gebhart/patrepeval huggingface dataset:
Interaction Trap/Two‐Hybrid System to Identify Interacting Proteins (2000)

This unit presents protocols designed to detect interacting proteins. Using yeast as a "test tube" and transcriptional activation of a reporter system, interacting proteins can be identified. The system can also be used to test complex formation for proteins for which there exists a reason to expect interaction.
Cloning, Characterization, and Serodiagnostic Evaluation of<i>Leishmania infantum</i>Tandem Repeat Proteins (2006)

Visceral leishmaniasis (VL) is a form of leishmaniasis, which is caused by infection with the protozoan parasite Leishmania, and is often fatal unless it is treated. Rapid and accurate diagnosis of VL is important for effective treatment. Here we report the cloning of previously undescribed tandem repeat (TR) proteins of Leishmania infantum and an evaluation of VL patient antibody responses to the corresponding proteins. By screening an L. infantum expression library with sera from human VL patients or infected hamsters, we identified 43 genes encoding B-cell antigens. Surprisingly, 19 of the 43 genes (44%) were TR proteins, and that percentage was significantly higher than that for genes picked randomly from the database. We then expressed the TR regions of LinJ16.1750, LinJ22.1590, and LinJ33.2870 and the entire LinJ28.2310 protein. These recombinant proteins were all recognized by Sudanese VL patient sera in an enzyme-linked immunosorbent assay. Recombinant LinJ16.1750 (rLinJ16.1750) showed the best performance among these antigens in terms of both sensitivity and specificity. Serological evaluation revealed that 97% (34 of 35) of Sudanese VL patients had significantly elevated antibody levels to rLinJ16.1750. Furthermore, when eight of the patient sera which had low reactivities to rK39 were tested with the novel recombinant antigens, some of the sera showed stronger antibody responses to these antigens than to rK39. Our results suggest that TR regions from the novel L. infantum proteins identified in this study are immunodominant B-cell epitopes and may represent good candidates for serodiagnosis of VL.
Automated particle mass-flow control system for high-temperature falling particle receivers (2018)

An automated particle mass-flow control system has been developed for high-temperature falling particle receivers. The system utilizes an electromechanically actuated slide gate that is designed to operate at 750°C to control the particle flow rate falling through the receiver. As the incoming irradiance changes, the particle mass flow rate is automatically adjusted to maintain a desired particle outlet temperature. The system uses the measured particle outlet temperature relative to a desired setpoint temperature and moves the slide gate to increase or decrease the mass flow rate accordingly in a closed-loop feedback control system. The control system components allow rapid movement of the slide gate with sub-millimeter accuracy resulting in a mass flow rate resolution less than 1 kg/m-s. Multiple slide gates can be used in parallel to accommodate large-scale receivers while independently controlling the particle mass flow rate along the width of the particle curtain. Using multiple slide gates (rather than a single larger slide gate) has the additional advantage of accommodating non-uniform irradiances on the particle curtain so that larger particle mass flow rates can be applied to regions of higher irradiance, and vice versa.
Developmental Expression of Tomato Heat-Shock Cognate Protein 80 (1992)

Heat-shock protein 80 (HSP80) is a major heat-shock protein induced in yeast and animals both by heat shock and by specific developmental events. In plants, a heat-shock-induced HSP80 cDNA has been described, although no information concerning developmental regulation of HSP80 genes is available. We have characterized a tomato (Lycopersicon esculentum) gene encoding a typical HSP80 protein. This gene, called HSC80, is interrupted by two introns, 995 and 109 bp long. Northern blot analyses and in situ RNA hybridization show that HSC80 mRNA is abundant in shoot and root apices and in fertilized ovaries up to 6 d postanthesis but is rare in mature leaves. Heat shock increased mRNA levels in mature leaves but only 3-fold. Developmental regulation of the HSC80 gene was confirmed by fusing 2 kb of its 5' region to the beta-glucuronidase reporter gene and introducing the chimeric gene into tomatoes. The roots of transformants showed high beta-glucuronidase expression in the apex and in lateral root primordia but not in mature tissue. Expression in the shoot was up to 10-fold higher in the apex than in mature leaves. Thus, HSC80 is preferentially expressed in shoot and root apices during normal development.
Therapeutic Cancer Vaccines in Combination with Conventional Therapy (2010)

The clinical efficacy of most therapeutic vaccines against cancer has not yet met its promise. Data are emerging that strongly support the notion that combining immunotherapy with conventional therapies, for example, radiation and chemotherapy may improve efficacy. In particular combination with chemotherapy may lead to improved clinical efficacy by clearing suppressor cells, reboot of the immune system, by rendering tumor cells more susceptible to immune mediated killing, or by activation of cells of the immune system. In addition, a range of tumor antigens have been characterized to allow targeting of proteins coupled to intrinsic properties of cancer cells. For example, proteins associated with drug resistance can be targeted, and form ideal target structures for use in combination with chemotherapy for killing of surviving drug resistant cancer cells. Proteins associated with the malignant phenotype can be targeted to specifically target cancer cells, but proteins targeted by immunotherapy may also simultaneously target cancer cells as well as suppressive cells in the tumor stroma.
Heat Flux-Based Emissivity Measurement (2005)

Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter Facebook Reddit LinkedIn Tools Icon Tools Reprints and Permissions Cite Icon Cite Search Site Citation Saeed Moghaddam, John Lawler, Collin McCaffery, Jungho Kim; Heat Flux‐Based Emissivity Measurement. AIP Conf. Proc. 6 February 2005; 746 (1): 32–37. https://doi.org/10.1063/1.1867115 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAIP Publishing PortfolioAIP Conference Proceedings Search Advanced Search |Citation Search
A Nanoscale Low-Power Resistorless Voltage Reference with High PSRR (2019)

In this paper, a nano-watt resistorless subthreshold voltage reference with high-power supply rejection ratio (PSRR) is presented. A self-biased MOS voltage divider is proposed to provide bias current for whole voltage reference, which is a positive temperature coefficient (TC) current containing threshold voltage characteristics. By injecting the generated current into a transistor with a different threshold voltage, a delta threshold voltage with a greatly reduced negative TC is realized and temperature-compensated by a generated positive TC item at the same time. Therefore, a temperature-stable voltage reference is achieved in the proposed compacted method with low power consumption and high PSRR. Verification results with 65-nm CMOS technology demonstrate that the minimum supply voltage can be as low as 0.35 V with a 0.00182-mm<sup>2</sup> active area. The generated reference voltage is 148 mV, with a TC of 28 ppm/°C for the - 30 to 80 °C temperature range. The line sensitivity is 1.8 mV/V, and the PSRR without any filtering capacitor at 100 Hz is 53 dB with a 2.28-nW power consumption.
Dispersion of Single-Walled Carbon Nanotubes in Poly(ε-caprolactone) (2007)

The dispersion of single-walled carbon nanotubes (SWNT) in poly(ε-caprolactone) with the aid of a zwitterionic surfactant is reported. Melt rheology and electrical conductivity measurements indicate geometrical percolation and electrical percolation for nanocomposites with ∼0.08 wt % SWNT, implying an effective anisotropy for the nanotubes of at least 600. Spectroscopic measurements and comparison of dispersion using other surfactants established that the excellent dispersion is a result of the compatibilizing effect of the zwitterionic surfactant.
Subproblem coupling in convolutional dictionary learning (2017)

The current leading algorithms for both convolutional sparse coding and dictionary learning are based on variable splitting and Augmented Lagrangian methods. The dictionary learning algorithms alternate between sparse coding and dictionary subproblems, typically interleaving the updates for each of these two subproblems. Due to the variable splitting, in each subproblem one of these two variables must be chosen to be passed to the other subproblem. We perform a careful comparison of the algorithm convergence resulting from the different choices in conjunction with a number of different algorithms for the dictionary subproblem, showing that one of these choices consistently provides the best convergence.
Evolution of Human Immunodeficiency Virus Type 1 Coreceptor Usage during Antiretroviral Therapy: a Bayesian Approach (2004)

There is substantial evidence for ongoing replication and evolution of human immunodeficiency virus type 1 (HIV-1), even in individuals receiving highly active antiretroviral therapy. Viral evolution in the presence of antiviral therapy needs to be considered when developing new therapeutic strategies. Phylogenetic analyses of HIV-1 sequences can be used for this purpose but may give rise to misleading results if rates of intrapatient evolution differ significantly. To improve analyses of HIV-1 evolution relevant to studies of pathogenesis and treatment, we developed a Bayesian hierarchical model that incorporates all available sequence data while simultaneously allowing the phylogenetic parameters of each patient to vary. We used this method to examine evolutionary changes in HIV-1 coreceptor usage in response to treatment. We examined patients whose viral populations exhibited a shift in coreceptor utilization in response to therapy. CXCR4 (X4) strains emerged in each patient but were suppressed following initiation of new antiretroviral regimens, so that CCR5-utilizing (R5) strains predominated. By phylogenetically reconstructing the evolutionary relationship of HIV-1 obtained longitudinally from each patient, it was possible to examine the origin of the reemergent R5 virus. Using our Bayesian hierarchical approach, we found that the reemergent R5 virus detectable after therapy was more closely related to the predecessor R5 virus than to the X4 strains. The Bayesian hierarchical approach, unlike more traditional methods, makes it possible to evaluate competing hypotheses across patients. This model is not limited to analyses of HIV-1 but can be used to elucidate evolutionary processes for other organisms as well.
Sn‐Pb Binary Perovskite Films with High Crystalline Quality for High Performance Solar Cells (2019)

Summary of main observation and conclusion As an environmentally friendly perovskite material with low bandgap, Tin (Sn)‐based perovskite has drawn much attention. A simple and effective method for fabricating high‐quality Sn‐Pb binary perovskite film is highly desired. Here, with methylammonium chloride (MACl) post‐treatment to assist vertical recrystallization, we fabricated high quality FA 0.75 Cs 0.25 Pb 0.5 Sn 0.5 I 3 perovskite film via one‐step processing method. This recrystallization method was first used in Sn‐based perovskite. The obtained film consists of vertically aligned grains with high crystallinity, which contributes to a power conversion efficiency (PCE) of 14.03% in corresponding perovskite solar cell (PVSC). The cells maintained 80% of their initial PCEs after being stored for 30 d in glove‐box. This simple, effective method provides an easy way to fabricate high performance Sn‐Pb binary PVSC.
Use of <i>Tomato yellow leaf curl virus</i> (TYLCV) <i>Rep</i> Gene Sequences to Engineer TYLCV Resistance in Tomato (2004)

ABSTRACT Tomato yellow leaf curl virus (TYLCV), a member of the genus Begomovirus (family Geminiviridae), causes severe losses in tomato production in the tropics and subtropics. In order to generate engineered resistance, eight different constructs of the TYLCV replication-associated protein (Rep) and C4 gene sequences were tested in transformed tomato inbred lines. Transgenic plants were screened for resistance to TYLCV using viruliferous whiteflies. No symptoms were observed and no TYLCV genomic DNA was detected by both hybridization and polymerase chain reaction in progenies of plants transformed with three constructs. This resistance was observed in plants that contained one of the following transgenes: 2/5Rep (81 nucleotides [nt] of the intergenic region [IR] plus 426 nt of the 5' end of the TYLCV Rep gene), Delta2/5Rep (85 nt of the IR plus 595 nt of the 5' end of the TYLCV Rep gene in the antisense orientation), and RepDelta2/5Rep (81 nt of the IR, the entire Rep gene, and 41 nt 3' to the end of the Rep gene fused to Delta2/5Rep). Our study differs from other transgenic Geminivirus resistance reports involving the Rep gene in that viruliferous whiteflies were used for challenge inoculation instead of agroinoculation or biolistic inoculation, and TYLCV resistance was evaluated under field conditions.
Application of the TLR9 Ligand CpG DNA to the Injured Corneal Epithelium Induces Intraocular Inflammation (2010)

This is the published version: Chinnery, H.R., McLenachan, S., Degli-Esposti, M., Forrester, J.V., Pearlman, E. and McMenamin, P.G. 2010, Application of the TLR9 ligand CpG DNA to the injured corneal epithelium induces intraocular inflammation, in ARVO 2010: Proceedings of the 2010 Association for Research in Vision and Opthalmology Conference, ARVO, Fort Lauderdale, Flo., pp. 1-1. Available from Deakin Research Online:
Studies of Prototype Live Hepatitis A Virus Vaccines in Primate Models (1988)

We have prepared two prototype live hepatitis A virus (HAV) vaccines by serial passage of the HM-175 strain of HAV in African green monkey kidney cells. Passage 21 (P-21) HM-175 virus shows evidence of attenuation for chimpanzees but not for marmosets; passage 32 (P-32) HM-175 virus shows evidence of attenuation for both species. Animals that received P-32 HAV had fewer elevations in levels of liver enzyme activity and evidence of less virus replication in the liver and excretion of virus in stool than did those that received wild-type virus. The P-21 and P-32 viruses were highly immunogenic in both species. The information provided by this study will aid in the development of a live HAV vaccine.
Synthesis–structure–performance correlation for polyaniline–Me–C non-precious metal cathode catalysts for oxygen reduction in fuel cells (2011)

In this report, we present the systematic preparation of active and durable non-precious metal catalysts (NPMCs) for the oxygen reduction reaction in polymer electrolyte fuel cells (PEFCs) based on the heat treatment of polyaniline/metal/carbon precursors. Variation of the synthesis steps, heat-treatment temperature, metal loading, and the metal type in the synthesis leads to markedly different catalyst activity, speciation, and morphology. Microscopy studies demonstrate notable differences in the carbon structure as a function of these variables. Balancing the need to increase the catalyst’s degree of graphitization through heat treatment versus the excessive loss of surface area that occurs at higher temperatures is a key to preparing an active catalyst. XPS and XAFS spectra are consistent with the presence of Me–Nx structures in both the Co and Fe versions of the catalyst, which are often proposed to be active sites. The average speciation and coordination environment of nitrogen and metal, however, depends greatly on the choice of Co or Fe. Taken together, the data indicate that better control of the metal-catalyzed transformations of the polymer into new graphitized carbon forms in the heat-treatment step will allow for even further improvement of this class of catalysts.
Development of an Electromagnetic Microscope for Eddy Current Evaluation of Materials (1991)

Superconductive quantum interference devices (SQUIDs) offer new technology for locating material flaws electromagnetically that promises to increase sensitivity and depth of field as well as to enhance resolution and imaging. The ultrahigh sensitivity of SQUIDs to magnetic flux allows use of microscopic pickup loops in a gradiometer configuration to give high resolution. To realize the advantages of SQUID technology for Air Force requirements in evaluating the integrity of airframes, SQM Technology, Inc. is developing an electromagnetic microscope that uses an array of microscopic pickup loops for imaging micro flaws in aluminum. The prototype comprises a triangular array of microscopic gradiometers that are coupled to SQUID sensors through a flexible, cryogenic umbilical, which enables convenient scanning. Development to date shows three main accomplishments: (1) a planar, azimuthal gradiometer configuration enables suppressing source interference, (2) instrument noise at drive currents of 1 A or so at frequencies below a few kilohertz is of the order of SQUID noise, and (3) a cryogenic umbilical can provide adequate cooling over a four to six foot length.
Abstract 1415: Anti-metastatic properties of tumor-entrained neutrophils (2012)

Abstract Metastasis represents the final stage in cancer progression and is the primary cause of cancer related mortality. Disseminated cells that are capable of colonizing distant organs and forming metastases therefore present an important therapeutic challenge. In recent years, primary tumors have been shown to prepare distal organs for later colonization of metastatic cells by stimulating organ-specific infiltration of bone marrow derived cells (BMDCs). Here, using mouse models of breast cancer, we demonstrate that neutrophils accumulate in the lung prior to the arrival of metastatic cells. In contrast to other BMDCs that promote metastatic colonization, tumor-entrained neutrophils (TENs), but not control neutrophils, inhibit seeding of metastatic tumor cells in the lungs. TENs protect the pre-metastatic lung by initiating physical contact, generating H2O2 and killing tumor cells. While tumor secreted CCL2 has a pro-tumorigenic effect at the primary site, our data show that it is both required and sufficient for optimal anti-metastatic entrainment at the metastatic site. As tumor-secreted TGFβ blocks cytotoxicity at the primary site, TENs cytotoxicity is limited to the pre-metastatic site where TGFβ levels are low. Additionally, we find that TENs are also present in the peripheral blood of human breast cancer patients prior to surgical resection but not in healthy individuals. Several chemokines known to be increased in the circulation of breast cancer patients have the capacity to induce a cytotoxic phenotype in naïve human neutrophils, providing a possible mechanism for neutrophil entrainment in cancer patients. Taken together, our data show that while tumor-secreted factors contribute to tumor progression at the primary site, they concomitantly induce a neutrophil-mediated inhibitory process at the metastatic site. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 1415. doi:1538-7445.AM2012-1415
Diffusion Stop-Layers for Superconducting Integrated Circuits and Qubits With Nb-Based Josephson Junctions (2010)

New technology for superconductor integrated circuits has been developed and is presented. It employs diffusion stop-layers (DSLs) to protect Josephson junctions (JJs) from interlayer migration of impurities, improve JJ critical current (I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">c</sub> ) targeting and reproducibility, eliminate aging, and eliminate pattern-dependent effects in I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">c</sub> and tunneling characteristics of Nb/Al/AlO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> /Nb junctions in integrated circuits. The latter effects were recently found in Nb-based JJs integrated into multi layered digital circuits. E.g., it was found that Josephson critical current density (J <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">c</sub> ) may depend on the JJ's environment, on the type and size of metal layers making contact to niobium base (BE) and counter electrodes (CE) of the junction, and also change with time. Such J <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">c</sub> variations within a circuit reduce circuit performance and yield, and restrict integration scale. This variability of JJs is explained as caused by hydrogen contamination of Nb layers during wafer processing, which changes the height and structural properties of AlO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> tunnel barrier. Redistribution of hydrogen impurities between JJ electrodes and other circuit layers by diffusion along Nb wires and through contacts between layers causes long-term drift of J <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">c</sub> . At least two DSLs are required to completely protect JJs from impurity diffusion effects-right below the junction BE and right above the junction CE. The simplest and the most technologically convenient DSLs we have found are thin (from ~3 nm to ~10 nm) layers of Al. They were deposited in-situ under the BE layer, thus forming an Al/Nb/Al/AlO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> /Nb penta-layer, and under the first wiring layer to junctions' CE, thus forming an Al/Nb wiring bi-layer. A significant improvement of J <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">c</sub> uniformity on 150-mm wafer has also been obtained along with large improvements in J <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">c</sub> targeting and run-to-run reproducibility.
High Resolution Image Reconstruction for Plenoptic Imaging Systems using System Response (2012)

Plenoptic imaging systems with a microlens array imaging the pupil at the sensor typically produce low resolution images. We introduce an inverse problem solver using the system response to obtain high resolution image reconstructions.