gebhart/patrepeval huggingface dataset:
Comparative Analysis of Hepatitis B Virus Polymerase Sequences Required for Viral RNA Binding, RNA Packaging, and Protein Priming (2013)

Hepatitis B virus replicates a DNA genome through reverse transcription of a pregenomic RNA (pgRNA) by using a multifunctional polymerase (HP). A critical function of HP is its specific association with a viral RNA signal, termed ε (Hε), located on pgRNA, which is required for specific packaging of pgRNA into viral nucleocapsids and initiation of viral reverse transcription. HP initiates reverse transcription by using itself as a protein primer (protein priming) and Hε as the obligatory template. HP is made up of four domains, including the terminal protein (TP), the spacer, the reverse transcriptase (RT), and the RNase H domains. A recently developed, Hε-dependent, in vitro protein priming assay was used in this study to demonstrate that almost the entire TP and RT domains and most of the RNase H domain were required for protein priming. Specific residues within TP, RT, and the spacer were identified as being critical for HP-Hε binding and/or protein priming. Comparison of HP sequence requirements for Hε binding, pgRNA packaging, and protein priming allowed the classification of the HP mutants into five groups, each with distinct effects on these complex and related processes. Detailed characterization of HP requirements for these related and essential functions of HP will further elucidate the mechanisms of its multiple functions and aid in the targeting of these functions for antiviral therapy.
Decrease of glutamate decarboxylase (GAD)-immunoreactive nerve terminals in the substantia nigra after kainic acid lesion of the striatum. (1981)

Antiserum sheep 3 against rat brain glutamate decarboxylase (GAD) was employed for the immunohistochemical localization of GAD-immunoreactive nerve terminals in the substantia nigra (SN). To test whether the antiserum specifically localized GAD-containing axon terminals, the effect of kainic acid-induced striatal lesions on the reactive nerve endings in the SN was investigated. Seven days after the injection of 1 microgram kainic acid into the striatum, a 65% decrease in GAD-enzyme activity occurred in the ipsilateral SN. On immunohistochemical examination there was correspondingly a marked reduction of GAD-positive terminals. The parallel decrease in biochemical and immunohistochemical GAD activity indicates that antiserum sheep 3 can be used as a specific immunohistochemical probed for GAD-containing elements.
Challenges of Ultra Large Scale Integration of Biomedical Computing Systems (2005)

The NCRI Informatics Initiative is overseeing the implementation of an informatics framework for the UK cancer research community. The framework advocates an integrated multidisciplinary method of working between scientific and medical communities. Key to this process is community adoption of high quality acquisition, storage, sharing and integration of diverse data elements to improve knowledge of the causes, prevention and treatment of cancer. The integration of the complex data and meta-data used by these multiple communities is a significant challenge and there are technical, resource-based and sociological issues to be addressed. In this paper we review progress aimed at establishing the framework and outline key challenges in ultra large scale integration of biomedical computing systems.
Basal glucagon hypersecretion and response to oral glucose load in prediabetes and mild type 2 diabetes (2019)

Dysregulation of glucagon secretion plays an important role in the pathogenesis of type 2 diabetes (T2DM). However it hasn't been elucidated involvement of glucagon dysregulation in pathophysiology of T2DM. Recently a new glucagon sandwich enzyme-linked immunosorbent assay (ELISA) became available that can measure plasma glucagon level with higher accuracy and simpler procedure than the conventional RIA method. We performed OGTT for adult subjects aged 20-69 years to define normal glucose tolerance (NGT, n = 25), borderline glucose intolerance (defined as pre-diabetes mellitus: preDM, n = 15), or diabetes mellitus (DM, n = 13), and we measured glucagon levels with this new ELISA method at fasting and during OGTT. Plasma glucose, insulin, glucagon and active GLP-1 were also measured. This study took place in diabetes outpatient clinic in Kitasato University Hospital and an affiliated outpatient clinic. PreDM and DM exhibited higher fasting plasma glucagon levels than NGT (34.4 ± 4.6 and 44.1 ± 5.0 vs. 20.6 ± 3.6 pg/mL), and statistical significance was observed between NGT and DM (p < 0.05). There was significant correlation between fasting glucagon level and indexes of insulin sensitivity. During OGTT, glucagon levels were less suppressed in DM and preDM than in NGT, whereas no apparent relationship was observed between glucagon and GLP-1 secretion. Significant positive correlation was observed between glucagon levels during OGTT and fasting TG. In conclusion, subjects with mild T2DM exhibited fasting hyperglucagonemia and insufficient suppression to oral glucose load compared to NGT subjects.
Perpendicular Magnetic Anisotropy of Co2FexMn1−xSi Heusler Alloy Ultra-Thin Films (2014)

Film thickness, composition, and buffer layer dependences of perpendicular magnetic anisotropy (PMA) were investigated for ultrathin Co <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> Fe <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> Mn <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1-x</sub> Si Heusler alloy films. The perpendicular magnetization was achieved when the thickness of the Co <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> MnSi on the Pd buffer layer was 0.6 and 0.8 nm. For Co <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> FeSi, only a 0.6 nm thick film exhibited perpendicular magnetization. Effective uniaxial magnetic anisotropy energy (Keffu ) was 1-2 × 106 erg/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> . From the buffer layer dependence, it was revealed that perpendicular magnetization of Co <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> FeSi films was not achieved for a MgO or Cr buffer layer. These results imply that contributions from the Pd/Heusler alloy interface plays an important role in the PMA of ultrathin Co <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> Fe <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> Mn <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1-x</sub> Si Heusler alloy films.
Effects of a Supersulfated Low Molecular Weight Heparin (IK-SSH) on Different Hemostatic Parameters (1998)

In a phase I trial effects of a new supersulfated low molecular weight heparin (IK-SSH) on different hemostatic parameters were investigated in healthy volunteers. Parameters studied were activated partial thromboplastin time (aPTT), thrombin time, Heptest, anti-activated factor II (anti-FIIa) and anti-activated factor X (anti-FXa) activity, platelet adhesion, platelet count, platelet-induced thrombin generation time (PITT), bleeding time, antithrombin III, fibrinogen and several safety parameters. After single intravenous (i.v.) injections of IK-SSH (0.14, 0.33 and 0.66 mg/kg) aPTT, Heptest and PITT were strongly and dose-dependently prolonged. After ascending subcutaneous (s.c.) doses of IK-SSH (0.33, 0.66 and 1 mg/kg) aPTT, Heptest and PITT were prolonged in a dose-dependent manner. Repeat s.c. injections of 1 mg/kg IK-SSH for 5 days markedly prolonged aPTT, Heptest and PITT. No cumulative effects were observed. Anti-FIIa and anti-FXa activity were not or only slightly increased. Bleeding time, thrombin time and platelet adhesion were not significantly changed after i.v. and s.c. injections of IK-SSH. However, tissue factor pathway inhibitor (TFPI) concentration was markedly increased after each injection of IK-SSH and returned to the preinjection value 24 h later. IK-SSH prolongs aPTT, Heptest and PITT in a similar manner as other low molecular weight heparins but without significantly affecting thrombin time, FIIa and FXa activity. The release of TFPI may well be responsible for the prolongation of aPTT, Heptest and PITT. IK-SSH may be further developed as an antithrombotic agent.
106Ruthenium eye plaque brachytherapy in the management of medium sized uveal melanoma (2020)

Our study proved <sup>106</sup>Ru -brachytherapy to be an excellent treatment option with regard to tumor control and preservation of the visual acuity in well-selected patients. Our data suggested that this treatment is also suitable for tumors with a depth of more than 5 mm.
Surface modification of vulcanized EPDM rubber by Ag (II): Kinetic study of Ag (II) generation and surface characterization (2018)

Ethylene propylene diene monomer (EPDM) rubber has been widely used in the various outdoor and industrial applications. However, in order to improve its adhesion properties it needs some surface modification. Mediated electrochemical oxidation by Ag (II) was thus employed to evaluate the feasibility of EPDM surface modification. The electrochemical behavior of Ag (I) /Ag (II) redox couple was initially studied at different temperatures in an electro-membrane cell using IrO2/Ta2O5anode. The reversibility of the redox reaction improved at low temperatures. The apparent rate constant for Ag (I) oxidation (k1) at 3 kA m-2 was  (s-1). The surface chemistry, morphology and wettability of the activated EPDM rubber by Ag (II) were then analyzed and the modified EPDM surface showed a significant decrease in the water contact angle resulting in an increase in the surface free energy and improved wettability. ATR analysis revealed presence of oxygen-containing polar groups on the modified rubber surface. SEM results showed that the short treatment time at room temperature only changed the morphology of the rubber surface, which is attributed to the etching of the outermost surface.
A note on the proposed UK VHF radar (1984)

The proposal for the establishment of a VHF radar in the UK is still under active consideration, although for financial reasons no start has yet been made on an installation. Several changes have been made to the scheme as described and these are listed. (1) The initial installation will be suitable for stratosphere-troposphere (ST) operation only using 64 antennas and 2 power modules. (2) An existing site is being examined on the west coast of Wales, which because it is a former Loran ground station is provided with the buildings, power and communications facilities to enable a radar to be assembled much more quickly than a green field site would allow. Because the site is not within a mountain valley as originally intended, careful early attention will have to be given to the possible problems of local interference and sea-surface returns. (3) Preliminary discussions with the UK licensing authorities suggest that a frequency of 47 MHz is more likely than 50 MHz. (4) Minor changes are planned in the antenna array connection scheme of the 400-element mesosphere-stratosphere-troposphere (MST) array to allow more precise sidelobe suppression to be achieved in the receive mode.
Thrombotic risk assessment in the antiphospholipid syndrome requires more than the quantification of lupus anticoagulants (2009)

Lupus anticoagulants (LACs) are associated with thromboembolic complications (TECs). LACs can be detected by their anticoagulant properties in thrombin generation assays, by the peak height (PH) and lag time (LT). To assess the thrombotic risk in LAC-positive patients, we have expressed the LAC activity quantitatively by PH/LT calibration curves, constructed for mixtures of monoclonal antibodies against beta2-glycoprotein I (beta2GPI) and prothrombin, spiked in normal plasma. PH/LT was determined in LAC patients, with (n = 38) and without (n = 21) TECs and converted into arbitrary LAC units. LAC titers ranged from 0 to 200 AU/mL, with 5 of 59 patients being negative. In the positive LAC titer population (54 of 59), LAC and anti-beta2GPI immunoglobulin G (IgG) titers correlated with TECs, with odds ratios of 3.54 (95% CI, 1.0-1.7) and 10.0 (95% CI, 1.98-50.6), respectively. In patients with single or combined low titers, useful predictions on thrombosis could be made only after additional measurements of soluble P-selectin and factor VII. This layered strategy yielded positive and negative predictive values, sensitivity, and specificity values approximately 90% in this subgroup. Hence, LAC and anti-beta2GPI IgG titers, when combined with selected markers of the hypercoagulable state, allow a relevant thrombotic risk assessment in nearly all patients with LACs.
Towards an industrially implementable PWM-injection scheme (2021)

We show how the rotor position of a PWM-fed PMSM can be recovered, even at low velocity or standstill, from the measured currents. The method is based on the excitation created by the PWM, without the need for an external probing signal. One originality of the approach is that we directly process the bitstream output by a Sigma-Delta modulator, hence do not require special derivative current sensors nor fast multibit ADCs, thereby opening the way for an effective implementation in an industrial drive.
Methods for the Investigation of Proteins (2004)

Relevance of Enzyme Mechanism Experimental Methods for the Investigation of an Enzyme Mechanism Distribution of Products (Curtin–Hammett Principle) Stationary Methods of Enzyme Kinetics Linear Free Enthalpy Relationships (LFERs): Brønsted and Hammett Effects Kinetic Isotope Effects Non-stationary Methods of Enzyme Kinetics: Titration of Active Sites Utility of the Elucidation of Mechanism: Transition-State Analog Inhibitors Methods of Enzyme Determination Quantification of Protein Isoelectric Point Determination Molecular Mass Determination of Protein Monomer: SDS-PAGE Mass of an Oligomeric Protein: Size Exclusion Chromatography (SEC) Mass Determination: Mass Spectrometry (MS) (after Kellner, Lottspeich, Meyer) Determination of Amino Acid Sequence by Tryptic Degradation, or Acid, Chemical or Enzymatic Digestion Enzymatic Mechanisms: General Acid–Base Catalysis Carbonic Anhydrase II Vanadium Haloperoxidase Nucleophilic Catalysis Serine Proteases Cysteine in Nucleophilic Attack Lipase, Another Catalytic Triad Mechanism Metalloproteases Electrophilic catalysis Utilization of Metal Ions: ADH, a Different Catalytic Triad Formation of a Schiff Base, Part I: Acetoacetate Decarboxylase, Aldolase Formation of a Schiff Base with Pyridoxal Phosphate (PLP): Alanine Racemase, Amino Acid Transferase Utilization of Thiamine Pyrophosphate (TPP): Transketolase
Further study on iterative control loop for aberration correction in imaging systems with single mode fibre aperture (2013)

An iterative control system was designed for compensation of wavefront aberration utilizing a micromachined deformable mirror through simulated annealing algorithm. 37 elements within a deformable mirror are controlled individually in a closed-loop to maximize the output optical intensity collected in a single mode aperture. In this paper, the design of the control system is explained comprehensively. The effect of the parameters involved on the achievable accuracy, computational load and speed of the algorithm are investigated. The shape of the mirror's surface throughout the runtime of the algorithm is also monitored and analyzed.
Coupling interactions in electromagnetic scattering from finite array of cavities with stratified dielectric coating (2012)

The coupling interactions in electromagnetic scattering from a finite array of two-dimensional identical cavities engraved in a perfectly electric conducting screen covered with stratified dielectric coating are presented using an algorithm based on the hybrid finite element-boundary integral method. The solution to the scattering from a finite array of cavities is approximated using the array factor method, which does not take into account the coupling between the cavities, and is compared to the recently developed finite element-boundary element method to demonstrate the importance of the inclusion of the coupling effect. Dependence of the coupling interactions between the cavities on various parameters such as separation periods, incident angle of the plane-wave excitation, and permittivity and thickness of the dielectric coating is demonstrated quantitatively through several numerical examples.
Conformations and conformational processes of pelargolactam (1995)

Abstract Pelargolactam (1‐azacyclodecan‐2‐one) was studied by 1 H and 13 C NMR spectroscopy in solution between 25 and −145°C. Equilibrium solutions of pelargolactam at 25°C consist mainly of the trans isomer together with 5–10% of the cis isomer. Solid pelargolactam consists of a mixture of cis and trans isomers, the cis form dissolving more rapidly than the trans form at −95°C. At temperatures above 90°C the 13 C NMR resonances for the cis and trans amides coalesce to one averaged set. A conformational process with a coalescence temperature of −30 to −50°C and a free energy of activation of Δ G ≠ = 46 kJ mol −1 observed in the 1 H spectrum of the trans isomer is interpreted as geminal exchange in the methylene groups. A lower barrier process was also observed, with a coalescence temperature of ca −115°C and Δ G ≠ = 32 kJ mol −1 . Only the latter process was observed in the 13 C spectrum, and below −120°C all 13 C lines split in two in the proportion 1:2. This process is interpreted as the interconversion between two trans conformers. Four conformational candidates were considered and their relative energies calculated by molecular mechanics.
A Bayesian Framework for Tilt Perception and Confidence (2005)

The misjudgement of tilt in images lies at the heart of entertaining vi-sual illusions and rigorous perceptual psychophysics. A wealth of find-ings has attracted many mechanistic models, but few clear computational principles. We adopt a Bayesian approach to perceptual tilt estimation, showing how a smoothness prior offers a powerful way of addressing much confusing data. In particular, we faithfully model recent results showing that confidence in estimation can be systematically affected by the same aspects of images that affect bias. Confidence is central to Bayesian modeling approaches, and is applicable in many other percep-tual domains. Perceptual anomalies and illusions, such as the misjudgements of motion and tilt evident in so many psychophysical experiments, have intrigued researchers for decades.1–3 A Bayesian view4–8 has been particularly influential in models of motion processing, treating such anomalies as the normative product of prior information (often statistically codify-
[Riboswitches]. (2005)

Riboswitches are RNA structures able to bind small molecules and regulate gene expression at both, transcriptional and translational level. They are present in a wide variety of bacterial species. In Bacillus subtilis more than 2% of the genome is regulated by riboswitches. Metabolite binding is highly specific and can be provided in cooperative manner. Several riboswitches has been identified and characterized to be specific for flavin mononucleotide, thiamine, thiamine pyrophosphate, adenosylcobalamin, S-adenosylmethionine, lysine, glycine, adenine, guanine and glucosamine-6-phosphate. Some of them have been found also in fungi (Neurospora crassa) and plants (Oryza sativa, Arabidopsis thaliana). In human only one riboswitch with binding capacity for 2-aminopurine, has been found. Occurrence of riboswitches in all of the phylogenetic groups suggests that they are one of the oldest regulatory systems. It provokes also the question about their involvement in regulation of gene expression in human.
274. Derivatives of 6-aminopenicillanic acid. Part III. 2,6-Dialkoxybenzoyl derivatives (1962)

F. P. Doyle, K. Hardy, J. H. C. Nayler, M. J. Soulal, E. R. Stove and H. R. J. Waddington, J. Chem. Soc., 1962, 1453 DOI: 10.1039/JR9620001453
Meningococcal group A lipooligosaccharides (LOS): preliminary structural studies and characterization of serotype-associated and conserved LOS epitopes (1994)

Structural studies indicate that the neisserial lipooligosaccharides (LOS) are composed of an oligosaccharide (OS) portion with a phosphorylated diheptose (Hep) core attached to the toxic lipid A moiety. A conserved meningococcal LOS epitope, defined by monoclonal antibody (MAb) D6A, is expressed on group A and many group B and C meningococci of different LOS serotypes (J. J. Kim, R. E. Mandrell, H. Zhen, M. A. Apicella, J. T. Poolman, and J. M. Griffiss, Infect. Immun. 56:2631-2638, 1988). This MAb-defined D6A epitope is immunogenic in humans (M. M. Estabrook, R. E. Mandrell, M. A. Apicella, and J. M. Griffiss, Infect. Immun. 58:2204-2213, 1990; M. M. Estabrook, C. J. Baker, and J. M. Griffiss, J. Infect. Dis. 197:966-970, 1993). In this study, we characterize this important MAb-defined LOS epitope. Serotype L10 and L11 group A meningococal LOS were chemically modified and used to investigate what portion of the LOS molecule is important for expression of the conserved (D6A) epitope and serotype-associated LOS epitopes by use of immunoblotting techniques and selected MAbs as probes. Preliminary structural characterization of the LOS was also accomplished by electrospray ionization-mass spectrometry. Our results indicate the following. (i) Antibodies that recognize the serotype-associated or conserved LOS epitopes recognize the OS portion of the LOS. (ii) The phosphorylated diheptose core region of the OS is essential for expression of the conserved D6A epitope. (iii) The lipid portion of the molecule is important for optimum expression of the LOS epitopes. (iv) The proposed compositions of the O-deacylated LOS are consistent with the presence of a phosphorylated diheptose core and are as follows: for O-deacylated L10 LOS, 3Hex (hexose), 1HexNAc (N-acetylhexosamine), 2KDO (2-keto-3-deoxy-D-manno-octulosonic acid), 2Hep (heptose), 1PEA or 2PEA (phosphoethanolamine), and O-deacylated lipid A; and for O-deacylated L11 LOS, 2Hex, 1HexNAc, 2KDO, 2Hep, 2PEA, and O-deacylated lipid A. Because the phosphorylated diheptose core region of the LOS is essential for the formation of a conserved LOS epitope (D6A) that is immunogenic in humans, care should be taken to maintain stereochemical requirements for the expression of this conserved epitope in the design of effective, nontoxic LOS vaccines.
Population transfer between molecular vibrational levels by stimulated Raman scattering with partially overlapping laser fields. A new concept and experimental results (1990)

The feasibility of a novel technique for efficient and selective population transfer from a thermally populated level 1 via an intermediate state 2 to level 3 is experimentally demonstrated. It is shown for sodium dimers that the process of on- or near-resonance stimulated Raman scattering with only partially overlapping laser beams is, in particular, useful for the selective population of high vibrational levels of particles in a molecular beam. This is achieved when the interaction with the Stokes laser, coupling levels 2 and 3, begins earlier than the interaction with the pump laser. The phenomenon, which is closely related to the formation of ‘‘trapped states,’’ is quantitatively explained using the basis of eigenstates of molecules strongly coupled to the radiation fields. The similarity and difference to related techniques such as rapid adiabatic passage phenomena in two-level systems, off-resonant stimulated Raman scattering, or stimulated emission pumping is briefly discussed.