gebhart/patrepeval huggingface dataset:
Virus-Neutralizing and Passively Protective Monoclonal Antibodies to Infectious Bursal Disease Virus of Chickens (1991)

Murine monoclonal antibodies (MAbs) were produced to assist in the identification and characterization of the virus-neutralizing epitopes of infectious bursal disease virus (IBDV). Only MAbs that reacted in Western blotting with viral protein 2 (VP2) or immunoprecipitated VP2 neutralized the infectivity of the virus in cell culture and passively protected young chickens from infection. Three of the neutralizing MAbs did not react with denatured viral proteins. Additivity enzyme-linked immunosorbent assays indicated that the six virus-neutralizing MAbs recognized two spatially independent epitopes. The ability of two of the virus-neutralizing MAbs to neutralize a variant of IBDV that had escaped neutralization by all the other MAbs confirmed the existence of two distinct neutralizing epitopes. The results support the hypothesis that there are at least two non-overlapping epitopes recognized by the virus-neutralizing MAbs reported in this study, although these may still be within one conformational site on VP2 of IBDV.
Designing fibre channel fabrics (2002)

The fibre channel standard, developed by the ANSI X3T9.3 task group, defines a serial I/O channel for interconnecting a number of peripheral devices and computer systems. In this paper we consider how fibre channel switches can be cascaded to form a fibre channel fabric. We begin with an analytical model of topology performance that provides a theoretical upper bound on fabric performance and a method for the practical evaluation of fabric topologies. Next, we present simulation results for a single fibre channel switch having 16 ports and a specific high-level architecture. Finally, we consider cascades of this switch, and discuss some subtleties, such as different routing strategies, deadlocks and unfairness.
Structure and function of cardiac sodium and potassium channels (1997)

The application of patch-clamp and molecular approaches has resulted in an increasingly refined understanding of the molecular entities underlying cardiac sodium and potassium currents. The sodium current results from expression of a single large alpha-subunit, whereas multiple potassium currents and potassium channel alpha-subunits have been identified. Recapitulation of some ion currents in heterologous expression systems requires not only expression of alpha-subunits but also ancillary (beta) subunits. Domains common to functions such as activation, inactivation, and drug block are now being identified in alpha- and beta-gene products. Variability in the expression or function of individual ion-channel genes is an increasingly recognized source of variability in the ion currents recorded in heart cells under physiological conditions (e.g. during development) as well as in disease.
Topologically Modified Biopolymers: Properties of Synthetic Circular DNAs and RNAs. (1995)

Circular nucleic acid molecules can have chemical and biological properties very different from those of the corresponding linear nucleic acid polymers. Described here are methods used recently for construction of such circular molecules, and some of the properties that can arise from making this topological change. Among the unusual properties found for circular nucleic acids are: strong resistance to degradation in biological media; high affinity of binding to other nucleic acids; high sequence selectivity in nucleic acid binding; topological linkage to biomolecules; and the ability to template the synthesis of specific repeating nucleic acid and protein polymers. These properties may be useful in biochemical, medical diagnostic and therapeutic applications.
General Synthesis of Potentially Antiviral α‐Adamantyl Carbonyl Compounds (1979)

The antiviral activity of some α-adamantyl carbonyl compounds of type (3) is greater than that of 1-amino-adamantane. Syntheses of the kind shown below are therefore of considerable interest.
VARIOT: a novel multilayer tunnel barrier concept for low-voltage nonvolatile memory devices (2003)

Low-voltage low-power nonvolatile floating-gate memory device operation can be achieved by using alternative tunnel barriers consisting of at least two dielectric layers with different dielectric constants k. Low-k/high-k (asymmetric) and low-k/high-k/low-k (symmetric) barriers enable steeper tunneling current-voltage characteristics. Their implementation is possible with high-k dielectric materials that are currently investigated for SiO/sub 2/ replacement in sub-100-nm CMOS technologies. We show that a reduction in programming voltages of up to 50% can be achieved. This would significantly reduce the circuitry required to generate the high voltages on a nonvolatile memory chip, while maintaining sufficient performance and reliability.
Cold trapping of volatile organic compounds on fused silica capillary columns (1983)

Abstract A 30 m, 0.25 mm ID, fused silica capillary column at temperatures from –60 to –100°C has been shown to be a quantitative trap for organic compounds with volatilities ranging from that of 1, 1 ‐dichloroethene that of chlorobenzene. This type of “whole column cryotrapping” provided sharp peaks (peak width approximately 4–7 seconds) for all compounds at a trapping temperature of –80°C and with high carrier gas pressures and linear velocities (30 psi and 110 cm/s, respectively). Whole column cryotrapping possesses great simplicity, chromatographic efficiency (no trapping loop connections), and a built‐in indicator of quality assurance for trapping efficiency ( i.e. , peak shape). These advantages are extremely attractive and are indicative of the fact that the potential of this approach has not yet been fully appreciated.
Characteristic Mode Based Tradeoff Analysis of Antenna-Chassis Interactions for Multiple Antenna Terminals (2011)

The design of multiple antennas in compact mobile terminals is a significant challenge, due to both practical and fundamental design tradeoffs. In this paper, fundamental antenna design tradeoffs of multiple antenna terminals are presented in the framework of characteristic mode analysis. In particular, interactions between the antenna elements and the characteristic modes and their impact on design tradeoffs are investigated in both theory and simulations. The results reveal that the characteristic modes play an important role in determining the optimal placement of antennas for low mutual coupling. Moreover, the ability of antenna elements to localize the excitation currents on the chassis can significantly influence the final performance. To demonstrate the effectiveness of the proposed approach, a dual-band, dual-antenna terminal is designed to provide an isolation of over 10 dB for the 900 MHz band without additional matching or decoupling structures. A tradeoff analysis of bandwidth, efficiency, effective diversity gain and capacity is performed over different antenna locations. Finally, three fabricated prototypes verify the simulation results for representative cases.
Gβγ Activation Site in Adenylyl Cyclase Type II (2005)

The Gbetagamma complex of heterotrimeric G proteins is the most outstanding example for the divergent regulation of mammalian adenylyl cyclases. The heterodimeric Gbetagamma complex inhibits some isoforms, e.g. ACI, and stimulates the isoforms ACII, -IV, and -VII. Although former studies identified the QEHA region located in the C2 domain of ACII as an important interaction site for Gbetagamma, the determinant of the stimulatory effect of Gbetagamma has not been detected. Here, we identified the C1b domain as the stimulatory region using full-length adenylyl cyclase. The relevant Gbetagamma signal transfer motif in IIC1b was determined as MTRYLESWGAAKPFAHL (amino acids 493-509). Amino acids of this PFAHL motif were absolutely necessary for ACII to be stimulated by Gbetagamma, whereas they were dispensable for Galpha(s) or forskolin stimulation. The PFAHL motif is present in all three adenylyl cyclase isoforms that are activated by Gbetagamma but is absent in other adenylyl cyclase isoforms as well as other known effectors of Gbetagamma. The emerging concept of two contact sites on different molecule halves for effective regulation of adenylyl cyclase is discussed.
Interleukin 10: a novel stimulatory factor for mast cells and their progenitors. (1991)

We have characterized the mast cell stimulating activity of murine cytokine synthesis inhibitory factor, referred to as interleukin 10 (IL-10). It was found that IL-10 alone failed to support the growth of mast cell lines and mast cell progenitors. Nevertheless, it dramatically enhanced their growth when combined with IL-3 or IL-4. Moreover, IL-4 plus IL-10 supported the proliferation of mast cells as well as IL-3, suggesting that these two factors may provide a pathway for their development independent of IL-3. However, optimal mast cell growth was stimulated by the combination of IL-10, IL-4, and IL-3. This particular set of cytokines are coordinately produced by activated T cells and may constitute an effective network regulating early and late stages of mast cell development during certain immune responses.
Modification of bladder structure in response to outflow obstruction and ageing. (1997)

The morphology of the normal bladder has been compared with that of the obstructed and the ageing bladder, using both light and electron microscopy. In the normal bladder the smooth muscle cells are closely packed together with relatively little intervening connective tissue. The smooth muscle bundles are innervated predominantly by autonomic presumptive cholinergic nerve fibres, while adrenergic nerves are usually observed in association with blood vessels. In the obstructed bladder, many smooth muscle cells are surrounded by large amounts of connective tissue and some of the muscle cells change their function from contracting to seemingly being involved in collagen synthesis. A significant reduction in the innervation of the smooth muscle cells is observed. In the ageing bladder, the smooth muscle cells have a normal morphology which is in contrast to the findings in the obstructed bladder. A reduction in the innervation of the ageing bladder is observed, although to a considerably lesser extent than that observed in the obstructed bladder. As the morphology of the obstructed bladder differs from that of the ageing bladder, it is unlikely that the changes seen in the obstructed bladder simply reflect a function of age.
Automated slide preparation system for the clinical laboratory (1996)

An automated device has been developed to prepare a wide variety of cytology preparations. Using the device, cells collected in suspension are mildly dispersed and transferred to a glass slide using filter-transfer technology. The cell density on the slide is controlled by the instrument. A companion product, the solution used in specimen transport and preparation, provides long-term preservation of diagnostic cells while lysing red blood cells. The overall process yields clean, uniform samples with better visualization of the diagnostic cells. The use of a disposable filter prevents sample-to-sample contamination. Collection of the sample in solution makes it possible to produce multiple slides from one sample.
Virtualization for Embedded Systems (2007)

1 Introduction 52 Virtualization 62.1 What Is It? 62.2 How Is It Done? 72.2.1 Pure virtualization 82.2.2 Impure virtualization 93 Virtualization for Embedded Systems 103.1 Virtualization Beneﬁts for Embedded Systems 103.1.1 Modern embedded systems software 103.1.2 Multiple concurrent operating systems 103.1.3 Security 113.1.4 Multicore chips 123.1.5 License separation 123.2 When “Virtualization” is not Virtualization 133.2.1 Security 133.2.2 License separation 133.3 Limits of Virtualization 143.3.1 Software complexity 143.3.2 Integration 143.3.3 Security policies 153.3.4 Trusted computing base 164 Microkernels — A Better Solution 174.1 Embedded Systems Requirements 174.2 Microkernels 174.2.1 What are microkernels? 174.2.2 General properties of microkernel systems 184.3 OKL4 Microkernel Technology 194.3.1 Low-overhead virtualization 194.3.2 Unbeaten IPC performance 204.3.3 Efﬁcient resource sharing 204.3.4 Flexible scheduling 214.3.5 Security 214.3.6 Small trusted computing base 224.3.7 Open-source software 234.4 Virtualization with OKL4 — Best of Both Worlds 235 The Future: Many Cores, Many Components, Many Nines 255.1 The Challenges 255.2 Future-Prooﬁng Embedded Technology 25Bibliography 27About the Author 28OK 40036:2007 Copyright
Effects of polymerase, template dilution and cycle number on PCR based 16 S rRNA diversity analysis using the deep sequencing method (2010)

These results highlight the PCR conditions, particularly the polymerase, have significant effect on the analysis of microbial diversity with next generation sequencing methods.
Optical nerve stimulation for a vestibular prosthesis (2009)

Infrared Nerve Stimulation (INS) offers several advantages over electrical stimulation, including more precise spatial selectivity and improved surgical access. In this study, INS and electrical stimulation were compared in their ability to activate the vestibular branch of the VIII<sup>th</sup> nerve, as a potential way to treat balance disorders. The superior and lateral canals of the vestibular system of Guinea pigs were identified and approached with the aid of precise 3-D reconstructions. A monopolar platinum stimulating electrode was positioned near the ampullae of the canals, and biphasic current pulses were used to stimulate vestibular evoked potentials and eye movements. Thresholds and input/output functions were measured for various stimulus conditions. A short pulsed diode laser (Capella, Lockheed Martin-Aculight, Inc., Bothell WA) was placed in the same anatomical position and various stimulus conditions were evaluated in their ability to evoke similar potentials and eye movements.
Natural Rubber Biosynthesis and Physic-Chemical Studies on Plant Derived Latex (2011)

Natural rubber is a biopolymer of high economic importance with incomparable performance properties such as high elasticity, resilience and efficient heat dispersion (van Beilen and Poirier, 2007a). This high molecular mass polymer is formed from isopentenyl diphosphate units (IPP) which are linked in cis-configuration building poly(cis-1,4-isoprene) 300 to 70,000 isoprene molecules are coupled to form an irregular structure that cannot crystallize under normal conditions mediating the amorphous, rubbery texture Upon harvest from plants and processing, along with the biopolymer itself also non-rubber compounds are co-extracted and remain in the natural rubber product Therefore, the final product consists of about 94% poly(cis-1,4-isoprene) and 6% non-rubber contents such as proteins and fatty acids These contaminations are thought to contribute to the extraordinary characteristics of natural rubber The plant-derived commodity is required for the production of more than 40,000 consumer products including tires, footwear and medical devices After harvest natural rubber is either kept in solution through addition of solvents and stabilizers or it is coagulated and dried. Solubilised natural rubber is used for products such as gloves or condoms but most of the harvested natural rubber is processed as so called bulk rubber in solid sheets or granules (van Beilen and Poirier, 2007b). Currently, the sole crop exploited for commercial production of high quality natural rubber in viable quantities is Hevea brasiliensis Muell. Arg. (Figure H. brasiliensis -a tree indigenous to the Amazon Basin -is the most recently domesticated plant among major crops. In their natural environment trees grow widely distributed within the forest, but for large-scale rubber production H. brasiliensis trees are planted in monoculture The main rubber-producing countries presently are Thailand, Indonesia, Malaysia, India and the People's Republic of China, which together accounted for 89% or 9.33 million tons of the global rubber production in 2005 (Figure With a yield potential of more than 2500 kg ha -1 year -1 H. brasiliensis is a valuable crop in tropical and subtropical countries where its cultivation is possible (Cornish, 2001a;
Nitriles in heterocyclic synthesis: Synthesis of pyrazolo[1, 5‐a] pyrimidine, pyrazolo[1, 5‐c][1, 2, 4]triazine and pyrazolo[4, 3‐e][1, 2, 4]triazine derivatives (1991)

Abstract 5‐Amino‐3‐phenylpyrazole ( 1 ) reacted with enaminonitriles 2a – c to afford the pyrazolopyrimidines 5a , b and the 5‐substituted aminopyrazole 8 . 5a reacted with arenediazonium chlorides and benzaldehyde to give 6 and 7 respectively. Also, o‐hydroxyacetophenone afforded the fused pyrazole derivative 9 on treatment with 1 . Enaminonitrile 3 coupled with 11 and arenediazonium chlorides to give 12 and 13 respectively. Cyclization of 13a , b afforded the pyrazolotriazines 15a , b .
Role of Oxidative Stress in Parkinson's Disease (2013)

Parkinson's disease (PD) is a progressive neurodegenerative movement disorder associated with a selective loss of the dopamine(DA)rgic neurons in the substantia nigra pars compacta and the degeneration of projecting nerve fibers in the striatum. Because there is currently no therapy that delays the neurodegenerative process, modification of the disease course by neuroprotective therapy is an important unmet clinical need. Toward this end, understanding cellular mechanisms that render the nigral neurons particularly vulnerable have been a subject of intensive research. Increasing evidence suggests that oxidative stress plays a major role. The metabolism of DA itself contributes to oxidative stress, resulting in modification of intracellular macromolecules whose functions are important for cell survival. Mitochondrial dysfunction and the consequent increase in reactive oxygen species also trigger a sequence of events that leads to cell demise. In addition, activated microglia produce nitric oxide and superoxide during neuroinflammatory responses, and this is aggravated by the molecules released by damaged DAergic neurons such as α-synuclein, neuromelanin and matrix metalloproteinase-3. Ways to reduce oxidative stress therefore can provide a therapeutic strategy. NAD(P)H:quinone reductase (NQO1) and other antioxidant enzymes, whose gene expression are commonly under the regulation of the transcription factor Nrf2, can serve as target proteins utilized toward development of disease-modifying therapy for PD.
Alveolar epithelial cells in idiopathic pulmonary fibrosis display upregulation of TRAIL, DR4 and DR5 expression with simultaneous preferential over-expression of pro-apoptotic marker p53. (2014)

Idiopathic pulmonary fibrosis (IPF) is a progressive, debilitating, and fatal lung disease of unknown aetiology with no current cure. The pathogenesis of IPF remains unclear but repeated alveolar epithelial cell (AEC) injuries and subsequent apoptosis are believed to be among the initiating/ongoing triggers. However, the precise mechanism of apoptotic induction is hitherto elusive. In this study, we investigated expression of a panel of pro-apoptotic and cell cycle regulatory proteins in 21 IPF and 19 control lung tissue samples. We reveal significant upregulation of the apoptosis-inducing ligand TRAIL and its cognate receptors DR4 and DR5 in AEC within active lesions of IPF lungs. This upregulation was accompanied by pro-apoptotic protein p53 overexpression. In contrast, myofibroblasts within the fibroblastic foci of IPF lungs exhibited high TRAIL, DR4 and DR5 expression but negligible p53 expression. Similarly, p53 expression was absent or negligible in IPF and control alveolar macrophages and lymphocytes. No significant differences in TRAIL expression were noted in these cell types between IPF and control lungs. However, DR4 and DR5 upregulation was detected in IPF alveolar macrophages and lymphocytes. The marker of cellular senescence p21(WAF1) was upregulated within affected AEC in IPF lungs. Cell cycle regulatory proteins Cyclin D1 and SOCS3 were significantly enhanced in AEC within the remodelled fibrotic areas of IPF lungs but expression was negligible in myofibroblasts. Taken together these findings suggest that, within the remodelled fibrotic areas of IPF, AEC can display markers associated with proliferation, senescence, and apoptotosis, where TRAIL could drive the apoptotic response. Clear understanding of disease processes and identification of therapeutic targets will direct us to develop effective therapies for IPF.
Efficient Synthesis of Empagliflozin, an Inhibitor of SGLT-2, Utilizing an AlCl<sub>3</sub>-Promoted Silane Reduction of a β-Glycopyranoside (2014)

An efficient production synthesis of the SGLT-2 inhibitor Empagliflozin (5) from acid 1 is described. The key tactical stage involves I/Mg exchange of aryl iodide 2 followed by addition to glucono lactone 3 in THF. Subsequent in situ treatment of the resulting lactol with HCl in MeOH produces β-anomeric methyl glycopyranoside 4 which is, without isolation, directly reduced with Et3SiH mediated by AlCl3 as a Lewis acid in CH2Cl2/MeCN to afford 5 in 50% overall yield. The process was implemented for production on a metric ton scale for commercial launch.
Desulphurisation–dimerisation of dithioacetals with W(CO)<sub>6</sub> (1987)

L. L. Yeung, Y. C. Yip and T. Luh, J. Chem. Soc., Chem. Commun., 1987, 981 DOI: 10.1039/C39870000981
Investigations on porous silicon as electrode material in electrochemical capacitors (2007)

Abstract In this study, we have demonstrated the possibility of using macroporous silicon electrodes in electrochemical capacitors. Macroporous silicon was used to increase the surface exchange between pore surface and electrolyte. The inherent resistivity of the porous silicon can be reduced through the use of subsequent doping and metallization processes of the macropore surface. A systematic study of the electrolyte concentration and the porous silicon depth influences was also performed. A unit cell capacitance value of 320 µF/cm 2 was obtained with doped and metallized p‐type macroporous silicon electrodes. (© 2007 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Therapeutic efficacy of fleroxacin for eliminating catheter-associated urinary tract infection in a rabbit model. (1993)

The efficacy of fleroxacin as therapy for experimentally induced catheter-associated urinary tract infection (CAUTI) was examined. A rabbit model of CAUTI using a closed urinary catheter drainage system and the mutant strain of Escherichia coli (WE 6933) were used to examine three dosage regimens (30 mg/kg q8h i.v.; 20 mg/kg q8h i.v.; and 10 mg/kg q8h++i.v.) of fleroxacin administered intravenously for 4 days. Quantitative bacterial counts, urinary concentrations of fleroxacin and desmethylferoxacin, histopathologic changes, and electron microscopic evaluation of catheter-associated biofilm and mucosal biofilm were performed. The results indicated that the bacterial biofilm on the urinary catheter could be eliminated by fleroxacin at 30 mg/kg q8h i.v. and 20 mg/kg q8h i.v. Fleroxacin concentrations in urine exceeded the levels necessary to destroy E. coli. Viable bacteria were eliminated with the third regimen (10 mg/kg q8h i.v.), but electron microscopy demonstrated remnants of bacterial biofilm. Histopathologic changes were significantly reduced in all fleroxacin-treated rabbits, and scanning electron microscopy showed deterioration of the bacterial biofilm on the surface of the Foley catheter in treated animals. These data suggest that fleroxacin may be useful for treating catheter-related infections because these therapeutic dosages limited ascending infections of the urethra and bladder, eliminated catheter-associated biofilms, and killed planktonic bacteria in urine.