gebhart/patrepeval huggingface dataset:
Domain structure of the endothelial cell receptor thrombomodulin as deduced from modulation of its anticoagulant functions. Evidence for a glycosaminoglycan-dependent secondary binding site for thrombin. (1990)

Rabbit thrombomodulin (TM) influences blood coagulation by serving as a cofactor for thrombin-induced protein C activation (activity a), by directly affecting the procoagulant activity of thrombin (activity b) and by accelerating the inhibition of thrombin by antithrombin III (AT III) (activity c). Although high molecular weight cationic compounds, such as poly-L-lysine and the ionophore-releasate from human platelets, only partly affected activity a in a concentration-dependent manner, activities b and c, however, were almost totally inhibited by these cationic compounds. Likewise, a heparin- and dermatan sulfate-binding peptide which represents a portion of the glycosaminoglycan-binding domain of vitronectin (VN) selectively inhibited activities b and c, indicating the presence of clustered acidic domain(s) in TM responsible for these activities. While heparinase or heparitinase did not affect rabbit TM function at all, digestion of rabbit TM with chondroitin ABC-lyase abolished activities b and c, whereas activity a remained unaffected. Modification of rabbit TM with chondroitin ABC-lyase was associated with a decrease in molecular mass of the receptor by about 10 kDa and a 2- to 3-fold decrease in affinity to thrombin as deduced from direct binding studies. These results suggest that at least two acidic thrombin binding domains are present in rabbit TM, whereby a dermatan sulfate-like glycosaminoglycan moiety constitutes the secondary binding domain for thrombin, eliciting both the direct as well as the AT III-dependent anticoagulant function of rabbit TM (activities b and c) but not protein C activation (activity a). In contrast to rabbit TM, human TM isolated from placenta only showed weak activities b and c. These differences in reactivity of TM from different sources appeared to be due to the masking (or absence) of the proposed secondary thrombin binding site in human TM, since VN could be identified as a major contamination in the human TM preparation as revealed by enzyme-linked immunosorbent assay and Western blot analysis. In addition, the major part of human TM could be immunoprecipitated by monospecific antibodies to VN. These findings indicate a possible modulatory function for VN in the human thrombin-TM system.
Extended serial passaging of mammalian neural stem cells in suspension bioreactors (1999)

Neural stem cells (NSCs) are primitive cells that are the "parent" cells of all the cells in the central nervous system (CNS). Their discovery in 1992 opened the door to a multitude of potential therapies and treatments to cure neurodegenerative diseases such as Parkinson's disease, multiple sclerosis, and Huntington's disease, which affect millions of people worldwide and cost billions of dollars in health care each year. This study proposes optimal serial passaging protocols so that mammalian neural stem cells can effectively be grown in suspension culture. We examined stationary culture passaging protocols and developed our own optimal procedure. Also examined was the effect of serially cultivating the neural stem cells in suspension culture for an extended period of time. The cells were grown for over 35 days in suspension with an overall multiplication ratio of over 10(7) with no decrease in growth rate, maximum cell density, or viability. The cells also remained karyotypically normal through 25 doublings and retained their ability to be differentiated into all the major cell types of the CNS-neurons, astrocytes, and oligodendrocytes. For the first time, mammalian neural stem cells were grown on a larger scale in suspension culture and maintained their stem cell characteristics. A semicontinuous scheme for large-scale production is also presented.
The Photoactivatable Inhibitor 7-Azido-8-iodoketanserin Labels the N Terminus of the Vesicular Monoamine Transporter from Bovine Chromaffin Granules (1997)

In monoaminergic cells, the hormone or neurotransmitter is concentrated into secretory vesicles by a tetrabenazine- and reserpine-sensitive vesicular monoamine transporter (VMAT), catalyzing a H+/monoamine antiport. Ketanserin is another powerful inhibitor of VMAT that binds to the tetrabenazine binding site. A photoactivatable derivative, 7-azido-8-iodoketanserin (AZIK), labels covalently the transporter from bovine chromaffin granules, VMAT-2. Digestion with endoproteinases V8 or Lys-C, which cleave peptide bonds at acidic or lysine residues, respectively, revealed that the AZIK label is located in a 7 kDa segment of the VMAT-2 polypeptide. The photolabeled chromaffin granule transporter was purified by DEAE and WGA chromatography followed by selective aggregation and size-exclusion HPLC. After treatment by V8 or Lys-C, digestion products were separated by electrophoresis in SDS and sequenced. For both enzymes, the material comigrating with the labeled peptide produced a sequence matching the N terminus of VMAT-2. A K55E mutant of the bovine VMAT-2 cDNA was constructed and expressed in COS-7 cells. The mutant protein exhibited a full VMAT activity and could be labeled by AZIK. However, the formation of the 7 kDa labeled peptide upon Lys-C proteolysis was prevented in the mutant, with a redistribution of the label in higher-molecular mass digestion products. The localization of the label upstream of lysine 55 was confirmed by an immunological and enzymatic analysis. We conclude that the segment 2-55 of bovine VMAT-2, which encompasses the cytosolic N terminus and the first transmembrane segment in the current topological model of the transporter, contains residues involved in the binding of ketanserin and, possibly, tetrabenazine.
Catalyst-trap microreactor for hydrogenation of a pharmaceutical intermediate (2006)

A silicon microreactor has been developed to investigate gas-liquid-solid catalytic reactions. The reactor employs a three-channel “catalyst-trap” design, whereby solid catalyst is suspended in the liquid channel by an arrangement of posts. Such a device has advantages in that commercial catalysts are supported, and that pressure drop across the bed can be reduced by engineering the packing density. A model incorporating the transport and kinetic effects is developed to design the reactor. The reaction chosen is one in a family of reactions relevant to the pharmaceutical industry, the liquid-phase hydrogenation of o-nitroanisole to oanisidine. The reaction is carried out across a range of gas and liquid flow rates that encompasses three distinct flow regimes, termed gas-dominated, liquid-dominated, and transitional. Experiments seek to assign a reaction conversion and selectivity to each point in this two-phase “flow map”, then reconcile differences in performance with the characteristics of the respective flow regime. We observe the highest reaction conversion in the transitional flow regime, where competition between the two phases results in the generation of a large amount of gas-liquid interfacial area. The experimental conversion is greater than that predicted by the model, an effect attributable to the mass transfer enhancement induced by transitional flow. Reaction time within the microchannel is sufficiently small so that selectivity towards production of o-anisidine is nearly 100% across all flow regimes. In this work we relate our map of conversion to the flow behavior and reactor geometry, and we discuss steps for further exploring the mass transfer characteristics of the transitional flow regime. This reactor architecture may be useful for catalyst evaluation through rapid screening, or in large numbers as an alternative to macro-scale production reactors.
A new fault simulator for large synchronous sequential circuits (2002)

A fault simulator for large synchronous sequential circuits is presented in this paper. There are four key ideas to the fault simulator. (1) It uses the critical path tracing method to screen out the single event faults that need not map into equivalent stem faults. (2) It uses the single fault propagation method to map the traced single event faults into equivalent stem faults. (3) All the multiple event faults are dynamically ordered for each test pattern such that the faults with the same faulty effects can be put into the same packet, so as to reduce the number of events created during simulation. (4) All the packets are propagated simultaneously; therefore, each gate is simulated only once for each test pattern, and while propagating packets, equivalent stem faults are also inserted into the packets and propagated as well. A memory sharing technique is used to reduce the memory overhead. Experimental results show that our fault simulator runs faster than PROOFS, HOPE, and improved HOPE (HOPE1.1) for large synchronous sequential benchmark circuits.
Structural Basis for Interaction of FGF-1, FGF-2, and FGF-7 with Different Heparan Sulfate Motifs<sup>,</sup> (2001)

Stromal cell-derived FGF-7 binds and activates only the resident FGFR2IIIb in epithelial cells while FGF-1 and FGF-2 exhibit a broader interaction with multiple isoforms of FGFR. Here we report the structure of FGF-7 that has been solved to 3.1 A resolution by molecular replacement with the structure of a dual function chimera of FGF-7 and FGF-1 (FGF-7/1) which was resolved to 2.3 A. Comparison of the FGF-7 structure to that of FGF-1 and FGF-2 revealed the strongly conserved Calpha backbone among the three FGF polypeptides and the surface hydrophobic patch that forms the primary receptor-binding domain. In contrast, a decrease and dispersion of the positive surface charge density characterized the heparin-binding domain of FGF-7 defined by homology to that of FGF-1 and FGF-2 in complexes with heparin. A simple heparin hexasaccharide that cocrystallized with FGF-1 and FGF-2 and protected both against protease in solution failed to exhibit the same properties with FGF-7. In contrast to FGF-1 and FGF-2, protection of FGF-7 was enhanced by heparin oligosaccharides of increased length with those exhibiting a 3-O-sulfate being the most effective. Protection of FGF-7 required interaction with specifically the fraction of crude heparin retained on antithrombin affinity columns. Conversely, heparin enriched by affinity for immobilized FGF-7 exhibited anti-factor Xa activity similar to that purified on an antithrombin affinity matrix. In contrast, an FGF-1 affinity matrix enriched the fraction of crude heparin with low anti-factor Xa activity. The results provide a structural basis to suggest that the unique FGF-7 heparin-binding (HB) domain underlies a specific restriction in respect to composition and length of the heparan sulfate motif that may impact specificity of localization, stability, and trafficking of FGF-7 in the microenvironment, and formation and activation of the FGFR2IIIb kinase signaling complex in epithelial cells.
Evidence of Interactions between the Nucleocapsid Protein NCp7 and the Reverse Transcriptase of HIV-1 (1999)

The human immunodeficiency virus (HIV-1) nucleocapsid protein NCp7 containing two CX2CX4HX4C-type zinc fingers was proposed to be involved in reverse transcriptase (RT)-catalyzed proviral DNA synthesis through promotion of tRNA3Lys annealing to the RNA primer binding site, improvement of DNA strand transfers, and enhancement of RT processivity. The NCp7 structural characteristics are crucial because mutations altering the finger domain conformation led to noninfectious viruses characterized by defects in provirus integration. These findings prompted us to study a putative RT/NCp7 protein-protein interaction. Binding assays using far Western analysis or RT immobilized on beads clearly showed the formation of a complex between NCp7 and RT. The affinity of NCp7 for p66/p51RT was 0.60 microM with a 1:1 stoechiometry. This interaction was confirmed by chemical cross-linking and co-immunoprecipitation of the two proteins in a viral environment. Competition experiments using different NCp7 mutants showed that alteration of the finger structure disrupted RT recognition, giving insights into the loss of infectivity of corresponding HIV-1 mutants. Together with structural data on RT, these results suggest that the role of NCp7 could be to enhance RT processivity through stabilization of a p51-induced active form of the p66 subunit and open the way for designing new antiviral agents.
Nitrogen incorporation in GaInP for novel heterojunction bipolar transistors (2002)

Novel device structures using GaInNP in a thin layer at the base-collector (BC) junction of a heterojunction bipolar transistor (HBT) are described. The proposed devices, blocked hole bipolar transistors (BHBTs) combine the benefits of single and double heterojunction bipolar transistors (DHBTs). In DHBTs there is typically a barrier to electrons at the BC junction. In the BHBT the barrier is eliminated by the incorporation of nitrogen into GaInP. In the new structures the majority of the collector remains GaAs, which yields a device with a higher cutoff frequency than achievable with GaInP collectors. Since the reduction in bandgap energy is primarily in the conduction band from the incorporation of nitrogen, there will remain a substantial valence band discontinuity. This will yield reduced saturation charge storage. The offset voltage will also be reduced by the greater symmetry of the base-emitter (BE) and BC junctions. Additionally, the eliminated barrier at the BC junction will yield devices with a reduced knee voltage. These attributes make the proposed devices very well suited for microwave power amplifiers.
Thermoforming of thermoplastic matrix composites. Part I (1992)

Long-fiber-reinforced polymer matrix composites find widespread use in a variety of commercial applications requiring properties that cannot be provided by unreinforced plastics or other common materials of construction. However, thermosetting matrix resins have long been plagued by production processes that are slow and difficult to automate. This has limited the use of long-fiber-reinforced composites to relatively low productivity applications in which higher production costs can be justified. Unreinforced thermoplastics, by their very nature, can easily be made into sheet form and processed into a variety of formed shapes by various pressure assisted thermoforming means. It is possible to incorporate various types of fiber reinforcement to suit the end use of the thermoformed shape. Recently developed thermoplastic resins can also sometimes correct physical property deficiencies in a thermoset matrix composite. Many forms of thermoplastic composite material now exist that meet all the requirements of present day automotive and aerospace parts. Some of these are presently in production, while others are still in the development stage. This opens the possibility that long-fiber-reinforced thermoplastics might break the barrier that has long limited the applications for fiber-reinforced composites. 37 refs., 8 figs., 5 tabs.
ChemInform Abstract: Oxidation Behavior of Mullite‐Coated SiC and SiC/SiC Composites under Thermal Cycling between Room Temperature and 1200 °‐1400 . degree.C. (1996)

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.
Polarization independent optical phase conjugation with pump-signal filtering in a monolithically integrated Mach-Zehnder interferometer semiconductor optical amplifier configuration (1998)

Demonstration of polarization independent optical phase conjugation by four-wave mixing in a monolithic Mach-Zehnder interferometric semiconductor optical amplifier (SOA) configuration. An integrated filtering mechanism for the pump-signal enhances the conjugate-to-pump ratio by 15 dB compared to the single SOA case.
The effect of aminoglycoside antibiotics on the thermodynamic properties of liposomal vesicles (2010)

Liposomes are ideal drug-delivery systems because they can alter the pharmacokinetic characteristics and biodistribution profile of the incorporated bioactive molecule. The effect of the aminoglycoside antibiotics, gentamicin (GN), tobramycin (TOB), and amikacin (AMI), on the thermodynamic properties of multilamellar vesicles composed of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) was studied by using differential scanning calorimetry (DSC), electron paramagnetic resonance (EPR), and (31)P nuclear magnetic resonance (NMR) spectroscopy. The relationship between the structure of aminoglycoside antibiotics and their effect on the physical properties of the liposomal bilayers was investigated. The incorporation of the drugs was achieved and an osmotic gradient created by controlling the mole ratio of the drug inside to that outside of the DPPC vesicles so that [drug(inside DPPC)]/[drug(outside DPPC)] was 1:0, 1:0.2, 1:1, or 1:2.5. Incorporation of the drugs into liposomes caused the T(m) to shift to a higher temperature and the delta H(m) and delta T(1/2) values to decrease. The 2A(max) and the order parameter (S), obtained from the EPR spectra, indicated that the fluidity of the liposomal membrane was affected by the type of drug and by the concentration used; GN and TOB decreased the fluidity and disturbed chain packing at mole ratios of [drug(inside DPPC)]/[drug(outside DPPC)] ranging from 1:0 to 1:0.2, while AMI increased the fluidity and disrupted chain packing at an osmotic gradient of 1:2.5. In conclusion, the molecular organization and thermotropic properties of the multilamellar DPPC vesicles were dependent on the osmotic gradient and structure of the aminoglycoside.
Future WSI technology: stacked monolithic WSI (1993)

Describes a methodology for stacking chips vertically and interconnecting them through the chips to achieve a three-dimensional (3D) circuit. This methodology involves the integration of two technologies: indium bump interconnect technology, historically used to fabricate hybrid focal plane arrays, and the precision thinning of bonded silicon wafers by a process called Acuthin. Substantial improvements in computing density, power dissipation, and signal propagation time can be realized. This paper describes some of the techniques and benefits of this 3D interconnect methodology.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Measurement of DNA synthesis by flow cytometry (1981)

Cells were stained for DNA content with Hoechst 33258 combined with propidium iodide and analyzed on an epi-fluorescence flow cytometer. Scatterplots of red versus blue fluorescence of control cells showed a straight line indicating that both dyes were measuring proportional amounts of cellular DNA. Scatterplots of cells incubated with the thymidine analog bromodeoxyuridine, however, showed a displacement from the control straight line that increased with longer exposure time to bromodeoxyuridine. These results suggest that bromodeoxyuridine incorporation in DNA can be detected by flow cytometry.
Automated underground residential distribution design. II. Prototype implementation and results (1993)

For pt.I see ibid., vol.8, no.2, p.637-43 (1993). The manual design of the underground electrical supply system for new residential developments (electrical plat design) often results in an overdesigned, costly, and nonstandardized solution. The intelligent decision support system for automated electrical plat design (DSS for AEPD) is an engineering tool aimed at automating electrical plat design. This tool combines the spatial analysis capabilities of a geographic information system (GIS) with the sophistication of artificial intelligence (AI) to deal with the complexity inherent in this type of problem. The results of the AEPD prototype implementation and an evaluation of the concept's feasibility are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Chronic insomnia: a practical review. (1999)

Insomnia has numerous, often concurrent etiologies, including medical conditions, medications, psychiatric disorders and poor sleep hygiene. In the elderly, insomnia is complex and often difficult to relieve because the physiologic parameters of sleep normally change with age. In most cases, however, a practical management approach is to first consider depression, medications, or both, as potential causes. Sleep apnea also should be considered in the differential assessment. Regardless of the cause of insomnia, most patients benefit from behavioral approaches that focus on good sleep habits. Exposure to bright light at appropriate times can help realign the circadian rhythm in patients whose sleep-wake cycle has shifted to undesirable times. Periodic limb movements during sleep are very common in the elderly and may merit treatment if the movements cause frequent arousals from sleep. When medication is deemed necessary for relief of insomnia, a low-dose sedating antidepressant or a nonbenzodiazepine anxiolytic may offer advantages over traditional sedative-hypnotics. Longterm use of long-acting benzodiazepines should, in particular, be avoided. Melatonin may be helpful when insomnia is related to shift work and jet lag; however, its use remains controversial.
An E. coli expression system which detoxifies the HIV protease. (1991)

Based on a variety of independent assays, the expression of HIV (human immunodeficiency virus type 1) protease in living bacterial cells results in their loss of viability. Although the mechanism is not proven, we have observed degradation of cellular proteins in E. coli expressing large amounts of active HIV protease. In order to avoid the loss of viability, we devised an expression system in which the viral protease is fused to beta-lactamase and is rapidly secreted to the periplasmic space, thus reducing its duration in the cytosol. Furthermore, we find the periplasmic form of the protease is soluble and enzymatically is several-fold more active than enzyme recovered from intracellular aggregates. The question of whether the viral protease may be toxic to infected cells is discussed.
Optical wavelength division multiplex (2002)

The author presents a brief overview of WDM (wavelength division multiplexing) technology, systems, and challenges, with emphasis on current research at AT&T Bell Laboratories. Particular attention is given to long-haul systems, local applications, and tunable WDM (e.g. the WDM digital crossconnect system and WDM multiple-access networks).< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Self-consistent particle simulation of radio-frequency CF4 discharge with implementation of all ion–neutral reactive collisions (1998)

The structures of the CF4 radio-frequency discharge between parallel electrodes are clarified by the use of the particle-in-cell/Monte Carlo method. The simulation is performed based on the most reliable collision data, i.e., detailed cross-section data for electron–CF4 collision, measured rate for positive–negative ion recombination, and the newly developed ion–CF4 collision model for endothermic reactions. Reactive collisions between positive ions (especially CF3+) and CF4 molecules are found to be important. The major loss process of negative ions is the recombination with positive ions. It is also found that the discharge sustaining mechanism is the ionization, not the electron detachment from negative ions.
A novel gene for autosomal dominant Stargardt-like macular dystrophy with homology to the SUR4 protein family. (2001)

ELOVL4 causes macular dystrophy in this large family distributed throughout North America and implicates fatty acid biosynthesis in the pathogenesis of macular degeneration. The PCR-based assay for the 5-bp deletion will facilitate more accurate genetic counseling and identification of other branches of the family.