gebhart/patrepeval huggingface dataset:
Computer Design of Anticancer Drugs. A New Enediyne Warhead (2000)

Seven criteria are developed and discussed that lead to the design of a new enediyne anticancer drug, which should have low toxicity but high biological selectivity and activity when attacking the DNA of tumor cells. These criteria concern (among others) the thermodynamic and kinetic stability of the species involved in the reaction of an enediyne, the biradical character and H-abstraction ability of the intermediate biradical generated in a Bergman reaction of the enediyne, and the basicity of the enediyne and its associated biradical. Thirteen different heteroenediynes were investigated with the help of B3LYP/6-31G(d,p) calculations to find a suitable candidate for a new enediyne anticancer drug, which fulfills the seven criteria. These calculations included the determination of reaction profiles for Bergman and retro-Bergman reactions, the calculation of singlet−triplet splittings of biradicals formed from enediynes, and the prediction of pKa values. Results were tested by using a larger basis set (6-311+G(3df,3pd)), another functional (BLYP), and coupled cluster methods such as CCSD(T) and the Brueckner orbitals-based BD(T) method. The best candidate for a new enediyne anticancer drug is an N,C-dialkynyl aldimine incorporated into a cyclodecaene ring.
Trilevel reactive ion etching processes for fabrication of 60 nm germanium structures with high aspect ratio (1993)

We investigated the influence of different parameters in reactive ion etching (RIE) on the anisotropy of 60 nm test structures in a 360-nm-thick layer of germanium. Structures of similar dimensions are required for zone plates in x-ray microscopy. A simple optical setup for the holographic exposure of gratings with a period of 120 nm is presented. The gratings cover an area of several mm2. This allows for splitting of the structures perpendicular to the grating lines and successive examination of the etch profiles in a scanning electron microscope. Two different trilevel systems were developed for structuring germanium in a CBrF3 plasma. Both trilevel systems use AZ 1350 photoresist on an intermediate layer of titanium. The bottom layer is either polyimide, which is structured by RIE in an oxygen plasma, or nickel, which is etched in a hydrogen plasma highly selective to titanium. The anisotropy of the germanium etch process has been found to increase with the ratio R of self-bias to gas pressure, whereas the selectivity decreases. The higher stability of the nickel mask allows us to choose higher values of R resulting in etch profiles with nearly vertical sidewalls.
The Steady-State Internal Redox State (NADH/NAD) Reflects the External Redox State and Is Correlated with Catabolic Adaptation in <i>Escherichia coli</i> (1999)

Escherichia coli MC4100 was grown in anaerobic glucose-limited chemostat cultures, either in the presence of an electron acceptor (fumarate, nitrate, or oxygen) or fully fermentatively. The steady-state NADH/NAD ratio depended on the nature of the electron acceptor. Anaerobically, the ratio was highest, and it decreased progressively with increasing midpoint potential of the electron acceptor. Similarly, decreasing the dissolved oxygen tension resulted in an increased NADH/NAD ratio. As pyruvate catabolism is a major switch point between fermentative and respiratory behavior, the fluxes through the different pyruvate-consuming enzymes were calculated. Although pyruvate formate lyase (PFL) is inactivated by oxygen, it was inferred that the in vivo activity of the enzyme occurred at low dissolved oxygen tensions (DOT </= 1%). A simultaneous flux from pyruvate through both PFL and the pyruvate dehydrogenase complex (PDHc) was observed. In anaerobic cultures with fumarate or nitrate as an electron acceptor, a significant flux through the PDHc was calculated on the basis of the redox balance, the measured products, and the known biochemistry. This result calls into question the common assumption that the complex cannot be active under these conditions. In vitro activity measurements of PDHc showed that the cellular content of the enzyme varied with the internal redox state and revealed an activity for dissolved oxygen tension of below 1%. Whereas Western blots showed that the E3 subunit of PDHc (dihydrolipoamide dehydrogenase) did not vary to a large extent under the conditions tested, the E2 subunit (dihydrolipoamide acetyltransferase) amount followed the trend that was found for the in vitro PDHc activity. From this it is concluded that regulation of the PDHc is exerted at the E1/E2 operon (aceEF). We propose that the external redox state (measured as the midpoint potentials of those terminal acceptors with which the cell has sufficient capacity to react) is reflected by the internal redox state. The latter may subsequently govern both the expression and the activity of the two pyruvate-catabolizing enzymes.
Neuregulin stimulation of cardiomyocyte regeneration in mice and human myocardium reveals a therapeutic window (2015)

Therapies developed for adult patients with heart failure have been shown to be ineffective in pediatric clinical trials, leading to the recognition that new pediatric-specific therapies for heart failure must be developed. Administration of the recombinant growth factor neuregulin-1 (rNRG1) stimulates regeneration of heart muscle cells (cardiomyocytes) in adult mice. Because proliferation-competent cardiomyocytes are more abundant in growing mammals, we hypothesized that administration of rNRG1 during the neonatal period might be more effective than in adulthood. If so, neonatal rNRG1 delivery could be a new therapeutic strategy for treating heart failure in pediatric patients. To evaluate the effectiveness of rNRG1 administration in cardiac regeneration, newborn mice were subjected to cryoinjury, which induced myocardial dysfunction and scar formation and decreased cardiomyocyte cell cycle activity. Early administration of rNRG1 to mice from birth to 34 days of age improved myocardial function and reduced the prevalence of transmural scars. In contrast, administration of rNRG1 from 4 to 34 days of age only transiently improved myocardial function. The mechanisms of early administration involved cardiomyocyte protection (38%) and proliferation (62%). We also assessed the ability of rNRG1 to stimulate cardiomyocyte proliferation in intact cultured myocardium from pediatric patients. rNRG1 induced cardiomyocyte proliferation in myocardium from infants with heart disease who were less than 6 months of age. Our results identify an effective time period within which to execute rNRG1 clinical trials in pediatric patients for the stimulation of cardiomyocyte regeneration.
Optimization of ion-atomic beam source for deposition of GaN ultrathin films (2014)

We describe the optimization and application of an ion-atomic beam source for ion-beam-assisted deposition of ultrathin films in ultrahigh vacuum. The device combines an effusion cell and electron-impact ion beam source to produce ultra-low energy (20-200 eV) ion beams and thermal atomic beams simultaneously. The source was equipped with a focusing system of electrostatic electrodes increasing the maximum nitrogen ion current density in the beam of a diameter of ≈15 mm by one order of magnitude (j ≈ 1000 nA/cm(2)). Hence, a successful growth of GaN ultrathin films on Si(111) 7 × 7 substrate surfaces at reasonable times and temperatures significantly lower (RT, 300 °C) than in conventional metalorganic chemical vapor deposition technologies (≈1000 °C) was achieved. The chemical composition of these films was characterized in situ by X-ray Photoelectron Spectroscopy and morphology ex situ using Scanning Electron Microscopy. It has been shown that the morphology of GaN layers strongly depends on the relative Ga-N bond concentration in the layers.
PS200. Effects of p11 on BDNF-induced changes in dendritic outgrowth and spine formation in primary hippocampal cells (2016)

73refractory depression, we have compared BDNF levels in frontal cortex, hippocampus, and amygdala in each group of animals.In addition, we have measured BDNF and BDNF expression related microRNA (miRNA206) contents in all exosome and brain-derived exosome in the peripheral blood, aimed at the identification of peripheral molecular dynamics that specifically reflect the changes in the brain.All experiments have carried out according to the approval of the Sapporo Medical University Animal Care and Use Committee with consideration so as not to give unnecessary pain to the animal.We have found that blood BDNF levels of refractory depression (7.4 ng/ml ± 1.50) showed significantly higher (p<0.05)than the controls (5.6 ng/ml ± 1.02) and simple depression models (4.5 ng/ml ± 0.84), and antidepressant tended to increase the BDNF levels in depression model (6.2 ng/ml ± 1.54), but reduced in refractory depression models (5.6 ng/ml ± 1.38).Furthermore, interestingly, the variation of blood BDNF levels and the way of the changes in the exosome is different.In considering the clinical report that indicated higher levels of blood BDNF in the non-reactive group of antidepressant treatment prior to administration, we are continuing analysis to identify the pathological mechanism that is common to the intractable depression.
Analytical prediction of the cogging torque in radial-field permanent magnet brushless motors (1992)

A method for predicting the cogging torque in radial-field permanent magnet brushless motors, based on the analytical calculation of the airgap field distribution and the net lateral force acting on the stator teeth, is developed and validated. The technique is applicable to both internal and external rotor motor topologies, modeled in a cylindrical coordinate system. It can also be applied to variants of the basic motor topologies, such as those with shifted magnets (i.e. spaced unsymmetrically) or unevenly distributed stator slots, and thus it can enable design features aimed at reducing the level of cogging torque to be evaluated. Based on the proposed analytical model, the effects of varying the leading design parameters on the cogging torque can be investigated. Hence, an optimal combination of design parameters can be identified to enable low cogging torque motors to be designed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Kinetic mechanism of glucose dehydrogenase from Halobacterium salinarum. (1999)

The kinetic mechanism of glucose dehydrogenase (EC 1.1.1.47) from Halobacterium salinarum was studied by initial velocity and product inhibition methods. The results suggest that both, in the forward and reverse direction, the reaction mechanism is of Bi Bi sequential ordered type involving formation of ternary complexes. NADP+ adds first and NADPH formed dissociates from the enzyme last. For the reverse direction, NADPH adds first and NADP+ leaves last. Product inhibition experiments indicate that (a), the coenzymes compete for the same site and form of the enzyme and (b), ternary abortive complexes of enzyme-NADP(+)-glucono-delta-lactone and enzyme-NADPH-glucose are formed. All the other inhibitions are noncompetitive.
Pharmacokinetic/pharmacodynamic serum and urine profile of cefditoren following single-dose and multiple twice- and thrice-daily regimens in healthy volunteers: a phase I study. (2007)

The objectives of this randomized, double-blind study were to evaluate the pharmacokinetics, and the pharmacodynamic and gastrointestinal (GI) tolerance of cefditoren pivoxil in healthy adult male volunteers when it is administered three times a day. Twenty healthy volunteers were included in the study. On day 1, 10 subjects received a 200-mg single dose of cefditoren pivoxil and 10 received a 400-mg dose. After a washout period of 8 days, eight subjects received cefditoren pivoxil 400 mg b.i.d., eight received 400 mg t.i.d., and four received placebo for 10 days. Medication was taken 30 min after meals. Blood and urine collections were carried out on days 1, 9, 14 and 19. Volunteers were asked about any GI change, especially about bowel habits, nausea, vomiting and abdominal pain. The maximum cefditoren concentration (C(max)) had a mean value of 3.77+/-0.66 mg/l, and was reached between 1.5 and 3 h in the thrice-daily administration. In the twice-daily regimen, the C(max) was 3.27+/-0.64 mg/l. The mean time above breakpoint minumum inhibitory concentration (MIC), calculated with data from each pharmacokinetic profile, was always above 40%, in both the twice- and thrice-daily regimens. The half-life of cefditoren was 1.19+/-0.2 h and 1.36+/-0.2 h in the twice-daily and thrice-daily regimens, respectively. The C(max) of cefditoren in urine was reached between 2 and 4 h postadministration, with a mean value of 154.53 mg/l in the twice-daily regimen, and 186.59 mg/l in the thrice-daily administration. There were no differences between the groups in the incidence of GI adverse events. The present data show that the administration of cefditoren pivoxil 400 mg t.i.d. is possible because it is well tolerated, and it increases the probability of success when the MIC of the causative bacteria is close to the susceptibility breakpoint. The high concentrations of active drug in the urine enable cefditoren to be considered as a useful candidate for the treatment of uncomplicated urinary tract infections (UTIs).
Everything Wired Must CONVERGE (1997)

The fusion of disparate information systems is creating new clarity for companies, their suppliers, and their customers.
Coupling membranes as energy-transmitting cables. I. Filamentous mitochondria in fibroblasts and mitochondrial clusters in cardiomyocytes. (1988)

An hypothesis considering mitochondria as intracellular power-transmitting protonic cables was tested in human fibroblasts where mitochondria are thin and long and in rat cardiomyocytes where they show cluster organization. Mitochondria in the cell were specifically stained with fluorescent-penetrating cation ethylrhodamine, which electrophoretically accumulates in the mitochondrial matrix. A 40-micron-long mitochondrial filament of fibroblast was illuminated by a very narrow (less than or equal to 0.5 micron) laser beam to induce local damage of the mitochondrial membranes. Such a treatment was found to induce quenching of the ethylrhodamine fluorescence in the entire filament. According to the electron microscope examination, the laser-treated filament retained its continuity after the laser illumination. Other mitochondrial filaments (some of which were localized at a distance less than 10 micron from the laser-treated one) remained fluorescent. In a cell where mitochondrial filaments seemed to be united in a network, laser illumination of one filament resulted in fluorescence quenching in the whole network, whereas fluorescence of small mitochondria not connected with the network was unaffected. The illumination of cardiomyocyte was found to result in the fluorescence quenching not only in a laser-illuminated mitochondrion but also in a large cluster of organelles composed of many mitochondria. Electron microscopy showed that all the mitochondria in the cluster change from the orthodox to the condensed state. It was also found that mitochondria in the cluster are connected to one another with specific junctions. If a mitochondrion did not form junctions with a quenched cluster, its fluorescence was not decreased even when this mitochondrion was localized close to an illuminated one. The size of the mitochondrial cluster may be as long as 50 micron. The cluster is formed by branched chains of contacting mitochondria, which may be defined as Streptio mitochondriale. In the cardiomyocyte there are several mitochondrial clusters or, alternatively, the quenched cluster is a result of decomposition of a supercluster uniting all the mitochondria of the cell. Cluster organization of mitochondria could also be revealed when a single mitochondrion was punctured in situ with a microcapillary. The obtained data are in agreement with the idea that mitochondrial junctions are H+ permeable so that, within the cluster, delta psi may be transmitted from one mitochondrion to another. The above results are consistent with the assumption that mitochondrial filaments or networks represent a united electrical system.(ABSTRACT TRUNCATED AT 400 WORDS)
Octopus rhodopsin Amino acid sequence deduced from cDNA (1988)

The primary structure of rhodopsin from the octopus Paroctopus defleini has been determined by parallel analysis of the protein and corresponding cDNA. The amino acid sequence is most similar to the recently cloned Drosophila opsins. Similarities to bovine and human opsins are also evident. The transmembrane topology of octopus rhodopsin is discussed.
Durability of Oilwell Cement Formulations Aged in H2S-Containing Fluids (2006)

Abstract In the next few decades, the production of oilfields with high contents of associated sour gases will increase. For instance, we estimate that 40% of the world remaining gas reserves contain more than 2% of CO2 and/or more than 100 ppm of H2S. Therefore, investigations on technologies to produce such fields are of utmost importance. Due to the presence of corrosive gas, special attention has to be paid to the design of well materials (casing, cementing materials). Corrosion of steel due to acid gas containing brines is well documented in the literature, and to a lesser extent, data about the degradation by wet CO2 or wet H2S can be found. For cementitious materials, one can find abundant literature dealing with deterioration of cement pastes due to CO2 environment. Published data on degradation mechanisms of cement-based materials exposed to H2S environments are more scarce. This paper addresses the problem of durability of oilwell cement in different hydrogen sulphide environments. Different periods of time can be identified in the lifetime of the wells: the production period (about 20 to 40 years), the post-abandonment period (some tens of years following the permanent well abandonment) and the abandonment period (several centuries). For each period of time, cementing materials (primary cementing, plugs) are in contact with different types of fluids. Therefore, to correctly assess the behaviour of oilwell cement, ageing tests have to be carried out in fluids representative of these different periods of time. In this paper, we present the methodology implemented under HP/HT conditions for ageing tests of materials in H2S-containing fluids and results obtained on cement-based materials. Main physico-chemical degradation mechanisms of cement-based materials due to H2S are identified using different characterization techniques. Depending of the nature of the fluid in contact with cementitious materials, severe degradation can occur with dramatic impairment of macroscopic properties.
New acoustic systems for AUV tracking, communications, and noise measurement at NSWCCD-ARD, Lake Pend Oreille, Idaho (2003)

This paper describes a newly developed acoustic system for AUV tracking and communications at the Naval Surface Warfare Center (NSWC), Acoustic Research Detachment (ARD) in Bayview, Idaho. This acoustic tracking and communications system (ATACS) has unique capabilities and is highly versatile to support a variety of AUV tests. ATACS software and hardware create a turn-key system which could be replicated and deployed in a wide variety of ocean or fresh-water environments. The system is currently supporting large scale vehicle (LSV) model experiments for NAVSEA sponsors but has capabilities that can support testing such as verification of guidance systems and operation of constellations of multiple AUVs. The system can be configured to simultaneously track and communicate with a large number of independent AUVs, each transmitting a unique identifier code. Global Positioning System (GPS) clocks are distributed to analog-to-digital (A/D) converters throughout the system to provide global synchronization of sampling. Calibration of system timing characteristics allow precise system timing and ranging accuracy. Software-based ranging receiver algorithms are highly flexible and support both coherent and non-coherent ping types. The system can receive pinger frequencies between 10 kHz and 120 kHz and effectively transmit between 25 kHz and 120 kHz. Real-time detection software runs on a VME-based multi-processor system. Detected signals are passed to a host processor for precise timing estimates and telemetry demodulation. Range and telemetry information is then broadcast across the Ethernet to various client applications such as vehicle tracking and control, beamsteering, etc. This instrumented test range covers over 2 square miles with a lake depth of 1100 feet. The effective tracking area extends over 10 square miles. Six bottom-mounted transceiver units provide bi-directional communications and ranging with AUVs. Each transceiver unit is buoyed 100 feet off the lake bottom and contains separate broadband source and hydrophone elements.
Yeast two-hybrid cloning of a novel zinc finger protein that interacts with the multifunctional transcription factor YY1 (1997)

Muscle-restricted transcription of sarcomeric actin genes is negatively controlled by the zinc finger protein YY1, which is down-regulated at the protein level during myogenic differentiation. To identify cellular proteins that might mediate the function/stability of YY1 in muscle cells, we screened an adult human muscle cDNA library using the yeast two-hybrid cloning system. We report the isolation and characterization of a novel protein termed YAF2 (YY1- associated factor 2) that interacts with YY1. The YAF2 cDNA encodes a 180 amino acid basic protein (pI 10.5) containing a single N-terminal C2-X10-C2 zinc finger. Lysine clusters are present that may function as a nuclear localization signal. Domain mapping analysis shows that the first and second zinc fingers of YY1 are targeted for YAF2 protein interaction. In contrast to the down-regulation of YY1, YAF2 message levels increase during in vitro differentiation of both rat skeletal and cardiac muscle cells. YAF2 appears to have a promyogenic regulatory role, since overexpression of YAF2 in C2 myoblasts stimulates myogenic promoter activity normally restricted by YY1. Co-transfection of YY1 reverses the stimulatory effect of YAF2. YAF2 also greatly potentiates proteolytic cleavage of YY1 by the calcium- activated protease m-calpain. The isolation of YAF2 may help in understanding the mechanisms through which inhibitors of myogenic transcription may be antagonized or eliminated by proteolysis during muscle development.
ChemInform Abstract: Chemical Vapor Deposition of Nitride Thin Films (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.