gebhart/patrepeval huggingface dataset:
Novel role of microtubules in thrombin‐induced endothelial barrier dysfunction (2004)

Disturbances in endothelial cell (EC) barrier regulation are critically dependent upon rearrangements of EC actin cytoskeleton. However, the role of microtubule (MT) network in the regulation of EC permeability is not well understood. We examined involvement of MT remodeling in thrombin-induced EC permeability and explored MT regulation by heterotrimeric G12/13 proteins and by small GTPase Rho. Thrombin induced phosphorylation of MT regulatory protein tau at Ser409 and Ser262 and peripheral MT disassembly, which was linked to increased EC permeability. MT stabilization by taxol attenuated thrombin-induced permeability, actin remodeling, and paracellular gap formation and diminished thrombin-induced activation of Rho and Rho-kinase. Expression of activated Galpha12/13 subunits involved in thrombin-mediated signaling or their effector p115RhoGEF involved in Rho activation caused MT disassembly, whereas p115RhoGEF-specific negative regulator RGS preserved MT from thrombin-induced disassembly. Consistent with these results, expression of activated RhoA and Rho-kinase induced MT disassembly. Conversely, thrombin-induced disassembly of peripheral MT network was attenuated by expression of dominant negative RhoA and Rho-kinase mutants or by pharmacological inhibition of Rho-kinase. Collectively, our data demonstrate for the first time a critical involvement of MT disassembly in thrombin-induced EC barrier dysfunction and indicate G-protein-dependent mechanisms of thrombin-induced MT alteration.
Mutational Analysis of the Adeno-Associated Virus Type 2 (AAV2) Capsid Gene and Construction of AAV2 Vectors with Altered Tropism (2000)

Adeno-associated virus type 2 (AAV2) has proven to be a valuable vector for gene therapy. Characterization of the functional domains of the AAV capsid proteins can facilitate our understanding of viral tissue tropism, immunoreactivity, viral entry, and DNA packaging, all of which are important issues for generating improved vectors. To obtain a comprehensive genetic map of the AAV capsid gene, we have constructed 93 mutants at 59 different positions in the AAV capsid gene by site-directed mutagenesis. Several types of mutants were studied, including epitope tag or ligand insertion mutants, alanine scanning mutants, and epitope substitution mutants. Analysis of these mutants revealed eight separate phenotypes. Infectious titers of the mutants revealed four classes. Class 1 mutants were viable, class 2 mutants were partially defective, class 3 mutants were temperature sensitive, and class 4 mutants were noninfectious. Further analysis revealed some of the defects in the class 2, 3, and 4 mutants. Among the class 4 mutants, a subset completely abolished capsid formation. These mutants were located predominantly, but not exclusively, in what are likely to be beta-barrel structures in the capsid protein VP3. Two of these mutants were insertions at the N and C termini of VP3, suggesting that both ends of VP3 play a role that is important for capsid assembly or stability. Several class 2 and 3 mutants produced capsids that were unstable during purification of viral particles. One mutant, R432A, made only empty capsids, presumably due to a defect in packaging viral DNA. Additionally, five mutants were defective in heparan binding, a step that is believed to be essential for viral entry. These were distributed into two amino acid clusters in what is likely to be a cell surface loop in the capsid protein VP3. The first cluster spanned amino acids 509 to 522; the second was between amino acids 561 and 591. In addition to the heparan binding clusters, hemagglutinin epitope tag insertions identified several other regions that were on the surface of the capsid. These included insertions at amino acids 1, 34, 138, 266, 447, 591, and 664. Positions 1 and 138 were the N termini of VP1 and VP2, respectively; position 34 was exclusively in VP1; the remaining surface positions were located in putative loop regions of VP3. The remaining mutants, most of them partially defective, were presumably defective in steps of viral entry that were not tested in the preliminary screening, including intracellular trafficking, viral uncoating, or coreceptor binding. Finally, in vitro experiments showed that insertion of the serpin receptor ligand in the N-terminal regions of VP1 or VP2 can change the tropism of AAV. Our results provide information on AAV capsid functional domains and are useful for future design of AAV vectors for targeting of specific tissues.
Toward Novel Antioxidants:  Preparation of Dihydrotellurophenes and Selenophenes by Alkyltelluride-Mediated Tandem S<sub>RN</sub>1/S<sub>H</sub>i Reactions<sup>1</sup> (1999)

Reaction of 1-(2-iodophenyl)-1-methyloxirane (12) with 2 equiv of sodium n-butyltellurolate (n-BuTeNa), generated by the sodium borohydride reduction of di-n-butyl ditelluride, in THF, affords 2,3-dihydro-3-hydroxy-3-methylbenzo[b]tellurophene (13) in 62% yield, together with a small quantity of 1-(n-butyltelluro)-2-phenyl-2-propanol (27). This transformation presumably involves a tandem S(RN)1/S(H)i sequence. Similar reactions of 1-(benzylseleno)-2-phenyl-2-propanol (5a, R = Me) and 1-allyloxy-2-iodobenzene (15) afforded 2,3-dihydro-3-hydroxy-3-methylbenzo[b]selenophene (17, 74%), and 3-(n-butyltelluro)methyl-2,3-dihydrobenzo[b]furan (18, 50%), respectively. Lithium alkyltellurolates, generated by direct tellurium insertion into the required alkyllithium, or sec-butyl or tert-butyl substitution on tellurium provide product distributions similar to those observed for reactions involving n-BuTeNa. Lithium or sodium phenyltellurolate returned only starting materials from these reaction mixtures. The 2-[2-(n-butyltelluro)-1-hydroxy-1-methyl]ethylphenyl radical (14) is estimated to cyclize with k(c) = 5 x 10(8) s(-)(1) at 25 degrees C. The tandem S(RN)1/S(H)i sequence has been applied to the preparation of the antioxidant analogues, 5-hydroxy-2,3-dihydrobenzo[b]tellurophene and selenophene (31, 32).
Inhibition of Benzo[<i>a</i>]pyrene‐Induced Forestomach Neoplasia in Mice by Citrus Limonoids (1989)

The limonoids, limonin and nomilin, are bitter principles found in common edible citrus fruits. Nomilin, when given three times (at 5 and 10 mg per animal) every two days, induced increased glutathione S-transferase activity 2.48 and 3.44 times over the control, respectively, in the liver of female ICR/Ha mice. The increases of GST activity in the small intestinal mucosa were 3.00 and 4.17, respectively, over the control. Limonin, when given at the same dose levels, was not active in the liver. However, marginal activity was obtained in the small intestinal mucosa. Nomilin, which is the more active enzyme inducer, was found to inhibit benzo[a]pyrene (BP)-induced neoplasia in the forestomach of ICR/Ha mice. The number of mice with tumors was reduced from 100 to 72%, and the number of tumors per mouse was significantly decreased as a result of nomilin treatment. Limonin, which is a weak enzyme inducer, was less potent as an inhibitor of BP-induced neoplasia. These findings suggest limonoids as a class of regularly consumed natural products may be effective chemopreventive agents.
A video-based optical system for rapid measurements of chest wall movement (2001)

We tested apparatus developed to measure the movement of the surface of the chest and abdomen, during breathing in the supine subject. A line of light is projected onto the chest wall. The line image from a video camera is analysed to estimate of the height of the surface profile, so that the shape and volume of the object can be derived. The data can provide direct or inferential volume estimates. We compared this system with the widely used inferential system of inductance bands in supine volunteers who breathed using patterns designed to emphasize variability in movements: normal and large breaths, and breathing through an expiratory resistance. We calculated the differences between a spirometer signal and continuous volume estimates using the linear regression method, obtained using signals from the two methods. The volume estimate differences obtained by the optical system and induction bands were not significantly different, but the optical system was more precise. Using the optical device, an acceptable interquartile range of differences from spirometric volume (50 ml) was significantly likely when the optical device was used. During resistive loaded breathing (mean tidal volume 390 ml) direct optical measurements of volume, and inductance band estimates, were compared with tidal volume. The optical system showed distortion of the shape of the abdomen during this breathing pattern. Mean error with the optical system was 64 ml and with the inductance band system was 108 ml (p < 0.05). The optical system gives accurate reproducible results in supine human subjects and additional valuable information on shape changes.
Reduction of atherosclerosis in apolipoprotein E knockout mice by activation of the retinoid X receptor (2001)

A common feature of many metabolic pathways is their control by retinoid X receptor (RXR) heterodimers. Dysregulation of such metabolic pathways can lead to the development of atherosclerosis, a disease influenced by both systemic and local factors. Here we analyzed the effects of activation of RXR and some of its heterodimers in apolipoprotein E -/- mice, a well established animal model of atherosclerosis. An RXR agonist drastically reduced the development of atherosclerosis. In addition, a ligand for the peroxisome proliferator-activated receptor (PPAR)gamma and a dual agonist of both PPARalpha and PPARgamma had moderate inhibitory effects. Both RXR and liver X receptor (LXR) agonists induced ATP-binding cassette protein 1 (ABC-1) expression and stimulated ABC-1-mediated cholesterol efflux from macrophages from wild-type, but not from LXRalpha and beta double -/-, mice. Hence, activation of ABC-1-mediated cholesterol efflux by the RXR/LXR heterodimer might contribute to the beneficial effects of rexinoids on atherosclerosis and warrant further evaluation of RXR/LXR agonists in prevention and treatment of atherosclerosis.
Affordable Air Services and Domestic Tourists' Dispersal beyond the Gateways (2008)

The proliferation of low cost airlines in recent years have resulted in an increase in air traffic flow into regional destinations in Australia. The aim of this research is to analyse the effects of increased 'air tourists' for those destinations relatively peripheral to the main gateways. This paper first outlines the research problem in more detail, then presents the findings from the preliminary analysis of the National Visitor Survey (NVS) data. Finally, this paper discusses the discrete choice modelling framework that will be applied to study the tourists' choice to travel beyond the gateways. The expected outcome from this research is information on underpinning preferences and constraints of tourists with respect to their destination choice, which can assist destination managers and planners in the gateways as well as in the periphery.
Preliminary Results on Optimization of Pilot Scale Pretreatment of Wheat Straw Used in Coproduction of Bioethanol and Electricity (2007)

The overall objective in this European Union-project is to develop cost and energy effective production systems for coproduction of bioethanol and electricity based on integrated biomass utilization. A pilot plan reactor for hydrothermal pretreatment (including weak acid hydrolysis, wet oxidation, and steam pretreatment) with a capacity of 100 kg/h was constructed and tested for pretreatment of wheat straw for ethanol production. Highest hemicellulose (C5 sugar) recovery and extraction of hemicellulose sugars was obtained at 190 degrees C whereas highest C6 sugar yield was obtained at 200 degrees C. Lowest toxicity of hydrolysates was observed at 190 degrees C; however, addition of H2O2 improved the fermentability and sugar recoveries at the higher temperatures. The estimated total ethanol production was 223 kg/t straw assuming utilisation of both C6 and C5 during fermentation, and 0.5 g ethanol/g sugar.
Vasculogenesis and angiogenesis: Extracellular matrix remodeling in coronary collateral arteries and the ischemic heart (1997)

Heart failure secondary to ischemic cardiomyopathy is the primary cause of cardiovascular mortality. The promise of the collateral circulation lies in its potential to alter the course of the natural history of coronary heart disease. The collateral circulation of the heart is responsible for supplying blood and oxygen to the myocardium at ischemic risk following severe stenosis and reduced vasoelasticity function of a major coronary artery. In response to flow, stress, and pressure, collateral vessels are restructured and remodeled. Vascular remodeling by its very nature implies synthesis and degradation of extracellular matrix components in the vessel wall. Under normal physiological conditions proteinases that break down the specialized matrix are tightly regulated by antiproteinases. The balance between proteinase and antiproteinase influences is discoordinated during collateral development which leads to adaptive changes in the structure, function, and regulation of extracellular matrix components in the vessel wall. The role of extracellular matrix components in coronary collateral vessel formation in a canine model of chronic coronary artery occlusion has been demonstrated. The role of matrix proteinases and antiproteinases in the collateral vessel play a significant role in the underlying mechanisms of collateral development. This review presents new and significant information regarding the role of extracellular matrix proteinases and antiproteinases in vascular remodeling, function, and collateral development. Such information will have a significant impact on the understanding of the basic biology of the vascular extracellular matrix turnover, remodeling, and function as well as on elucidating potential avenues for pharmacological approaches designed to increase collateral formation and optimize myocardial blood flow in the treatment of ischemic heart disease.
Effect of Fish Oil on Ventricular Tachyarrhythmia and Death in Patients With Implantable Cardioverter Defibrillators (2006)

clinicaltrials.gov Identifier: NCT00110838.
On velocity estimation and correlation properties of narrow-band mobile communication channels (2001)

The estimation of the maximum Doppler spread or, equivalently, the vehicle velocity, is useful in improving handoff algorithms and necessary for the optimal tuning of parameters for systems that adapt to changing channel conditions. We provide a novel velocity estimator based on the spectral moments of the in-phase and the quadrature phase components or the envelope of the received signal. We characterize the joint effects of the Ricean K factor, the directivity and the angle of nonisotropic scattering, and the effects of additive white noise on our estimator and other covariance-based velocity estimators analytically. We also prove the mean-square consistency of the covariance-based velocity estimators under some assumptions on the angle of arrival distribution. Simulations illustrate our approach and compare with existing techniques.
TNF Activates Syk Protein Tyrosine Kinase Leading to TNF-Induced MAPK Activation, NF-κB Activation, and Apoptosis (2004)

Spleen tyrosine kinase (Syk), a nonreceptor protein kinase initially found to be expressed only in hemopoietic cells, has now been shown to be expressed in nonhemopoietic cells and to mediate signaling of various cytokines. Whether Syk plays any role in TNF signaling was investigated. Treatment of Jurkat T cells with TNF activated Syk kinase but not ZAP70, another member of Syk kinase family, and the optimum activation occurred at 10 s and with 1 nM TNF. TNF also activated Syk in myeloid and epithelial cells. TNF-induced Syk activation was abolished by piceatannol (Syk-selective inhibitor), which led to the suppression of TNF-induced activation of c- JNK, p38 MAPK, and p44/p42 MAPK. Jurkat cells that did not express Syk (JCaM1, JCaM1/lck) showed lack of TNF-induced Syk, JNK, p38 MAPK, and p44/p42 MAPK activation, as well as TNF-induced IkappaBalpha phosphorylation, IkappaBalpha degradation, and NF-kappaB activation. TNF-induced NF-kappaB activation was enhanced by overexpression of Syk by Syk-cDNA and suppressed when Syk expression was down-regulated by expression of Syk-small interfering RNA (siRNA-Syk). The apoptotic effects of TNF were reduced by up-regulation of NF-kappaB by Syk-cDNA, and enhanced by down-regulation of NF-kappaB by siRNA-Syk. Immunoprecipitation of cells with Syk Abs showed TNF-dependent association of Syk with both TNFR1 and TNFR2; this association was enhanced by up-regulation of Syk expression with Syk-cDNA and suppressed by down-regulation of Syk using siRNA-Syk. Overall, our results demonstrate that Syk activation plays an essential role in TNF-induced activation of JNK, p38 MAPK, p44/p42 MAPK, NF-kappaB, and apoptosis.
Positive regulatory elements (HF-1a and HF-1b) and a novel negative regulatory element (HF-3) mediate ventricular muscle-specific expression of myosin light-chain 2-luciferase fusion genes in transgenic mice. (1994)

The cardiac myosin light-chain 2v (MLC-2v) gene has served as a model system to identify the pathways which restrict the expression of cardiac muscle genes to particular chambers of the heart during cardiogenesis. To identify the critical cis regulatory elements which mediate ventricular chamber-specific expression of the MLC-2v gene in the in vivo context, a series of transgenic mice which harbor mutations in putative MLC-2 cis regulatory elements in a 250-bp MLC-2-luciferase fusion gene which is expressed in a ventricular chamber-specific fashion in transgenic mice were generated. These studies demonstrate that both components of HF-1 (HF-1a and HF-1b/MEF-2) are required to maintain ventricular chamber-specific expression and function as positive regulatory elements. Mutations in another conserved element (HF-2) are without statistically significant effect on ventricular chamber expression. Transgenics harboring mutations in the E-box site also displayed significant upregulation of reporter activity in the soleus, gastrocnemius, and uterus, with a borderline effect on expression in liver. Mutations in another conserved element (HF-3) result in a marked (&gt; 75-fold) upregulation of the luciferase reporter activity in the soleus muscle of multiple independent or transgenic founders. Since the HF-3 mutations appeared to have only a marginal effect on luciferase reporter activity in liver tissue, HF-3 appears to function as a novel negative regulatory element to primarily suppress expression in muscle tissues. Thus, a combination of positive (HF-1a/HF-1b) and negative (E-box and HF-3) regulatory elements appear to be required to maintain ventricular chamber-specific expression in the in vivo context.
Transgenic Mouse Strains as Platforms for the Successful Discovery and Development of Human Therapeutic Monoclonal Antibodies (2014)

Transgenic mice have yielded seven of the ten currently-approved human antibody drugs, making them the most successful platform for the discovery of fully human antibody therapeutics. The use of the in vivo immune system helps drive this success by taking advantage of the natural selection process that produces antibodies with desirable characteristics. Appropriately genetically-engineered mice act as robust engines for the generation of diverse repertoires of affinity- matured fully human variable regions with intrinsic properties necessary for successful antibody drug development including high potency, specificity, manufacturability, solubility and low risk of immunogenicity. A broad range of mAb drug targets are addressable in these mice, comprising both secreted and transmembrane targets, including membrane multi-spanning targets, as well as human target antigens that share high sequence identity with their mouse orthologue. Transgenic mice can routinely yield antibodies with sub-nanomolar binding affinity for their antigen, with lead candidate mAbs frequently possessing affinities for binding to their target of less than 100 picomolar, without requiring any ex vivo affinity optimization. While the originator transgenic mice platforms are no longer broadly available, a new generation of transgenic platforms is in development for discovery of the next wave of human therapeutic antibodies.
A scalable low power issue queue for large instruction window processors (2006)

Large instruction windows and issue queues are key to exploiting greater instruction level parallelism in out-of-order superscalar processors. However, the cycle time and energy consumption of conventional large monolithic issue queues are high. Previous efforts to reduce cycle time segment the issue queue and pipeline wakeup. Unfortunately, this results in significant IPC loss. Other proposals which address energy efficiency issues by avoiding only the unnecessary tag-comparisons do not reduce broadcasts. These schemes also increase the issue latency.To address both these issues comprehensively, we propose the Scalable Lowpower Issue Queue (SLIQ). SLIQ augments a pipelined issue queue with direct indexing to mitigate the problem of delayed wakeups while reducing the cycle time. Also, the SLIQ design naturally leads to significant energy savings by reducing both the number of tag broadcasts and comparisons required.A 2 segment SLIQ incurs an average IPC loss of 0.2% over the entire SPEC CPU2000 suite, while achieving a 25.2% reduction in issue latency when compared to a monolithic 128-entry issue queue for an 8-wide superscalar processor. An 8 segment SLIQ improves scalability by reducing the issue latency by 38.3% while incurring an IPC loss of only 2.3%. Further, the 8 segment SLIQ significantly reduces the energy consumption and energy-delay product by 48.3% and 67.4% respectively on average.
Two subsets of human alphoid repetitive DNA show distinct preferential localization in the pericentric regions of chromosomes 13, 18, and 21 (1986)

We have isolated and characterized two human middle repetitive alphoid DNA fragments, L1.26 and L1.84, which localize to two different sets of chromosomes. In situ hybridization revealed both repeats to have major and minor binding sites on the pericentric regions of several chromosomes. Probe L1.26 maps predominantly to chromosomes 13 and 21. Probe L1.84 locates to chromosome 18. Minor hybridization sites for both probes include chromosomes 2, 8, 9, and 20; in addition, L1.26 revealed minor sites on chromosomes 18 and 22. The binding to these sites strongly depends on hybridization conditions. In Southern blot hybridizations to total human DNA, both L1.26 and L1.84 give the same ladder pattern, with a step size of 170 bp, indicating their presence as tandem repeats, but with different band intensities for each probe. The chromosome-specific nature of particular multimers was confirmed by Southern blot analyses of a human-rodent hybrid cell panel. We conclude that L1.26 and L1.84, with their related sequences, constitute subfamilies of alphoid DNA that are specific for subsets of chromosomes and, in some cases, possibly even for single chromosomes.