gebhart/patrepeval huggingface dataset:
Enzymatically-Active ADAMTS13 Variants Are Not Inhibited by Anti-ADAMTS13 Autoantibodies - A Potential Novel Therapeutic Strategy. (2005)

Abstract ADAMTS13, a reprolysin-type zinc metalloprotease consisting of a metalloprotease (MP), a disintegrin, a thrombospondin-1 (TSP), a cysteine-rich region (Cys), a spacer, seven additional TSP, and two CUB domains, is critical for preventing unwarranted VWF-platelet interaction in the circulation. Profound deficiency of ADAMTS13, due to genetic mutations of the ADAMTS13 gene or autoimmune inhibitors of the protease, causes microvascular thrombosis characteristic of TTP. Plasma exchange is a conventional but complex therapy of TTP that may be ineffective for patients with high inhibitor titers. In this study we produce recombinant ADAMTS13 variant proteins and analyze their binding with and suppression by TTP inhibitors. TTP IgG binds the ADAMTS13 variants ending downstream of the spacer domain but not those truncated upstream, consistent with recent reports that the spacer domain is essential for interaction between TTP IgG and ADAMTS13. Nevertheless, the spacer domain sequence alone may be insufficient since TTP IgG does not bind a fragment consisting solely of the spacer domain sequence but binds a fragment encompassing the sequence between the distal 2/3 of the MP and the spacer. ADAMTS13 ending at the TSP#1 or downstream are proteolytically active in cleaving either VWF multimers or a 73-amino acid fragment of the VWF A2 domain. Mixing studies show that each of ten TTP plasma samples tested suppresses the protease activity of ADAMTS13 ending downstream of the spacer domain, but not the activity of the variants truncated at the TSP#1 or Cys domain. The variant proteins truncated at TSP#1, when added to a series of plasma samples from a TTP patient with rising inhibitor titers, consistently yield the expected protease activity levels, even in those samples whose high inhibitor titers abolish the activity of the full-length ADAMTS13 at 15x of its concentration. These findings indiate that it is feasible to design ADAMTS13 variant proteins that are proteolytically active yet refractory to suppression by inhibitors of TTP. Such ADAMTS13 variants may be exploited to circumvent the inhibitors of TTP, potentially eliminating the need of performing plasma exchanges in the future.
ChemInform Abstract: Triply Convergent Synthesis of (‐)‐Prostaglandin E2 Methyl Ester. (1988)

Abstract Starting from cyclopentadiene (I), a six‐step procedure involving asymmetric semihydrolysis of the meso‐diacetate (V) leads to the optically active enone (+)‐(VII).
An electric double-layer capacitor with high capacitance and low resistance (1992)

The development of the electric double-layer capacitor with ultra-high capacitance and extremely low DC resistance is described. The capacitance ranges from 1 to 500 F and the DC resistance is less than one fifth of that of the conventional capacitor with organic electrolytes. The capacitor consists of an activated carbon layer on aluminum foil collector electrodes, a separator, and an organic electrolyte. Details of the electrical characteristics and reliability of the capacitors are presented. Several features of activated carbon electrodes and the mechanism for the improvement of the DC resistance are discussed. Some examples of the potential application of the capacitor for high current load uses are also discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
SEM-contour shape analysis method for advanced semiconductor devices (2013)

The new measuring method that we developed executes a contour shape analysis that is based on the pattern edge information from a SEM image. This analysis helps to create a highly precise quantification of every circuit pattern shape by comparing the contour extracted from the SEM image using a CD measurement algorithm and the ideal circuit pattern. The developed method, in the next phase, can generate four shape indices by using the analysis mass measurement data. When the shape index measured using the developed method is compared the CD, the difference of the shape index and the CD is negligibly small for the quantification of the circuit pattern shape. In addition, when the 2D patterns on a FEM wafer are measured using the developed method, the tendency for shape deformations is precisely caught by the four shape indices. This new method and the evaluation results will be presented in detail in this paper.
Practical nanoscale field emission devices for integrated circuits (2017)

Nanoscale field emission devices promise many advantages over traditional solid-state devices including fast switching speeds, extreme operating temperatures, and radiation hardness. Despite this, practical circuits have long been hampered by the extreme requirements of nanoscale field emitters. Devices have required vacuum packaging, or extremely sharp emission points that are difficult to reproduce, or cannot be integrated on a single wafer with independent gating. We demonstrate CMOS compatible, integratable two- and three-terminal devices operating at near atmospheric pressures with high single tip currents at low voltages that can be used as building blocks for future circuits.
Shape memory effect related to thin plate martensite with large thermal hysteresis in ausaged Fe-Ni-Co-Ti alloy. (1989)

Behavior of martensitic transformation and shape memory effect in an Fe–31%Ni–10%Co–3% alloy were studied. The specimen which was ausaged at 873 K for 3.6 ks produces a thin plate martensite (Ms=193 K) with a large thermal hysteresis (i.e., As – Ms=150 K, Af – Ms=315 K). Despite the large thermal hysteresis, the forward and reverse transformations of thin plate martensite occur by a reversible movement of interface in the same manner as thermoelastic martensite. The ausaged specimen which is fully austenitic at room temperature shows a complete shape memory effect when the specimen is heated up above Af after the deformation at temperatures near or below Ms. The ausaged specimen hardly exhibits the shape memory effect when deformed at room temperature. However, when the ausaged specimen is once subzero cooled to liquid nitrogen to produce a large amount of martensite (about 70%), the almost complete shape memory effect occurs even by the deformation at room temperature. Furthermore, the subzero cooled specimen shows the partial shape memory effect when the specimen is cooled below Ms after the deformation at temperature around As. The deformation mode of specimen at various temperatures was investigated by microstructural observations and the origin of the shape memory effect in the present alloy was discussed.
Analog gradient beamformer for a wireless ultrasound scanner (2016)

This paper presents a novel beamformer architecture for a low-cost receiver front-end, and investigates if the image quality can be maintained. The system is oriented to the development of a hand-held wireless ultrasound probe based on Synthetic Aperture Sequential Beamforming, and has the advantage of effectively reducing circuit complexity and power dissipation. The array of transducers is divided into sub-apertures, in which the signals from the single channels are aligned through a network of cascaded gradient delays, and summed in the analog domain before A/D conversion. The delay values are quantized to simplify the shifting unit, and a single A/D converter is needed for each sub-aperture yielding a compact, low-power architecture that can be integrated in a single chip. A simulation study was performed using a 3:75MHz convex array, and the point spread function (PSF) for different configurations was evaluated in terms of lateral full-width-at-half-maximum (FWHM) and −20 dB cystic resolution (CR). Several setups were simulated varying the sub-aperture size <i>N</i> and the quantization step, and design constraints were obtained comparing the PSF to that of an ideal non-quantized system. The PSF is shown for <i>N</i> = 32 with a quantization step of 12 ns. For this configuration, the FWHM is degraded by 0.25% and the CR is 8.70% lower compared to the ideal situation. The results demonstrate that the gradient beamformer provides an adequate image quality, and open the way to a fully-integrated chip for a compact, low-cost, wireless ultrasound probe.
New Efficient Organic Scintillators Derived from Pyrazoline (2016)

We report on the synthesis, spectroscopic and scintillation properties of three new pyrazoline core based fluorophores. Fluorescence properties of the fluorophores have been studied both in a solution state and in a solid polyvinyltoluene (PVT) resin matrix of different porosity. The synthesized fluorophores were found to be promising candidates for application in plastic scintillators for detection of ionizing radiation (alpha, beta particles, γ rays and neutrons) and demonstrated superior efficiency in comparison to the existing commercially used fluorophores (2-(1-naphthyl)-5-phenyloxazole (αNPO), 9,10-diphenylanthracene, etc.). Moreover, the suggested synthetic route allows functionalization of the fluorophores with a vinyl group for further covalent bound to the PVT or other vinyl polymer matrices, which dramatically improves chemical stability of the system simultaneously improving the photoluminescence quantum yield. Possible mechanisms of the enhanced scintillation properties are discussed based on preliminary quantum mechanical calculations and spectroscopic characteristics of the fluorophores under study.
Practical, Stereoselective Synthesis of Palinavir, a Potent HIV Protease Inhibitor (1997)

Palinavir is a potent peptidomimetic-based HIV protease inhibitor. We have developed a highly convergent and stereoselective synthesis which is amenable to the preparation of multikilogram quantities of this compound. The synthetic sequence proceeds in 24 distinct chemical steps (with several integrated, multistep operations) from commercially available starting materials. No chromatographies are required throughout the process, and the final product is purified by crystallization of its dihydrochloride salt to >99% homogeneity.
Hepatitis B virus as an insertional mutagene in a human hepatocellular carcinoma. (1990)

Chronic hepatitis B virus (HBV) infection is etiologically related to human hepatocellular carcinoma (HCC). Most HCCs contain integrated HBV DNA in the liver cellular DNA, suggesting that the integration may be involved in carcinogenesis. From a comparison of a single HBV integration site present in a hepatoma with the corresponding unoccupied site in the non-tumourous tissue of the same liver, we have shown that HBV DNA inserted in a putative cellular exon with striking similarity to the DNA-binding domain of the thyroid/steroid hormone receptors. The corresponding cDNA has been isolated (hap gene) and shown to encode the retinoic acid receptor. In the original patient, integration took place so that the first codons of the viral surface protein gene became fused in frame with most of the hap gene. Because retinoic acid is known to regulate the transcription of target genes crucial for cellular growth and differentiation, it is most probable that consequent to the HBV insertion, hap, usually transcribed at a very low level in normal hepatocytes, became inappropriately expressed as an altered chimaeric retinoic acid receptor, thus contributing to the cell transformation. These results strongly support the possibility that HBV may play a direct role in liver carcinogenesis by insertional mutagenesis.
NIMG-24HIGH SPATIOTEMPORAL DYNAMIC SUSCEPTIBILITY CONTRAST (DSC) PERFUSION MRI USING MULTIBAND ECHOPLANAR IMAGING (MB-EPI) (2015)

NIMG-24. HIGH SPATIOTEMPORAL DYNAMIC SUSCEPTIBILITY CONTRAST (DSC) PERFUSION MRI USING MULTIBAND ECHOPLANAR IMAGING (MB-EPI) Benjamin Ellingson, Kevin Leu, Whitney Pope, Albert Lai, Phioanh Nghiemphu, Linda Liau, and Timothy Cloughesy; University of California Los Angeles, Los Angeles, CA, USA BACKGROUND: Dynamic susceptibility contrast (DSC)-MRI is a commonlyusedperfusion imaging techniqueused toassessbrain tumorvascularity and angiogenesis by estimation of relative cerebral blood volume (rCBV). Despite widespread use, technical limitations lead to compromises in terms of resolution, slice coverage, and temporal resolution when acquiring dynamic data using the current single-shot echoplanar (EPI) imaging approach. In the current study we demonstrate the use of a new “multiband” (MB)-EPI sequence for multislice excitation, originally developed for fMRI as part of the Human Connectome Project, to obtain DSC perfusion MRI with whole brain coverage, higher spatial resolution, and twice the temporal resolution of current strategies. METHODS: DSC data collected using standard EPI were compared with DSC obtained using MB-EPI in 20 prospective GBM patients. Standard DSC-MRI were collected on conventional 1.5T or 3T MR scanners using a temporal resolution of 1250-1900ms, matrix size 1⁄4 96x96–128x128, and 5-20 slices with 5mm slice thickness. High spatiotemporalDSC-MRI datawere collectedona3TSiemensPrismawith temporal resolution of 600-750ms, matrix size 1⁄4 100x100–200x200, and 30-32 slices with 4mm slice thickness. Both DSC-MRI datasets were post-processed using standard leakage correction and deconvolution techniques to calculate rCBV and rCBF. RESULTS: Data collected using standard and MB-EPI showed similar dynamic contrast-to-noise, although MB-EPI showed more T1-weighting and leakage effects. RCBV maps obtained using both techniques provided similar information regarding the extent of hypervascularity within the tumor after leakage correction; however, rCBV maps calculated from MB-EPI data had more brain coverage and higher spatial resolution. Parametric maps of blood flow differed slightly due to higher temporal resolution MB-EPI data. CONCLUSION: High spatiotemporal DSC perfusion MRI is desirable and clinically feasible using MB-EPI. DSC using MB-EPI provides comparablequantitativedataand dataqualitywith betteraccuracyandspatial resolution. Neuro-Oncology 17:v153–v171, 2015. doi:10.1093/neuonc/nov225.24 Published by Oxford University Press on behalf of the Society for Neuro-Oncology 2015.
Very important pharmacogene summary: sulfotransferase 1A1 (2009)

Hildebrandt, Michelle; Adjei, Araba; Weinshilboum, Richard; Johnson, Julie A.; Berlin, Dorit S.; Klein, Teri E.; Altman, Russ B. Author Information
Image destabilization: Programmable defocus using lens and sensor motion (2009)

We propose a novel camera setup in which both the lens and the sensor are perturbed during the exposure. We analyze the defocus effects produced by such a setup, and use it to demonstrate new methods for simulating a lens with a larger effective aperture size (i.e., shallower depth of field) and methods for achieving approximately depth-independent defocus blur size. We achieve exaggerated, programmable, and pleasing bokeh with relatively small aperture sizes such as those found on cell phone cameras. Destabilizing the standard alignment of the sensor and lens allows us to introduce programmable defocus effects and achieve greater flexibility in the image capture process.
The Self‐Assembly of Catenated Cyclodextrins (1993)

The Schotten–Baumann reaction between a diamine with a central bitolyl unit and terephthaloyl chloride in the presence of heptakis(2,6-di-O-methyl)-β-cyclodextrin (DM-β-CD) in dilute solution affords the [2]catenanes 1 and 2 as well as two analogous [3]catenanes, in which two DM-β-CD units are threaded on a tetrakislactam ring. In catenane 1 the bitolyl unit is found to be situated inside the Cyclodextrin torus.
Adaptive deep-learning algorithm for signal recovery of broadband microwave photonic receiving systems based on supervised training (2021)

We show an adaptive deep-learning algorithm that recovers the distorted broadband signals of defective microwave photonic (MWP) receiving systems. With data-driven supervised training, the adopted neural network automatically learns the end-to-end distortion effects of the photonic analog links and recovers the received signals in the digital domain. Through changing the training data sets and retraining the same neural network, this algorithm can be applied in various MWP receiving systems. Two MWP receiving systems are set up for experimentally demonstrating the capability of broadband signal recovery. Results show that the neural network can reduce the signal distortion (measured with mean square error) by <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:mo>∼</mml:mo> </mml:mrow> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:mn>18</mml:mn> </mml:mrow> <mml:mspace width="thickmathspace"/> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:mi mathvariant="normal">d</mml:mi> <mml:mi mathvariant="normal">B</mml:mi> </mml:mrow> </mml:math> . Moreover, visualization analysis indicates that the proposed algorithm is potentially adaptive to more MWP receiving systems and applications. The noise robustness of this algorithm is also verified so that it is applicable in noisy situations. The proposed algorithm improves the performance of MWP receiving systems through appending a deep learning digital processor whose deployment is low cost.
Improved liquid phase separation processes for generating biodegradable microspheres loaded with high concentrations of drugs for tumor embolization (2018)

Drug-eluting microspheres are the most commonly used particulate embolic agents for transarterial chemoembolization of liver tumors. However, drug loading of degradable embolic particles is often insufficient. In the current study, microspheres prepared from poly(D,L-lactic-co-glycolic acid) were investigated as a biodegradable embolic agent for arterial embolization applications. Through modified solvent evaporation and liquid-induced phase separation, high drug loading (as high as 32%) and low solvent residue (as low as 0.03%) was achieved. Degradation performance, 1H NMR, and the nonsolvent’s influence on solvent residue content were assessed. These drug-loading microspheres with biodegradability hold promise for embolization therapies.
Crystal structure of Grimontia hollisae collagenase provides insights into its novel substrate specificity toward collagen (2022)

Collagenase from the gram-negative bacterium Grimontia hollisae strain 1706B (Ghcol) degrades collagen more efficiently even than clostridial collagenase, the most widely used industrial collagenase. However, the structural determinants facilitating this efficiency are unclear. Here, we report the crystal structures of ligand-free and Gly-Pro-hydroxyproline (Hyp)-complexed Ghcol at 2.2 and 2.4 Å resolution, respectively. These structures revealed that the activator and peptidase domains in Ghcol form a saddle-shaped structure with one zinc ion and four calcium ions. In addition, the activator domain comprises two homologous subdomains, whereas zinc-bound water was observed in the ligand-free Ghcol. In the ligand-complexed Ghcol, we found two Gly-Pro-Hyp molecules, each bind at the active site and at two surfaces on the duplicate subdomains of the activator domain facing the active site, and the nucleophilic water is replaced by the carboxyl oxygen of Hyp at the P1 position. Furthermore, all Gly-Pro-Hyp molecules bound to Ghcol have almost the same conformation as Pro-Pro-Gly motif in model collagen (Pro-Pro-Gly)<sub>10</sub>, suggesting these three sites contribute to the unwinding of the collagen triple helix. A comparison of activities revealed that Ghcol exhibits broader substrate specificity than clostridial collagenase at the P2 and P2' positions, which may be attributed to the larger space available for substrate binding at the S2 and S2' sites in Ghcol. Analysis of variants of three active-site Tyr residues revealed that mutation of Tyr564 affected catalysis, whereas mutation of Tyr476 or Tyr555 affected substrate recognition. These results provide insights into the substrate specificity and mechanism of G. hollisae collagenase.
MicroRNA-146a Deficiency Leads to Increased Myeloid Cell Proliferation and Activation (2011)

Abstract Abstract 2815 NF-κB is a key regulator of inflammation and the immune activation against pathogens. On the other hand, constitutive and dysregulated NF-κB activation has been shown to lead to hematologic malignancies. Thus, NF-κB activity has to be properly regulated to achieve this delicate balance. Recent studies on microRNA-146a (miR-146a) suggest it to be an important negative regulator of NF-κB activation by targeting TRAF6 and IRAK1. To characterize the function of miR-146a in the context of NF-κB activation in the hematopoietic system, we have created a knockout (KO) mouse with germline deletion of miR-146a gene. We have shown that over time miR-146a KO mice develop a myeloproliferative condition in spleen and bone marrow that progresses to splenic myeloid sarcoma and bone marrow fibrosis. The myeloproliferative disease is driven by dysregulated NF-κB activation as the KO spleen and bone marrow cells show increased NF-κB activity and reduction in NF-κB level effectively rescues the myeloproliferative disease. In addition, the KO mice exhibit a chronic inflammatory state with increased cytokine production and macrophages from the KO are hyper-activated upon primary LPS stimulation and secondary re-stimulation. In this study, we have provided genetic evidence that miR-146a functions as a tumor suppressor in the hematopoietic system and highlighted the important role of miR-146a as a negative regulator of NF-κB activation and inflammation. Disclosures: Taganov: Regulus Therapeutics Inc: Employment.
Pulsed operation of a miniature scalar optically pumped magnetometer (2017)

A scalar magnetic field sensor based on a millimeter-size <sup>87</sup>Rb vapor cell is described. The magnetometer uses nearly copropagating pump and probe laser beams, amplitude modulation of the pump beam, and detection through monitoring the polarization rotation of the detuned probe beam. The circularly polarized pump laser resonantly drives a spin precession in the alkali atoms at the Larmor frequency. A modulation signal on the probe laser polarization is detected with a lock-in amplifier. Since the Larmor precession is driven all-optically, potential cross talk between sensors is minimized. And since the pump light is turned off during most of the precession cycle, large offsets of the resonance, typically present in a single-beam Bell-Bloom scheme, are avoided. At the same time, relatively high sensitivities can be reached even in millimeter-size vapor cells: The magnetometer achieves a sensitivity of 1 pT/Hz<sup>1/2</sup> in a sensitive volume of 16 mm<sup>3</sup>, limited by environmental noise. When a gradiometer configuration is used to cancel the environmental noise, the magnetometer sensitivity reaches 300 fT/Hz<sup>1/2</sup>. We systematically study the dependence of the magnetometer performance on the optical duty cycles of the pump light and find that better performance is achieved with shorter duty cycles, with the highest values measured at 1.25% duty cycle.
Dataflow-driven memory allocation for multi-dimensional signal processing systems (1994)

Memory cost is responsible for a large amount of the chip and/or board area of customized video and image processing systems. In this paper, a novel background memory allocation and assignment technique is presented. It is intended for a behavioural algorithm specification, where the procedural ordering of the memory related operations is not yet fully fixed. Instead of the more restricted classical scheduling-based explorations, starting from procedurally interpreted specifications in terms of loops, a novel optimization approach—driven by data flow analysis—is proposed. Employing the estimated silicon area as a steering cost, this allocation/assignment technique yields one or (optionally) several distributed (multi-port) memory architecture(s) with fully-determined characteristics, complying with a given clock cycle budget for read/write operations. Moreover, our approach can accurately deal with complex multi-dimensional signals by means of a polyhedral data-flow analysis operating with groups of scalars.