensive numerical experiments involving 4,414 protein-ligand complexes from the PDBBind database and 128,374 ligand-target and decoy-target pairs in the DUD database are performed to test respectively the scoring power and the discriminatory power of the proposed topological learning strategies. It is demonstrated that the present topological learning outperforms other existing methods in protein-ligand binding affinity prediction and ligand-decoy discrimination.
Ionizing Energy Depositions After Fast Neutron Interactions in Silicon (2016)

In this study we present the ionizing energy depositions in a 300 μm thick silicon layer after fast neutron impact. With the Time-of-Flight (ToF) technique, the ionizing energy deposition spectra of recoil silicons and secondary charged particles were assigned to (quasi-)monoenergetic neutron energies in the range from 180 keV to hundreds of MeV. We show and interpret representative measured energy spectra. By separating the ionizing energy losses of the recoil silicon from energy depositions by products of nuclear reactions, the competition of ionizing (IEL) and non-ionizing energy losses (NIEL) of a recoil silicon within the silicon lattice was investigated. The data give supplementary information to the results of a previous measurement and are compared with different theoretical predictions.
Tribenzo [b.e.h] [1.4.7] trioxacyclononatrien und Tetrabenzo [b.e.h.k] [1.4.7.10] tetroxacyclododecatetraen / Tribenzo [b,e,h] [1,4,7] trioxonin and Tetrabenzo [b,e,h,k] [1,4,7,10] tetroxadodecin (1974)

The syntheses of the oligomeric o-phenyleneoxides tribenzo [b, e, h] [ 1, 4, 7] trioxonin and tetrabenzo [b, e, h,k] [ 1, 4, 7, 10] tetroxadodecin are described.
High resolution optical fiber-integrated resonant biosensors (2004)

Optical sensors based on resonating periodic waveguides are presented. Spectral shifts of 6.4nm are measured as protein chemically binds to a sensor surface. Measured transmission notches agree with theory for a double-layer fibertip device.
Variants of human chorionic gonadotropin from pregnant women and tumor patients recognized by monoclonal antibodies (1993)

In biological fluids, hCG and its free alpha- (hCG alpha) and beta-subunits (hCG beta), occur in multiple forms. These various forms differ at the molecular level primarily in glycosylation, but also differ in protein backbone modifications corresponding to the urinary low molecular weight fragment of the hCG beta-subunit (beta-core fragment). This microheterogeneous nature can be demonstrated by isoelectric focusing in which variants are separated into bands with different isoelectric points (pI). To determine whether such isoelectric variants differ in antigenicity and consequently might escape immunoassay detection due to overspecificity of monoclonal antibodies (MCA), urinary pregnancy hCG (NIH, CR123) and tumor hCG preparations, such as a tumor-specific acidic variant of hCG (hCGav) and the hCG beta-core fragment, were separated by isoelectric focusing in the absence or presence of 8 M urea, or by sodium docedyl sulfate-polyacrylamide gel electrophoresis and enzymatically immunostained using an MCA panel directed against 17 different hCG epitopes. MCA against 14 different epitopes accessible on holo-hCG recognized all pI variants of pregnancy holo-hCG or tumor-derived hCGav, as was true for the three MCA recognizing epitopes hidden on holo-hCG but accessible on the free subunits after hCG dissociation by urea. We conclude that each individual pI-isoform of holo-hCG and its free subunits expresses the entire set of epitopes recognized by our MCA panel. The carbohydrate moieties that form a biochemical basis for hCG heterogeneity seem to be neither of major antigenic relevance, nor are they structurally related to any particular epitope. Thus, various glycosylation forms of hCG, hCG alpha, hCG beta, and hCG beta-core in normal as well as in pathological samples should safely be detectable and measureable by immunoassays employing MCA with appropriate subunit specificity.
Electronic health records and communication for better health care : Proceedings of EuroRec '01 (2002)

The annual EuroRec Working Conference has become the traditional gathering for all the partners involved on the scene of Electronic Health Records (EHRs). While the existence of relevant technical specifications is acknowledged as of utmost importance, ahead or beyond the technical concern lie key issues that are of cultural, economic, ethical, and political nature. Questions include Which incentives, which business model, which solutions are available for communicating EHRs in hospital and ambulatory care? These key questions have been the thread for s series of specific workshops that have been taken place over the two conference days, each one addressing a specific topic: does the use of EHRs reveal a cultural gap?; an ethical concern; an economic concern; a political concern and a technical concern.
Visualization of In Vivo Olfactory Uptake and Transfer Using Fluorescein Dextran (2002)

Nasal administration of a 3 kDa fluorescein dextran (FD3) solution to rats resulted in transcellular absorption across the olfactory epithelium and transfer to the olfactory bulb within 15 min. After entering the lamina propria, FD3 was transferred in the connective tissue surrounding the olfactory nerve bundles to the olfactory bulb of the brain. More FD3 was absorbed across the olfactory epithelium than across the respiratory epithelium and to the nasal associated lymphoid tissue. Further, the amount of FD3 crossing the olfactory epithelium was region-dependent, with higher amounts absorbed in the turbinates than in the nasal septum. Plastic embedding and sectioning followed by fluorescence microscopy, enabled simultaneous visualization of FD3 in the mucosa and olfactory bulb, as well as the opportunity to store the tissue blocks for a prolonged period of time.
Activation of p53 in cervical carcinoma cells by small molecules (2000)

In over 90% of cervical cancers and cancer-derived cell lines, the p53 tumor suppressor pathway is disrupted by human papillomavirus (HPV). The HPV E6 protein promotes the degradation of p53 and thus inhibits the stabilization and activation of p53 that would normally occur in response to HPV E7 oncogene expression. Restoration of p53 function in these cells by blocking this pathway should promote a selective therapeutic affect. Here we show that treatment with the small molecule nuclear export inhibitor, leptomycin B, and actinomycin D leads to the accumulation of transcriptionally active p53 in the nucleus of HeLa, CaSki, and SiHa cells. Northern blot analyses showed that both actinomycin D and leptomycin B reduced the amount of HPV E6-E7 mRNA whereas combined treatment with the drugs showed almost complete disappearance of the viral mRNA. The combined treatment activated p53-dependant transcription, and increases in both p21(WAF1/CIP1) and Hdm2 mRNA were seen. The combined treatment resulted in apoptotic death in the cells, as evidenced by nuclear fragmentation and PARP-cleavage indicative of caspase 3 activity. These effects were greatly reduced by expressing a dominant negative p53 protein. The present study shows that small molecules can reactivate p53 in cervical carcinoma cells, and this reactivation is associated with an extensive biological response, including the induction of the apoptotic death of the cells.
Long-Lived Near-Infrared MLCT Emitters (2001)

A series of near-infrared emitters based on metal-to-ligand charge transfer (MLCT) excited states has been prepared. In the series, systematic variation of the coordinated ligands in polypyridyl complexes of RuII and OsII are used to vary the excited-to-ground-state energy gap. Emission energies are shifted by a combination of electron donor ligands and ligands with low-energy π* acceptor orbitals. Excited-state lifetimes are enhanced by use of acceptor ligands which are rigid and extensively delocalized. Emission from [(Ru(bpy)2)2(dpop)]4+ in acetonitrile is illustrated, along with a spectrum calculated by using a standard Franck−Condon analysis of the spectral profile.
Cannabidiol Reduces Intestinal Inflammation through the Control of Neuroimmune Axis (2011)

Enteric glial cells (EGC) actively mediate acute and chronic inflammation in the gut; EGC proliferate and release neurotrophins, growth factors, and pro-inflammatory cytokines which, in turn, may amplify the immune response, representing a very important link between the nervous and immune systems in the intestine. Cannabidiol (CBD) is an interesting compound because of its ability to control reactive gliosis in the CNS, without any unwanted psychotropic effects. Therefore the rationale of our study was to investigate the effect of CBD on intestinal biopsies from patients with ulcerative colitis (UC) and from intestinal segments of mice with LPS-induced intestinal inflammation. CBD markedly counteracted reactive enteric gliosis in LPS-mice trough the massive reduction of astroglial signalling neurotrophin S100B. Histological, biochemical and immunohistochemical data demonstrated that S100B decrease was associated with a considerable decrease in mast cell and macrophages in the intestine of LPS-treated mice after CBD treatment. Moreover the treatment of LPS-mice with CBD reduced TNF-α expression and the presence of cleaved caspase-3. Similar results were obtained in ex vivo cultured human derived colonic biopsies. In biopsies of UC patients, both during active inflammation and in remission stimulated with LPS+INF-γ, an increased glial cell activation and intestinal damage were evidenced. CBD reduced the expression of S100B and iNOS proteins in the human biopsies confirming its well documented effect in septic mice. The activity of CBD is, at least partly, mediated via the selective PPAR-gamma receptor pathway. CBD targets enteric reactive gliosis, counteracts the inflammatory environment induced by LPS in mice and in human colonic cultures derived from UC patients. These actions lead to a reduction of intestinal damage mediated by PPARgamma receptor pathway. Our results therefore indicate that CBD indeed unravels a new therapeutic strategy to treat inflammatory bowel diseases.
Fluoropolymer-Based Flexible Neural Prosthetic Electrodes for Reliable Neural Interfacing (2017)

We covalently bound fluoropolymer (FP) films by plasma treatment followed by thermal pressing at temperatures below their melting point and fabricated an adhesion-metal-free flexible gold electrode array entirely encapsulated by the FP film, excepting the active electrode openings. The fabricated device was chemically resistant and was modified to have a lower impedance and efficient charge injection capability. The fabricated device was evaluated in vivo in rats and was confirmed to record the epidural epileptiform activity induced by chemical administration. The chemically inert nature of FPs and the gold electrode is expected to facilitate reliable neural interfacing without abiotic issues. Plasma treatment-induced covalent binding of FP films can also be utilized in a variety of applications requiring durability, such as implantable biosensors and sensor platforms operating under chemically harsh environments, including humid conditions.
Selecting industrial research projects (1968)

INDUSTRIAL research covers a wide spectrum of research activity, from fundamental research through applied research to development work. Fundamental research in industry is the counterpart of pure research elsewhere: it is the search for new knowledge in scientific fields which are relevant to an organization's short‐ or long‐term objectives. In fundamental research one cannot predict beforehand what each project will achieve and relate this to the organization's objectives. The research workers should choose individual projects within a particular field on their scientific merits. The effectiveness of fundamental research depends on selecting the fields in which to carry it out and on the ability of the research workers to make discoveries. Fundamental research in industry aims to provide a flow of discoveries and new ideas that may, after applied research and development, produce technology that the organization can exploit to promote its objectives.
Thiazolidinediones for the prevention of diabetes in the non‐obese diabetic (NOD) mouse: implications for human type 1 diabetes (2002)

RGL reduces diabetes incidence in the NOD mouse model of type 1 diabetes. This may be an effect resulting from its action as on inhibitor of pro-inflammatory genes such as cytokines and metabolic proteases. Its use may be considered for trials designed to protect beta-cell function in humans, especially in patients with latent autoimmune diabetes of adults (LADA) and also for disease prevention.
The Chemistry of Curcumin: From Extraction to Therapeutic Agent (2014)

Curcumin, a pigment from turmeric, is one of the very few promising natural products that has been extensively investigated by researchers from both the biological and chemical point of view. While there are several reviews on the biological and pharmacological effects of curcumin, chemistry reviews are comparatively scarcer. In this article, an overview of different aspects of the unique chemistry research on curcumin will be discussed. These include methods for the extraction from turmeric, laboratory synthesis methods, chemical and photochemical degradation and the chemistry behind its metabolism. Additionally other chemical reactions that have biological relevance like nucleophilic addition reactions, and metal chelation will be discussed. Recent advances in the preparation of new curcumin nanoconjugates with metal and metal oxide nanoparticles will also be mentioned. Directions for future investigations to be undertaken in the chemistry of curcumin have also been suggested.
A GENERALIZED RHEOLOGICAL MODEL FOR INELASTIC FLUID FOODS1 (1987)

A versatile four‐parameter model is presented for the rheological characterization of inelastic fluid foods. The model has been shown to accurately represent shear stress versus shear rate, and apparent viscosity versus shear rate relationships for several food materials. By appropriate specification of the four parameters of the model, conventional rheological models used in fluid food analyses (power law, Bingham plastic, Herschel‐Bulkley, Casson, Heinz‐Casson, and Mizrahi‐Berk) can be obtained from the generalized equation.
Wavelength demultiplexing optical switch (1992)

A novel wavelength demultiplexing optical switch (WDMOS) with completely optical input/output capabilities is demonstrated. The WDMOS input elements can be applied to optical logic circuits in which discrete wavelengths are utilized as an added dimension to the intensity levels of the optical signals. The WDMOS can be viewed as a resonant cavity-enhanced heterojunction phototransistor vertically integrated with a quantum well light emitting diode. The resulting device is an N-p-n-p optical switch situated in an optical cavity which serves to combine the wavelength selective spectral response of the optical cavity with the bistable switching characteristics of the N-p-n-p structure.
69. Combination Therapy of Reovirus and PD-1 Blockade Effectively Establishes Tumor Control Via Innate and Adaptive Immune Responses (2015)

Combination therapy of Reovirus and PD-1 blockade effectively establishes tumor control via innate and adaptive immune responses Karishma Rajani1, Christopher Parrish2, Kevin Shim1, Liz Ilett2, Jill Thompson1, Tim Kottke1, Jose Pulido1, Fiona Errington-Mais2, Peter Selby2, Hardev Pandha3, Kevin Harrington4, Alan Melcher2, Rosa Maria Diaz1, Shane Zaidi1,4 Matt Coffey5, and Richard Vile1,2,6 Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, USA. 2Leeds Institute of Cancer and Pathology, St. James University Hospital, Leeds, UK. 3University of Surrey, Guildford, UK. 4. The Institute of Cancer Research, 237 Fulham Road, London, SW3.5Oncolytics Biotech Inc., Calgary, Canada. 6Department of Immunology, Mayo Clinic, Rochester, Minnesota, USA. Reovirus has oncolytic activity against many human/murine tumor cells, partly because of disruption of the PKR-mediated anti-viral response in malignant cells. We have shown that anti-tumor therapy is directly associated with immune activation by virus replication in tumors. The immune mechanisms of therapy include both innate immune activation against virally infected tumor cells, as well as the generation of adaptive anti tumor immune responses as a result of in vivo priming against tumor associated antigens released during that killing. To exploit the immune components of reovirus anti-tumor therapy, we hypothesized that the combination of reovirus therapy with systemic checkpoint inhibition would augment therapeutic efficacy. To establish this, subcutaneous (SC) B16 melanomas were treated with reovirus alone or in combination with antibody against PD-1. In this model, intra-tumoral (IT) injection of reovirus into SC tumors generated moderate therapy. Systemic treatment of anti-PD-1 antibody along with IT reovirus, significantly enhanced survival compared to IT reovirus alone (p < 0.01) and led to > 40% of mice being cured long term. Immune analysis suggested that the enhanced therapeutic benefit of reovirus plus checkpoint inhibition is contributed by at least two factors. First, blockade of PD-1 significantly enhanced the ability of NK cells to recognize (TNF-α secretion), and kill, reovirus-infected tumor cells. Second, anti PD-1 antibody led to a significant reduction in Treg activity in reovirus-treated mice, with the overall effect of increasing the adaptive CD8+ anti-tumor T cell response. In vivo depletion studies demonstrated that NK cells had a dramatic effect in reducing the therapeutic efficacy of reovirus plus anti-PD-1 therapy. These results indicate that combination therapy of reovirus with PD-1 blockade confers significant survival benefit, by augmenting tumor-specific NK responses and attenuating tumor-specific immunosuppression and is a viable treatment modality with far greater efficacy than either therapy alone.