gebhart/patrepeval huggingface dataset:
Structure-Based Redesign of Corepressor Specificity of the Escherichia coli Purine Repressor by Substitution of Residue 190, (1998)

Guanine or hypoxanthine, physiological corepressors of the Escherichia coli purine repressor (PurR), promote formation of the ternary PurR-corepressor-operator DNA complex that functions to repress pur operon gene expression. Structure-based predictions on the importance of Arg190 in determining 6-oxopurine specificity and corepressor binding affinity were tested by mutagenesis, analysis of in vivo function, and in vitro corepressor binding measurements. Replacements of Arg190 with Ala or Gln resulted in functional repressors in which binding of guanine and hypoxanthine was retained but specificity was relaxed to permit binding of adenine. X-ray structures were determined for ternary complexes of mutant repressors with purines (adenine, guanine, hypoxanthine, and 6-methylpurine) and operator DNA. These structures indicate that R190A binds guanine, hypoxanthine, and adenine with nearly equal, albeit reduced, affinity in large part because of a newly made compensatory hydrogen bond between the rotated hydroxyl side chain of Ser124 and the exocyclic 6 positions of the purines. Through direct and water-mediated contacts, the R190Q protein binds adenine with a nearly 75-fold higher affinity than the wild type repressor while maintaining wild type affinity for guanine and hypoxanthine. The results establish at the atomic level the basis for the critical role of Arg190 in the recognition of the exocyclic 6 position of its purine corepressors and the successful redesign of corepressor specificity.
THE CHEMILUMINESCENCE OF CERTAIN INDOLES* (1965)

Abstract— A series of twenty‐four indoles and related compounds have been examined for chemiluminescent activity in aqueous solution and in dimethylsulfoxide. Seven compounds were found to chemiluminesce in the presence of base and peroxydisulfate in aqueous solution and eleven compounds gave chemiluminescence in dimethylsulfoxide with base using oxygen as the oxidizing agent. The relative intensities have been determined. There is no clear correlation between substitution patterns and the presence of chemiluminescence in either series. Some preliminary kinetic studies have been made on the indole system. Product studies indicate that the indole is degraded by at least two different pathways and that chemiluminescent process is probably only a small fraction of the total chemical change occurring.
The properties of a dielectric containing semiconducting particles of various shapes (1937)

It is pointed out that, although dielectric losses in certain materials are frequently attributed to the presence of particles of conducting impurity, any discussion as to the type and magnitude of loss produced by a given quantity and disposition of impurity is often extremely vague or entirely lacking. A description is given of some experiments with a suspension of water droplets in wax, the results of which did not agree with the predictions of Wagner&apos;s theory except when the suspension was kept at a temperature near to the melting point of the wax. The behaviour of a model inhomogeneous material containing spheroidal particles is investigated analytically and it is concluded that a minute amount of conducting impurity in the form of fine needles could produce a serious loss at low frequencies, although the effect of the same quantity of impurity in spherical form would be negligible.
Atomic-Scale Heterogeneity of a Multicomponent Bulk Metallic Glass with Excellent Glass Forming Ability (2009)

We report the atomic structure of a multicomponent Cu45Zr45Ag10 bulk metallic glass investigated by state-of-the-art experimental and computational techniques. In comparison with a binary Cu50Zr50 metallic glass, Zr-rich interpenetrating clusters centered by paired and stringed Ag atoms and Cu-rich icosahedra are widely observed in the ternary Cu45Zr45Ag10 alloy. The atomic-scale heterogeneity caused by chemical short- and medium-range order is found to play a key role in stabilizing the liquid phase and in improving the glass forming ability of the multicomponent alloy.
Understanding leaky modes: slab waveguide revisited (2009)

Computational methods for determining the complex propagation constants of leaky waveguide modes have become so powerful and so readily available that it is possible to use these methods with little understanding of what they are calculating. We compare different computational methods for calculating the propagation constants of the leaky modes, focusing on the relatively simple context of a W-type slab waveguide. In a lossless medium with infinite transverse extent, a direct determination of the leaky mode by using mode matching is compared with complete mode decomposition. The mode matching method is analogous to the multipole method in two dimensions. We then compare these results with a simple finite-difference scheme in a transverse region with absorbing boundaries that is analogous to finite-difference or finite-element methods in two dimensions. While the physical meaning of the leaky modes in these different solution methods is different, they all predict a nearly identical evolution for an initial, nearly confined mode profile over a limited spatial region and a limited distance. Finally, we demonstrate that a waveguide that uses bandgap confinement with a central defect produces analogous results.
Dantrolene – A review of its pharmacology, therapeutic use and new developments (2004)

Human malignant hyperthermia is a life-threatening genetic sensitivity of skeletal muscles to volatile anaesthetics and depolarizing neuromuscular blocking drugs occurring during or after anaesthesia. The skeletal muscle relaxant dantrolene is the only currently available drug for specific and effective therapy of this syndrome in man. After its introduction, the mortality of malignant hyperthermia decreased from 80% in the 1960s to < 10% today. It was soon discovered that dantrolene depresses the intrinsic mechanisms of excitation-contraction coupling in skeletal muscle. However, its precise mechanism of action and its molecular targets are still incompletely known. Recent studies have identified the ryanodine receptor as a dantrolene-binding site. A direct or indirect inhibition of the ryanodine receptor, the major calcium release channel of the skeletal muscle sarcoplasmic reticulum, is thought to be fundamental in the molecular action of dantrolene in decreasing intracellular calcium concentration. Dantrolene is not only used for the treatment of malignant hyperthermia, but also in the management of neuroleptic malignant syndrome, spasticity and Ecstasy intoxication. The main disadvantage of dantrolene is its poor water solubility, and hence difficulties are experienced in rapidly preparing intravenous solutions in emergency situations. Due to economic considerations, no other similar drugs have been introduced into routine clinical practice.
Genotype‐phenotype correlation in adult‐onset acid maltase deficiency (1995)

We performed a clinical, biochemical, and genetic study in 16 patients from 11 families with adult-onset acid maltase deficiency. All patients were compound heterozygotes and carried the IVS1(-13T --> G) transversion on one allele; the second allele harbored either a deletion of a T at position 525 in exon 2 (7 probands, 64%) or a deletion of exon 18 (1 proband, 9%). Deterioration of handicap was related to age, and decrease in vital capacity to duration of the symptomatic stage. Respiratory insufficiency was never the first manifestation. The levels of activity of serum creatine kinase and of alpha-glucosidase in peripheral blood cells or muscle were helpful for the diagnosis, but did not have prognostic value. The adult form of acid maltase deficiency appears to be both clinically and genetically rather homogeneous; decrease of alpha-glucosidase activity is the final common pathway leading to destruction of muscle fibers and progression of muscle weakness over a period of years.
Topical negative pressure may help chronic wound healing (2002)

EDITOR—Harding et al's review article on healing chronic wounds1 fails to mention treatment with topical negative pressure, which has an emerging role in the management of chronic wounds. 2 3

The simple technique entails applying an open-pore foam dressing (polyurethane ether) to the wound. This dressing is sealed with transparent adhesive drape. A negative pressure or suction force is then applied across the wound via a drainage …
Swine As Models in Biomedical Research (1992)

MHC- Homozygous Miniature Swine Swine as a Model for Pancreatic Beta-Cell Transplantation Renal Transplantation in Swine Orthotopic Liver Transplantation in Outbred and Partially Inbred Swine The Role of the Hanford Minipig as an Animal Model in PediatricSurgery and Neonatal Intensive Care The Anephric Micropig as a Model for Peritoneal Dialysis Vascular Pharmacology of the Micropig: Importance of the Endothelium Use of Swine in the Study of Anesthetics Atherosclerotic Yucatan Microswine as a Model for Novel Cardiovascular Interventions and Imaging The spontaneously Hypercholesterolemic Pig as an Animal Model ofHuman Hypercholesterolemia The Yucatan Miniature Swine: An Atherogenic Model to Assess theEarly Patency rates of an Endovascular Stent Studies in the Physiology of Cardiopulmonary Bypass Using aSwine Model Hemorrhage and Hemorrhagic Shock in Swine: A Review Awake Porcine Model of Intraperitoneal Sepsis Wound-Healing Models in the Miniature Yucatan Pig DOCA-Treated Yucatan Miniature Swine: A Neurogenic Model of Essential Hypertension.
Epileptic seizure during patient-controlled analgesia with tramadol (2009)

Editor, A 26-year-old woman (ASA-I) was tested for pain after caesarean section with 3 mg ml−1 tramadol intravenous (i.v.) patient-controlled anaesthesia (PCA). She had no history of epilepsy, head injury or drug use. Anaesthesia was induced with propofol and succinyl choline, maintained with sevoflurane in 50% N2O/O2 with a fresh gas flow of 4 l min−1 and with fentanyl (2 μg kg−1) after delivery. Thereafter, she received tramadol (PCA) with a 50 mg initial loading dose, 20 mg incremental dose, 15-min lockout interval and 4-h limit of 200 mg. Diclofenac 75 mg intramuscular (i.m.) was also given owing to insufficient pain relief. After 8 hours of PCA (total tramadol dose 300 mg), she had generalized tonic clonic convulsions lasting 2–3 min. Diazepam 10 mg i.v. was given. Blood chemistry, electroencephalography and cranial magnetic resonance imaging were all normal. Seizures did not recur as tramadol treatment was stopped. She was discharged after a 3-day uneventful hospital stay. In a retrospective series of 190 cases, Marquardt et al.[1] reported on the adverse effects of tramadol overdose: central nervous system depression in 27.4%, nausea–vomiting in 21.1%, tachycardia in 17.4% and seizures in 13.7% were observed. The minimum dose causing seizures was 200 mg and 86.4% of the cases ensued within the first 6 h. Results of various studies have been controversial regarding the incidence of epileptic seizures in association with tramadol. Thundiyil et al.[2] found that tramadol cases constituted 7.5% of 386 patients with drug-induced epilepsy. Two other studies concluded that tramadol-related seizures were not any different from those related to other analgesics and that tramadol did not increase the frequency of idiopathic epilepsy [3,4]. In our case, we believe that rapid (300 mg in 8 h) i.v. use of tramadol may have increased the risk of convulsions. To the best of our knowledge, our patient is the first report of tramadol-induced seizures during PCA. Overall, in drawing attention to the increased use of PCA in postoperative pain management, we recommend that physicians should be aware of such complications.
Three-dimensional actuators transformed from the programmed two-dimensional structures via bending, twisting and folding mechanisms (2011)

Combining the physical principle of actuators with the basic concept of photonic crystals, colour-tunable three-dimensional (3D) photonic actuators were successfully fabricated. By controlling the d-spacings and the refractive index contrasts of the self-assembled 3D colloidal photonic crystals, colours of the photonic actuators were tuned. Various shapes of these 3D actuating objects were constructed by transforming the programmed 2D structures via bending, twisting and folding mechanisms. These 2D structures were first programmed by breaking the symmetry. The selective swellings were then applied as driving forces to control the shapes and colours of the photonic actuators. Scroll photonic actuators had been first demonstrated by bending the traditional 2D cantilever structure (K.-U. Jeong, et al., J.Mater.Chem., 2009, 19, 1956). By breaking the symmetry of a cantilever structure perpendicular to its long axis, polypeptide-/DNA-like 3D helical photonic actuators were obtained from the programmed 2D structure via twisting processes. Both left- and right-handed scrolls and helices with various colours can be achieved by changing the polarity of solvents. Different types of 3D actuators, such as cube, pyramid and phlat ball, were also demonstrated via the folding mechanism. The reversible 3D photonic actuators transformed from the programmed 2D structures via the bending, twisting and folding mechanisms may be applied in the field of mechanical actuators, and optoelectronic and bio-mimetic devices.
Tumor-Directed Targeting of Liposomes (2002)

Tumor-specific targeting is a critical goal in the research area of liposomal drug delivery. Identification of the specific interactions between ligands and target tumor cells is a principle prerequisite in achieving this goal. Generally, tumor cells aberrantly express tumor-associated antigens that can be utilized as appropriate target molecules. Monoclonal antibodies against tumor-associated antigens have been successfully adopted for targeting to various types of cancer cells. The incorporation of humanized monoclonal antibodies or single chain human antibodies, instead of rodent antibodies into immunoliposomes has resulted in better clinical applicability. Tumor-specific ligands other than monoclonal antibodies have also been investigated as in vivo tumor-directing molecules. However, the number of pre-clinical studies of anticancer treatments using tumor-specific liposomal drugs reporting successful targeting and enhanced therapeutic efficacy has been limited. Further refinement of tumor-specific interactions and liposomal formulations will be necessary for the application of the tumor-specific liposomal drug strategy for anticancer chemotherapy or gene therapy.
Regulation of DNA synthesis in fat cells and stromal elements from rat adipose tissue (1968)

The incorporation of tritiated thymidine into the deoxyribonucleic acid (DNA) of adipose fat and stromal cells was followed under a variety of conditions. After in vitro incubation of adipose slices or up to 2 days after in vivo injection of the isotope, all DNA radioactivity was in the stromal cell fraction. From 2 to 15 days after thymidine injection total tissue DNA radioactivity was constant, while between 2 and 5 days after injection label in fat cell DNA increased markedly. Thus new labeled fat cells, initially collected in the stromal pool, required 2-5 days after completion of DNA synthesis to accumulate sufficient lipid to be harvested in the fat cell fraction. Fasting before thymidine injection practically abolished DNA synthesis in primordial fat cells and reduced less drastically formation of stromal elements. However fasting sufficient to deplete lipid stores by 50% neither destroyed mature fat cells nor impaired their capacity to reaccumulate fat with refeeding. Other studies evaluated the role of new fat cell formation in the process of lipid accretion accompanying refeeding. These experiments indicated that at least during the early phase of rapid weight gain, accumulation of fat was due to deposition of triglyceride in existing cells rather than to accelerated formation of new fat cells. Studies with hypophysectomized rats demonstrated that pituitary ablation variably affected stromal DNA synthesis and nearly abolished the formation and (or) maturation of primordial fat cells. In these animals growth hormone markedly enhanced thymidine incorporation into stromal DNA but had no effect on fat cell precursors. In intact animals the predominant effect of growth hormone was also on the stromal fraction, although an action of the hormone of lesser magnitude on fat cell precursors was also evident.
Experimental status of the 100 MW Gyroklystron system at the University of Maryland (2002)

Summary form only given. A test bed for implementation of first harmonic and second harmonic coaxial gyroklystrons is nearing its completion stages. This presentation includes the details of each major component's construction status as well as any relevant physical parameters. Designs of a fundamental frequency (8.568 GHz) and second-harmonic (17.136 GHz) microwave circuit have already been accomplished after selection among various two and three cavity designs. Predicted efficiencies near 40% for both these circuits using a large signal code have made them acceptable candidates for high power testing on the new test bed. The first harmonic circuit consists only of an input and output cavity while the second harmonic system has an additional buncher cavity situated between the input and output cavity to boost gain and efficiency up to 49 dB and 41% respectively. Cold testing of the constructed cavity parts are performed to verify their resonant frequency and Q with those predicted from our scattering matrix codes. These microwave circuits are ultimately studied using a 320 MW electron beam from the newly designed and constructed magnetron injection gun (MIG). Cold test results of the first harmonic output cavity indicate that its resonant frequency and Q are 8.568 GHz/spl plusmn/2 MHz and 134/spl plusmn/6 respectively. Because the input cavity's Q derives mostly from lossy properties introduced via ceramics, the required Q of 52 as dictated by the large signal codes are obtained purely from empirical methods during cold testing. The measured resonant frequency and Q of the input and buncher cavities along with descriptions and schematics of all these coaxial circuit cold test setups are presented.
Tolerance Band Modulation Methods for Modular Multilevel Converters (2014)

Modular multilevel converters (M2Cs) are increasingly used in high-voltage direct current (HVDC) systems. The efficiency of M2Cs is influenced by the modulation and cell selecting methods, which determines the switching frequency and capacitor voltage ripple in the converter station. A new approach to modulation of the M2C is presented in this paper. Tolerance band methods are employed to obtain the switching instants, and also cell selection. The proposed methods overcome the modulation problem for converters with few cells on one hand and also reduce the sorting efforts for cell balancing purposes of many cells converter on the other hand. Three different algorithms are also proposed to balance the cell capacitor voltages. The evaluation is done in time-domain simulation by which the performance of each method is studied in both the steady-state and transient cases. It is observed that using tolerance band methods not only reduces the switching frequency but also allows for handling severe fault cases in a grid-connected system. Eventually, the most promising tolerance band method has been implemented and verified in a real-time digital simulator, RTDS®. The average switching frequency of 70 Hz has been achieved for the system under study, while the capacitor voltage ripple is limited to 10% of the nominal cell voltage.
CALCIUM BINDING TO THERMITASE. CRYSTALLOGRAPHIC STUDIES OF THERMITASE AT 0, 5 AND 100 MM CALCIUM (1990)

The three-dimensional crystal structure of thermitase complexed with eglin-c in the presence of 100 mM calcium has been determined and refined at 2.0-A resolution to a R-factor of 16.8%. This crystal structure is compared with previously determined structures of thermitase at 0 and 5 mM calcium concentration. In the presence of 100 mM calcium all three calcium binding sites in thermitase are fully occupied. At 100 mM CaCl2 the "weak" calcium binding is occupied by a calcium ion, which is chelated by three protein ligands and four water molecules in a pentagonal bipyramid geometry. Thermitase has, apparently, a monovalent and divalent cation binding position at 2.5-A distance from each other at this site. At low calcium concentrations the monovalent-ion position is occupied by a sodium or potassium ion. The "medium strength" binding site shows in the presence of 100 mM CaCl2 a square antiprism arrangement with eight ligands, of which seven are donated by the protein. At low calcium concentrations we observe a distorted pentagonal bipyramid coordination at this site. The largest difference between these two conformations is observed for ligand Asp-60, which has two conformations with 0.8-A difference in C alpha positions. The "strong" calcium binding site has a pentagonal bipyramid coordination and is fully occupied in all three structures. Structural changes on binding calcium to the weak and "medium strength" calcium binding sites of thermitase are limited to the direct surroundings of these sites. Thermitase resembles in this respect subtilisin BPN' and does not exhibit long-range shifts as have been reported for proteinase K.
Interlaced Kalman filtering of 3D angular motion based on Euler's nonlinear equations (1994)

A novel Kalman filtering technique is presented that reduces the mean-square-error (MSE) between three-dimensional (3D) actual angular velocity values and estimated ones by an order of magnitude (when compared with the MSE resulting from direct measurements) even under extremely low signal-to-noise ratio conditions. The filtering problem is nonlinear in nature because the dynamics of 3D angular motion are described by Euler's equations. This nonlinear set of differential equations state that the angular acceleration in one axis is proportional to the torque applied to that axis, and to the products of angular velocity components in the other two axes of rotation. Instead of using extended Kalman filtering techniques to solve this complex problem, the authors developed a new approach where the nonlinear Euler's model is decomposed into two pseudolinear models (primary and secondary). The first model describes the time progression of the state vector containing the linear terms, while the other characterizes the propagation of the state vector containing the nonlinearities. This makes it possible to run two interlaced discrete-linear Kalman filters simultaneously. One filter estimates the values of the state vector containing the linear terms, while the other estimates the values of the state vector containing the nonlinear terms in the system. These estimates are then recombined, solving the nonlinear estimation process without linearizing the system. Thus, the new approach takes advantage of the simplicity, computational efficiency and higher convergence speed of the linear Kalman filter form and it overcomes many of the drawbacks typical of conventional extended Kalman filtering techniques. The high performance and effectiveness of this method is demonstrated through a computer simulation case study.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>