gebhart/patrepeval huggingface dataset:
Determination of minimum bactericidal concentrations of oxacillin for Staphylococcus aureus: influence and significance of technical factors (1983)

The minimum bactericidal concentration of oxacillin for Staphylococcus aureus was shown to be considerably influenced by technical and definitional factors, particularly by the survival of some organisms on the walls of test tubes and by the growth phase of the inoculum. Attention to technical detail greatly improved reproducibility, and log-phase cultures of all strains showed greater than 99.9% killing in 24 h, at or close to the minimum inhibitory concentration, including eight strains described as tolerant. Some strains showed the paradoxical phenomenon of having more survivors in higher concentrations above the minimum bactericidal concentration. An accepted reference minimum bactericidal concentration procedure is needed for establishing clinical correlates and for a review of endpoint criteria. Routine minimum bactericidal concentration tests on S. aureus should be interpreted with great caution.
A simple in vivo assay for increased protein solubility (1999)

Low solubility is a major stumbling block in the detailed structural and functional characterization of many proteins and isolated protein domains. The production of some proteins in a soluble form may only be possible through alteration of their sequences by mutagenesis. The feasibility of this approach has been demonstrated in a number of cases where amino acid substitutions were shown to increase protein solubility without altering structure or function. However, identifying residues to mutagenize to increase solubility is difficult, especially in the absence of structural knowledge. For this reason, we have developed a method by which soluble mutants of an insoluble protein can be easily distinguished in vivo in Escherichia coli. This method is based on our observation that cells expressing fusions of an insoluble protein to chloramphenicol acetyltransferase (CAT) exhibit decreased resistance to chloramphenicol compared to fusions with soluble proteins. We found that a soluble mutant of an insoluble protein fused to CAT could be selected by plating on high levels of chloramphenicol.
CROSSLINKING CHEMISTRY FOR FLUOROCARBON ETHER BIBENZOXAZOLE POLYMERS (1976)

Curable and hydrolytically stable FEB copolymers were synthesized by the acetic acid-promoted copolycondensation of tetrafluoroethylene oxide: hexafluoropropylene oxide-derive dithioimidate esters with fluorocarbon ether bis(o-aminophenol) monomers and a fluorocarbon bis(o-aminophenol) monomer containing an aliphatic hydrocarbon cure site. The structure of the cure site monomer was molecularly tailored to possess sufficient solubility and reactivity during the polycondensation reactions to permit incorporation of the appropriately structured cure sites into the FEB copolymer backbone. Thermogravimetric analysis and isothermal aging studies indicated high thermooxidative stability almost comparable to analogous FEB polymers void of the hydrocarbon cure sites. Isothermal aging in air at 260C (500F) and 288C (550F) for 200 hours led to weight losses of 7 and 17 percent, respectively. Preliminary formulation and curing studies demonstrated the reactivity of the cure sites to radical-induced cure reactions. Based on the low temperature viscoelastic properties, the high thermooxidative and hydrolytic stability, as well as the ready curability of the FEB copolymers, a broader use temperature range capability than currently available in state-of-the-art elastomer materials is envisioned.
New miniaturized tunneling-based gyro for inertial measurement applications (1999)

Microelectromechanical (MEM) technology promises to significantly reduce the size, weight, and cost of a variety of sensor systems. For vehicular, tactical, or personal inertial/GPS navigation systems, high performance MEM gyroscopes are required with 1–100°/h resolution and stability. To date, this goal has proven difficult to achieve with low cost manufacturing for many of the previous approaches using Coriolis-based devices due, in part, to the need to precisely tune the drive and sense resonant frequencies or to employ large millimeter-size structures. We have designed, fabricated, and tested a new highly miniaturized tunneling-based gyro that employs the high displacement sensitivity of quantum tunneling to obtain the desired resolution without the need for precise mechanical frequency matching. Our first tested devices with 300-μm-long cantilevers have demonstrated 27°/h/√Hz noise floors. Measurements indicate that this number can be reduced to near the thermal noise floor of 3°/h/√Hz when a closed loop servo, operating at the device’s oscillation frequency, is implemented around the sensor.
Quaternary dynamics and plasticity underlie small heat shock protein chaperone function (2010)

Small Heat Shock Proteins (sHSPs) are a diverse family of molecular chaperones that prevent protein aggregation by binding clients destabilized during cellular stress. Here we probe the architecture and dynamics of complexes formed between an oligomeric sHSP and client by employing unique mass spectrometry strategies. We observe over 300 different stoichiometries of interaction, demonstrating that an ensemble of structures underlies the protection these chaperones confer to unfolding clients. This astonishing heterogeneity not only makes the system quite distinct in behavior to ATP-dependent chaperones, but also renders it intractable by conventional structural biology approaches. We find that thermally regulated quaternary dynamics of the sHSP establish and maintain the plasticity of the system. This extends the paradigm that intrinsic dynamics are crucial to protein function to include equilibrium fluctuations in quaternary structure, and suggests they are integral to the sHSPs' role in the cellular protein homeostasis network.
Purification and characterization of the recombinant alginate lyase from Pseudomonas sp. leaked by Escherichia coli upon addition of glycine (1995)

The plasmid pAL205 encodes an alginate lyase gene of Pseudomonas sp. OS-ALG-9, fused in frame to the β-galactosidase α-peptide gene. The alginate lyase (Aly) expressed in Escherichia coli (pAL205) was significantly secreted into the medium by the addition of glycine. The extracellular enzyme isolated from the culture of E. coli JM109 (pAL205) was purified over 15 000-fold by successive chromatography and subjected to amino acid sequence analysis. The sequence determined was identical to that of the intracellular protein. Since the activity and molecular size of the extracellular Aly is identical to the intracellular protein and to the Aly isolated from Pseudomonas, the glycine does not affect or modify the Aly during its leakage into the medium.
Motion Artifact Reduction Using a Convolutional Neural Network for Dynamic Contrast Enhanced MR Imaging of the Liver (2019)

A deep learning-based method for removing motion artifacts in images obtained via DCE-MRI of the liver was demonstrated and validated.
Intrinsic near-24-h pacemaker period determines limits of circadian entrainment to a weak synchronizer in humans (2001)

Endogenous circadian clocks are robust regulators of physiology and behavior. Synchronization or entrainment of biological clocks to environmental time is adaptive and important for physiological homeostasis and for the proper timing of species-specific behaviors. We studied subjects in the laboratory for up to 55 days each to determine the ability to entrain the human clock to a weak circadian synchronizing stimulus [scheduled activity-rest cycle in very dim (approximately 1.5 lux in the angle of gaze) light-dark cycle] at three approximately 24-h periods: 23.5, 24.0, and 24.6 h. These studies allowed us to test two competing hypotheses as to whether the period of the human circadian pacemaker is near to or much longer than 24 h. We report here that imposition of a sleep-wake schedule with exposure to the equivalent of candle light during wakefulness and darkness during sleep is usually sufficient to maintain circadian entrainment to the 24-h day but not to a 23.5- or 24.6-h day. Our results demonstrate functionally that, in normally entrained sighted adults, the average intrinsic circadian period of the human biological clock is very close to 24 h. Either exposure to very dim light and/or the scheduled sleep-wake cycle itself can entrain this near-24-h intrinsic period of the human circadian pacemaker to the 24-h day.
Planar native-oxide index-guided AlxGa1−xAs-GaAs quantum well heterostructure lasers (1991)

A new form of planar index-guided laser diode is demonstrated with a relatively thick (∼0.4 μm) native oxide employed to define the lateral optical waveguide (transverse to the laser stripe). Oxidation of high-gap AlxGa1−xAs in a ‘‘wet’’ ambient results in the transformation of most of the upper confining layer to a lower-index current-blocking native oxide outside of the active stripe. Planar quantum well heterostructure (QWH) AlxGa1−xAs-GaAs laser diodes fabricated by this process exhibit both optical and current confinement. Continuous 300 K threshold currents as low as 10 mA (uncoated facets) and kink-free single-longitudinal-mode operation are demonstrated for ∼2-μm-wide active region devices.
The effect of aspirin, ticlopidine and their low‐dose combination on platelet aggregability in acute ischemic stroke: a short duration follow‐up study (1999)

We investigated the effects of aspirin (300 mg/d), ticlopidine (500 mg/d) and their low-dose combination (aspirin 100 mg/d plus ticlopidine 250 mg/d) on the platelet aggregability using the Wu and Hoak method. Each treatment group consisted of 25 patients with acute ischemic stroke. Platelet aggregation ratios (PAR) were measured on the 1(st) (before treatment), 10(th) and 90(th) days in the treatment groups and compared with those of 25 control cases. On the first day, comparison of PAR in each treatment group with the control was significant, while the differences between treatment groups were not significant. On the 90(th) day, differences of PAR between aspirin and control were significant, but differences between the other treatment groups and the control group were not significant, indicating a lower anti-aggregant efficacy of aspirin. Our study suggests that PAR determination can be used to assess the efficacy of anti-aggregant drugs. Our crude observation also suggests a higher anti-aggregant efficacy of ticlopidine, and aspirin plus ticlopidine, than aspirin. In addition, proper doses of aspirin plus ticlopidine may be a good choice for the prevention of ischemic stroke. Further studies are required to assess whether PAR determination could be useful for assessing patients at risk of stroke, and for drug selection for the prevention of stroke.
Buspirone (1999)

The Food and Drug Administration approved the use of buspirone for generalized anxiety disorder (GAD) in 1986. Since then, numerous studies have examined the efficacy and safety of buspirone for patients with not only generalized feelings of anxiety, but also panic disorder, major depressive disorder, obsessive-compulsive disorder, body dysmorphic disorder, social phobia, posttraumatic stress disorder, selective serotonin reuptake inhibitor-induced adverse events, dementia, behavioral disturbances, attention deficit-hyperactivity disorder, and tobacco dependency. Although relatively few placebo-controlled trials have been conducted on patients with problems other than GAD, an ever-growing body of research suggests future directions for the use of buspirone. This article reviews the body of research relating to new uses for buspirone.
Identification of a common nucleotide sequence in the 3'-untranslated region of mRNA molecules specifying inflammatory mediators. (1986)

Recently, cDNA sequences have been reported for both human and murine tumor necrosis factor (TNF; cachectin). The coding region of the TNF genes is highly conserved between man and mouse; 80% homology is apparent at the amino acid level. We now observe that a 33-nucleotide sequence, comprised entirely of A and T residues and located in the 3'-untranslated region, is conserved in toto in the murine and human TNF mRNAs. Since the 3'-untranslated region is normally not conserved, we reasoned that this sequence might play a regulatory role. We identified a consensus sequence (TTATTTAT) present in the 3'-untranslated region of both human and mouse TNF mRNAs, as well as the mRNAs encoding human lymphotoxin, human colony stimulating factor, human and mouse interleukin 1, human and rat fibronectin, and most of the sequenced human and mouse interferons. All of these mRNAs, except the lymphotoxin mRNA, lack homology to the TNF mRNAs in the coding region. The consensus sequence is uncommon among mammalian mRNAs in general, but it appears with a frequency greater than chance alone would dictate, suggesting that it may serve a specific regulatory function among the mRNAs in which it is found. It is particularly prevalent among mRNAs encoding proteins related to the inflammatory response.
Optimizing HTHP Cementing Operations (2002)

Abstract Successful cementing jobs are critical to economically completing HTHP wells. BP and Schlumberger Dowell have consistently been successful cementing wells at total depths between 22,000′ and 23,000′ and maximum temperatures of 400°F. The proof of successful cement work is demonstrated with record production rates for the state of Louisiana and achieving isolation in sands with over 10,000 psi depletion. The optimization methods and approach will be discussed along with problems experienced and subsequent solutions. Over 15 such wells have been drilled in Louisiana during the last 5 years. This paper will also address the philosophy and procedure of cementing production tieback casing to the surface by reverse circulating.
Annealed Silver-Island Films for Applications in Metal-Enhanced Fluorescence: Interpretation in Terms of Radiating Plasmons (2005)

The effects of thermally annealed silver island films have been studied with regard to their potential applicability in applications of metal-enhanced fluorescence, an emerging tool in nano-biotechnology. Silver island films were thermally annealed between 75 and 250 degrees C for several hours. As a function of both time and annealing temperature, the surface plasmon band at approximately 420 nm both diminished and was blue shifted. These changes in plasmon resonance have been characterized using both absorption measurements, as well as topographically using Atomic Force Microscopy. Subsequently, the net changes in plasmon absorption are interpreted as the silver island films becoming spherical and growing in height, as well as an increased spacing between the particles. Interestingly, when the annealed surfaces are coated with a fluorescein-labeled protein, significant enhancements in fluorescence are observed, scaling with annealing temperature and time. These observations strongly support our recent hypothesis that the extent of metal-enhanced fluorescence is due to the ability of surface plasmons to radiate coupled fluorophore fluorescence. Given that the extinction spectrum of the silvered films is comprised of both an absorption and scattering component, and that these components are proportional to the diameter cubed and to the sixth power, respectively, then larger structures are expected to have a greater scattering contribution to their extinction spectrum and, therefore, more efficiently radiate coupled fluorophore emission. Subsequently, we have been able to correlate our increases in fluorescence emission with an increased particle size, providing strong experiment evidence for our recently reported metal-enhanced fluorescence, facilitated by radiating plasmons hypothesis.
The Yin and Yang of Oxidation in the Development of the Fatty Streak (1996)

Recent data support the hypothesis that the fatty streak develops in response to specific phospholipids contained in LDL that become trapped in the artery wall and become oxidized as a result of exposure to the oxidative waste of the artery wall cells. The antioxidants present within both LDL and the microenvironments in which LDL is trapped function to prevent the formation of these biologically active, oxidized lipids. Enzymes associated with LDL and HDL (eg, platelet activating factor acetylhydrolase) or with HDL alone (eg, paraoxonase) destroy these biologically active lipids. The regulation and expression of these enzymes are determined genetically and are also significantly modified by environmental influences, including the acute-phase response or an atherogenic diet. The balance of these multiple factors leads to an induction or suppression of the inflammatory response in the artery wall and determines the clinical course.
Ototoxicity. Amelioration by protective agents. (1999)

The findings of studies from this laboratory are summarized to compare the efficacy of four chemoprotective agents against the effects of cisplatin-induced hearing loss and biochemical damage in the rat cochlea. A number of studies have shown that cisplatin is ototoxic, resulting in hearing loss, morphologic damage, and biochemical changes in the cochlea. These studies used Wistar rats, which underwent pre- and posttreatment ABR testing using clicks and tonebursts stimuli at 8, 16, and 32 kHz. Controls received i.p. saline injection. Cisplatin-treated rats were given 16 mg/kg cisplatin i.p. Animals received protective agents in the following dosage: DDTC protected rats received 600 mg/kg subcutaneously an hour after cisplatin. MTBA-protected animals were given 250 mg/kg i.p. 30 minutes before cisplatin. Animals protected with ebselen received 16 mg/kg i.p. an hour before cisplatin. One hundred mg/kg of alpha-lipoic acid was injected i.p. 30 minutes before cisplatin. Rats were sacrificed three days after treatment and the cochleae were harvested and frozen in liquid nitrogen and stored at -80 degrees C until analysis of glutathione (GSH), the activity of antioxidant enzymes (superoxide dismutase, catalase, glutathione peroxidase, and glutathione reductase) and malondialdehyde was performed. Cisplatin-treated rats were found to have ABR threshold shifts of 27-40 dB, and rats treated with chemoprotective agents plus cisplatin all had ABR thresholds shifts of less than 10 dB. Significant depletion of glutathione and decrease of the activities of the antioxidant enzymes were observed in cisplatin-treated rats. These changes were accompanied by a marked elevation of malondialdehyde. These changes were almost completely prevented by the use of the chemoprotective agents. These findings suggest that cisplatin ototoxicity is related to lipid peroxidation and that the use of protective agents prevents hearing loss and lipid peroxidation by sparing the antioxidant defense system in the cochlea.
Variable heparan sulfate proteoglycan binding of apolipoprotein E variants may modulate the expression of type III hyperlipoproteinemia. (1994)

The initial step in the clearance of apolipoprotein (apo) E-enriched remnant lipoproteins from the plasma appears to be sequestration within the liver mediated by their binding to heparan sulfate proteoglycans (HSPG). The surface-bound remnants are believed to be internalized by their interaction with the low density lipoprotein (LDL) receptor-related protein or by the LDL receptor. Cholesterol-induced rabbit beta-very low density lipoproteins (beta-VLDL) enriched in human apoE3 display 4-5-fold enhanced binding to cultured cells. The present study attempts to determine whether recessive versus dominant type III hyperlipoproteinemia might be explained, at least in part, by a variable interaction of the mutant forms of apoE with the HSPG and impaired uptake. The beta-VLDL+apoE2(Arg158-->Cys), which is associated with recessive type III hyperlipoproteinemia, bound more poorly than beta-VLDL+apoE3 but still possessed significant enhanced binding (approximately 2-2.5-fold compared with beta-VLDL without added apoE) to HepG2 and McA-RH7777 cells. In comparison, beta-VLDL+apoE(Arg142-->Cys), beta-VLDL+apoE(Arg145-->Cys), and beta-VLDL+apoE-Leiden, which are associated with dominant type III hyperlipoproteinemia, bound more poorly. This same hierarchy of binding and uptake was determined by [14C]oleate incorporation into cholesteryl esters in LDL receptor-negative cells and by secretion of apoE3 and the variant apoE forms from McA-RH7777 cells. Furthermore, the enhanced binding of the apoE-enriched beta-VLDL was almost totally inhibited by heparinase treatment of the cells, and the basal binding activity was inhibited by 80-90% following addition of an LDL receptor antibody capable of blocking receptor-ligand interaction. The beta-VLDL enriched in apoE or apoE-dimyristoylphosphatidylcholine complexes bound to isolated HSPG from McA-RH7777 cells or the rat liver to a very similar degree. Likewise, the binding of beta-VLDL plus the various forms of apoE to the LDL receptor-related protein on ligand blots paralleled the results of other studies. In conclusion, all of the type III hyperlipoproteinemic apoE variants are defective in displaying enhanced binding to HSPG and in the cellular uptake initiated by HSPG. However, apoE2(Arg158-->Cys) displayed more activity than the variants associated with the dominant forms of type III hyperlipoproteinemia. The hierarchy of binding and uptake was as follows: apoE3 > apoE2(Arg158-->Cys) > apoE(Arg145-->Cys) > apoE(Arg142-->Cys) approximately apoE-Leiden (the latter two usually displaying very little, if any, enhanced binding and uptake). Thus, a correlation exists between the mode of expression of type III hyperlipoproteinemia and the binding and uptake of the specific apoE mutation.
Carving fiber-top optomechanical transducers from an optical fiber (2006)

In a recent paper (Iannuzzi et al 2006 Monolithic fiber-top sensor for critical environments and standard applications Appl. Phys. Lett. 88 053501) we have presented the principle of the fiber-top position sensor, having a monolytical structure carved out of a single-mode optical fiber. The device alleviates sensing in a critical environment via interferometric readout, and because of its monolithic construction, facilitates plug-and-play utilization without alignment. In this paper we describe the fabrication method of a similar device which, however, was also equipped with a pyramidal tip on the top of the cantilever, an important detail for future implementation in scanning probe microscopy. A silicon surface was then periodically put in contact and moved out of contact with the device. The output signal resembles force curves that can be similarly obtained with atomic force microscopes. © 2006 IOP Publishing Ltd.