gebhart/patrepeval huggingface dataset:
Phototoxicity of Zinc Oxide Nanoparticle Conjugatesin Human Ovarian Cancer NIH: OVCAR-3 Cells (2008)

Zinc oxide (ZnO) nanoparticles conjugated to porphyrin (ZnO-MTAP) have been designed, synthesized and evaluated for photodynamic therapy (PDT) against ovarian cancer. Based on the self-lighting photodynamic therapy (SLPDT) concept, photoactivation of ZnO-MTAP conjugates will lead to release of reactive oxygen species which, if effectively targeted to tumor cells, can elicit selective cytotoxicity. Following synthesis, conjugated nanoparticles were purified using gel exclusion chromatography and tumoricidal activity was evaluated using the human ovarian cancer cell line, NIH: OVCAR-3. Conjugates generated reactive oxygen species (ROS) in a concentration- and illumination-dependent manner following exposure to ultraviolet A light (365 nm). Cellular uptake of nanoparticle conjugates was detected using laser scanning confocal microscopy. Under dark conditions, ZnO-MTAP conjugates (1–10 μ M, 24 hr) exhibited little cytotoxic potential. Ultraviolet radiation alone (UVA, 9 kJ/m 2 ) also had little effect on cell viability. Co-exposure to both UVA radiation (9 kJ/m 2 ) and ZnO nanoparticle conjugates however, elicited concentration-dependent cytotoxicity (40% and 92%, respectively). Furthermore, caspase 3/7 activity was markedly elevated 3–6 hours after irradiation, suggesting apoptosis was induced by the phototherapy. These findings provide proof-of-concept that photoactivation of ZnO-MTAP conjugates can be useful for targeted destruction of tumor cells.
The control of airway mucus secretion. (1987)

Airway mucus is essential for the effectiveness of cough and mucociliary transport. Even the resting airway produces some mucus but, under a great variety of threats to airway function, this production increases. A number of mechanisms may be responsible for augmenting secretion; these include reflexes, initiated by nervous receptors in the airways, and with their efferent limbs in the autonomic nerves to the airways. Cigarette smoke short circuits this reflex pathway; nicotine absorbed from the smoke stimulates ganglion cells directly and so drives secretion. Secretomotor nerves which control the output from submucosal glands include cholinergic, adrenergic and NANC fibres. A number of mediators of the sort released during inflammation and antigen challenge, including prostaglandins and leukotrienes, can also elicit secretion into the airway lumen. Other stimuli act at least partly on unknown mechanisms to release mucus from the surface epithelium into the airway lumen. For example inhalation of dust, which stimulates cough receptors and so acts partly by driving mucus secretion reflexly, also initiates secretion into the denervated airway. Similarly, during the inhalation of cool dry air, the airway lining secretes more mucus, probably by a non-nervous mechanism which responds to drying of the airway surface. More needs to be learned about such apparently direct mechanisms. Different control systems appear to stimulate the production of a variety of mucins from distinct cell types. We do not yet know the physiological and pathological importance of these differences.
SEIZURES IN WOMEN WITH PREECLAMPSIA: MECHANISMS AND MANAGEMENT (2011)

Eclampsia is defined in the obstetrical literature as the occurrence of unexplained seizure during pregnancy in a woman with preeclampsia. In the Western world, the incidence of eclampsia is ~1 per 2000 to 1 per 3000 pregnancies, but the incidence is 10-fold higher in tertiary referral centers and undeveloped countries where there is poor prenatal care, and in multi-fetal gestations. Nearly 1 in 50 women with eclampsia die as do 1 in 14 of their offspring, and mortality rates are considerably higher in undeveloped countries. Eclampsia is also associated with significant life-threatening complications, including neurological events. Seizure acutely can cause stroke, haemorrhage, oedema and brain herniation and thus lead to epilepsy and cognitive impairment later in life.
An evaluation of automaticity and triggered activity in the canine heart one to four days after myocardial infarction. (1985)

Both abnormal automaticity and triggered activity induced by delayed afterdepolarizations have been proposed as the primary mechanism for ventricular tachycardia (VT) occurring in dogs 24 hr after ligation of the left anterior descending coronary artery. Because of this controversy, we studied the effects of ventricular pacing and therapeutic concentrations of lidocaine and ethmozin on sustained rhythmic activity of isolated subendocardial preparations excised from the infarct, and on VT in conscious dogs. There were differences in the sustained rhythmic activity cycle length of isolated preparations and the VT cycle length that were attributable to the absence of sympathetic input in the former and its presence in the latter. In isolated tissues, pacing for 1 or 10 beats reset the sustained rhythmic activity and pacing for 1 min induced overdrive suppression. Lidocaine (5 micrograms/ml) had no effect on sustained rhythmic activity but ethmozin (2 micrograms/ml) suppressed it. Delayed afterdepolarizations occurred but appeared to be induced by pacing or by the hyperpolarization associated with recovery. Although delayed afterdepolarizations were infrequent at 24 hr, their frequency increased with the hyperpolarization of the membrane that occurred at 48 to 96 hr after infarction. Delayed afterdepolarizations also occurred more readily when superfusate temperature was lowered. In conscious dogs, pacing the VT for 1 or 10 beats or 1 min had no effect. Lidocaine (2 to 10 micrograms/ml) did not affect the VT but ethmozin (2 to 5 micrograms/ml) increased VT cycle length significantly. Pacing for 1 min in the presence of ethmozin, but not lidocaine, converted VT to sinus rhythm. Our results suggest that although delayed afterdepolarizations occur at 24 hr after infarction in the standard Harris preparation, they are most readily seen as an accompaniment of hyperpolarization, pacing, or lowering of bath temperature. The predominant rhythm at 24 hr appears to be automatic.
New BODIPY chromophores bound to polyhedral oligomeric silsesquioxanes (POSS) with improved thermo- and photostability (2011)

New hybrid dyes, analogs of the BODIPY laser dye PM567, with the chromophore group covalently bound to a POSS T8 group, have been prepared and their photophysical properties in ethyl acetate solution and in poly(methyl methacrylate) (PMMA) thin film solution have been studied. In PMMA solution and under comparative conditions, the dyes show higher thermostability than the parent dye PM567, the related compound POSS(iBu)8, and the corresponding unbound model dyes, because the first mass loss takes place at higher temperatures. In addition, their photostabilities in the same medium under irradiation with 365 nm light are much higher than those of the dye PM567 or an equimolar mixture of PM567 plus POSS(iBu)8 under the same conditions, indicating that the POSS moiety photostabilizes the bound BODIPY group. The different photostabilities could be a consequence of different reactivities of the hybrid dyes with self-generated singlet oxygen, because they show lower reaction rate constant values than PM567, although the observed tendency of these values does not correlate with that of the photodegradation quantum yield values. The new hybrid materials can be employed in applications where highly photostable and highly emissive dyes are required.
Étude par RMN et par microcalorimétrie de la solubilité de certains halons et de leur interaction avec la sérum albumine humaine (1986)

La solubilité de différents halogenoalcanes (Halons) dans l'eau, l'acide oléique, la sérum albumine humaine (SAH) et le plasma humain a été étudiée par RMN du Fluor.
A KBE Application for Automatic Aircraft Wire Harness Routing (2012)

Wire harness design is an increasingly complex task. Knowledge Based Engineering (KBE) and optimization techniques can be used to support designers in handling this complexity. The wire harness design process can be divided in three main parts, namely electrical design, configuration design and geometrical routing. This paper describes the latest progress in the development of a KBE application aiming at the automation of the routing phase. Discrete optimization techniques are used to design shortest path harnesses, while complying with different type of constraints. Some preliminary results have been presented in a previous paper, where only geometrical constraints were addressed. However, wire harness design is affected also by other types of rules and constraints, which need to be accounted to obtain more realistic design results from the optimization process. This paper describes some new developments in the routing application to account for the presence of critical zones inside the aircraft. As study case, the presence of heat sources inside the airframe is considered, which either force the harness to be routed elsewhere, or require the use of wire protections, with obvious consequences on weight and manufacturing. First, some mathematic transformation techniques are used to model the presence of heat sources inside the routing environment. Then the A* algorithm is used for compute the 3D routing, aiming at minimum wire harness weight. The main architecture of the routing application is presented and its functionality is demonstrated with samples of wire harness routing inside a wing. The results show that the proposed KBE application can automate the routing of wire harness while taking into account different rules and constraints. The modeling approach for a heat source can be generalized and extended to address other criticality such as abrasion, electromagnetic interference, corrosion, etc. The achieved level of automation relieves designers from the repetitive work associated with the frequent changes affecting the design environment.
Genotator: A Workbench for Sequence Annotation (1997)

Sequencing centers such as the Human Genome Center at LBNL are producing an ever-increasing flood of genetic data. Annotation can greatly enhance the biological value of these sequences. Useful annotations include possible gene locations, homologies to known genes, and gene signals such as promoters and splice sites. Genotator is a workbench for automated sequence annotation and annotation browsing. The back end runs a series of sequence analysis tools on a DNA sequence, handling the various input and output formats required by the tools. Genotator currently runs five different gene-finding programs, three homology searches, and searches for promoters, splice sites, and ORFs. The results of the analyses run by Genotator can be viewed with the interactive graphical browser. The browser displays color-coded sequence annotations on a canvas that can be scrolled and zoomed, allowing the annotated sequence to be explored at multiple levels of detail. The user can view the actual DNA sequence in a separate window; when a region is selected in the map display, it is highlighted automatically in the sequence display, and vice versa. By displaying the output of all of the sequence analyses, Genotator provides an intuitive way to identify the significant regions (for example, probable exons) in a sequence. Users can interactively add personal annotations to label regions of interest. Additional capabilities of Genotator include primer design and pattern searching. [Further details for obtaining Genotator are available at http://www.cshl.org/gr .]
pH-Induced Conformational Change of the Influenza M2 Protein C-Terminal Domain (2008)

The M2 protein from influenza A is a pH-activated proton channel that plays an essential role in the viral life cycle and serves as a drug target. Using spin labeling EPR spectroscopy, we studied a 38-residue M2 peptide spanning the transmembrane region and its C-terminal extension. We obtained residue-specific environmental parameters under both high- and low-pH conditions for nine consecutive C-terminal sites. The region forms a membrane surface helix at both high and low pH, although the arrangement of the monomers within the tetramer changes with pH. Both electrophysiology and EPR data point to a critical role for residue Lys 49.
Antibodies to cannabinoid type 1 receptor co‐react with stomatin‐like protein 2 in mouse brain mitochondria (2013)

Anti-cannabinoid type 1 receptor (CB1 ) polyclonal antibodies are widely used to detect the presence of CB1 in a variety of brain cells and their organelles, including neuronal mitochondria. Surprisingly, we found that anti-CB1 sera, in parallel with CB1 , also recognize the mitochondrial protein stomatin-like protein 2. In addition, we show that the previously reported effect of synthetic cannabinoid WIN 55,212-2 on mitochondrial complex III respiration is not detectable in purified mitochondrial preparations. Thus, our study indicates that a direct relationship between endocannabinoid signaling and mitochondrial functions in the cerebral cortex seems unlikely, and that caution should be taken interpreting findings obtained using anti-CB1 antibodies.
Structural Characterization and Oxidative Dehydrogenation Activity of V<sub>2</sub>O<sub>5</sub>/Ce<i><sub>x</sub></i>Zr<sub>1-</sub><i><sub>x</sub></i>O<sub>2</sub>/SiO<sub>2</sub> Catalysts (2006)

The thermal stability of a nanosized Ce(x)Zr(1-x)O2 solid solution on a silica surface and the dispersion behavior of V2O5 over Ce(x)Zr(1-x)O2/SiO2 have been investigated using XRD, Raman spectroscopy, XPS, HREM, and BET surface area techniques. Oxidative dehydrogenation of ethylbenzene to styrene was performed as a test reaction to assess the usefulness of the VOx/Ce(x)Zr(1-x)O2/SiO2 catalyst. Ce(x)Zr(1-x)O2/SiO2 (1:1:2 mol ratio based on oxides) was synthesized through a soft-chemical route from ultrahigh dilute solutions by adopting a deposition coprecipitation technique. A theoretical monolayer equivalent to 10 wt % V2O5 was impregnated over the calcined Ce(x)Zr(1-x)O2/SiO2 sample (773 K) by an aqueous wet impregnation technique. The prepared V2O5/Ce(x)Zr(1-x)O2/SiO2 sample was subjected to thermal treatments from 773 to 1073 K. The XRD measurements indicate the presence of cubic Ce0.75Zr0.25O2 in the case of Ce(x)Zr(1-x)O2/SiO2, while cubic Ce0.5Zr0.5O2 and tetragonal Ce0.16Zr0.84O2 in the case of V2O5/Ce(x)Zr(1-x)O2/SiO2 when calcined at various temperatures. Dispersed vanadium oxide induces more incorporation of zirconium into the ceria lattice, thereby decreasing its lattice size and also accelerating the crystallization of Ce-Zr-O solid solutions at higher calcination temperatures. Further, it interacts selectively with the ceria portion of the composite oxide to form CeVO4. The RS measurements provide good evidence about the dispersed form of vanadium oxide and the CeVO4 compound. The HREM studies show the presence of small Ce-Zr-oxide particles of approximately 5 nm size over the surface of amorphous silica and corroborate with the results obtained from other techniques. The catalytic activity studies reveal the ability of vanadium oxide supported on Ce(x)Zr(1-x)O2/SiO2 to efficiently catalyze the ODH of ethylbenzene at normal atmospheric pressure. The remarkable ability of Ce(x)Zr(1-x)O2 to prevent the deactivation of supported vanadium oxide leading to stable activity in the time-on-stream experiments and high selectivity to styrene are other important observations.
BREED:  Generating Novel Inhibitors through Hybridization of Known Ligands. Application to CDK2, P38, and HIV Protease (2004)

In this work we describe BREED, a method for the generation of novel inhibitors from structures of known ligands bound to a common target. The method is essentially an automation of the common medicinal chemistry practice of joining fragments of two known ligands to generate a new inhibitor. The ligand-bound target structures are overlaid, all overlapping bonds in all pairs of ligands are found, and the fragments on each side of each matching bond are swapped to generate the new molecules. Since the method is automated, it can be applied recursively to generate all possible combinations of known ligands. In an application of this method to HIV protease inhibitors and protein kinase inhibitors, hundreds of new molecular structures were generated. These included known inhibitor scaffolds not included in the initial set, entirely novel scaffolds, and novel substituents on known scaffolds. The method is fast, and since all of the ligand functional groups are known to bind the target in the precise position and orientation present in the novel ligand, the success rate of this method should be superior to more traditional de novo design techniques. In an era of increasingly high-throughput structural biology, such methods for high-throughput utilization of structural information will become increasingly valuable.
Novel aryl diketo-containing inhibitors of HIV-1 integrase (2002)

HIV-1 integrase is a promising therapeutic target for the development of drugs to treat HIV infection. Aryl diketo-based analogs, disclosed independently by scientists from Merck and Shionogi pharmaceutical companies, are a unique class of compounds that exhibit potent integrase inhibition and display good antiviral effects in HIV-infected cells. The progress of Merck's L-870810 and Shionogi's S-1360 to phase II clinical trials has promised the inclusion of integrase inhibitors in cocktail combination therapies in the near future. This review presents a critical overview of research related to this new class of integrase inhibitors.
Molecular three-terminal devices: fabrication and measurements (2005)

Incorporation of a third, gate electrode in the device geometry of molecular junctions necessary to identify the transport mechanism. At present, the most popular technique fabricate three-terminal molecular devices makes use of electromigration. Although it statistical process, we show that control over the gap resistance can be obtained. A detailed analysis of the current-voltage characteristics of gaps without molecules, however, shows that they reveal features that can mistakenly be attributed to molecular transport. This observation raises questions about which gaps with molecules can be disregarded which not. We show that electrical characteristics can be controlled by the rational design of the molecular bridge and that vibrational modes probed by electrical transport are potential interest as molecular fingerprints.
Photopyroelectric thin-film instrumentation and impulse-response detection. Part III: Performance and signal recovery techniques (1987)

Frequency-modulation time-delay spectrometry (FM-TDS) was compared with stochastic excitation in photopyroelectric measurements on thin solid samples. These methods involve broadband signal excitation with simultaneous detection of all frequency components within the response bandwidth of the photothermal system. Fast signal recovery was achieved by FFT methods. Both FM-TDS and wideband random-noise excitation were found to yield high-quality, band-limited impulse-response information. Random noise measurements were found to be much less susceptible to distortions and nonlinearities in the excitation wave train. FM-TDS showed superior coherence and signal-to-noise ratio (SNR) to random methods. The results of this work demonstrate a photopyroelectric effect spectrometer capable of yielding fast, time-resolved information equivalent to the response of a pulsed laser, with low peak power. This important feature shows excellent potential for nondestructive thickness, thermal diffusivity, and thermal conductivity measurements on materials which are susceptible to optical damage.
Realistic rendering and modeling of plants (2010)

The simulation and modeling of nature scenes with thousands of plants is challenging because of its complexity. In this paper, we devise an efficient interactive system for solving this problem and decompose the process of scenes synthesis into steps: modeling the individual plants, modeling the terrain, specification the plants distribution, and rendering the landscape. What's more, we give a new fractal noise function, a new algorithm to describe the natural phenomenon of clustering and two efficient interactive editors for generating all kinds of terrains and plants. We compound computer graphic and image technique in rendering to improve the speed and also propose a landscapes walk-through framework to achieve more realistic.
Carbon in III-V Compounds: A Theoretical Approach (1992)

Carbon as a very well behaved acceptor dopant in GaAs/AlGaAs is already successfully used in many device applications. However, the physics governing its incorporation behavior (amphoteric impurity) into III-V semiconductors is currently not well understood. We present a calculation from first principles of the change in total energy accompanying the incorporation of carbon onto lattice sites in the III-V compounds AlP, GaP, InP; and AlAs, GaAs and InAs. Taking into account the energy gained by filling a group III or group V vacancy with carbon, the obtained p -type conduction in carbon doped GaAs, AlAs, GaP (and presumably AlP) as well as the n -type conduction in InP can be explained based on the results of our total energy calculations. Additionally, the observed trends in the energy gain can explain the observed differences in tendency for carbon incorporation into the compounds under study.
Graft Copolymerization of Vinyl Monomers onto Cellulosic Fibers (1982)

Graft copolymerization of vinyl monomers - in this case acrylonitrile - onto cellulosic fibers is initiated by Mn3+ ions as pyrophosphate complex in aqueous solution at pH 1.5 to 2 and about 30°C under a nitrogen blanket in a process similar to what we previously reported for grafting onto starch. The following substrates are used: dissolving pulp (MDC) and grease-proof pulp (GP), both bleached sulfite pulps from spruce, ethyl cellulose (EC) and hydroxyethyl cellulose (HEC) of low degree of substitution (0.25, 0.40 and 0.60). At low Mn3+-complex concentration (1-2 mmole/1) and substrates in never-dried form the reaction is completed in 2 to 3 h giving high conversion to polymer (70 to 85%) and high grafting efficiency (80 to 98% of the polymer is grafted). The grafted substrates retain their fiber morphology and their liquid water retention (5 to 8 g/g). After hydrolysis of the graft copolymers in aqueous NaOH solution (1% NaOH at 100°C), which saponifies the nitrile groups to amide and carboxyl groups, the retention of liquid water increases 5 to 10 times. The grafted and hydrolyzed MDC and GP samples, containing native cellulose lattice (cellulose I) reach saturation in water retention in a few minutes, while the corresponding EC and HEC samples, containing disordered mercerized cellulose lattice (cellulose II), show gradually increased water retention for a long time (> 60 min.).