gebhart/patrepeval huggingface dataset:
Gene-Based Vaccination with a Mismatched Envelope Protects against Simian Immunodeficiency Virus Infection in Nonhuman Primates (2012)

The RV144 trial demonstrated that an experimental AIDS vaccine can prevent human immunodeficiency virus type 1 (HIV-1) infection in humans. Because of its limited efficacy, further understanding of the mechanisms of preventive AIDS vaccines remains a priority, and nonhuman primate (NHP) models of lentiviral infection provide an opportunity to define immunogens, vectors, and correlates of immunity. In this study, we show that prime-boost vaccination with a mismatched SIV envelope (Env) gene, derived from simian immunodeficiency virus SIVmac239, prevents infection by SIVsmE660 intrarectally. Analysis of different gene-based prime-boost immunization regimens revealed that recombinant adenovirus type 5 (rAd5) prime followed by replication-defective lymphocytic choriomeningitis virus (rLCMV) boost elicited robust CD4 and CD8 T-cell and humoral immune responses. This vaccine protected against infection after repetitive mucosal challenge with efficacies of 82% per exposure and 62% cumulatively. No effect was seen on viremia in infected vaccinated monkeys compared to controls. Protection correlated with the presence of neutralizing antibodies to the challenge viruses tested in peripheral blood mononuclear cells. These data indicate that a vaccine expressing a mismatched Env gene alone can prevent SIV infection in NHPs and identifies an immune correlate that may guide immunogen selection and immune monitoring for clinical efficacy trials.
The study of high-speed surface dynamics using a pulsed proton beam (2012)

We present experimental results supporting physics based ejecta model development, where we assume ejecta form as a special limiting case of a Richtmyer-Meshkov (RM) instability with Atwood number A = -1. We present and use data to test established RM spike and bubble growth rate theory through application of modern laser Doppler velocimetry techniques applied in a novel manner to coincidentally measure bubble and spike velocities from shocked metals. We also explore the link of ejecta formation from a solid material to its plastic flow stress at high-strain rates ($107/s) and high strains (700%).
Platelet-Platelet Recognition During Aggregation: Distinct Mechanisms Determined by the Release Reaction (1984)

Fixed platelets, bearing covalently bound fibrinogen, were previously shown to participate passively in aggregation induced by thrombin or A23187. The bound fibrinogen was specifically required for the interaction. The present study examines the role of the release reaction in controlling the passive participation of the fixed platelets in aggregation. Aggregation of fresh platelets induced by low ADP concentration (less than or equal to 2 microM) was not augmented by the fixed platelets, but was augmented when higher concentrations of ADP were employed. Fixed platelets failed to enhance aggregation of aspirin-treated fresh platelets induced by 10 microM ADP; the augmentation capability was reconstituted by a supernatant fraction from platelets activated by 10 microM ADP in the presence of EDTA. The binding of soluble fibrinogen to activated fresh platelets occurred regardless of the release reaction, but the interaction of fragmented fixed platelets bearing bound fibrinogen with aggregating fresh platelets was apparent only when release took place. It is concluded that fibrinogen covalently bound to fixed platelets is selectively recognized by released compound(s).
Answering XML Queries over Heterogeneous Data Sources. (2001)

This work describes an architecture for integrating heterogeneous data sources under an XML global schema, following the local-as-view approach (local sources&amp;apos; schemas are described as views over the global schema). In this context, we focus on the problem of translating the user&amp;apos;s query against the XML global schema into a SQL query over the local data sources.
Erythropoietin Treatment Improves Liver Regeneration and Survival in Rat Models of Extended Liver Resection and Living Donor Liver Transplantation (2008)

Erythropoietin treatment significantly improved liver regeneration and survival after PH and pLTx and may therefore represent a promising strategy to optimize the clinical outcome after extended liver resection and LDLT in the future.
IMO-8400, a novel TLR7, TLR8 and TLR9 antagonist, inhibits disease development in lupus-prone NZBW/F1 mice (119.12) (2012)

Abstract Several studies have implicated Toll-like receptors (TLRs) 7, 8 and 9 in the development and progression of lupus. We have developed IMO-8400, a synthetic DNA-based antagonist that has shown potent inhibition of TLR7-, TLR8-, and TLR9-mediated immune responses in cell-based assays and in non-human primates. To assess the therapeutic potency of IMO-8400, we have tested this compound in lupus-prone NZBW/F1 mice. Mice were injected subcutaneously with IMO-8400 at 1.9, 3.8 or 7.5 mg/kg once a week or 7.5 mg/kg once every two weeks from the age of week 21 to 33, and sacrificed at week 34. NZBW/F1 mice treated with IMO-8400 at the weekly dose of 3.8 or 7.5 mg/kg or 7.5 mg/kg every two weeks showed a significant reduction in urine protein and blood urea nitrogen levels in compression to that of untreated mice. Additionally, anti-DNA, anti-RNP and anti-SM IgG levels were also lower in treated mice than untreated controls. No treatment-related side-effects were observed. Histological examination of kidney sections revealed improvement in nephritis (reduced glomerular sclerosis and decreased interstitial inflammation), accompanied by decreased glomerular deposits of IgG immune complex in mice treated with IMO-8400. These results indicate that IMO-8400 suppressed autoimmune antibody production and improved renal function by inhibiting immune responses in lupus-prone NZBW/F1 mice. Thus, IMO-8400 has the potential for the treatment of lupus and other autoimmune diseases.
CO<sub>2</sub> and argon laser vascular welding: Acute histologic and thermodynamic comparison (1988)

CO2 and argon lasers have been used successfully for vascular welding in both experimental and clinical settings. This study compared the thermodynamics during CO2 and argon laser welding of 1-cm longitudinal arteriotomies in a canine model. Continuous recordings using an AGA 782 digital thermographic system with spatial and thermal resolution of +/-0.2 mm and +/-0.2 degree C, respectively, were analyzed. A HGM argon laser using a 300-microns optic fiber held at 1 cm from the vessel edges (spot diameter = 2.8 mm) with concomitant room temperature saline irrigation (1 drop/sec) was used for argon welds. Total exposure time was 150 sec/cm. CO2 welds were performed with a Sharplan CO2 laser (spot diameter = 0.22 mm) with no irrigation for total exposure time of 10 sec/cm. Thermodynamic results and laser parameters are summarized as follows: Argon-n = 20; power = 500 mW; energy fluence = 1,400 J/cm2; Tmax = 48.8 degrees C; T mean +/- S.D. = 45.1 +/- 2.7 degrees C; CO2-n = 20; power = 150 mW; energy fluence = 3,000 J/cm2; Tmax 84.0 degrees C; T mean +/- S.D. = 60.7 +/- 9.8 degrees C. There was a significant difference (P less than .05) in thermal measurements between successful CO2 and argon vascular welds. Temperature rise during the argon welds was limited by saline irrigation. In contrast, during CO2 laser welding, the temperature rose quickly to its maximum and was maintained at a relatively high level as the laser progressed (0.1 cm/sec) along the anastomosis.(ABSTRACT TRUNCATED AT 250 WORDS)
Nanopore Analysis of Nucleic Acids Bound to Exonucleases and Polymerases (2010)

When a voltage is imposed across a thin membrane containing a nanoscopic pore, the electric field generated within the pore captures linear ionized polymers, such as nucleic acids, that are present in the solution bathing the pore. The nucleic acid molecule transiently blocks ionic current as it is translocated through the pore, and modulations of the current provide information about the structure and dynamic motion of the molecule. Altering the imposed voltage allows movement of the DNA molecule in the pore to be controlled. If a DNA-processing enzyme such as an exonuclease or polymerase is present, the enzyme-DNA complex is also drawn to the pore, and further modulations of the ionic current reflect enzyme function at the single-molecule level on millisecond timescales. The combined enzymatic and voltage control of a DNA molecule in the nanopore can be used to sequence the DNA.
Geographical sampling bias and its implications for conservation priorities in Africa (2003)

Abstract Aim To design and apply statistical tests for measuring sampling bias in the raw data used to the determine priority areas for conservation, and to discuss their impact on conservation analyses for the region. Location Sub‐Saharan Africa. Methods An extensive data set comprising 78,083 vouchered locality records for 1068 passerine birds in sub‐Saharan Africa has been assembled. Using geographical information systems, we designed and applied two tests to determine if sampling of these taxa was biased. First, we detected possible biases because of accessibility by measuring the proximity of each record to cities, rivers and roads. Second, we quantified the intensity of sampling of each species inside and surrounding proposed conservation priority areas and compared it with sampling intensity in non‐priority areas. We applied statistical tests to determine if the distribution of these sampling records deviated significantly from random distributions. Results The analyses show that the location and intensity of collecting have historically been heavily influenced by accessibility. Sampling localities show dense, significant aggregation around city limits, and along rivers and roads. When examining the collecting sites of each individual species, the pattern of sampling has been significantly concentrated within and immediately surrounding areas now designated as conservation priorities. Main conclusions Assessment of patterns of species richness and endemicity at the scale useful for establishing conservation priorities, below the continental level, undoubtedly reflects biases in taxonomic sampling. This is especially problematic for priorities established using the criterion of complementarity because the estimated spatial costs of this approach are highly sensitive to sampling artefacts. Hence such conservation priorities should be interpreted with caution proportional to the bias found. We argue that conservation priority setting analyses require (1) statistical tests to detect these biases, and (2) data treatment to reflect species distribution rather than patterns of collecting effort.
Cloning and Molecular Analysis of the Pea Seedling Copper Amine Oxidase (1995)

A pea seedling amine oxidase cDNA has been isolated and sequenced. A single long open reading frame has amino acid sequences corresponding to those determined from active site peptide (Janes, S.M., Palcic, M.M., Scaman, C.H., Smith, A.J., Brown, D.E., Dooley, D.M., Mure, M., and Klinman, J.P. (1992) Biochemistry 31, 12147-12154) and N-terminal sequencing experiments. The latter reveals the protein to have a 25-amino acid leader sequence with characteristics of a secretion signal peptide, as expected for this extracellular enzyme. Comparisons of the amino acid sequence of the mature pea enzyme (649 amino acids) with that of the mature lentil enzyme (569 amino acids; Rossi, A., Petruzzelli, R., and Finazzi-Agrò, A. (1992) FEBS Lett. 301, 253-257) reveal important and unexpected differences particularly with regard to protein length. Sequencing of part of the lentil gene identified several frameshift differences within the coding region resulting in a mature lentil protein of exactly the same length, 649 amino acids, as the pea enzyme. Multiple alignments of 10 copper amine oxidase sequences reveal 33 completely conserved residues of which 10 are found within 41 aligned residues at the C-terminal tails, the region missing from the original lentil sequence. One of only four conserved histidines is found in this region and may represent the third ligand to the copper. The pea enzyme contains around 3-4% carbohydrate as judged by deglycosylation experiments. We have also demonstrated by hybridization analysis that copper amine oxidase genes are present in a range of mono- and dicotyledonous plants.
Mechanical and dynamic mechanical properties of polyurethane and polyurethane/polyurea elastomers based on 4,4?-diisocyanatodicyclohexyl methane (1997)

The physical and thermal properties of hand-cast polyurethane and polyurethane/polyurea elastomers prepared from prepolymers of 20 and 97% trans,trans-4,4′-diisocyanatodicyclohexyl methane (t,t-rMDI) and C3- and C4-polyethers chain extended with either 1,4-butanediol (XB) or a commercial mixture of diethyl toluenediamine isomers (DETDA) were determined. The influence of the distribution of geometric isomers of the diisocyanate and of the chain-extender building blocks on these properties is significant. Urethane/ureas are harder and have higher modulus than polyurethanes formed from the same prepolymer. The polyurethane/polyurea elastomers all have somewhat high compression set. Dynamic Mechanical Analysis (DMA) suggests that DETDA extended systems based on 20% t,t-rMDI are phase separated, as illustrated by extended rubbery plateau regions and significantly higher softening points than the corresponding XB extended ones. Uniquely, these elastomers are transparent rather than opaque as typical with most other phase-segregated elastomers. Polyurethanes based on 97% t,t-rMDI are harder and have higher modulus than those based on 20% t,t-rMDI (Desmodur™ W). They have good phase separation and high softening points but they are opaque. Surprisingly, there is not much difference between the physical or thermal properties of polyurethane/polyureas and polyurethanes based on 97% t,t-rMDI. Replacing XB with DETDA gives only moderate improvement in properties, but it does make the elastomers optically clear. © 1997 John Wiley & Sons, Inc. J Appl Polym Sci 64: 957–970, 1997
In vivo induction kinetics of the arabinose promoters in Escherichia coli (1995)

In Escherichia coli, the AraC protein represses transcription from its own promoter, PC, and when associated with arabinose, activates transcription from three other promoters, PBAD, PE, and PFGH. Expression from all four of these promoters is also regulated by cyclic AMP-catabolite activator protein; however, the arrangement of the protein binding sites is not identical for each promoter. We are interested in determining how the AraC protein is able to activate PBAD, PE, and PFGH despite their differences. We have characterized the induction response of the wild-type arabinose operons from their native chromosomal locations by primer extension analysis. In this analysis, mRNA from the four arabinose operons plus an internal standard could all be assayed in the RNA obtained from a single sample of cells. We found that each of the operons shows a rapid, within 15 to 30 s, response to arabinose. We also found that the expression of araFGH is more sensitive to catabolite repression but not to arabinose concentration than are araE and araBAD. Finally, we have determined the relative levels of inducibility in wild-type cells of araBAD, araFGH, and araE to be 6.5, 5, and 1, respectively. These results provide a basis for subsequent studies to determine the mechanism(s) by which AraC protein activates transcription from the different arabinose promoters.
Impact of a Cu-zeolite SCR Catalyst on the Performance of a Diesel LNT+SCR System (2009)

&lt;div class="htmlview paragraph"&gt;Advanced Cu-zeolite based SCR (selective catalytic reduction) catalyst technologies were evaluated in a laboratory reactor as a component of a diesel LNT (lean NOx trap) plus in-situ SCR system (i.e., NH&lt;sub&gt;3&lt;/sub&gt; generation over the LNT vs injection via urea). New-generation LNT formulations, with lower desulfation temperatures and improved durability characteristics relative to previous LNTs, were also evaluated. The combined new-generation LNT+Cu-zeolite SCR systems showed a much wider temperature window of high NOx conversion compared to either LNT catalysts alone or LNT+SCR systems utilizing Fe-zeolite SCR catalysts. The new-generation Cu-zeolite SCR catalysts retained high activity even after repeated exposure to high-temperature rich DeSOx conditions in a laboratory 3-mode aging cycle simulating 120,000 mile vehicle driving.&lt;/div&gt;
Phorbol ester modulation of a novel cytoplasmic protein binding activity at the 3'-untranslated region of mammalian ribonucleotide reductase R2 mRNA and role in message stability. (1994)

The R2 gene of ribonucleotide reductase is elevated in BALB/c 3T3 fibroblasts treated with the tumor promotor, 12-O-tetradecanoylphorbol-13-acetate (TPA). TPA treatment increased the half-life of the R2 message by 3-fold, showing that TPA regulates R2 gene expression by a post-transcriptional mechanism(s). A 20-nucleotide (nt) TPA-responsive region was found within the R2 mRNA 3'-untranslated region (3'UTR). Ultraviolet cross-linking detected a novel 45-kDa protein-R2 mRNA complex migration band that bound selectively to the 20-nt fragment and did not bind to the 5'UTR or the coding region of the R2 message, or to the 3'UTRs of mRNA from several other genes, or to the homopolymer poly(A) sequence. The-45 kDa protein-R2 mRNA binding activity observed in unstimulated cells was markedly down-regulated after TPA treatment. Deletion of a 201-nt region, containing the 20-nt sequence, from the 3'UTR caused stabilization of hybrid chloramphenicol acetyltransferase mRNA in the absence of TPA treatment. Furthermore, in vitro decay reaction mixtures supplemented with the 20-nt sense RNA transcript resulted in stabilization of R2 message. A model is presented of R2 message regulation in which a cis-element within the 20-nt sequence of the 3'UTR interacts with a cytosolic protein to form a 45-kDa protein-mRNA binding complex. The TPA-induced alteration of R2 message stability is at least in part due to the down-regulation of the 45-kDa protein-mRNA binding activity which is linked to a reduction in the rate of R2 mRNA degradation.
Multinode Cooperative Communications in Wireless Networks (2006)

In this paper, a class of cooperative communication protocols with arbitrary N-relay nodes is proposed for wireless networks, in which each relay coherently combines the signals received from m (1lesmlesN-1) previous relays in addition to the signal from the source. Exact symbol-error-rate (SER) expressions for an arbitrary N-node network employing M'ary phase-shift-keying (MPSK) modulation or quadrature-amplitude modulation (QAM) are provided for the proposed class of protocols. Further, approximate expressions for the SER are derived and shown to be tight at high enough signal-to-noise ratio (SNR). Our analysis reveals an interesting result: The class of cooperative protocols shares the same asymptotic performance at high enough SNR and does not depend on m, the number of previous nodes involving in coherent detection, hence, the asymptotic performance of a simple cooperative scenario in which each relay combines the signals from the source and the previous relay is exactly the same as that for a much more complicated scenario in which each relay combines the signals from the source and all the previous relays. The theoretical results also confirm that full diversity equal to the number of cooperating nodes is indeed achievable by the proposed protocols. Finally, we formulate a power-allocation problem in order to minimize the SER of the system. The analysis shows that the optimum power allocation at different nodes follows a certain ordering, and that the power-allocation scheme at high SNR does not depend on the channel quality of the direct link between the source and the destination. Closed-form solutions for the optimal power-allocation problem are provided for some network topologies. Simulation results confirm our theoretical analysis
The Politics of Geography (2012)

This chapter offers a theoretical discussion of the contributions Japanese-American writer Karen Tei Yamashita in relation to debates over postmodern space and location, literary avant-garde and commercial and mass cultural forms, and the question of referent in Asian American cultural studies. It identifies three primary contributions that she has made to transnational Asian American literary practice. These include her reconstitution of knowledge about Asian American experiences, her intervention in an increasingly commercialized American culture, and her fashioning of a micropolitical strategy for building interethnic and interdisciplinary alliances through literary representation.
Evidence for Calpain-Mediated Androgen Receptor Cleavage as a Mechanism for Androgen Independence (2007)

Prostate carcinoma is the most commonly diagnosed cancer in men and the second leading cause of death due to cancer in Western civilization. Androgen ablation therapy is effective in treating androgen-dependent tumors, but eventually, androgen-independent tumors recur and are refractory to conventional chemotherapeutics. Hence, the emergence of androgen independence is the most challenging problem in managing prostate tumors. We report a novel mechanism of androgen independence: calpain cleaves the androgen receptor (AR) into an androgen-independent isoform. In vitro and in vivo analyses show that calpain removes the COOH-terminal ligand binding domain generating a constitutively active molecule. Analysis of human prostate tumors indicates that several tumors express higher levels of this truncated AR than noncancerous prostate tissue. In transient transfection studies, the truncated AR is three to five times more potent than the full-length receptor in transactivating transcription. The androgen-independent Rv1 cells express high levels of the truncated AR, and treatment of these cells with a calpain inhibitor reduces truncated AR expression. In the absence of androgen, inhibition of calpain activity induces apoptosis. The HIV protease inhibitor amprenavir inhibits calpain activity and is also effective in inducing apoptosis in the Rv1 cell line. The cell culture studies were reproduced in a mouse xenograft model, where, in the absence of androgens, amprenavir significantly reduces tumor growth. Together, these studies indicate that calpain-dependent proteolysis of the AR may be a mechanism of androgen independence. The calpain inhibition studies suggest that inhibiting this activity may be a potential treatment for some androgen-independent prostate tumors.
Spectral domain analysis of circularly polarized rectangular patch antennas with a dielectric superstrate (2002)

Circularly polarized patch antennas are finding increasing use in far-distance communications such as the satellite broadcasting and communication, and in near-distance communications such as the indoor wireless LAN system and the wireless card system, because of their features of lower cost, less weight and lower profile. Practical patch antennas are often covered with a dielectric superstrate for protection against environmental hazards. It is important to predict the effect of this superstrate on the operating characteristics such as the resonant frequency and input impedance. The spectral domain approach using two entire basis functions, respectively corresponding to electric currents flowing on the patch surface of two degenerate modes, is extended to study the resonant frequencies of two degenerate modes, the circular polarization condition and the input impedance of a circularly polarized rectangular patch antenna with a superstrate, excited by a coaxial probe.