gebhart/patrepeval huggingface dataset:
AGIPD, a high dynamic range fast detector for the European XFEL (2015)

AGIPD-(Adaptive Gain Integrating Pixel Detector) is a hybrid pixel X-ray detector developed by a collaboration between Deutsches Elektronen-Synchrotron (DESY), Paul-Scherrer-Institut (PSI), University of Hamburg and the University of Bonn. The detector is designed to comply with the requirements of the European XFEL. The radiation tolerant Application Specific Integrated Circuit (ASIC) is designed with the following highlights: high dynamic range, spanning from single photon sensitivity up to 10<sup>4</sup> 12.5keV photons, achieved by the use of the dynamic gain switching technique using 3 possible gains of the charge sensitive preamplifier. In order to store the image data, the ASIC incorporates 352 analog memory cells per pixel, allowing also to store 3 voltage levels corresponding to the selected gain. It is operated in random-access mode at 4.5MHz frame rate. The data acquisition is done during the 99.4ms between the bunch trains. The AGIPD has a pixel area of 200×200 <em>μ</em>m<sup>2</sup> and a 500<em>μ</em>m thick silicon sensor is used. The architecture principles were proven in different experiments and the ASIC characterization was done with a series of development prototypes. The mechanical concept was developed in the close contact with the XFEL beamline scientists and is now being manufactured. A first single module system was successfully tested at APS.
Flicker (2013)

Future microprocessors may become so power constrained that not all transistors will be able to be powered on at once. These systems will be required to nimbly adapt to changes in the chip power that is allocated to general-purpose cores and to specialized accelerators.
Novel bimodular DNA aptamers with guanosine quadruplexes inhibit phylogenetically diverse HIV-1 reverse transcriptases (2008)

DNA aptamers RT5, RT6 and RT47 form a group of related sequences that inhibit HIV-1 reverse transcriptase (RT). The essential inhibitory structure is identified here as bimodular, with a 5' stem-loop module physically connected to a 3'-guanosine quadruplex module. The stem-loop tolerates considerable sequence plasticity. Connections between the guanosine triplets in the quadruplex could be simplified to a single nucleotide or a nonnucleic acid linker, such as hexaethylene glycol. All 12 quadruplex guanosines are required in an aptamer retaining most of the original loop sequence from RT6; only 11 are required for aptamer R1T (single T residue in intra-quadruplex loops). Circular dichroism (CD) spectroscopy gave ellipticity minima and maxima at 240 nm and 264 nm, indicating a parallel arrangement of the quadruplex strands. The simplified aptamers displayed increased overall stability. An aptamer carrying the original intra-quadruplex loops from RT6 inhibited RT in K(+) buffers but not in Na(+) buffers and displayed significant CD spectral broadening in Na(+) buffers, while R1T inhibited RT in both buffers and displayed less broadening in Na(+) buffers. The bimodular ssDNA aptamers inhibited RT from diverse primate lentiviruses with low nM IC(50) values. These data provide insight into the requirements for broad-spectrum RT inhibition by nucleic acid aptamers.
An Adult Stem Cell Proliferation Assay in the Flatworm Model <i>Macrostomum lignano</i> to Predict the Carcinogenicity of Compounds (2015)

Flatworms possess adult pluripotent stem cells whose dynamics can easily be experimentally assessed in vivo. This feature provides the unique opportunity to be used in a pharmacological context to test the safety of chemicals. The objective of this study was to develop and assess the applicability of an alternative in vivo test with a low-level organism where stem cell proliferation is used as an endpoint to predict the carcinogenicity of chemicals. As a start, to obtain proof of concept with this new test model, we tested 4 known carcinogens (2 DNA-reactive and 2 non-DNA-reactive) and 2 noncarcinogens as negative controls. We evaluated our carcinogenicity prediction model and advocate for its future use in pharmacological safety screenings.
ChemInform Abstract: Selective Thromboxane Synthetase Inhibitors. Part 1. 1‐[(Aryloxy)alkyl]‐1H‐ imidazoles. (1986)

Abstract Ether wie (III) und (IV) werden dargestellt und auf Inhibierung von TxAz‐Synthetase, PGIZ‐Synthetase, Cyclooxygenase und Steroid‐1 lß‐Hydroxylase untersucht.
Prediction of a pure-carbon planar covalent metal (1996)

Carbon is well-known as an insulator, a semimetal, a molecular solid, and a one-dimensional semiconductor or low-density-of-states metal. We propose a pure-carbon planar structure composed of pentagons and heptagons that is metallic with a density of states at the Fermi level of \ensuremath{\sim}0.1 state per eV per atom. This structure, planar carbon pentaheptite, is metastable with a total energy per carbon atom comparable to that of ${\mathrm{C}}_{60}$. The structure can be rolled into tubes in a manner similar to graphite. Possible synthetic pathways are discussed.
Method and device for controlling a synchronous motor with permanent magnet (Procédé et dispositif de commande d'un moteur synchrone à aimant permanent) (1997)

NOVELTY - For control mono-phase or multiphase machines in motor or generating mode with or without pulse width modulation. USE - Control of electrical rotating machines. ADVANTAGE - Can be used for control of single phase and three phase machines. DETAILED DESCRIPTION - The method for control of a permanent magnet synchronous motor (10) from a supply source (11) without direct sensing, having at least a phase, a winding, and a rotor. The supply to each phase of the motor is controlled. The output signals from the voltage measured at each phase is sampled at variable frequency and the control of the supply to each phase is determined from the sampled signals. The control device uses a converter (12), a bridge network (13) which supplies the motor winding, a winding supply control unit, a measuring circuit (14) for the voltage at each phase, and a control unit (15). The control unit is composed of a microprocessor (16) and a comparator (17) which compares the instantaneous value of the total motor current to a reference value. The controller also has a sensor (18) which determines the real position of the rotor as a function of the induced voltage due to rotor displacement. All the components are contained on a printed circuit board.. DESCRIPTION OF DRAWING(S) - The drawing a schematic of the system motor (10) supply source (11) convertor (12) bridge network (13) measuring circuit (14) control unit (15) micro-processor (16) comparator (17) sensor (18)
Cross-phase modulation resonances in wavelength-division-multiplexed lightwave transmission (2002)

We have observed cross-phase-modulation-impairment resonances in wavelength-division-multiplexed lightwave transmission. The resonances occur in a system with equal amplifier span lengths when channels have an integral number of bit walk-throughs per amplifier span. In a five-channel experiment over 8/spl times/80 km of standard single-mode fiber at 2.5 Gb/s with +7 dBm/channel, Q measurements predict on-resonance error rates several orders of magnitude higher than off-resonance error rates.
Pharmacokinetics of a fusion inhibitor of the hepatitis B virus (2006)

1911 Objectives: Chronic infection with the human hepatitis B virus (HBV) is still a major health problem to the world’s population today. Interference with HBV infection by externally applied fragments of viral surface proteins that interfere with receptor interaction or membrane fusion might allow the development of novel antiviral strategies that interfere with the hepadnaviral entry process, as gp-41-derived T 20-peptides in HIV-therapy. Proteins that interfere with the fusion of the virus might be used as diagnostic tracers for viral diseases. Methods: We have recently demonstrated that peptides encompassing the 47 terminal amino acids of the N-terminal part of a major envelope protein block HBV infection of primary human hepatocytes with surprising efficacy, at already picomolar concentrations, probably by sustained inactivation of a receptor on hepatocytes (Gripon P, Cannie I, Urban S. Efficient inhibition of hepatitis B virus infection by acylated peptidesderived from the large viral surface protein. J Virol. 2005; 79: 1613-22). The biodistribution of the I-125-labelled peptide was determined in RAG-2 mice bearing hepatocytes susceptible to infection with HBV. The stability of the peptide was determined in human serum. Results: A tyrosine bearing derivative of the peptide Myr-GQNLSTSNPLGFFPDHQLDPAFRANTANPDWDFNPNKDWTPDANKVG-COOH was obtained by Fmoc solid phase synthesis. The peptide was labelled with 125-I using the Chloramine-T method. No significant increase of the I-125-labelled peptide was determined in mice bearing infection susceptible hepatocytes at 1 h post injection. The peptide was cleared by the kidneys that were the major sites of accumulation. However, a high concentration (5.1 %ID/g at 1 h post injection) was found in the blood. The biological half live of the peptide was > 60 h in human serum. Conclusions: Using the labelled lipopeptide we investigated the organ distribution with respect to a specific targeting to the transplanted hepatocytes, as well as the peptide stability in serum. At the levels determined, this preclinical study did not reveal a targeting of the hepatocytes. However, the peptide is circulating in the blood at concentration that is high enough to prevent infections with the virus. It can be speculated that the peptide is protected against degradation due to an association via its lipophilic end to serum proteins. Consequently, the peptide is a promising candidate for future clinical applications, e.g. prevention of HBV reinfection after liver transplantation.
Ultrasound Imaging of Peyronie’s Plaques (1981)

We herein present the results of our successful attempts to depict and to measure the plaques of Peyronie’s disease with an ultrasound technique. The potential use of this technique also is discussed.
Design of polarization beam splitter based on coupled rods in a square-lattice photonic crystal (2013)

In this paper, we design a polarization splitter by combining a photonic crystal waveguide and internal polarization-selective rods leading to a spatial separation of two orthogonal polarizations for mid-infrared applications. The performance of the splitter is investigated by tuning the length of the polarization-selection rods or defect rods for both the polarization extinction ratio (PER) and degree of polarization (DoP). At optimized parameter of the selective rods, the DoP obtained a high value as 1 and the PER obtained a higher value greater than 30 dB for both TE- and TM-polarized lights.
Methoxyethylamino-numonafide Is an Efficacious and Minimally Toxic Amonafide Derivative in Murine Models of Human Cancer (2011)

Amonafide is a DNA intercalator in clinical development for the treatment of cancer. The drug has a 5-position amine that is variably acetylated to form a toxic metabolite in humans, increasing adverse effects and complicating the dosing of amonafide. Numonafides, 6-amino derivatives of amonafide that avoid the toxic acetylation, also show in vitro anticancer activity, as we have previously described. Here, we report the in vitro and in vivo activities of two numonafides, 6-methoxyethylamino-numonafide (MEAN) and 6-amino-numonafide (AN) with comparisons to amonafide. The in vitro potencies and cellular anticancer mechanisms are similar for the two numonafides and amonafide. Results from several mouse models of human cancer demonstrate that AN and MEAN require slightly higher doses than amonafide for equal efficacy in short-term dosing models, but the same dose of all three compounds in long-term dosing models are equally efficacious. MEAN is tolerated much better than amonafide and AN at equally efficacious doses based on weight change, activity, stool consistency, and dose tolerance with survival as the end point. The studies presented here demonstrate that MEAN is much less toxic than amonafide or AN in mouse models of human liver and gastric cancers while being equally efficacious in vivo and inhibiting cancer cells through similar mechanisms. These findings demonstrate that numonafides can be less toxic than amonafide and support further preclinical development and novel anticancer agents or as replacements or amonafide.
Identification and Manipulation of Antigen Specific T-Cells with Artificial Antigen Presenting Cells (2007)

T-cells specific for a particular antigen represent a small percentage of the overall T-cell population. Detecting the presence of antigen specific T-cells in patients, animal models or populations of cultured cells has presented a challenge to researchers. The T-cell capture method described here utilizes a truly artificial method of antigen presentation and requires only 50,000 cells for the detection of the major histomcompatibility complex (MHC) class II and antigen restricted T-cells. With this method, liposomes, prepared with readily available materials, are loaded with neutravidin "rafts" comprised of MHC/peptide complexes, anti-CD28, a costimulatory molecule, and anti-LFA-1, an adhesion molecule. These artificial APCs are easily manipulated to include any MHC, antibodies to cell surface markers and/or costimulatory signals of interest thereby enabling not only T-cell identification but also the manipulation of mechanisms of T-cell activation.
Modification and <i>de novo</i> design of non-ribosomal peptide synthetases (NRPS) using specific assembly points within condensation domains (2018)

Abstract Many important natural products are produced by non-ribosomal peptide synthetases (NRPSs) 1 .These giant enzyme machines activate amino acids in an assembly line fashion in which a set of catalytically active domains is responsible for the section, activation, covalent binding and connection of a specific amino acid to the growing peptide chain 1,2 . Since NRPS are not restricted to the incorporation of the 20 proteinogenic amino acids, their efficient manipulation would give access to a diverse range of peptides available biotechnologically. Here we describe a new fusion point inside condensation (C) domains of NRPSs that enables the efficient production of peptides, even containing non-natural amino acids, in yields higher than 280 mg/L. The technology called eXchange Unit 2.0 (XU 2.0 ) also allows the generation of targeted peptide libraries and therefore might be suitable for the future identification of bioactive peptide derivatives for pharmaceutical and other applications.
Physically Based Shape Matching (2022)

Abstract The shape matching method is a popular approach to simulate deformable objects in interactive applications due to its stability and simplicity. An important feature is that there is no need for a mesh since the method works on arbitrary local groups within a set of particles. A major drawback of shape matching is the fact that it is geometrically motivated and not derived from physical principles which makes calibration difficult. The fact that the method does not conserve volume can yield visual artifacts, e.g. when a tire is compressed but does not bulge. In this paper we present a new meshless simulation method that is related to shape matching but derived from continuous constitutive models. Volume conservation and stiffness can be specified with physical parameters. Further, if the elements of a tetrahedral mesh are used as groups, our method perfectly reproduces FEM based simulations.
Abstract 2990: Notch1 monoclonal antibody inhibits tumor growth and modulates angiogenesis (2014)

Abstract AVEO Oncology has developed a series of inducible mouse models of cancer, which through the preservation of critical tumor/stromal interactions, facilitate identification of cell-surface and secreted proteins that represent viable targets for therapeutic antibodies and other biologics. Functional genetic screens performed in vivo in these models identified the Notch pathway as a critical regulator of tumor maintenance. This finding was consistent with emerging evidence that activation of Notch signaling via receptor point mutation, receptor amplification, and elevated receptor and ligand expression, plays a key role in various human cancers. Moreover, the Notch pathway controls diverse aspects of tumorigenesis and tumor maintenance, regulating tumor autonomous processes and interactions with the microenvironment, including angiogenesis. To further understand the role of the Notch pathway in tumor maintenance, and to assess the therapeutic potential of targeting the Notch pathway in cancer, we have generated monoclonal antibodies that inhibit the Notch1 receptor. Characterization of monoclonal antibodies targeting Notch1 through cell-based and biochemical studies demonstrated that the Notch1 monoclonal antibody bound with high affinity and high specificity to the Notch1 receptor, prevented ligand-mediated activation of the target receptor, and specifically repressed Notch-dependent signaling with high potency. Significantly, specific inhibition by the Notch1 monoclonal antibody did not result in the dose-limiting gut toxicity observed with Notch1 mAb resulted in tumor inhibition that was accompanied by increased vascular density, inhibition of Notch target gene expression, and increased expression of angiogenesis-related genes, consistent with expected changes resulting from Notch1/Dll4 pathway inhibition. In addition, several tumor models treated in combination with Notch1 mAb and an investigational VEGF pathway inhibitor, tivozanib, demonstrated increased tumor inhibition compared to either agent alone. Interestingly, combination treatment resulted in decreased vascular density and downregulated expression of angiogenesis genes, similar to treatment with VEGF inhibitor alone. Collectively, our work suggests that combination therapy of Notch1 antibodies with VEGF inhibitors should be evaluated as a potential viable therapeutic option for VEGF-resistant tumors. Citation Format: Heidi Okamura, Theresa Proia, Alisa Bell, Qing Liu, Zakir Siddiquee, Jie Lin, Jeno Gyuris. Notch1 monoclonal antibody inhibits tumor growth and modulates angiogenesis. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2990. doi:10.1158/1538-7445.AM2014-2990
Improving cytotoxicity against cancer cells by chemo-photodynamic combined modalities using silver-graphene quantum dots nanocomposites (2015)

The combination of chemotherapy and photodynamic therapy has emerged as a promising strategy for cancer therapy due to its synergistic effects. In this work, PEGylated silver nanoparticles decorated with graphene quantum dots (Ag-GQDs) were tested as a platform to deliver a chemotherapy drug and a photosensitizer, simultaneously, in chemo-photodynamic therapy against HeLa and DU145 cancer cells in vitro. Ag-GQDs have displayed high efficiency in delivering doxorubicin as a model chemotherapy drug to both cancer cells. The Ag-GQDs exhibited a strong antitumor activity by inducing apoptosis in cancer cells without affecting the viability of normal cells. Moreover, the Ag-GQDs exhibited a cytotoxic effect due to the generation of the reactive singlet oxygen upon 425 nm irradiation, indicating their applicability in photodynamic therapy. In comparison with chemo or photodynamic treatment alone, the combined treatment of Ag-GQDs conjugated with doxorubicin under irradiation with a 425 nm lamp significantly increased the death in DU145 and HeLa. This study suggests Ag-GQDs as a multifunctional and efficient therapeutic system for chemo-photodynamic modalities in cancer therapy.
HIGH-RATE CATHODIC ARC DEP'OSITION* (1998)

Vacuum deposition of thin films on large area substrates has enjoyed a steady growth during the last years. This development is strongly coupled to the continuous improvement of PVDl techniques like magnetron or evaporation. Using the traditional thermal evaporation, highest rates can be achieved at the lowest costs, but there are a lot of potential applications which would need an improved quality of the films (nanocrystalline instead of columnar growth, higher density, no pin-holes, etc.). There are several new developments directed onto a (moderate) increase of the activation of the thermal vapor. Vacuum arc evaporation, as characterized for the highest degree of ionization between the industrial deposition sources, will be used in different concepts to realize an activated high rate deposition, suitable for industrial large area coating. A shiort revue of arc based activated deposition technologies will be given in the paper. Advantages and problems of combinations (thermal evaporation together with a dc- or pulsed arc source) activated sources (activation of the neutral vapor by additional arc discharge) and new sources (electron beams sustained high current arc: ,,spotless arc, anodic arc) are discussed in relation of their possible applications. Large area coating is a very complex problem with many aspects such as deposition rate, investment costs, technology reliability, safety demands and film properties. For each technological process the activation must be adapted to the specific demands and conditions.
The Elongin B Ubiquitin Homology Domain (1999)

Mammalian Elongin B is a 118-amino acid protein composed of an 84-amino acid amino-terminal ubiquitin-like domain and a 34-amino acid carboxyl-terminal tail. Elongin B is found in cells as a subunit of the heterodimeric Elongin BC complex, which was originally identified as a positive regulator of RNA polymerase II elongation factor Elongin A and subsequently as a component of the multiprotein von Hippel-Lindau tumor suppressor and suppressor of cytokine signaling complexes. As part of our effort to understand how the Elongin BC complex regulates the activity of Elongin A, we are characterizing Elongin B functional domains. In this report, we show that the Elongin B ubiquitin-like domain is necessary and sufficient for interaction with Elongin C and for positive regulation of Elongin A transcriptional activity. In addition, by site-directed mutagenesis of the Elongin B ubiquitin-like domain, we identify a short Elongin B region that is important for its interaction with Elongin C. Finally, we observe that both the ubiquitin-like domain and carboxyl-terminal tail are conserved in Drosophila melanogaster and Caenorhabditis elegans Elongin B homologs that efficiently substitute for mammalian Elongin B in reconstitution of the transcriptionally active Elongin ABC complex, suggesting that the carboxyl-terminal tail performs an additional function not detected in our assays.
An efficient architecture for energy recovery in hydraulic elevators (2015)

This study introduces an efficient architecture for hydraulically counter-weighting an elevator system while controlling for cab speed. A physical model of the architecture is developed and posed as a single-input single-output system in which the ratio of two hydraulic pump/motor swash plate angles serve as the control input for regulating the output cab speed. Heuristic control rules based on efficiency considerations and elevator operation are posed for the swash plate angles. A high-fidelity simulation tool is then employed to assess the new architecture and control approach. Simulations demonstrate the effectiveness of the devised control strategy and the overall satisfactory operation of the elevator system. Simulations also provide comparisons of the new architecture’s efficiency vs. an electrohydraulic elevator architecture employing a motor/generator for energy capture and return. It’s shown that the introduced architecture yields up to a 13% increase in actuation efficiency over the electrohydraulic system, and up to a 23% reduction in input energy over a day’s operation. It is anticipated that the gains in energy efficiency, and the reduced complexity and cost (vs. electrohydraulic systems), make the new architecture attractive for continued exploration.