gebhart/patrepeval huggingface dataset:
Dynamics of Thermal Motions within a Large Catalytic RNA Investigated by Cross-linking with Thiol−Disulfide Interchange (1997)

Conformational dynamics have been studied in proteins, but the extent of thermal motion within large compact RNA molecules, including ribozymes, has not been systematically explored. Methods are developed for the incorporation of the alkyl-phenyl disulfide 1 and the alkyl thiol 2 at specific ribose 2‘-positions within RNA. These groups react under mild conditions to form disulfide cross-links by thiol−disulfide interchange. When incorporated on opposite faces of a short, continuous RNA helix, these reactants do not form a disulfide cross-link. In contrast, in an active 310-nucleotide group I ribozyme prepared by semisynthetic methods, sites separated by a distance of up to 50 Å in the structure are cross-linked at rates only 3- to 15-times slower than cross-linking between proximal sites. Furthermore, ribozymes with normally distant sites held together by a disulfide cross-link retain substantial catalytic activity. These results reveal unexpectedly large thermal motions between domains of a compact folded ribozyme.
ChemInform Abstract: A New Stereospecific Annulation. (1986)

Abstract Das Lithium‐enolat (I) reagiert mit dem Butenolid (II) zu dem Addukt (III), das mit Persäure zu (IV) entschwefelt oder mit Vinyllithium in das Addukt (V) übergeführt wird.
Loss of PHD3 allows tumours to overcome hypoxic growth inhibition and sustain proliferation through EGFR (2014)

Solid tumours are exposed to microenvironmental factors such as hypoxia that normally inhibit cell growth. However, tumour cells are capable of counteracting these signals through mechanisms that are largely unknown. Here we show that the prolyl hydroxylase PHD3 restrains tumour growth in response to microenvironmental cues through the control of EGFR. PHD3 silencing in human gliomas or genetic deletion in a murine high-grade astrocytoma model markedly promotes tumour growth and the ability of tumours to continue growing under unfavourable conditions. The growth-suppressive function of PHD3 is independent of the established PHD3 targets HIF and NF-κB and its hydroxylase activity. Instead, loss of PHD3 results in hyperphosphorylation of epidermal growth factor receptor (EGFR). Importantly, epigenetic/genetic silencing of PHD3 preferentially occurs in gliomas without EGFR amplification. Our findings reveal that PHD3 inactivation provides an alternative route of EGFR activation through which tumour cells sustain proliferative signalling even under conditions of limited oxygen availability.
Recent advance in transflective liquid crystal displays (2006)

Three new transflective liquid crystal displays (LCDs) are reported in this paper. The first one uses color sequential method for transmissive mode with an LED backlight. The second utilizes a wire-grid-polarizer in the reflective part without any phase retardation film. The third is a polarizer-free transflective LCD based on the absorption and scattering mechanisms of dye-doped negative LC gel.
1.54 µm GaSb/AlGaSb multi-quantum-well monolithic laser at 77 K grown on miscut Si substrate using interfacial misfit arrays (2007)

A GaSb quantum-well (QW) laser diode grown monolithically on a 5° miscut Si (001) substrate is presented. The III-Sb epi-structure is grown monolithically on the miscut Si substrate via a thin (50 nm) AlSb nucleation layer. The 13% lattice mismatch between AlSb and Si is accommodated by a self-assembled, 2D array of interfacial misfit dislocations (IMF). The 5° miscut geometry enables simultaneous IMF formation and anti-phase domain suppression. The 1 mm × 100 µm GaSb QW laser diode operates under pulsed conditions at 77 K with a threshold current density of 2 kA/cm2 and a maximum peak power of ∼20 mW. Furthermore, the device is characterised by a 9.1 Ω forward resistance and a leakage current density of 0.7 A/cm2 at −5 V.
Generation of Cation Radicals from Enamines and Their Reactions with Olefins (1992)

Abstract Cation radicals of enamines, generated by the oxidation with CeIV compounds, react with electron-rich olefins to give the addition products. The formal α-alkylation of formylacetate is realized by the reaction of 3-(1-pyrrolidinyl)propenoate and olefins by the use of tetrabutylammonium cerium(IV) nitrate as an oxidant.
Magnetic Recording: Magnetic‐Pole Flip by Millimeter Wave (Adv. Mater. 48/2020) (2020)

In article number 2004897, Shin-ichi Ohkoshi and co-workers propose a new magnetic recording methodology, “focused-millimeter-wave-assisted magnetic recording (F-MIMR)”, to drastically increase the recording density of magnetic tapes. Demonstrations are performed using magnetic films based on a series of epsilon iron oxide, ε-Fe2O3. Irradiation of the focused millimeter wave generated from terahertz (THz) light flips the magnetic pole direction, leading to a breakthrough technology for high-density magnetic recordings.
Modeling and Simulation of Si IGBTs (2020)

Technology CAD (TCAD) has been recognized as a powerful design tool for Si insulated gate bipolar transistors (IGBTs). Here, physical models, such as a mobility model for carrier-carrier scattering, were investigated for a predictive TCAD. Simulated currentvoltage characteristics of the trench-gate IGBTs were compared with measurements. The difference between 3D- and 2D-TCAD simulations was observed in a high current region, which was explained by a bias-dependent current flow. A test element group (TEG) for separation of the emitter currents for holes and electrons was also determined as effective for calibration of lifetime model parameters.
The effect of methylphenidate treatment on suspiciousness in children with ADHD alone or comorbid with ODD (2017)

In addition to the beneficial effect of MPH treatment on ADHD and ODD symptoms it also diminishes suspiciousness. However, due to the small sample size further studies are needed to confirm the present results.
Integrated multi-omics analysis of the clinical relevance and potential regulatory mechanisms of splicing factors in hepatocellular carcinoma (2021)

Splicing factors (SFs) have been increasingly documented to perturb the genome of cancers. However, little is known about the alterations of SFs in hepatocellular carcinoma (HCC). This study comprehensively delineated the genomic and epigenomic characteristics of 404 SFs in HCC based on the multi-omics data from the Cancer Genome Atlas database. The analysis revealed several clinically relevant SFs that could be effective biomarkers for monitoring the onset and prognosis of HCC (such as, HSPB1, DDX39A, and NELFE, which were the three most significant clinically relevant SFs). Functional enrichment analysis of these indicators showed the enrichment of pathways related to splicing and mRNA processes. Furthermore, the study found that SF copy number variation is common in HCC and could be a typical characteristic of hepato-carcinogenesis; the complex expression regulation of SFs was significantly affected by copy number variant and methylation. Several SFs with significant mutation patterns were identified (such as, RNF213, SF3B1, SPEN, NOVA1, and EEF1A1), and the potential regulatory network of SFs was constructed to identify their potential mechanisms for regulating clinically relevant alternative splicing events. Therefore, this study established a foundation to uncover the broad molecular spectrum of SFs for future functional and therapeutic studies of HCC.
Methods for the Characterization of Phosphatase-Stabilized 2−5A-Antisense Chimeras (1998)

We have developed chromatographic and spectrophotometric assays for determining the degree of thiolation in phosphatase-resistant 5'-monothiophosphate-capped 2-5A-antisense chimeras. Concomitantly, we have explored the reactivity of this 5'-monophosphorothioate moiety with reporter reagents such as 5-iodoacetomidofluorescein and 5,5'-dithiobis(2-nitrobenzoic acid). On the basis of these reactions, analyses for 5'-monothiophosphate-functionalized 2-5A-antisense chimeras were made possible. Kinetic experiments demonstrated that oligonucleotide backbone negative charge could retard mixed disulfide formation in the reaction of 5,5'-dithiobis(2-nitrobenzoic acid) with 5'-monothiophosphorylated 2-5A-antisense chimeras.
Comparison of topological descriptors for similarity-based virtual screening using multiple bioactive reference structures (2004)

This paper reports a detailed comparison of a range of different types of 2D fingerprints when used for similarity-based virtual screening with multiple reference structures. Experiments with the MDL Drug Data Report database demonstrate the effectiveness of fingerprints that encode circular substructure descriptors generated using the Morgan algorithm. These fingerprints are notably more effective than fingerprints based on a fragment dictionary, on hashing and on topological pharmacophores. The combination of these fingerprints with data fusion based on similarity scores provides both an effective and an efficient approach to virtual screening in lead-discovery programmes.
From Femtoseconds To Biology: Mechanism Of The Light-Driven Proton Pump In Bacteriorhodopsin (1989)

Femtosecond time-resolved absorption and time-resolved resonance Raman spectroscopy are used to examine the molecular mechanism of the light-driven proton pump in bacteriorhodopsin. Transient absorption spectroscopy with 6-fs pulses is used to directly observe the excited-state, double bond torsional isomerization of the retinal chromophore. Time-resolved resonance Raman spectroscopy is used to determine the structure of the retinal prosthetic group in each of the subsequent photolytic intermediates. Based on these results, a new &quot;C-T Model&quot; for the molecular mechanism of the proton pump has been developed. The key feature of this model is an isomerization-driven conformational change of the protein from the T-form to the C-form which acts as a &quot;reprotonation switch&quot; and stores energy to drive later events in the photocycle.
Targeted Ephemeris Decorrelation Parameter Inflation for Improved LAAS Availability during Severe Ionosphere Anomalies (2008)

The Local Area Augmentation System (LAAS) is a ground-based differential GNSS system designed to provide precision approach for aircraft landing at a LAASequipped airport. While most anomalies affecting the system can be mitigated in the range domain, positiondomain geometry screening is essential to mitigate threats from anomalous ionosphere spatial gradients. These can potentially cause large range-domain errors before detection by the LAAS Ground Facility (LGF). Existing algorithms for position-domain screening inflate the sigma values (ovig and opr_gnd) broadcast by the LAAS Ground Facility (LGF). This ensures that subset satellite geometries (i.e. subsets of a set of approved GPS satellites for which the LGF broadcasts valid corrections) for which unacceptable errors can result are made unavailable to the user. These unsafe subsets are found by comparing the resulting Maximum Ionosphere-Induced Error in Vertical (MIEV) with maximum “safe” navigation system error (NSE) values derived from Obstacle Clearance Surface (OCS) applicable to CAT I precision approaches. Recent analyses of past ionosphere spatial gradients observed over the Conterminous United States (CONUS) resulted in very high maximum gradients for both low and high-elevation satellites. The new ionosphere anomaly “threat model” for LAAS CAT I specifies a maximum spatial gradient of 375 mm/km for low-elevation satellites (below 15o) while high-elevation (above 65o) satellites can experience gradients as high as 425 mm/km. Uniform inflation of the broadcast sigmas for all approved satellites results in a significant drop in system availability under the new threat model. To minimize this decline, this paper proposes a new algorithm to implement position-domain screening by inflating satellite-specific, targeted ephemeris decorrelation parameters (called “P-values”) and opr_gnd values. Availability is assessed for ten major airports in the USA. Under normal conditions, 100% availability is achieved for eight airports, while availability for the two remaining airports exceeds 99%. Targeted inflation consistently results in better system availability compared to strategies that inflate all satellites by the same amount, such as the ovig approach.
Activation of Postsynaptic Ca2+Stores Modulates Glutamate Receptor Cycling in Hippocampal Neurons (2004)

We show that activation of postsynaptic inositol 1,4,5-tris-phosphate receptors (IP(3)Rs) with the IP(3)R agonist adenophostin A (AdA) produces large increases in AMPA receptor (AMPAR) excitatory postsynaptic current (EPSC) amplitudes at hippocampal CA1 synapses. Co-perfusion of the Ca(2+) chelator bis-(o-aminophenoxy)-N,N,N',N'-tetraacetic acid strongly inhibited AdA-enhanced increases in EPSC amplitudes. We examined the role of AMPAR insertion/anchoring in basal synaptic transmission. Perfusion of an inhibitor of synaptotagmin-soluble n-ethylmaleimide-sensitive factor attachment protein (SNAP) receptor SNARE-mediated exocytosis depressed basal EPSC amplitudes, whereas a peptide that inhibits GluR2/3 interactions with postsynaptic density-95 (PDZ) domain proteins glutamate receptor interacting protein (GRIP)/protein interacting with C-kinase-1 (PICK1) enhanced basal synaptic transmission. These results suggest that constitutive trafficking and anchoring of AMPARs help maintain basal synaptic transmission. The regulation of postsynaptic AMPAR trafficking involves synaptotagmin-SNARE-mediated vesicle exocytosis and interactions between AMPARs and the PDZ domains in GRIP/PICK1. We show that inhibitors of synaptotagmin-SNARE-mediated exocytosis, or interactions between AMPARs and GRIP/PICK1, attenuated AdA-enhanced increases in EPSC amplitudes. These results suggest that IP(3)R-mediated Ca(2+) release can enhance AMPAR EPSC amplitudes through mechanisms that involve AMPAR-PDZ interactions and/or synaptotagmin-SNARE-mediated receptor trafficking.
Centroid adapted frequency selective extrapolation for reconstruction of lost image areas (2015)

Lost image areas with different size and arbitrary shape can occur in many scenarios such as error-prone communication, depth-based image rendering or motion compensated wavelet lifting. The goal of image reconstruction is to restore these lost image areas as close to the original as possible. Frequency selective extrapolation is a block-based method for efficiently reconstructing lost areas in images. So far, the actual shape of the lost area is not considered directly. We propose a centroid adaption to enhance the existing frequency selective extrapolation algorithm that takes the shape of lost areas into account. To enlarge the test set for evaluation we further propose a method to generate arbitrarily shaped lost areas. On our large test set, we obtain an average reconstruction gain of 1.29 dB.
Dual cure photocatalyst systems (1990)

A family of dual cure photocatalyst systems is being developed to be used in the solventless processing of organic coatings. The photocatalyst systems consist of organometallic compounds often in combination with other agents. Upon photolysis, the photocatalyst system generates a Lewis acid and a free radical. The Lewis acid can initiate the polymerization of epoxies or the addition of isocyanates and polyols to form polyurethanes while the free radical can initiate the polymerization of acrylates. The performance of the various photocatalyst systems will be compared on the basis of the physical properties of the cured compositions they produce. 17 figs.
Bacteriophage PMB12 conversion of the sporulation defect in RNA polymerase mutants of Bacillus subtilis (1977)

The pseudotemperate phage PMB12 was isolated from soil on the basis of its ability to enhance the rate of sporulation of Bacillus subtilis 168. PMB12 was subsequently shown to convert the sporulation defect in two genetically distinct classes of sporulation mutants. One class includes those rifampin-resistant mutants that are also spore-negative (mutated at the rif locus). The other class includes a strain carrying the sporulation mutation spoCM-1. The spoCM-1 mutation is linked to cysA15 by PBS1 transduction but is distinct from the rif locus. Several other sporulation mutants were not converted by PMB12. PMB12 is related to phage PBS1. However, PBS1 did not convert the above sporulation mutants. The replication of PBS2, a clear-plaquing derivative of PBS1, is rifampin insensitive, apparently due to a phage-induced rifampin-insensitive RNA polymerase. PMB12 replication is also rifampin insensitive.
Fast Solutions in Power System Simulation through Coupling with Data-Driven Power Flow Models for Voltage Estimation (2020)

Power systems solvers are vital tools in planning, operating, and optimizing electrical distribution networks. The current generation of solvers employ computationally expensive iterative methods to compute sequential solutions. To accelerate these simulations, this paper proposes a novel method that replaces the physics-based solvers with data-driven models for many steps of the simulation. In this method, computationally inexpensive data-driven models learn from training data generated by the power flow solver and are used to predict system solutions. Clustering is used to build a separate model for each operating mode of the system. Heuristic methods are developed to choose between the model and solver at each step, managing the trade-off between error and speed. For the IEEE 123 bus test system this methodology is shown to reduce simulation time for a typical quasi-steady state time-series simulation by avoiding the solver for 86.7% of test samples, achieving a median prediction error of 0.049%.
Role of glucose transporters in the cellular insulin resistance of type II non-insulin-dependent diabetes mellitus. (1988)

To examine the role of glucose transport proteins in cellular insulin resistance, we studied subcutaneous adipocytes isolated from lean control, obese control (body mass index [BMI] 33.4 +/- 0.9), and untreated obese non-insulin-dependent diabetes mellitus (NIDDM) patients (BMI 35.2 +/- 2.1; fasting glucose 269 +/- 20 mg/dl). Glucose transporters were measured in plasma membrane (PM), low-density (LDM), and high-density (HDM) microsomal subfractions from basal and maximally insulin-stimulated cells using the cytochalasin B binding assay, and normalized per milligram of membrane protein. In all subgroups, insulin led to an increase in PM glucose transporters and a corresponding depletion of transporters in the LDM. Insulin recruited 20% fewer transporters to the PM in the obese subgroup when compared with lean controls, and this was associated with a decline in LDM transporters with enlarging cell size in the control subjects. In NIDDM, PM, and LDM, transporters were decreased 50% in both basal and stimulated cells when compared with obese controls having similar mean adipocyte size. Cellular depletion of glucose transporters was not the only cause of insulin resistance, because the decrease in rates of [14C]-D-glucose transport (basal and insulin-stimulated) was greater than could be explained by reduced numbers of PM transporters in both NIDDM and obesity. In HDM, the number of transporters was not influenced by insulin and was similar in all subgroups. We conclude that (a) in NIDDM and obesity, both reduced numbers and impaired activity of glucose transporters contribute to cellular insulin resistance, and (b) in NIDDM, more profound cellular insulin resistance is associated primarily with a further depletion of cellular transporters.
A study of the interaction of paper substrates on printed forensic imaging (2011)

At the microscopic level, printing on a substrate exhibits imperfections that can be used as a unique identifier for labels, documents and other printed items. In previous work, we have demonstrated using these minute imperfections around a simple forensic mark such as a single printed character for robust authentication of the character with a low cost (and mobile) system. This approach allows for product authentication even when there is only minimal printing (e.g. on a small label or medallion), supporting a variety of secure document workflows. In this paper, we present an investigation on the influence that the substrate type has on the imperfections of the printing process that are used to derive the character 'signature'. We also make a comparison between two printing processes, dry electro photographic process (laser) and (thermal) inkjet. Understanding the sensitivity of our methods to these factors is important so that we know the limitations of the approach for document forensics.
Virtual fluoroscopy for intraoperative C-arm positioning and radiation dose reduction (2018)

Positioning of an intraoperative C-arm to achieve clear visualization of a particular anatomical feature often involves repeated fluoroscopic views, which cost time and radiation exposure to both the patient and surgical staff. A system for virtual fluoroscopy (called FluoroSim) that could dramatically reduce time- and dose-spent "fluoro-hunting" by leveraging preoperative computed tomography (CT), encoded readout of C-arm gantry position, and automatic 3D-2D image registration has been developed. The method is consistent with existing surgical workflow and does not require additional tracking equipment. Real-time virtual fluoroscopy was achieved via mechanical encoding of the C-arm motion, C-arm geometric calibration, and patient registration using a single radiograph. The accuracy, time, and radiation dose associated with C-arm positioning were measured for FluoroSim in comparison with conventional methods. Five radiology technologists were tasked with acquiring six standard pelvic views pertinent to sacro-illiac, anterior-inferior iliac spine, and superior-ramus screw placement in an anthropomorphic pelvis phantom using conventional and FluoroSim approaches. The positioning accuracy, exposure time, number of exposures, and total time for each trial were recorded, and radiation dose was characterized in terms of entrance skin dose and in-room scatter. The geometric accuracy of FluoroSim was measured to be [Formula: see text]. There was no significant difference ([Formula: see text]) observed in the accuracy or total elapsed time for C-arm positioning. However, the total fluoroscopy time required to achieve the desired view decreased by 4.1 s ([Formula: see text] for conventional, compared with [Formula: see text] for FluoroSim, [Formula: see text]), and the total number of exposures reduced by 4.0 ([Formula: see text] for conventional, compared with [Formula: see text] for FluoroSim, [Formula: see text]). These reductions amounted to a 50% to 78% decrease in patient entrance skin dose and a 55% to 70% reduction in in-room scatter. FluoroSim was found to reduce the radiation exposure required in C-arm positioning without diminishing positioning time or accuracy, providing a potentially valuable tool to assist technologists and surgeons.
Supercritical solvothermal flow synthesis of advanced functional nanomaterials (2019)

Invited talk
Dynamic Nuclear Polarization of Oxygen-17 (2012)

Oxygen-17 detected DNP NMR of a water/glycerol glass enabled an 80-fold enhancement of signal intensities at 82 K, using the biradical TOTAPOL. The >6,000-fold savings in acquisition time enables (17)O-(1)H distance measurements and heteronuclear correlation experiments. These experiments are the initial demonstration of the feasibility of DNP NMR on quadrupolar (17)O.